The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Department of Bioinformatics Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures Brunswick Germany

Department of Energy Joint Genome Institute Berkeley CA United States

Department of Microorganisms Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures Brunswick Germany

Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Prague Czechia

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Abdad M. Y., Abdallah R. A., El Karkouri K., Beye M., Stenos J., Owen H., et al. (2017). Rickettsia gravesii sp. nov.: a novel spotted fever group rickettsia in Western Australian Amblyomma triguttatum triguttatum ticks. Int. J. Syst. Evol. Microbiol. 67 3156–3161. 10.1099/ijsem.0.001865 PubMed DOI

Abraham W. R., de Carvalho M. P., da Costa Neves T. S. P., Memoria M. T., Tartuci I. T., Vancanneyt M., et al. (2017). Proposal of Henriciella barbarensis sp. nov. and Henriciella algicola sp. nov., stalked species of the genus and emendation of the genus Henriciella. Int. J. Syst. Evol. Microbiol. 67 2804–2810. 10.1099/ijsem.0.002024 PubMed DOI

Abraham W.-R., Lünsdorf H., Vancanneyt M., Smit J. (2013). Cauliform bacteria lacking phospholipids from an abyssal hydrothermal vent: proposal of Glycocaulis abyssi gen. nov., sp. nov., belonging to the family Hyphomonadaceae. Int. J. Syst. Evol. Microbiol. 63 2207–2215. 10.1099/ijs.0.047894-0 PubMed DOI

Abraham W. R., Macedo A. J., Lünsdorf H., Fischer R., Pawelczyk S., Smit J., et al. (2008). Phylogeny by a polyphasic approach of the order Caulobacterales, proposal of Caulobacter mirabilis sp. nov., Phenylobacterium haematophilum sp. nov. and Phenylobacterium conjunctum sp. nov., and emendation of the genus Phenylobacterium. Int. J. Syst. Evol. Microbiol. 58(Pt 8) 1939–1949. 10.1099/ijs.0.65567-0 PubMed DOI

Abraham W.-R., Strömpl C., Meyer H., Lindholst S., Moore E. R. B., Christ R., et al. (1999). Phylogeny and polyphasic taxonomy of Caulobacter species. Proposal of Maricaulis gen. nov. with Maricaulis maris (Poindexter) comb. nov. as the type species, and emended description of the genera Brevundimonas and Caulobacter. Int. J. Syst. Bacteriol. 49(Pt 3) 1053–1073. 10.1099/00207713-49-3-1053 PubMed DOI

Abraham W.-R., Strömpl C., Vancanneyt M., Bennasar A., Swings J., Lünsdorf H., et al. (2004). Woodsholea maritima gen. nov., sp. nov., a marine bacterium with a low diversity of polar lipids. Int. J. Syst. Evol. Microbiol. 54(Pt 4) 1227–1234. 10.1099/ijs.0.02943-0 PubMed DOI

Abt B., Göker M., Scheuner C., Han C., Lu M., Misra M., et al. (2013). Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1T), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema. Stand. Genomic Sci. 8 88–105. 10.4056/sigs.3096473 PubMed DOI PMC

Abt B., Han C., Scheuner C., Lu M., Lapidus A., Nolan M., et al. (2012). Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1T), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta. Stand. Genomic Sci. 6 194–209. 10.4056/sigs.2796069 PubMed DOI PMC

Addison S. L., Foote S. M., Reid N. M., Lloyd-Jones G. (2007). Novosphingobium nitrogenifigens sp. nov., a polyhydroxyalkanoate-accumulating diazotroph isolated from a New Zealand pulp and paper wastewater. Int. J. Syst. Evol. Microbiol. 57 2467–2471. 10.1099/ijs.0.64627-0 PubMed DOI

Akinola R. O. (2013). A systems level comparison of Mycobacterium tuberculosis, Mycobacterium leprae and Mycobacterium smegmatis based on functional interaction network analysis. J. Bacteriol. Parasitol. 4:173 10.4172/2155-9597.1000173 DOI

Aksenova H. Y., Rainey F. A., Janssen P. H., Zavarzin G. A., Morgan H. W. (1992). Spirochaeta thermophila sp. nov., an obligately anaerobic, polysaccharolytic, extremely thermophilic bacterium. Int. J. Syst. Evol. Microbiol. 42 175–177. 10.1099/00207713-42-1-175 DOI

Alain K., Tindall B. J., Intertaglia L., Catala P., Lebaron P. (2008). Hellea balneolensis gen. nov., sp. nov., a prosthecate alphaproteobacterium from the Mediterranean Sea. Int. J. Syst. Evol. Microbiol. 58 2511–2519. 10.1099/ijs.0.65424-0 PubMed DOI

Alarico S., Rainey F. A., Empadinhas N., Schumann P., Nobre M. F., da Costa M. S. (2002). Rubritepida flocculans gen. nov., sp. nov., a new slightly thermophilic member of the α-1 subclass of the Proteobacteria. Syst. Appl. Microbiol. 25 198–206. 10.1078/0723-2020-00116 PubMed DOI

Albuquerque L., França L., Taborda M., La Cono V., Yakimov M., da Costa M. S. (2015). Palleronia abyssalis sp. nov., isolated from the deep Mediterranean Sea and the emended description of the genus Palleronia and of the species Palleronia marisminoris. Antonie Van Leeuwenhoek 107 633–642. 10.1007/s10482-014-0358-2 PubMed DOI

Albuquerque L., Rainey F. A., Nobre M. F., da Costa M. S. (2008). Elioraea tepidiphila gen. nov., sp. nov., a slightly thermophilic member of the Alphaproteobacteria. Int. J. Syst. Evol. Microbiol. 58 773–778. 10.1099/ijs.0.65294-0 PubMed DOI

Albuquerque L., Rainey F. A., Nobre M. F., da Costa M. S. (2012). Oceanicella actignis gen. nov., sp. nov., a halophilic slightly thermophilic member of the Alphaproteobacteria. Syst. Appl. Microbiol. 35 385–389. 10.1016/j.syapm.2012.07.001 PubMed DOI

Albuquerque L., Rainey F. A., Pena A., Tiago I., Veríssimo A., Nobre M. F., et al. (2010). Tepidamorphus gemmatus gen. nov., sp. nov., a slightly thermophilic member of the Alphaproteobacteria. Syst. Appl. Microbiol. 33 60–66. 10.1016/j.syapm.2010.01.002 PubMed DOI

Albuquerque L., Santos J., Travassos P., Nobre M. F., Rainey F. A., Wait R., et al. (2002). Albidovulum inexpectatum gen. nov., sp. nov., a nonphotosynthetic and slightly thermophilic bacterium from a marine hot spring that is very closely related to members of the photosynthetic genus Rhodovulum. Appl. Environ. Microbiol. 68 4266–4273. 10.1128/AEM.68.9.4266 PubMed DOI PMC

Almpanis A., Swain M., Gatherer D., McEwan N. (2018). Correlation between bacterial G+C content, genome size and the G+C content of associated plasmids and bacteriophages. Microb. Genomics 4:e000168. 10.1099/mgen.0.000168 PubMed DOI PMC

Amoozegar M. A., Makhdoumi-kakhki A., Ramezani M., Nikou M. M., Abolhassan S., Fazeli S., et al. (2013). Limimonas halophila gen. nov., sp. nov., an extremely halophilic bacterium in the family Rhodospirillaceae. Int. J. Syst. Evol. Microbiol. 63 1562–1567. 10.1099/ijs.0.041236-0 PubMed DOI

Anil Kumar P., Aparna P., Srinivas T. N. R., Sasikala C., Ramana C. V. (2008). Rhodovulum kholense sp. nov. Int. J. Syst. Evol. Microbiol. 58(Pt 7) 1723–1726. 10.1099/ijs.0.65620-0 PubMed DOI

Anil Kumar P., Srinivas T. N. R., Manasa P., Madhu S., Shivaji S. (2012). Lutibaculum baratangene gen. nov., sp. nov., a proteobacterium isolated from a mud volcano. Int. J. Syst. Evol. Microbiol. 62 2025–2031. 10.1099/ijs.0.036350-0 PubMed DOI

Anil Kumar P., Srinivas T. N. R., Takaichi S., Maoka T., Sasikala C., Ramana C. V. (2009). Phaeospirillum chandramohanii sp. nov., a phototrophic alphaproteobacterium with carotenoid glycosides. Int. J. Syst. Evol. Microbiol. 59 2089–2093. 10.1099/ijs.0.009019-0 PubMed DOI

Arahal D. R., La Mura A., Lucena T., Rodrigo-Torres L., Aznar R., Pujalte M. J. (2019). Shimia thalassica sp. nov., and reclassification of Pseudopelagicola gijangensis as Shimia gijangensis comb. nov., and Thalassobius activus as Cognatishimia activa comb. nov. Int. J. Syst. Evol. Microbiol. 69 3405–3413. 10.1099/ijsem.0.003629 PubMed DOI

Arahal D. R., Macián M. C., Garay E., Pujalte M. J. (2005). Thalassobius mediterraneus gen. nov., sp. nov., and reclassification of Ruegeria gelatinovorans as Thalassobius gelatinovorus comb. nov. Int. J. Syst. Evol. Microbiol. 55 2371–2376. 10.1099/ijs.0.63842-0 PubMed DOI

Arroua B., Ranchou-Peyruse A., Ranchou-Peyruse M., Magot M., Urios L., Grimaud R. (2017). Pleomorphochaeta caudata gen. nov., sp. nov., an anaerobic bacterium isolated from an offshore oil well, reclassification of Sphaerochaeta multiformis MO-SPC2T as Pleomorphochaeta multiformis MO-SPC2T comb. nov. as the type strain of this novel genus and emended description of the genus Sphaerochaeta. Int. J. Syst. Evol. Microbiol. 67 417–424. 10.1099/ijsem.0.001641 PubMed DOI

Arun A. B., Schumann P., Chu H.-I., Tan C.-C., Chen W.-M., Lai W.-A., et al. (2008). Pseudoxanthobacter soli gen. nov., sp. nov., a nitrogen-fixing alphaproteobacterium isolated from soil. Int. J. Syst. Evol. Microbiol. 58 1571–1575. 10.1099/ijs.0.65206-0 PubMed DOI

Arunasri K., Venkata Ramana V., Spröer C., Sasikala C., Ramana C. V. (2008). Rhodobacter megalophilus sp. nov., a phototroph from the Indian Himalayas possessing a wide temperature range for growth. Int. J. Syst. Evol. Microbiol. 58 1792–1796. 10.1099/ijs.0.65642-0 PubMed DOI

Asker D., Beppu T., Ueda K. (2007). Sphingomonas jaspsi sp. nov., a novel carotenoid-producing bacterium isolated from Misasa, Tottori, Japan. Int. J. Syst. Evol. Microbiol. 57 1435–1441. 10.1099/ijs.0.64828-0 PubMed DOI

Auch A. F., Henz S. R., Holland B. R., Göker M. (2006). Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences. BMC Bioinformatics 7:350. 10.1186/1471-2105-7-350 PubMed DOI PMC

Auling G., Hans-Jürgen B., Egli T., El-banna T., Stackebrandt E. (1993). Description of the Gram-Negative, obligately aerobic, nitrilotriacetate (NTA)-utilizing bacteria as Chelatobacter heintzii, gen. nov., sp. nov., and Chelatococcus asaccharovorans, gen. nov., sp. nov. Syst. Appl. Microbiol. 16 104–112. 10.1016/S0723-2020(11)80254-7 DOI

Babudieri B. (1950). Natura delle cosidette “S-formen” delle leptospire. Loro identificazione con Hyphomicrobium vulgare Stutzer e Hartleb. Studio di quest. Ultimo germe. R. C. 1 St. Suppl. Sanita Roma 13 580–591. PubMed

Baek K., Choi A., Kang I., Cho J.-C. (2014). Celeribacter marinus sp. nov., isolated from coastal seawater. Int. J. Syst. Evol. Microbiol. 64 1323–1327. 10.1099/ijs.0.060673-0 PubMed DOI

Baik K. S., Choe H. N., Park S. C., Hwang Y. M., Kim E. M., Park C., et al. (2013). Sphingopyxis rigui sp. nov. and Sphingopyxis wooponensis sp. nov., isolated from wetland freshwater, and emended description of the genus Sphingopyxis. Int. J. Syst. Evol. Microbiol. 63 1297–1303. 10.1099/ijs.0.044057-0 PubMed DOI

Bala K., Sharma P., Lal R. (2010). Sphingobium quisquiliarum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH-contaminated soil. Int. J. Syst. Evol. Microbiol. 60 429–433. 10.1099/ijs.0.010868-0 PubMed DOI

Balcázar J. L., Planas M., José P. (2012). Oceanibacterium hippocampi gen. nov., sp. nov., isolated from cutaneous mucus of wild seahorses (Hippocampus guttulatus). Antonie Van Leeuwenhoek 102 187–191. 10.1007/s10482-012-9726-y PubMed DOI

Bambauer A., Rainey F. A., Stackebrandt E., Winter J. (1998). Characterization of Aquamicrobium defluvii gen. nov. sp. nov., a thiophene-2-carboxylate-metabolizing bacterium from activated sludge. Arch. Microbiol. 169 293–302. 10.1007/s002030050575 PubMed DOI

Bao Z., Sato Y., Fujimura R., Ohta H. (2014). Alsobacter metallidurans gen. nov., sp. nov., a thallium-tolerant soil bacterium in the order Rhizobiales. Int. J. Syst. Evol. Microbiol. 64 775–780. 10.1099/ijs.0.054783-0 PubMed DOI

Bapteste E., Boucher Y. (2009). “Epistemological impacts of horizontal gene transfer on classification in microbiology,” in Horizontal Gene Transfer. Methods in Molecular Biology, eds Gogarten M. B., Gogarten J. P., Olendzenski L. C. (Totowa, NJ: Humana Press; ), 55–72. 10.1007/978-1-60327-853-9 PubMed DOI

Baranton G. U. Y., Postic D., Girons S., Boerlin P., Piffaretti J., Assous M., et al. (1992). Delineation of Borrelia burgdorferi sensu stricto, Borrelia garinii sp. nov., and group VS461 associated with Lyme borreliosis. Int. J. Syst. Bacteriol. 42 378–383. 10.1099/00207713-42-3-378 PubMed DOI

Baraúna A. C., Rouws L. F. M., Simoes-Araujo J. L., dos Reis F. B., Jr., Iannetta P. P. M., Maluk M., et al. (2016). Rhizobium altiplani sp. nov., isolated from effective nodules on Mimosa pudica growing in untypically alkaline soil in central Brazil. Int. J. Syst. Evol. Microbiol. 66 4118–4124. 10.1099/ijsem.0.001322 PubMed DOI

Barberán A., Velazquez H. C., Jones S., Fierer N. (2017). Hiding in plain sight: mining bacterial species records for phenotypic trait information. mSphere 2:e00237-17. 10.1128/mSphere.00237-17 PubMed DOI PMC

Bates S. T., Cropsey G. W. G., Caporaso J. G., Knight R., Fierer N. (2011). Bacterial communities associated with the lichen symbiosis. Appl. Environ. Microbiol. 77 1309–1314. 10.1128/AEM.02257-10 PubMed DOI PMC

Bazylinski D. A., Williams T. J., Lefèvre C. T., Berg R. J., Zhang C. L., Bowser S. S., et al. (2013a). Magnetococcus marinus gen. nov., sp. nov., a marine, magnetotactic bacterium that represents a novel lineage (Magnetococcaceae fam. nov., Magnetococcales ord. nov.) at the base of the Alphaproteobacteria. Int. J. Syst. Evol. Microbiol. 63 801–808. 10.1099/ijs.0.038927-0 PubMed DOI

Bazylinski D. A., Williams T. J., Lefèvre C. T., Trubitsyn D., Fang J., Beveridge T. J., et al. (2013b). Magnetovibrio blakemorei gen. nov., sp. nov., a magnetotactic bacterium (Alphaproteobacteria: Rhodospirillaceae) isolated from a salt marsh. Int. J. Syst. Evol. Microbiol. 63 1824–1833. 10.1099/ijs.0.044453-0 PubMed DOI

Beijerinck M. W. (1898). Ueber die arten der essigbakterien. Cent. für Bakteriol. Parasitenkd. und Infekt. 4 209–216.

Beijerinck M. W., Folpmers T. (1916). Verslagen van de gewone vergadering der wis- en natuurkundige afdeeling. K. Akad. van Wet. te Amsterdam 18 1198–1200.

Belas R., Horikawa E., Aizawa S.-I., Suvanasuthi R. (2009). Genetic determinants of Silicibacter sp. TM1040 motility. J. Bacteriol. 191 4502–4512. 10.1128/JB.00429-09 PubMed DOI PMC

Ben Hania W., Joseph M., Schumann P., Bunk B., Fiebig A., Spröer C., et al. (2015). Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat. Stand. Genomic Sci. 10 1–14. 10.1186/1944-3277-10-7 PubMed DOI PMC

Bibi F., Chung E. J., Khan A., Jeon C. O., Chung Y. R. (2013). Martelella endophytica sp. nov., an antifungal bacterium associated with a halophyte. Int. J. Syst. Evol. Microbiol. 63 2914–2919. 10.1099/ijs.0.048785-0 PubMed DOI

Bibi F., Jeong J. H., Chung E. J., Jeon C. O., Chung Y. R. (2014). Labrenzia suaedae sp. nov., a marine bacterium isolated from a halophyte, and emended description of the genus Labrenzia. Int. J. Syst. Evol. Microbiol. 64 1116–1122. 10.1099/ijs.0.052860-0 PubMed DOI

Biebl H., Pukall R., Lünsdorf H., Schulz S., Allgaier M., Tindall B. J., et al. (2007). Description of Labrenzia alexandrii gen. nov., sp. nov., a novel alphaproteobacterium containing bacteriochlorophyll α, and a proposal for reclassification of Stappia aggregata as Labrenzia aggregata comb. nov., of Stappia marina as Labrenzia marina comb. Int. J. Syst. Evol. Microbiol. 57 1095–1107. 10.1099/ijs.0.64821-0 PubMed DOI

Billerbeck S., Orchard J., Tindall B. J., Giebel H.-A., Brinkhoff T., Simon M. (2015). Description of Octadecabacter temperatus sp. nov., isolated from the southern North Sea, emended descriptions of the genus Octadecabacter and its species and reclassification of Octadecabacter jejudonensis Park and Yoon 2014 as Pseudooctadecabacter jejudonensis gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 65(Pt 6) 1967–1974. 10.1099/ijs.0.000205 PubMed DOI

Birtles R. J., Harrison T. G., Saunders N. A., Molyneux D. H. (1995). Proposals to unify the genera Grahamella and Bartonella, with descriptions of Bartonella talpae comb. nov., Bartonella peromysci comb. nov., and three new species, Bartonella grahamii sp. nov., Bartonella taylorii sp. nov., and Bartonella doshiae sp. nov. Int. J. Syst. Bacteriol. 45 1–8. 10.1099/00207713-45-1-1 PubMed DOI

Boone D. R., Castenholz R. W., Garrity G. M. (2001a). Bergey’s Manual of Systematic Bacteriology: The Archaea and the Deeply Branching and Phototrophic Bacteria, 2nd Edn, Vol. 1 New York, NY: Springer, 10.1007/978-0-387-68489-5 DOI

Boone D. R., Castenholz R. W., Garrity G. M. (2001b). “Taxonomic outline of the Archaea and Bacteria,” in Bergey’s Manual of Systematic Bacteriology: The Archaea and the Deeply Branching and Phototrophic Bacteria, Vol. 1 ed. Whitman W. B. (New York, NY: Springer; ), 155–166.

Borsodi A. K., Micsinai A., Kovács G., Tóth E., Schumann P., Kovács A. L., et al. (2003). Pannonibacter phragmitetus gen. nov., sp. nov., a novel alkalitolerant bacterium isolated from decomposing reed rhizomes in a Hungarian soda lake. Int. J. Syst. Evol. Microbiol. 53 555–561. 10.1099/ijs.0.02356-0 PubMed DOI

Bouzar H., Jones J. B. (2001). Agrobacterium larrymoorei sp. nov., a pathogen isolated from aerial tumours of Ficus benjamina. Int. J. Syst. Evol. Microbiol. 51 1023–1026. 10.1099/00207713-51-3-1023 PubMed DOI

Bowman J. P. (2005). “Family V. Methylocystaceae fam. nov,” in Bergey’s Manual of Systematic Bacteriology: The Proteobacteria, Part C, the Alpha-, Beta-, Delta-, and Epsilonbacteria, Vol. 2 eds Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. (New York, NY: Springer; ), 411–422.

Bowman J. P., Sly L. I., Nichols P. D., Hayward A. C. (1993). Revised taxonomy of the methanotrophs: description of Methylobacter gen. nov., emendation of Methylococcus, validation of Methylosinus and Methylocystis species, and a proposal that the family Methylococcaceae includes only the group I methanotrophs. Int. J. Syst. Evol. Microbiol. 43 735–753. 10.1099/00207713-43-4-735 DOI

Breed R. S., Murray E. G. D., Smith N. (eds) (1957). Bergey’s Manual of Determinative Bacteriology, 7th Edn Baltimore, MD: The Williams & Wilkins Co.

Breider S., Scheuner C., Schumann P., Fiebig A., Petersen J., Pradella S., et al. (2014). Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov. Front. Microbiol. 5:416. 10.3389/fmicb.2014.00416 PubMed DOI PMC

Brenner D. J., Hollis D. G., Moss C. W., English C. K., Hall G. S., Vincent J., et al. (1991). Proposal of Afipia gen. nov., with Afipia felis sp. nov. (formerly the cat scratch disease bacillus), Afipia clevelandensis sp. nov. (formerly the Cleveland clinic foundation strain), Afipia broomeae sp. nov., and three unnamed genospecies. J. Clin. Microbiol. 29 2450–2460. 10.1128/jcm.29.11.2450-2460.1991 PubMed DOI PMC

Brenner D. J., Kaufmann A. F., Sulzer K. R., Steigerwalt A. G., Rogers F. C., Weyant R. (1999). Further determination of DNA relatedness between serogroups and serovars in the family Leptospiraceae with a proposal for Leptospira alexanderi sp. nov. and four new Leptospira genomospecies. Int. J. Syst. Bacteriol. 49 839–858. 10.1099/00207713-49-2-839 PubMed DOI

Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. (eds) (2005). Bergey’s Manual of Systematic Bacteriology: The Proteobacteria; Part C, the Alpha-, Beta-, Delta-, and Epsilonproteobacteria, 2nd Edn, Vol. 2 Bosten, MA: Springer.

Brenner D. J., O’Connor S. P., Winkler H. H., Steigerwalt A. G. (1993). Proposals to unify the genera Bartonella and Rochalimaea, with descriptions of Bartonella quintana comb. nov., Bartonella vinsonii comb. nov., Bartonella henselae comb. nov. and Bartonella elizabethae comb. nov. and to remove the family Bartonellaceae from the order Rickettsiales. Int. J. Syst. Bacteriol. 43 777–786. 10.1099/00207713-43-4-777 PubMed DOI

Brettar I., Christen R., Bötel J., Lünsdorf H., Höfle M. G. (2007). Anderseniella baltica gen. nov., sp. nov., a novel marine bacterium of the Alphaproteobacteria isolated from sediment in the central Baltic Sea. Int. J. Syst. Evol. Microbiol. 57 2399–2405. 10.1099/ijs.0.65007-0 PubMed DOI

Breznak J. A., Warnecke F. (2008). Spirochaeta cellobiosiphila sp. nov., a facultatively anaerobic, marine spirochaete. Int. J. Syst. Evol. Microbiol. 58 2762–2768. 10.1099/ijs.0.2008/001263-0 PubMed DOI

Brinkhoff T., Giebel H.-A., Simon M. (2008). Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch. Microbiol. 189 531–539. 10.1007/s00203-008-0353-y PubMed DOI

Brinkmann H., Göker M., Koblížek M., Wagner-Döbler I., Petersen J. (2018). Horizontal operon transfer, plasmids, and the evolution of photosynthesis in Rhodobacteraceae. ISME J. 12 1994–2010. 10.1038/s41396-018-0150-9 PubMed DOI PMC

Brumpt E. (1932). Longévité du virus de la fièvre boutonneuse (Rickettsia conori, n. sp.) chez la Tique, Rhipicephalus sanguineus. C. R. Soc. Biol. Fil. 110 1199–1202.

Buchanan R. E. (1917). Studies on the nomenclature and classification of the bacteria: III. the families of the Eubacteriales. J. Bacteriol. 2 347–350. 10.1128/jb.2.4.347-350.1917 PubMed DOI PMC

Buddle M. B. (1956). Studies on Brucella ovis (n. sp.), a cause of genital disease of sheep in New Zealand and Australia. J. Hyg. (Lond) 54 351–364. 10.1017/s0022172400044612 PubMed DOI PMC

Bundesanstalt für Arbeitsschutz und Arbeitsmedizin (2015). Technische regel für biologische arbeitsstoffe TRBA 466, einstufung von Prokaryonten (Bacteria und Archaea) in Risikogruppen. Einstufung von Prokaryonten (Bacteria und Archaea) Risikogruppen 25 1–382.

Buonaurio R., Stravato V. M., Kosako Y., Fujiwara N., Naka T., Kobayashi K., et al. (2002). Sphingomonas melonis sp. nov., a novel pathogen that causes brown spots on yellow Spanish melon fruits. Int. J. Syst. Evol. Microbiol. 52 2081–2087. 10.1099/ijs.0.02063-0 PubMed DOI

Busse H. J., Denner E. B. M., Buczolits S., Salkinoja-Salonen M., Bennasar A., Kämpfer P. (2003). Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air- and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas. Int. J. Syst. Evol. Microbiol. 53 1253–1260. 10.1099/ijs.0.02461-0 PubMed DOI

Cai H., Cui H., Zeng Y., An M., Jiang H. (2018a). Sandarakinorhabdus cyanobacteriorum sp. nov., a novel bacterium isolated from cyanobacterial aggregates in a eutrophic lake. Int. J. Syst. Evol. Microbiol. 68 730–735. 10.1099/ijsem.0.002571 PubMed DOI

Cai H., Cui H., Zeng Y., Wang Y., Jiang H. (2018b). Niveispirillum lacus sp. nov., isolated from cyanobacterial aggregates in a eutrophic lake. Int. J. Syst. Evol. Microbiol. 68 507–512. 10.1099/ijsem.0.002526 PubMed DOI

Cai H., Wang Y., Xu H., Yan Z., Jia B., Maszenan A. M., et al. (2015). Niveispirillum cyanobacteriorum sp. nov., a nitrogen-fixing bacterium isolated from cyanobacterial aggregates in a eutrophic lake. Int. J. Syst. Evol. Microbiol. 65 2537–2541. 10.1099/ijs.0.000299 PubMed DOI

Cai M., Wang L., Cai H., Li Y., Tang Y. Q., Wu X. L. (2011a). Rubrimonas shengliensis sp. nov. and Polymorphum gilvum gen. nov., sp. nov., novel members of Alphaproteobacteria from crude oil contaminated saline soil. Syst. Appl. Microbiol. 34 321–327. 10.1016/j.syapm.2011.03.004 PubMed DOI

Cai M., Wang L., Cai H., Li Y., Wang Y.-N., Tang Y.-Q., et al. (2011b). Salinarimonas ramus sp. nov. and Tessaracoccus oleiagri sp. nov., isolated from a crude oil-contaminated saline soil. Int. J. Syst. Evol. Microbiol. 61 1767–1775. 10.1099/ijs.0.025932-0 PubMed DOI

Cai X., Wang Y., Yang X., Liu J., Wu Y., Zhang X.-H. (2017). Paraphaeobacter pallidus gen. nov., sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol. 67 2520–2526. 10.1099/ijsem.0.001935 PubMed DOI

Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., et al. (2009). BLAST+: architecture and applications. BMC Bioinformatics 10:421. 10.1186/1471-2105-10-421 PubMed DOI PMC

Camacho M., Redondo-Gómez S., Rodríguez-Llorente I., Rohde M., Spröer C., Schumann P., et al. (2016). Labrenzia salina sp. nov., isolated from the rhizosphere of the halophyte Arthrocnemum macrostachyum. Int. J. Syst. Evol. Microbiol. 66 5173–5180. 10.1099/ijsem.0.001492 PubMed DOI

Carmichael L. E., Bruner D. W. (1968). Characteristics of a newly-recognized species of Brucella responsible for infectious canine abortions. Cornell Vet. 48 579–592. PubMed

Carro L., Nouioui I., Sangal V., Meier-Kolthoff J. P., Trujillo M. E., Montero-Calasanz M., et al. (2018). Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Sci. Rep. 8:525. 10.1038/s41598-017-17392-0 PubMed DOI PMC

Casida L. E. (1982). Ensifer adhaerens gen. nov., sp. nov.: a bacterial predator of bacteria in soil? Int. J. Syst. Bacteriol. 32 339–345. 10.1099/00207713-32-3-339 DOI

Celador-lera L., Menéndez E., Peix A., Igual J. M., Velázquez E., Rivas R. (2017). Rhizobium zeae sp. nov., isolated from maize (Zea mays L.) roots. Int. J. Syst. Evol. Microbiol. 67 2306–2311. 10.1099/ijsem.0.001944 PubMed DOI

Cha I.-T., Park I., Lee H.-W., Lee H., Park J.-M., Roh S. W., et al. (2016). Pseudoruegeria aestuarii sp. nov., of the family Rhodobacteraceae, isolated from a tidal flat. Int. J. Syst. Evol. Microbiol. 66 3125–3131. 10.1099/ijsem.0.001156 PubMed DOI

Chan E. C. S., Siboo R., Keng T., Psarra N., Hurley R., Cheng S.-L., et al. (1993). Treponema denticola (ex Brumpt 1925) sp. nov., nom. rev., and identification of new Spirochete isolates from periodontal pockets. Int. J. Syst. Bacteriol. 43 196–203. 10.1099/00207713-43-2-196 PubMed DOI

Chang R., Bird L., Barr C., Osburn M., Wilbanks E., Nealson K., et al. (2018). Thioclava electrotropha sp. nov., a versatile electrode and sulfur-oxidizing bacterium from marine sediments. Int. J. Syst. Evol. Microbiol. 68 1652–1658. 10.1099/ijsem.0.002723 PubMed DOI

Chang Y. L., Wang J. Y., Wang E. T., Liu H. C., Sui X. H., Chen W. X. (2011). Bradyrhizobium lablabi sp. nov., isolated from effective nodules of Lablab purpureus and Arachis hypogaea. Int. J. Syst. Evol. Microbiol. 61 2496–2502. 10.1099/ijs.0.027110-0 PubMed DOI

Chen C., Zheng Q., Wang Y. N., Yan X. J., Hao L. K., Du X., et al. (2010). Stakelama pacifica gen. nov., sp. nov., a new member of the family Sphingomonadaceae isolated from the Pacific Ocean. Int. J. Syst. Evol. Microbiol. 60 2857–2861. 10.1099/ijs.0.018945-0 PubMed DOI

Chen C.-X., Zhang X.-Y., Liu C., Yu Y., Liu A., Li G.-W., et al. (2013). Pseudorhodobacter antarcticus sp. nov., isolated from Antarctic intertidal sandy sediment, and emended description of the genus Pseudorhodobacter Uchino et al., 2002 emend. Jung et al. 2012. Int. J. Syst. Evol. Microbiol. 63(Pt 3) 849–854. 10.1099/ijs.0.042184-0 PubMed DOI

Chen H., Jogler M., Rohde M., Klenk H. P., Busse H. J., Tindall B. J., et al. (2012). Reclassification and emended description of Caulobacter leidyi as Sphingomonas leidyi comb. nov., and emendation of the genus Sphingomonas. Int. J. Syst. Evol. Microbiol. 62 2835–2843. 10.1099/ijs.0.039636-0 PubMed DOI

Chen H., Jogler M., Tindall B. J., Klenk H. P., Rohde M., Busse H. J., et al. (2013). Sphingomonas starnbergensis sp. nov., isolated from a prealpine freshwater lake. Int. J. Syst. Evol. Microbiol. 63 1017–1023. 10.1099/ijs.0.042887-0 PubMed DOI

Chen I. M. A., Chu K., Palaniappan K., Pillay M., Ratner A., Huang J., et al. (2019). IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res. 47 D666–D677. 10.1093/nar/gky901 PubMed DOI PMC

Chen M.-H., Sheu S.-Y., Chen C. A., Wang J.-T., Chen W.-M. (2011a). Paracoccus isoporae sp. nov., isolated from the reef-building coral Isopora palifera. Int. J. Syst. Evol. Microbiol. 61 1138–1143. 10.1099/ijs.0.023333-0 PubMed DOI

Chen M.-H., Sheu S.-Y., Chen C. A., Wang J.-T., Chen W.-M. (2011b). Shimia isoporae sp. nov., isolated from the reef-building coral Isopora palifera. Int. J. Syst. Evol. Microbiol. 61 823–827. 10.1099/ijs.0.022848-0 PubMed DOI

Chen M.-H., Sheu S.-Y., Chen C. A., Wang J.-T., Chen W.-M. (2012). Roseivivax isoporae sp. nov., isolated from a reef-building coral, and emended description of the genus Roseivivax. Int. J. Syst. Evol. Microbiol. 62 1259–1264. 10.1099/ijs.0.032961-0 PubMed DOI

Chen M. H., Zhou X. Y., Ou F. H., Xia F., Lv Y. Y., Qiu L. H. (2017a). Aliidongia dinghuensis gen. nov., sp. nov., a poly-β-hydroxybutyrate-producing bacterium isolated from pinus massoniana forest soil. Int. J. Syst. Evol. Microbiol. 67 212–217. 10.1099/ijsem.0.001588 PubMed DOI

Chen S., Xu Y., Zheng C., Ke L. X. (2017b). Marivibrio halodurans gen. nov., sp. nov., a marine bacterium in the family Rhodospirillaceae isolated from underground rock salt. Int. J. Syst. Evol. Microbiol. 67 4266–4271. 10.1099/ijsem.0.002309 PubMed DOI

Chen W., Sheng X.-F., He L.-Y., Huang Z. (2015). Rhizobium yantingense sp. nov., a mineral-weathering bacterium. Int. J. Syst. Evol. Microbiol. 65 412–417. 10.1099/ijs.0.064428-0 PubMed DOI

Chen W. H., Yang S. H., Li Z. H., Zhang X. X., Sui X. H., Wang E. T., et al. (2017c). Ensifer shofinae sp. nov., a novel rhizobial species isolated from root nodules of soybean (Glycine max). Syst. Appl. Microbiol. 40 144–149. 10.1016/j.syapm.2017.01.002 PubMed DOI

Chen W.-M., Cho N.-T., Huang W.-C., Young C.-C., Sheu S.-Y. (2013). Description of Gemmobacter fontiphilus sp. nov., isolated from a freshwater spring, reclassification of Catellibacterium nectariphilum as Gemmobacter nectariphilus comb. nov., Catellibacterium changlense as Gemmobacter changlensis comb. nov., Catellibacterium aquatile as Gemmobacter aquaticus nom. nov., Catellibacterium caeni as Gemmobacter caeni comb. nov., Catellibacterium nanjingense as Gemmobacter nanjingensis comb. nov., and emended description of the genus Gemmobacter and of Gemmobacter aquatilis. Int. J. Syst. Evol. Microbiol. 63 470–478. 10.1099/ijs.0.042051-0 PubMed DOI

Chen W.-M., Zhu W.-F., Bontemps C., Young J. P. W., Wei G. H. (2010). Mesorhizobium alhagi sp. nov., isolated from wild Alhagi sparsifolia in north-western China. Int. J. Syst. Evol. Microbiol. 60 958–962. 10.1099/ijs.0.014043-0 PubMed DOI

Chen W.-X., Tan Z.-Y., Gao J.-L., Li Y., Wang E.-T. (1997). Rhizobium hainanense sp. nov., isolated from tropical legumes. Int. J. Syst. Evol. Microbiol. 47 870–873. 10.1099/00207713-47-3-870 PubMed DOI

Chen X., Li Q. L. G.-D., Lei H., Jiang Y., Han L., Huang X.-S., et al. (2017d). Enterovirga rhinocerotis gen. nov., sp. nov., isolated from Rhinoceros unicornis faeces. Antonie Van Leeuwenhoek 110 553–562. 10.1007/s10482-016-0823-1 PubMed DOI

Chen X., Wang H., Xu J., Song D., Sun G., Xu M. (2016). Sphingobium hydrophobicum sp. nov., a hydrophobic bacterium isolated from electronic-waste-contaminated sediment. Int. J. Syst. Evol. Microbiol. 66 3912–3916. 10.1099/ijsem.0.001287 PubMed DOI

Chen Z., Liu Y., Liu L.-Z., Zhong Z.-P., Liu Z.-P., Liu Y. (2014). Cribrihabitans marinus gen. nov., sp. nov., isolated from a biological filter in a marine recirculating aquaculture system. Int. J. Syst. Evol. Microbiol. 64 1257–1263. 10.1099/ijs.0.059576-0 PubMed DOI

Chen Z., Zhang J., Lei X., Lai Q., Yang L., Zhang H., et al. (2015). Mameliella phaeodactyli sp. nov., a member of the family Rhodobacteraceae isolated from the marine algae Phaeodactylum tricornutum. Int. J. Syst. Evol. Microbiol. 65 1617–1621. 10.1099/ijs.0.000146 PubMed DOI

Chernikova T. N., Dallimore J., Lünsdorf H., Heipieper H. J., Golyshin P. N. (2017). Monaibacterium marinum, gen. nov, sp. nov, a new member of the Alphaproteobacteria isolated from seawater of Menai Straits. Wales, UK. Int. J. Syst. Evol. Microbiol. 67 3310–3317. 10.1099/ijsem.0.002111 PubMed DOI

Cho J.-C., Giovannoni S. J. (2004). Oceanicola granulosus gen. nov., sp. nov. and Oceanicola batsensis sp. nov., poly-β-hydroxybutyrate-producing marine bacteria in the order ‘Rhodobacterales.’. Int. J. Syst. Evol. Microbiol. 54 1129–1136. 10.1099/ijs.0.03015-0 PubMed DOI

Cho J.-C., Giovannoni S. J. (2006). Pelagibaca bermudensis gen. nov., sp. nov., a novel marine bacterium within the Roseobacter clade in the order Rhodobacterales. Int. J. Syst. Evol. Microbiol. 56 855–859. 10.1099/ijs.0.64063-0 PubMed DOI

Cho Y.-J., Yi H., Seo B., Cho K. H., Chun J. (2013). Fretibacter rubidus gen. nov., sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol. 63 4633–4638. 10.1099/ijs.0.053751-0 PubMed DOI

Choi D. H., Cho B. C. (2006). Citreimonas salinaria gen. nov., sp. nov., a member of the Roseobacter clade isolated from a solar saltern. Int. J. Syst. Evol. Microbiol. 56 2799–2803. 10.1099/ijs.0.64373-0 PubMed DOI

Choi D. H., Cho J.-C., Lanoil B. D., Giovannoni S. J., Cho B. C. (2007). Maribius salinus gen. nov., sp. nov., isolated from a solar saltern and Maribius pelagius sp. nov., cultured from the Sargasso Sea, belonging to the Roseobacter clade. Int. J. Syst. Evol. Microbiol. 57(Pt 2) 270–275. 10.1099/ijs.0.64552-0 PubMed DOI

Choi D. H., Hwang C. Y., Cho B. C. (2009). Pelagibius litoralis gen. nov., sp. nov., a marine bacterium in the family Rhodospirillaceae isolated from coastal seawater. Int. J. Syst. Evol. Microbiol. 59 818–823. 10.1099/ijs.0.002774-0 PubMed DOI

Choi D. H., Yi H., Chun J., Cho B. C. (2006). Jannaschia seosinensis sp. nov., isolated from hypersaline water of a solar saltern in Korea. Int. J. Syst. Evol. Microbiol. 56 45–49. 10.1099/ijs.0.63835-0 PubMed DOI

Choi E. J., Lee H. J., Kim J. M., Jeon C. O. (2013). Roseovarius lutimaris sp. nov., isolated from a marine tidal flat. Int. J. Syst. Evol. Microbiol. 63(Pt 10) 3835–3840. 10.1099/ijs.0.050807-0 PubMed DOI

Choi G., Gao M., Lee D., Choi H. (2017). Mabikibacter ruber gen. nov., sp. nov., a bacterium isolated from marine sediment, and proposal of Mabikibacteraceae fam. nov. in the class Alphaproteobacteria. Int. J. Syst. Evol. Microbiol. 67 3375–3380. 10.1099/ijsem.0.002121 PubMed DOI

Chu C., Yuan C., Liu X., Yao L., Zhu J., He J., et al. (2015). Phenylobacterium kunshanense sp. nov., isolated from the sludge of a pesticide manufacturing factory. Int. J. Syst. Evol. Microbiol. 65(Pt 2) 325–330. 10.1099/ijs.0.063644-0 PubMed DOI

Cleenwerck I., Vandemeulebroecke K., Janssens D., Swings J. (2002). Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov. Int. J. Syst. Evol. Microbiol. 52(Pt 5) 1551–1558. 10.1099/ijs.0.02064-0 PubMed DOI

Coenye T., Goris J., Spilker T., Vandamme P., LiPuma J. J. (2002). Characterization of unusual bacteria isolated from respiratory secretions of cystic fibrosis patients and description of Inquilinus limosus gen. nov., sp. nov. J. Clin. Microbiol. 40 2062–2069. 10.1128/JCM.40.6.2062-2069.2002 PubMed DOI PMC

Coil D. A., Flanagan J. C., Stump A., Alexiev A., Lang J. M., Eisen J. A. (2015). Porphyrobacter mercurialis sp. nov., isolated from a stadium seat and emended description of the genus Porphyrobacter. PeerJ 3:e1400. 10.7717/peerj.1400 PubMed DOI PMC

Cole J. K., Morton B. R., Cardamone H. C., Lake H. R. R., Dohnalkova A. C., Kim Y. M., et al. (2018). Salinivirga fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from a photosynthetic mat, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu Y. et al., 2010 into Salinarimonadaceae. 2010 into Salinarimonadaceae. Int. J. Syst. Evol. Microbiol. 68 1591–1598. 10.1099/ijsem.0.002715 PubMed DOI

Cole S. T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., et al. (1998). Deciphering the biology of mycobacterium tuberculosis from the complete genome sequence. Nature 393 537–544. 10.1038/31159 PubMed DOI

Colwell R. R. (1970). Polyphasic taxonomy of the genus vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J. Bacteriol. 104 410–433. 10.1128/jb.104.1.410-433.1970 PubMed DOI PMC

Conn H. J. (1938). Taxonomic relationships of certain non-sporeforming rods in soil. J. Bacteriol. 36 320–321.

Conn H. J. (1942). Validity of the genus Alcalignes. J. Bacteriol. 44 353–360. PubMed PMC

Cordeiro A. B., Ribeiro R. A., Helene L. C. F., Hungria M. (2017). Rhizobium esperanzae sp. nov., a N2-fixing root symbiont of Phaseolus vulgaris from Mexican soils. Int. J. Syst. Evol. Microbiol. 67 3937–3945. 10.1099/ijsem.0.002225 PubMed DOI

Coton M., Laplace J. M., Auffray Y., Coton E. (2006). Polyphasic study of Zymomonas mobilis strains revealing the existence of a novel subspecies Z. mobilis subsp. francensis subsp. nov., isolated from French cider. Int. J. Syst. Evol. Microbiol. 56 121–125. 10.1099/ijs.0.63732-0 PubMed DOI

Cwyk W. M., Canale-Parola E. (1979). Treponema succinifaciens sp. nov., an aerobic Spirochete from the swine intestine. Arch. Microbiol. 122 231–239. 10.1007/bf00411285 PubMed DOI

da Rocha-Lima H. (1916). Zur aetiologie des fleckfeibers. Berliner Klin. Wochenschr. 53 567–569.

Dadhwal M., Jit S., Kumari H., Lal R. (2009). Sphingobium chinhatense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite. Int. J. Syst. Evol. Microbiol. 59 3140–3144. 10.1099/ijs.0.005553-0 PubMed DOI

Dahal R. H., Chaudhary D. K., Kim J. (2018). Pinisolibacter ravus gen. nov., sp. nov., isolated from pine forest soil and allocation of the genera Ancalomicrobium and pinisolibacter to the family ancalomicrobiaceae fam. nov., and emendation of the genus Ancalomicrobium staley 1968. Int. J. Syst. Evol. Microbiol. 68 1955–1962. 10.1099/ijsem.0.002772 PubMed DOI

Dai X., Shi X., Gao X., Liang J., Zhang X.-H. (2015). Salipiger nanhaiensis sp. nov., a bacterium isolated from deep sea water. Int. J. Syst. Evol. Microbiol. 65 1122–1126. 10.1099/ijs.0.000066 PubMed DOI

Dai X., Wang B.-J., Yang Q.-X., Jiao N.-Z., Liu S.-J. (2006). Yangia pacifica gen. nov., sp. nov., a novel member of the Roseobacter clade from coastal sediment of the East China Sea. Int. J. Syst. Evol. Microbiol. 56 529–533. 10.1099/ijs.0.64013-0 PubMed DOI

Daneshvar M. I., Hollis D. G., Weyant R. S., Steigerwalt A. G., Whitney A. M., Douglas Michael P., et al. (2003). Paracoccus yeeii sp. nov. (formely CDC group EO-2), a novel bacterial species associated with human infection. J. Clin. Microbiol. 41 1289–1294. 10.1128/JCM.41.3.1289 PubMed DOI PMC

Das S. K., Mishra A. K., Tindall B. J., Rainey F. A., Stackebrandt E. (1996). Oxidation of Thiosulfate by a new bacterium, Bosea thiooxidans (strain BI-42) gen. nov., sp. nov.: analysis of phylogeny based on chemotaxonomy and 16s ribosomal DNA sequencing. Int. J. Syst. Bacteriol. 46 981–987. 10.1099/00207713-46-4-981 PubMed DOI

Davis D. H., Doudoroff M., Stanier R. Y., Mandel M. (1969). Proposal to reject the genus Hydrogenomonas: taxonomic implications. Int. J. Syst. Bacteriol. 19 375–390. 10.1099/00207713-19-4-375 DOI

de Lajudie P., Laurent-Fulele E., Wiilerns A., Torck U., Coopman R., Collin M. D., et al. (1998). Allorhizobium undicola gen. nov., sp. nov., nitrogen-fixing bacteria that efficiently nodulate Neptunia natans in Senegal. Int. J. Syst. Evol. Microbiol. 48 1277–1290. 10.1099/00207713-48-4-1277 PubMed DOI

De Ley J., Frateur J. (1974). “Genus Acetobacter Beijerinck, 1898,” in Bergey’s Manual of Determinative Bacteriology, 8th Edn, eds Buchanan R. E., Gibbons N. E. (Baltimore, MD: The Williams & Wilkins Co; ), 276–278.

De Ley J., Swings J. (1976). Phenotypic description, numerical analysis, and proposal for an improved taxonomy and nomenclature of the genus Zymomonas Kluyver and van Niel 1936. Int. J. Syst. Evol. Microbiol. 26 146–157. 10.1099/00207713-26-2-146 DOI

De Meyer S. E., Willems A. (2012). Multilocus sequence analysis of Bosea species and description of Bosea lupini sp. nov., Bosea lathyri sp. nov. and Bosea robiniae sp. nov., isolated from legumes. Int. J. Syst. Evol. Microbiol. 62 2505–2510. 10.1099/ijs.0.035477-0 PubMed DOI

Dedysh S. N., Haupt E. S., Dunfield P. F. (2016). Emended description of the family Beijerinckiaceae and transfer of the genera Chelatococcus and Camelimonas to the family Chelatococcaceae fam. nov. Int. J. Syst. Evol. Microbiol. 66 3177–3182. 10.1099/ijsem.0.001167 PubMed DOI

Dedysh S. N., Khmelenina V. N., Suzina N. E., Trotsenko Y. A., Semrau J. D., Liesack W., et al. (2002). Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog. Int. J. Syst. Evol. Microbiol. 52 251–261. 10.1099/00207713-52-1-251 PubMed DOI

Defosse D. L., Johnson R. C., Paster B. J., Dewhirst F. E., Fraser G. J. (1995). Brevinema andersonii gen. nov., sp. nov., an infectious spirochete isolated from the short-tailed shrew (Blarina brevicauda) and the white-footed mouse (Peromyscus leucopus). Int. J. Syst. Bacteriol. 45 78–84. 10.1099/00207713-45-1-78 PubMed DOI

Dehio C., Lanz C., Pohl R., Behrens P., Bermond D., Piémont Y., et al. (2001). Bartonella schoenbuchii sp. nov., isolated from the blood of wild roe deer. Int. J. Syst. Evol. Microbiol. 51 1557–1565. 10.1099/00207713-51-4-1557 PubMed DOI

Delamuta J. R. M., Ribeiro R. A., Ormeño-Orillo E., Parma M. M., Melo I. S., Martínez-Romero E., et al. (2015). Bradyrhizobium tropiciagri sp. nov. and Bradyrhizobium embrapense sp. nov., nitroen-fixing symbionts of tropical forage legumes. Int. J. Syst. Evol. Microbiol. 65 4424–4433. 10.1099/ijsem.0.000592 PubMed DOI

Deng Z.-S., Zhao L.-F., Xu L., Kong Z.-Y., Zhao P., Qin W., et al. (2011). Paracoccus sphaerophysae sp. nov, a siderophore-producing, endophytic bacterium isolated from root nodules of Sphaerophysa salsula. Int. J. Syst. Evol. Microbiol. 61 665–669. 10.1099/ijs.0.021071-0 PubMed DOI

Denner E. B. M., Kämpfer P., Busse H.-J., Moore E. R. B. (1999). Reclassification of Pseudomonas echinoides Heumann 1962, 343AL, in the genus Sphingomonas as Sphingomonas echinoides comb. nov. Int. J. Syst. Bacteriol. 49 1103–1109. 10.1099/00207713-49-3-1103 PubMed DOI

Denner E. B. M., Paukner S., Kämpfer P., Moore E. R. B., Abraham W.-R., Busse H.-J., et al. (2001). Sphingomonas pituitosa sp. nov., an exopolysaccharide-producing bacterium that secretes an unusual type of sphingan. Int. J. Syst. Evol. Microbiol. 51 827–841. 10.1099/00207713-51-3-827 PubMed DOI

Derx H. G. (1950). Beijerinckia, a new genus of nitrogen-fixing bacteria occurring in tropical soils. Proc. K. Ned. Akad. van Wet. Ser. C 53 140–147.

Desper R., Gascuel O. (2004). Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol. Biol. Evol. 21 587–598. 10.1093/molbev/msh049 PubMed DOI

Desper R., Gascuel O. (2006). Getting a tree fast: neighbor joining, FastME, and distance-based methods. Curr. Protoc. Bioinformatics Chapter 6 Unit 6.3. 10.1002/0471250953.bi0603s15 PubMed DOI

Díaz-Cárdenas C., Patel B. K. C., Baena S. (2010). Tistlia consotensis gen. nov., sp. nov., an aerobic, chemoheterotrophic, freel-living, nitrogen-fixing alphaproteobacterium, isolated from a Colombian saline spring. Int. J. Syst. Evol. Microbiol. 60 1437–1443. 10.1099/ijs.0.010926-0 PubMed DOI

Donachie S. P., Bowman J. P., Alam M. (2006). Nesiotobacter exalbescens gen. nov., sp. nov., a moderately thermophilic alphaproteobacterium from an Hawaiian hypersaline lake. Int. J. Syst. Evol. Microbiol. 56 563–567. 10.1099/ijs.0.63440-0 PubMed DOI

Dong C., Lai Q., Chen L., Sun F., Shao Z., Yu Z. (2010). Oceanibaculum pacificum sp. nov., isolated from hydrothermal field sediment of the south-west Pacific Ocean. Int. J. Syst. Evol. Microbiol. 60 219–222. 10.1099/ijs.0.011932-0 PubMed DOI

Doronina N. V., Braus-Stromeyer S. A., Leisinger T., Trotsenko Y. A. (1995). Isolation and characterization of a new facultatively methylotrophic bacterium: description of Methylorhabdus multivorans, gen. nov., sp. nov. Syst. Appl. Microbiol. 18 92–98. 10.1016/S0723-2020(11)80454-6 DOI

Doronina N. V., Kaparullina E. N., Trotsenko Y. A., Nörtemann B., Bucheli-Witschel M., Weilenmann H.-U., et al. (2010). Chelativorans multitrophicus gen. nov., sp. nov. and Chelativorans oligotrophicus sp. nov., aerobic EDTA-degrading bacteria. Int. J. Syst. Evol. Microbiol. 60 1044–1051. 10.1099/ijs.0.003152-0 PubMed DOI

Doronina N. V., Poroshina M. N., Kaparullina E. N., Ezhov V. A., Trotsenko Y. A. (2013). Methyloligella halotolerans gen. nov., sp. nov. and Methyloligella solikamskensis sp. nov., two non-pigmented halotolerant obligately methylotrophic bacteria isolated from the Ural saline environments. Syst. Appl. Microbiol. 36 148–154. 10.1016/j.syapm.2012.12.001 PubMed DOI

Doronina N. V., Trotsenko Y. A., Tourova T. P. (2000). Methylarcula marina gen. nov., sp. nov. and Methylarcula terricola sp. nov.: novel aerobic, moderately halophilic, facultatively methylotrophic bacteria from coastal saline environments. Int. J. Syst. Evol. Microbiol. 50 1849–1859. 10.1099/00207713-50-5-1849 PubMed DOI

Douglas H. C. (1957). “Order III. Hyphomicrobiales Douglas, ordo nov,” in Bergey’s Manual of Determinative Bacteriology, 7th Edn, eds Breed R. S., Murray E. G. D., Smith N. R. (Baltimore, MD: The Williams and Wilkins Co; ), 276.

Dreyfus B., Garcia J. L., Gillis M. (1988). Characerization of Azorhizobium caulinodans gen. nov., sp. nov., a stem-nodulating nitrogen-fixing bacterium isolated from Sesbania rostrata. Int. J. Syst. Bacteriol. 38 89–98. 10.1099/00207713-38-1-89 DOI

Droz S., Chi B., Horn E., Steigerwalt A. G., Whitney A. M., Brenner D. J. (1999). Bartonella koehlerae sp. nov., isolated from cats. J. Clin. Microbiol. 37 1117–1122. 10.1128/jcm.37.4.1117-1122.1999 PubMed DOI PMC

Duchow E., Douglas H. C. (1949). Rhodomicrobium vannielii, a new photoheterotrophic bacterium. J. Bacteriol. 58 409–416. 10.1128/jb.58.4.409-416.1949 PubMed DOI PMC

Duh D., Punda-Polic V., Avsic-Zupanc T., Bouyer D., Walker D. H., Popov V. L., et al. (2010). Rickettsia hoogstraalii sp. nov., isolated from hard- and soft-bodied ticks. Int. J. Syst. Evol. Microbiol. 60 977–984. 10.1099/ijs.0.011049-0 PubMed DOI

Dumler J. S., Barbet A. F., Bekker C. P. J., Dasch G. A., Palmer G. H., Ray S. C., et al. (2001). Reorganization of genera in the families Rickettsiaceae and Anaplasmataceae in the order Rickettsiales: unification of some species of Ehrlichia with Anaplasma, Cowdria with Ehrlichia and Ehrlichia with Neorickettsia, descriptions of six new species combinations and designation of Ehrlichia equi and ‘HGE agent’ as subjective synonyms of Ehrlichia phagocytophila. Int. J. Syst. Evol. Microbiol. 51 2145–2165. 10.1099/00207713-51-6-2145 PubMed DOI

Dunfield P. F., Khmelenina V. N., Suzina N. E., Trotsenko Y. A., Dedysh S. N. (2003). Methylocella silvestris sp. nov., a novel methanotroph isolated from an acidic forest cambisol. Int. J. Syst. Evol. Microbiol. 53 1231–1239. 10.1099/ijs.0.02481-0 PubMed DOI

Dutta D., Gachhui R. (2006). Novel nitrogen-fixing Acetobacter nitrogenifigens sp. nov., isolated from Kombucha tea. Int. J. Syst. Evol. Microbiol. 56 1899–1903. 10.1099/ijs.0.64101-0 PubMed DOI

Dziuba M., Koziaeva V., Grouzdev D., Burganskaya E., Baslerov R., Kolganova T., et al. (2016). Magnetospirillum caucaseum sp. nov., Magnetospirillum marisnigri sp. nov. and Magnetospirillum moscoviense sp. nov., freshwater magnetotactic bacteria isolated from three distinct geographical locations in European Russia. Int. J. Syst. Evol. Microbiol. 66 2069–2077. 10.1099/ijsem.0.000994 PubMed DOI

Emerson D., Rentz J. A., Lilburn T. G., Davis R. E., Aldrich H., Chan C., et al. (2007). A novel lineage of Proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities. PLoS One 2:e667. 10.1371/journal.pone.0000667 PubMed DOI PMC

Enright A. J., Van Dongen S., Ouzounis C. A. (2002). An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30 1575–1584. 10.1093/nar/30.7.1575 PubMed DOI PMC

Eremeeva M. E., Gerns H. L., Lydy S. L., Goo J. S., Ryan E. T., Mathew S. S., et al. (2007). Bacteremia, fever, and splenomegaly caused by a newly recognized Bartonella species. N. Engl. J. Med. 356 2381–2387. 10.1056/nejmoa065987 PubMed DOI

Faine S., Stallman N. D. (1982). Amended descriptions of the genus Leptospira Noguchi 1917 and the species L. interrogans (Stimson 1907) Wenyon 1926 and L. biflexa (Wolbach and Binger 1914) Noguchi 1918. Int. J. Syst. Bacteriol. 32 461–463. 10.1099/00207713-32-4-461 DOI

Falk E. C., Döbereiner J., Johnson J. L., Krieg N. R. (1985). Deoxyribonucleic acid homology of Azospirillum amazonense Magalhães et al. 1984 and emendation of the description of the genus Azospirillum. Int. J. Syst. Bacteriol. 35 117–118. 10.1099/00207713-35-1-117 DOI

Falush D., Torpdahl M., Didelot X., Conrad D. F., Wilson D. J., Achtman M. (2006). Mismatch induced speciation in Salmonella: model and data. Philos. Trans. R. Soc. B Biol. Sci. 361 2045–2053. 10.1098/rstb.2006.1925 PubMed DOI PMC

Farrand S. K., van Berkum P. B., Oger P. (2003). Agrobacterium is a definable genus of the family Rhizobiaceae. Int. J. Syst. Evol. Microbiol. 53 1681–1687. 10.1099/ijs.0.02445-0 PubMed DOI

Farris J. S. (1974). Formal definitions of paraphyly and polyphyly. Syst. Zool. 23 548–554. 10.2307/2412474 PubMed DOI

Farris J. S. (1977). Phylogenetic analysis under Dollo’s Law. Syst. Zool. 26 77–88. 10.1093/sysbio/26.1.77 DOI

Farris J. S. (1989). The retention index and homoplasy excess. Syst. Biol. 38 406–407. 10.2307/2992406 DOI

Felföldi T., Vengring A., Márialigeti K., András J., Schumann P., Tóth E. M. (2014). Hephaestia caeni gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from activated sludge. Int. J. Syst. Evol. Microbiol. 64 738–744. 10.1099/ijs.0.053736-0 PubMed DOI

Feng G., Da Yang S. Z., Wang Y. H., Zhang X. X., Zhao G. Z., Deng M. R., et al. (2014). Description of a Gram-negative bacterium, Sphingomonas guangdongensis sp. nov. Int. J. Syst. Evol. Microbiol. 64 1697–1702. 10.1099/ijs.0.056853-0 PubMed DOI

Feng X.-M., Mo Y.-X., Han L., Nogi Y., Zhu Y.-H., Lv J. (2015). Qipengyuania sediminis gen. nov., sp. nov., a member of the family Erythrobacteraceae isolated from subterrestrial sediment. Int. J. Syst. Evol. Microbiol. 65 3658–3665. 10.1099/ijsem.0.000472 PubMed DOI

Flores-Félix J. D., Carro L., Velázquez E., Valverde Á, Cerda-Castillo E., García-Fraile P., et al. (2013). Phyllobacterium endophyticum sp. nov., isolated from nodules of Phaseolus vulgaris. Int. J. Syst. Evol. Microbiol. 63 821–826. 10.1099/ijs.0.038497-0 PubMed DOI

Foesel B. U., Drake H. L., Schramm A. (2011). Defluviimonas denitrificans gen. nov., sp. nov., and Pararhodobacter aggregans gen. nov. sp. nov., non-phototrophic Rhodobacteraceae from the biofilter of a marine aquaculture. Syst. Appl. Microbiol. 34 498–502. 10.1016/j.syapm.2011.08.006 PubMed DOI

Foesel B. U., Größner A. S., Drake H. L., Schramm A. (2007). Geminicoccus roseus gen. nov., sp. nov., an aerobic phototrophic Alphaproteobacterium isolated from a marine aquaculture biofilter. Syst. Appl. Microbiol. 30 581–586. 10.1016/j.syapm.2007.05.005 PubMed DOI

Foster G., Osterman B. S., Godfroid J., Jacques I., Cloeckaert A. (2007). Brucella ceti sp. nov. and Brucella pinnipedialis sp. nov. for Brucella strains with cetaceans and seals as their preferred hosts. Int. J. Syst. Evol. Microbiol. 57 2688–2693. 10.1099/ijs.0.65269-0 PubMed DOI

Fournier P.-E., Dumler J. S., Greub G., Zhang J., Wu Y., Raoult D. (2003). Gene sequence-based criteria for identification of new Rickettsia isolates and description of Rickettsia heilongjiangensis sp. nov. J. Clin. Microbiol. 41 5456–5465. 10.1128/JCM.41.12.5456 PubMed DOI PMC

Fournier P.-E., Grunnenberger F., Jaulhac B., Gastinger G., Raoult D. (2000). Evidence of Rickettsia helvetica infection in Humans, eastern France. Emerg. Infect. Dis. 6 389–392. 10.3201/eid0604.000412 PubMed DOI PMC

Fournier P.-E., Takada N., Fujita H., Raoult D. (2006). Rickettsia tamurae sp. nov., isolated from Amblyomma testudinarium ticks. Int. J. Syst. Evol. Microbiol. 56 1673–1675. 10.1099/ijs.0.64134-0 PubMed DOI

Fox J. E., Gulledge J., Engelhaupt E., Burow M. E., McLachlan J. A. (2007). Pesticides reduce symbiotic efficiency of nitrogen-fixing rhizobia and host plants. PNAS 104 10282–10287. 10.1073/pnas.0611710104 PubMed DOI PMC

Francis I. M., Jochimsen K. N., De Vos P., van Bruggen A. H. C. (2014). Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. Int. J. Syst. Evol. Microbiol. 64 1340–1350. 10.1099/ijs.0.058909-0 PubMed DOI

Frank B. (1889). Über die pilzsymbiose der leguminosen. Ber. Dtsch. Bot. Ges. 7 332–346.

Frank O., Goker M., Pradella S., Petersen J. (2015). Ocean’s twelve: flagellar and biofilm chromids in the multipartite genome of Marinovum algicola DG898 exemplify functional compartmentalization. Environ. Microbiol. 17 4019–4034. 10.1111/1462-2920.12947 PubMed DOI

Fritz I., Strömpl C., Abraham W.-R. (2004). Phylogenetic relationships of the genera Stella, Labrys and Angulomicrobium within the “Alphaproteobacteria” and description of Angulomicrobium amanitiforme sp. nov. Int. J. Syst. Evol. Microbiol. 54 651–657. 10.1099/ijs.0.02746-0 PubMed DOI

Fuerst J. A., Hawkins J. A., Holmes A., Sly L. I., Moore C. J., Stackebrandt E. (1993). Porphyrobacter neustonensis gen. nov., sp. nov., an aerobic bacteriochlorophyll-synthesizing budding bacterium from fresh water. Int. J. Syst. Bacteriol. 43 125–134. 10.1099/00207713-43-1-125 PubMed DOI

Fujii K., Satomi M., Morita N., Motomura T., Tanaka T., Kikuchi S. (2003). Novosphingobium tardaugens sp. nov., an oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo. Int. J. Syst. Evol. Microbiol. 53 47–52. 10.1099/ijs.0.02301-0 PubMed DOI

Fukuda W., Chino Y., Araki S., Kondo Y., Imanaka H., Kanai T., et al. (2014). Polymorphobacter multimanifer gen. nov., sp. nov., a polymorphic bacterium isolated from antarctic white rock. Int. J. Syst. Evol. Microbiol. 64 2034–2040. 10.1099/ijs.0.050005-0 PubMed DOI

Fukuda W., Yamada K., Miyoshi Y., Okuno H., Atomi H., Imanaka T. (2012). Rhodoligotrophos appendicifer gen. nov., sp. nov., an appendaged bacterium isolated from a freshwater Antarctic lake. Int. J. Syst. Evol. Microbiol. 62 1945–1950. 10.1099/ijs.0.032953-0 PubMed DOI

Fukui Y., Abe M., Kobayashi M., Saito H., Oikawa H., Yano Y., et al. (2013). Algimonas porphyrae gen. nov., sp. nov., a member of the family Hyphomonadaceae, isolated from the red alga Porphyra yezoensis. Int. J. Syst. Evol. Microbiol. 63 314–320. 10.1099/ijs.0.040485-0 PubMed DOI

Furuhata K., Miyamoto H., Goto K., Kato Y., Hara M., Fukuyama M. (2008). Roseomonas stagni sp. nov., isolated from pond water in Japan. J. Gen. Appl. Microbiol. 54 167–171. 10.2323/jgam.54.167 PubMed DOI

Galatis H., Martin K., Kämpfer P., Glaeser S. P. (2013). Devosia epidermidihirudinis sp. nov. isolated from the surface of a medical leech. Antonie Van Leeuwenhoek 103 1165–1171. 10.1007/s10482-013-9895-3 PubMed DOI

Gallego S., Vila J., Nieto J. M., Urdiain M., Rosselló-Móra R., Grifoll M. (2010). Breoghania corrubedonensis gen. nov. sp. nov., a novel alphaproteobacterium isolated from a Galician beach (NW Spain) after the prestige fuel oil spill, and emended description of the family Cohaesibacteraceae and the species Cohaesibacter gelatinilyticus. Syst. Appl. Microbiol. 33 316–321. 10.1016/j.syapm.2010.06.005 PubMed DOI

Gao J., Sun P., Wang X., Lv F., Mao X., Sun J. (2017). Rhizobium wenxiniae sp. nov., an endophytic bacterium isolated from maize root. Int. J. Syst. Evol. Microbiol. 67 2798–2803. 10.1099/ijsem.0.002025 PubMed DOI

Gao J.-L., Turner S. L., Kan F. L., Wang E. T., Tan Z. Y., Qiu Y. H., et al. (2004). Mesorhizobium septentrionale sp. nov. and Mesorhizobium temperatum sp. nov., isolated from Astragalus adsurgens growing in the northern regions of China. Int. J. Syst. Evol. Microbiol. 54 2003–2012. 10.1099/ijs.0.02840-0 PubMed DOI

García-Fraile P., Rivas R., Willems A., Peix A., Martens M., Martínez-Molina E., et al. (2007). Rhizobium cellulosilyticum sp. nov., isolated from sawdust of Populus alba. Int. J. Syst. Evol. Microbiol. 57 844–848. 10.1099/ijs.0.64680-0 PubMed DOI

Garg N., Bala K., Lal R. (2012). Sphingobium lucknowense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from HCH-contaminated soil. Int. J. Syst. Evol. Microbiol. 62 618–623. 10.1099/ijs.0.028886-0 PubMed DOI

Garrity G. M., Bell J. A., Lilburn T. (2005a). “Class I. Alphaproteobacteria class. nov,” in Bergey’s Manual of Systematic Bacteriology: The Proteobacteria, (Part C), Vol. 2 eds Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. (New York, NY: Springer; ).

Garrity G. M., Bell J. A., Lilburn T. (2005b). “Family I. Rhodobacteraceae fam. nov,” in Bergey’s Manual of Systematic Bacteriology: The Proteobacteria, (Part C), Vol. 2 eds Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. (New York, NY: Springer; ), 161.

Garrity G. M., Bell J. A., Lilburn T. (2005c). “Family IX. Methylobacteriaceae fam. nov,” in Bergey’s Manual of Systematic Bacteriology: The Proteobacteria, (Part C), Vol. 2 eds Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. (New York, NY: Springer; ), 567.

Garrity G. M., Bell J. A., Lilburn T. (2005d). “Family VI. Beijerinckiaceae fam. nov,” in Bergey’s Manual of Systematic Bacteriology: The Proteobacteria, (Part C), Vol. 2 eds Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. (New York, NY: Springer; ), 422.

Garrity G. M., Bell J. A., Lilburn T. (2005e). “Family VII. Bradyrhizobiaceae fam. nov,” in Bergey’s Manual of Systematic Bacteriology: The Proteobacteria, (Part C), Vol. 2 eds Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. (New York, NY: Springer; ), 438.

Garrity G. M., Bell J. A., Lilburn T. (2005f). “Family X. Rhodobiaceae fam. nov,” in Bergey’s Manual of Systematic Bacteriology: The Proteobacteria, (Part C), Vol. 2 eds Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. (New York, NY: Springer; ), 571.

Garrity G. M., Bell J. A., Lilburn T. G. (2003a). Taxonomic Outline of the Procaryotes, 2nd Edn New York, NY: Springer.

Garrity G. M., Bell J. A., Lilburn T. G. (2003b). Taxonomic Outline of the Prokaryotes, Bergey’s Manual of Systematic Bacteriology, Release 4.0, 2nd Edn New York, NY: Springer.

Garrity G. M., Lilburn T. G., Cole J. R., Harrison S. H., Euzéby J., Tindall B. J. (2007). Taxonomic Outline of the Bacteria and Archaea, Release 7.7 March 6, 2007. Part 3 – the bacteria: phylum “Proteobacteria”, class Alphaproteobacteria (East Lansing: Michigan State University; ).

Geng S., Pan X. C., Mei R., Wang Y. N., Sun J. Q., Liu X. Y., et al. (2014). Paradevosia shaoguanensis gen. nov. sp. nov. isolated from a Coking Wastewater. Curr. Microbiol. 70 110–118. 10.1007/s00284-014-0689-2 PubMed DOI

Gerpe D., Buján N., Diéguez A. L., Lasa A., Romalde J. L. (2017). Kiloniella majae sp. nov., isolated from spider crab (Maja brachydactyla) and pullet carpet shell clam (Venerupis pullastra). Syst. Appl. Microbiol. 40 274–279. 10.1016/j.syapm.2017.05.002 PubMed DOI

Geueke B., Busse H.-J., Fleischmann T., Kämpfer P., Kohler H. E. (2007). Description of Sphingosinicella xenopeptidilytica sp. nov., a β-peptide-degrading species, and emended descriptions of the genus Sphingosinicella and the species Sphingosinicella microcystinivorans. Int. J. Syst. Evol. Microbiol. 57 107–113. 10.1099/ijs.0.64509-0 PubMed DOI

Ghosh W., Mandal S., Roy P. (2006). Paracoccus bengalensis sp. nov., a novel sulfur-oxidizing chemolithoautotroph from the rhizospheric soil of an Indian tropical leguminous plant. Syst. Appl. Microbiol. 29 396–403. 10.1016/j.syapm.2005.10.004 PubMed DOI

Gich F., Overmann J. (2006). Sandarakinorhabdus limnophila gen. nov., sp. nov., a novel bacteriochlorophyll α-containing, obligately aerobic bacterium isolated from freshwater lakes. Int. J. Syst. Evol. Microbiol. 56 847–854. 10.1099/ijs.0.63970-0 PubMed DOI

Giesberger G. (1947). Some observations on the culture, physiology and morphology of some brown-red Rhodospirillum-species. Antonie Van Leeuwenhoek 13 135–148. 10.1007/bf02272755 DOI

Gillis M., De Ley J. (1980). Intra- and intergeneric similarities of the ribosomal ribonucleic acid cistrons of Acetobacter and Gluconobacter. Int. J. Syst. Bacteriol. 30 7–27. 10.1099/00207713-30-1-7 DOI

Gillis P., Vandamme P., De Vos P., Swings J., Kersters K. (2005). “Polyphasic taxonomy,” in Bergey’s Manual of Systematic Bacteriology: The Proteobacteria (Part A), Vol. 2 eds Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. (New York, NY: Springer Verlag; ), 43–48. 10.1007/0-387-28021-9_7 DOI

Girija K. R., Sasikala C., Ramana C. V., Spröer C., Takaichi S., Thiel V., et al. (2010). Rhodobacter johrii sp. nov., an endospore-producing cryptic species isolated from semi-arid tropical soils. Int. J. Syst. Evol. Microbiol. 60 2099–2107. 10.1099/ijs.0.011718-0 PubMed DOI

Glaeser J., Overmann J. (1999). Selective enrichment and characterization of Roseospirillum parvum, gen. nov. and sp. nov., a new purple nonsulfur bacterium with unusual light absorption properties. Arch. Microbiol. 11 405–416. 10.1007/s002030050727 PubMed DOI

Glaeser S. P., Galatis H., Martin K., Kämpfer P. (2013). Niabella hirudinis and Niabella drilacis sp. nov., isolated from the medicinal leech Hirudo verbana. Int. J. Syst. Evol. Microbiol. 63 3487–3493. 10.1099/ijs.0.050823-0 PubMed DOI

Glaeser S. P., Kämpfer P. (2015). Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst. Appl. Microbiol. 38 237–245. 10.1016/j.syapm.2015.03.007 PubMed DOI

Glaeser S. P., Kämpfer P., Busse H.-J., Langer S., Glaeser J. (2009). Novosphingobium acidiphilum sp. nov., an acidophilic salt-sensitive bacterium isolated from the humic acid-rich Lake Grosse Fuchskuhle. Int. J. Syst. Evol. Microbiol. 59 323–330. 10.1099/ijs.0.65852-0 PubMed DOI

Goloboff P. A., Farris J. S., Nixon K. C. (2008). TNT, a free program for phylogenetic analysis. Cladistics 24 774–786. 10.1111/j.1096-0031.2008.00217.x DOI

González J. M., Covert J. S., Whitman W. B., Henriksen J. R., Mayer F., Scharf B., et al. (2003). Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. Int. J. Syst. Evol. Microbiol. 53 1261–1269. 10.1099/ijs.0.02491-0 PubMed DOI

Gossling J., Moore W. E. C. (1975). Gemmiger formicilis, n.gen., n.sp., an anaerobic budding bacterium from intestines. Int. J. Syst. Bacteriol. 25 202–207. 10.1099/00207713-25-2-202 DOI

Gray P. H. H., Thornton H. G. (1928). Soil bacteria that decompose certain aromatic compounds. Zentralblatt für Bakteriol. Parasitenkunde Infekt. und Hyg. Abteilung II 73 74–96.

Green P. N., Ardley J. K. (2018). Review of the genus Methylobacterium and closely related organisms: a proposal that some Methylobacterium species be reclassified into a new genus, Methylorubrum gen. nov. Int. J. Syst. Evol. Microbiol. 68 2727–2748. 10.1099/ijsem.0.002856 PubMed DOI

Green P. N., Bousfield I. J. (1983). Emendation of Methylobacterium Patt, Cole, and Hanson 1976; Methylobacterium rhodinum (Heumann 1962) comb. nov. corrig.; Methylobacterium radiotolerans (Ito and Iizuka 1971) comb. nov. corrig.; and Methylobacterium mesophilicum (Austin and Goodfellow 1979) comb. nov. Int. J. Syst. Bacteriol. 33 875–877. 10.1099/00207713-33-4-875 DOI

Gu C. T., Wang E. T., Tian C. F., Han T. X., Chen W. F., Sui X. H., et al. (2008). Rhizobium miluonense sp. nov., a symbiotic bacterium isolated from Lespedeza root nodules. Int. J. Syst. Evol. Microbiol. 58 1364–1368. 10.1099/ijs.0.65661-0 PubMed DOI

Gu T., Sun L. N., Zhang J., Sui X. H., Li S. P. (2014). Rhizobium flavum sp. nov., a triazophos-degrading bacterium isolated from soil under the long-term application of triazophos. Int. J. Syst. Evol. Microbiol. 64 2017–2022. 10.1099/ijs.0.061523-0 PubMed DOI

Gu X., Zhang H. (2004). Genome phylogenetic analysis based on extended gene contents. Mol. Biol. Evol. 21 1401–1408. 10.1093/molbev/msh138 PubMed DOI

Gundi V. A. K. B., Taylor C., Raoult D., La Scola B. (2009). Bartonella rattaustraliani sp. nov., Bartonella queenslandensis sp. nov. and Bartonella coopersplainsensis sp. nov., identified in Australian rats. Int. J. Syst. Evol. Microbiol. 59 2956–2961. 10.1099/ijs.0.002865-0 PubMed DOI

Guo L.-L., Wu Y.-H., Xu X.-W., Huang C.-J., Xu Y.-Y., Cheng H., et al. (2017). Actibacterium pelagium sp. nov., a novel alphaproteobacterium, and emended description of the genus Actibacterium. Int. J. Syst. Evol. Microbiol. 67 5080–5086. 10.1099/ijsem.0.002417 PubMed DOI

Guo P., Wang B.-Z., Hang B.-J., Li L., Li S.-P., He J. (2010). Sphingobium faniae sp. nov., a pyrethroid-degrading bacterium isolated from activated sludge treating wastewater from pyrethroid manufacture. Int. J. Syst. Evol. Microbiol. 60 408–412. 10.1099/ijs.0.009795-0 PubMed DOI

Gupta R. S., Mahmood S., Adeolu M. (2013). A phylogenomic and molecular signature based approach for characterization of the phylum Spirochaetes and its major clades: proposal for a taxonomic revision of the phylum. Front. Microbiol. 4:217 10.3389/fmicb.2013.00217 PubMed DOI PMC

Gupta S. K., Lal D., Lal R. (2009). Novosphingobium panipatense sp. nov. and Novosphingobium mathurense sp. nov., from oil-contaminated soil. Int. J. Syst. Evol. Microbiol. 59 156–161. 10.1099/ijs.0.65743-0 PubMed DOI

Hahnke R. L., Meier-Kolthoff J. P., García-López M., Mukherjee S., Huntemann M., Ivanova N. N., et al. (2016). Genome-based taxonomic classification of Bacteroidetes. Front. Microbiol. 7:2003. 10.3389/fmicb.2016.02003 PubMed DOI PMC

Hahnke S., Tindall B. J., Schumann P., Simon M., Brinkhoff T. (2013). Pelagimonas varians gen. nov., sp. nov., isolated from the southern North Sea. Int. J. Syst. Evol. Microbiol. 63 835–843. 10.1099/ijs.0.040675-0 PubMed DOI

Hameed A., Shahina M., Lai W.-A., Lin S.-Y., Young L.-S., Liu Y.-C., et al. (2015). Oricola cellulosilytica gen. nov., sp. nov., a cellulose-degrading bacterium of the family Phyllobacteriaceae isolated from surface seashore water, and emended descriptions of Mesorhizobium loti and Phyllobacterium myrsinacearum. Antonie Van Leeuwenhoek 107 759–771. 10.1007/s10482-014-0370-6 PubMed DOI

Hameed A., Shahina M., Lin S.-Y., Nakayan P., Liu Y.-C., Lai W.-A., et al. (2014). Youngimonas vesicularis gen. nov., sp. nov., of the family Rhodobacteraceae, isolated from surface seawater, reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. and emended description of the g. Int. J. Syst. Evol. Microbiol. 64 2729–2737. 10.1099/ijs.0.060962-0 PubMed DOI

Hampson D. J., La T. (2006). Reclassification of Serpulina intermedia and Serpulina murdochii in the genus Brachyspira as Brachyspira intermedia comb. nov. and Brachyspira murdochii comb. nov. Int. J. Syst. Evol. Microbiol. 56 1009–1012. 10.1099/ijs.0.64004-0 PubMed DOI

Han S.-B., Su Y., Hu J., Wang R.-J., Sun C., Wu D., et al. (2016). Terasakiella brassicae sp. nov., isolated from the wastewater of a pickle-processing factory, and emended descriptions of Terasakiella pusilla and the genus Terasakiella. Int. J. Syst. Evol. Microbiol. 66 1807–1812. 10.1099/ijsem.0.000946 PubMed DOI

Han T. X., Wang E. T., Wu L. J., Chen W. F., Gu J. G., Gu C. T., et al. (2008). Rhizobium multihospitium sp. nov., isolated from multiple legume species native of Xinjiang. China. Int. J. Syst. Evol. Microbiol. 58 1693–1699. 10.1099/ijs.0.65568-0 PubMed DOI

Hansen T. A., Imhoff J. F. (1985). Rhodobacter veldkampii, a new species of phototrophic purple nonsulfur bacteria. Int. J. Syst. Bacteriol. 35 115–116. 10.1099/00207713-35-1-115 PubMed DOI

Harwati T. U., Kasai Y., Kodama Y. (2009a). Tropicimonas isoalkanivorans gen. nov., sp. nov., a branched-alkane-degrading bacterium isolated from Semarang Port in Indonesia. Int. J. Syst. Evol. Microbiol. 59 388–391. 10.1099/ijs.0.65822-0 PubMed DOI

Harwati T. U., Kasai Y., Kodama Y., Susilaningsi D., Watanabe K. (2009b). Tropicibacter naphthalenivorans gen. nov., sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from Semarang Port in Indonesia. Int. J. Syst. Evol. Microbiol. 59 392–396. 10.1099/ijs.0.65821-0 PubMed DOI

Harwati T. U., Kasai Y., Kodama Y., Susilanngsih D., Watanabe K. (2008). Tranquillimonas alkanivorans gen. nov., sp. nov., an alkane-degrading bacterium isolated from Semarang Port in Indonesia. Int. J. Syst. Evol. Microbiol. 58 2118–2121. 10.1099/ijs.0.65817-0 PubMed DOI

Hedges L. M., Brownlie J. C., O’Neill S. L., Johnson K. N. (2008). Wolbachia and virus protection in insects. Science 322:702. 10.1126/science.1162418 PubMed DOI

Helsel L. O., Hollis D., Steigerwalt A. G., Morey R. E., Jordan J., Aye T., et al. (2007). Identification of “Haematobacter,” a new genus of aerobic gram-negative rods isolated from clinical specimens, and reclassification of Rhodobacter massiliensis as “Haematobacter massiliensis comb. nov.”. J. Clin. Microbiol. 45 1238–1243. 10.1128/JCM.01188-06 PubMed DOI PMC

Helsel L. O., Hollis D. G., Steigerwalt A. G., Levett P. N. (2006). Reclassification of Roseomonas fauriae Rihs et al. 1998 as a later heterotypic synonym of Azospirillum brasilense Tarrand et al. 1979. Int. J. Syst. Evol. Microbiol. 56 2753–2755. 10.1099/ijs.0.64549-0 PubMed DOI

Hennig W. (1965). Phylogenetic systematics. Annu. Rev. Entomol. 10 97–116.

Henrici A. T., Johnson D. E. (1935). Studies of freshwater bacteria: II. stalked bacteria, a new order of schizomycetes. J. Bacteriol. 30 61–93. PubMed PMC

Henz S. R., Huson D. H., Auch A. F., Nieselt-Struwe K., Schuster S. C. (2005). Whole-genome prokaryotic phylogeny. Bioinformatics 21 2329–2335. 10.1093/bioinformatics/bth324 PubMed DOI

Hildebrand F., Meyer A., Eyre-Walker A. (2010). Evidence of selection upon genomic GC-content in bacteria. PLoS Genet. 6:e1001107. 10.1371/journal.pgen.1001107 PubMed DOI PMC

Hiraishi A. (1997). Transfer of the bacteriochlorophyll β-containing phototrophic bacteria Rhodopseudomonas viridis and Rhodopseudomonas sulfoviridis to the genus Blastochloris gen. nov. Int. J. Syst. Bacteriol. 47 217–219. 10.1099/00207713-47-1-217 PubMed DOI

Hiraishi A., Kuraishi H., Kawahara K. (2000). Emendation of the description of Blastomonas natatoria (Sly 1985) Sly and Cahill, 1997 as an aerobic photosynthetic bacterium and reclassification of Erythromonas ursincola Yurkov et al. 1997 as Blastomonas ursincola comb. nov. Int. J. Syst. Evol. Microbiol. 50 1113–1118. 10.1099/00207713-50-3-1113 PubMed DOI

Hiraishi A., Muramatsu K., Ueda Y. (1996). Molecular genetic analyses of Rhodobacter azotoformans sp. nov. and related species of phototrophic bacteria. Syst. Appl. Microbiol. 19 168–177. 10.1016/S0723-2020(96)80042-7 DOI

Hiraishi A., Ueda Y. (1994a). Intrageneric structure of the genus Rhodobacter: transfer of Rhodobacter sulfidophilus and related marine species to the genus Rhodovulum gen. nov. Int. J. Syst. Bacteriol. 44 15–23. 10.1099/00207713-44-1-15 DOI

Hiraishi A., Ueda Y. (1994b). Rhodoplanes gen. nov., a new genus of phototrophic bacteria including Rhodopseudomonas rosea as Rhodoplanes roseus comb. nov. and Rhodoplanes elegans sp. nov. Int. J. Syst. Bacteriol. 44 665–673. 10.1099/00207713-44-4-665 DOI

Hiraishi A., Urata K., Satoh T. (1995). A new genus of marine budding phototrophic bacteria, Rhodobium gen. nov., which includes Rhodobium orientis sp. nov. and Rhodobium marinum comb. nov. Int. J. Syst. Bacteriol. 45 226–234. 10.1099/00207713-45-2-226 PubMed DOI

Hirsch P. (1989). “Genus Hyphomicrobium Stutzer and Hartleb 1898, 76AL,” in Bergey’s Manual of Systematic Bacteriology, Vol. 3 eds Staley J. T., Bryant M. P., Pfennig N., Holt J. G. (Baltimore, MD: The Williams & Wilkins Co; ), 1895–1904.

Hirsch P., Hoffmann B. (1989). Dichotomicrobium thermohalophilum, gen. nov., spec. nov., budding prosthecate bacteria from the solar lake (Sinai) and some related strains. Syst. Appl. Microbiol. 11 291–301. 10.1016/S0723-2020(89)80027-X DOI

Holmes B., Popoff M., Kiredjian M., Kersters K. (1988). Ochrobactrum anthropi gen. nov., sp. nov. from human clinical specimens and previously known as group Vd. Int. J. Syst. Bacteriol. 38 406–416. 10.1099/00207713-38-4-406 DOI

Hong Z., Lai Q., Luo Q., Jiang S., Zhu R., Liang J., et al. (2015). Sulfitobacter pseudonitzschiae sp. nov., isolated from the toxic marine diatom Pseudo-nitzschia multiseries. Int. J. Syst. Evol. Microbiol. 65 95–100. 10.1099/ijs.0.064972-0 PubMed DOI

Hosokawa T., Koga R., Kikuchi Y., Meng X.-Y., Fukatsu T. (2010). Wolbachia as a bacteriocyte-associated nutritional mutualist. PNAS 107 769–774. 10.1073/pnas.0911476107 PubMed DOI PMC

Hosoya S., Yokota A. (2007). Loktanella atrilutea sp. nov., isolated from seawater in Japan. Int. J. Syst. Evol. Microbiol. 57 1966–1969. 10.1099/ijs.0.64978-0 PubMed DOI

Hou L., Zhang Y., Sun J., Xie X. (2015). Acuticoccus yangtzensis gen. nov., sp. nov., a novel member in the family Rhodobacteraceae, isolated from the surface water of the Yangtze estuary. Curr. Microbiol. 70 176–182. 10.1007/s00284-014-0698-1 PubMed DOI

Hovind-Hougen K. (1979). Leptospzraceae, a new family to include Leptospira Noguchi 1917 and Leptonema gen. nov. Int. J. Syst. Bacteriol. 29 245–251. 10.1099/00207713-29-3-245 DOI

Hu Q., Zhang L., Hang P., Zhou X.-Y., Jia W.-B., Li S.-P., et al. (2018). Xinfangfangia soli gen. nov., sp. nov., isolated from a diuron-polluted soil. Int. J. Syst. Evol. Microbiol. 68 2622–2626. 10.1099/ijsem.0.002887 PubMed DOI

Huang M. M., Guo L. L., Wu Y. H., Lai Q. L., Shao Z. Z., Wang C. S., et al. (2018). Pseudooceanicola lipolyticus sp. nov., a marine alphaproteobacterium, reclassification of oceanicola flagellates as Pseudooceanicola flagellatus comb. nov. and emended description of the genus Pseudooceanicola. Int. J. Syst. Evol. Microbiol. 68 409–415. 10.1099/ijsem.0.002521 PubMed DOI

Huang Z., Guo F., Lai Q., Shao Z. (2017). Notoacmeibacter marinus gen. nov., sp. nov., isolated from the gut of a limpet and proposal of notoacmeibacteraceae fam. nov. in the order rhizobiales of the class alphaproteobacteria. Int. J. Syst. Evol. Microbiol. 67 2527–2531. 10.1099/ijsem.0.001951 PubMed DOI

Huber B., Scholz H. C., Kämpfer P., Falsen E., Langer S., Busse H.-J. (2010). Ochrobactrum pituitosum sp. nov., isolated from an industrial environment. Int. J. Syst. Evol. Microbiol. 60 321–326. 10.1099/ijs.0.011668-0 PubMed DOI

Huddleson I. F. (1929). The differentiation of the species of the genus Brucella. Michigan State Coll. Agric. Exp. Stn. Tech. Bull. 100 1–16.

Humrighouse B. W., Emery B. D., Kelly A. J., Metcalfe M. G., Mbizo J., McQuiston J. R. (2016). Haematospirillum jordaniae gen. nov., sp. nov., isolated from human blood samples. Antonie Van Leeuwenhoek 109 493–500. 10.1007/s10482-016-0654-0 PubMed DOI

Hunter W. J., Kuykendall L. D., Manter D. K. (2007). Rhizobium selenireducens sp. nov.: a selenite-reducing α-Proteobacteria isolated from a bioreactor. Curr. Microbiol. 55 455–460. 10.1007/s00284-007-9020-9 PubMed DOI

Huo Y.-Y., Xu X.-W., Liu S.-P., Cui H.-L., Li X., Wu M. (2011). Sphingomonas rubra sp. nov., isolated from bioreactor wastewater. Int. J. Syst. Evol. Microbiol. 61 1028–1032. 10.1099/ijs.0.020958-0 PubMed DOI

Huson D. H., Steel M. (2004). Phylogenetic trees based on gene content. Bioinformatics 20 2044–2049. 10.1093/bioinformatics/bth198 PubMed DOI

Hwang C. Y., Bae G. D., Yih W., Cho B. C. (2009a). Marivita cryptomonadis gen. nov., sp. nov. and Marivita litorea sp. nov., of the family Rhodobacteraceae, isolated from marine habitats. Int. J. Syst. Evol. Microbiol. 59 1568–1575. 10.1099/ijs.0.005462-0 PubMed DOI

Hwang C. Y., Cho B. C. (2008a). Cohaesibacter gelatinilyticus gen. nov., sp. nov. a marine bacterium that forms a distinct branch in the order Rhizobiales, and proposal of Cohaesibacteraceae fam. nov. Int. J. Syst. Evol. Microbiol. 58 267–277. 10.1099/ijs.0.65016-0 PubMed DOI

Hwang C. Y., Cho B. C. (2008b). Cucumibacter marinus gen. nov., sp. nov., a marine bacterium in the family Hyphomicrobiaceae. Int. J. Syst. Evol. Microbiol. 58 1591–1597. 10.1099/ijs.0.65587-0 PubMed DOI

Hwang C. Y., Cho K. D., Yih W., Cho B. C. (2009b). Maritalea myrionectae gen. nov., sp. nov., isolated from a culture of the marine ciliate Myrionecta rubra. Int. J. Syst. Evol. Microbiol. 59 609–614. 10.1099/ijs.0.002881-0 PubMed DOI

Hyatt D., Chen G.-L., LoCascio P. F., Land M. L., Larimer F. W., Hauser L. J. (2010). Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. 10.1186/1471-2105-11-119 PubMed DOI PMC

Hyun D.-W., Kim M.-S., Shin N.-R., Kim J. Y., Kim P. S., Whon T. W., et al. (2013a). Shimia haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai. Int. J. Syst. Evol. Microbiol. 63 4248–4253. 10.1099/ijs.0.053140-0 PubMed DOI

Hyun D.-W., Shin N.-R., Kim M.-S., Kim P. S., Kim J. Y., Whon T. W., et al. (2013b). Pseudoruegeria haliotis sp. nov., isolated from the gut of the abalone Haliotis discus hannai. Int. J. Syst. Evol. Microbiol. 63 4626–4632. 10.1099/ijs.0.053892-0 PubMed DOI

Iino T., Suzuki R., Kosako Y., Ohkuma M., Komagata K., Uchimura T. (2012). Acetobacter okinawensis sp. nov., Acetobacter papayae sp. nov., and Acetobacter persicus sp. nov.; novel acetic acid bacteria isolated from stems of sugarcane, fruits, and a flower in Japan. J. Gen. Appl. Microbiol. 58 235–243. 10.2323/jgam.58.235 PubMed DOI

Im W.-T., Kim S.-H., Kim M. K., Ten L. N., Lee S.-T. (2006). Pleomorphomonas koreensis sp. nov., a nitrogen-fixing species in the order Rhizobiales. Int. J. Syst. Evol. Microbiol. 56 1663–1666. 10.1099/ijs.0.63499-0 PubMed DOI

Im W.-T., Yokota A., Kim M.-K., Lee S.-T. (2004). Kaistia adipata gen. nov., sp. nov., a novel α-proteobacterium. J. Gen. Appl. Microbiol. 50 249–254. 10.2323/jgam.50.249 PubMed DOI

Imhoff J. F. (2001). Transfer of Rhodopseudomonas acidophila to the new genus Rhodoblastus as Rhodoblastus acdidophilus gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 51 1863–1866. 10.1099/00207713-51-5-1863 PubMed DOI

Imhoff J. F., Petri R., Süling J. (1998). Reclassification of species of the spiral-shaped phototrophic purple non-sulfur bacteria of the α-Proteobacteria: description of the new genera Phaeospirillum gen. nov., Rhodovibrio gen. nov., Rhodothalassium gen. nov. and Roseospira gen. nov. as well as. Int. J. Syst. Bacteriol. 48 793–798. 10.1099/00207713-48-3-793 PubMed DOI

Imhoff J. F., Trüpper H. G., Pfenning N. (1984). Rearrangement of the species and genera of the phototrophic “purple nonsulfur bacteria.”. Int. J. Syst. Bacteriol. 34 340–343. 10.1099/00207713-34-3-340 DOI

Imran A., Hafeez F. Y., Frühling A., Schumann P., Malik K. A., Stackebrandt E. (2010). Ochrobactrum ciceri sp. nov., isolated from nodules of Cicer arietinum. Int. J. Syst. Evol. Microbiol. 60 1548–1553. 10.1099/ijs.0.013987-0 PubMed DOI

Irgens R. L., Kersters K., Segers P., Gillis M., Staley J. T. (1991). Aquabacter spiritensis, gen. nov., sp. nov. an aerobic, gas-vacuolate aquatic bacterium. Arch. Microbiol. 155 137–142. 10.1007/bf00248607 DOI

Ivanova E. P., Gorshkova N. M., Sawabe T., Zhukova N. V., Hayashi K., Kurilenko V. V., et al. (2004). Sulfitobacter delicatus sp. nov. and Sulfitobacter dubius sp. nov., respectively from a starfish (Stellaster equestris) and sea grass (Zostera marina). Int. J. Syst. Evol. Microbiol. 54 475–480. 10.1099/ijs.0.02654-0 PubMed DOI

Ivanova E. P., Webb H., Christen R., Zhukova N. V., Kurilenko V. V., Kalinovskaya N. I., et al. (2010). Celeribacter neptunius gen. nov., sp. nov., a new member of the class Alphaproteobacteria. Int. J. Syst. Evol. Microbiol. 60 1620–1625. 10.1099/ijs.0.014159-0 PubMed DOI

Ivanova E. P., Zhukova N. V., Lysenko A. M., Gorshkova N. M., Sergeev A. F., Mikhailov V. V., et al. (2005). Loktanella agnita sp. nov. and Loktanella rosea sp. nov., from the north-west Pacific Ocean. Int. J. Syst. Evol. Microbiol. 55 2203–2207. 10.1099/ijs.0.63461-0 PubMed DOI

Iwaki H., Nishimura A., Hasegawa Y. (2012). Tropicibacter phthalicus sp. nov., a phthalate-degrading bacterium from seawater. Curr. Microbiol. 64 392–396. 10.1007/s00284-012-0085-8 PubMed DOI

Iwaki H., Yasukawa N., Fujioka M., Takada K., Hasegawa Y. (2013). Isolation and characterization of a marine cyclohexylacetate-degrading bacterium Lutimaribacter litoralis sp. nov., and reclassification of Oceanicola pacificus as Lutimaribacter pacificus comb. nov. Curr. Microbiol. 66 588–593. 10.1007/s00284-013-0321-x PubMed DOI

Jang G. Il, Hwang C. Y., Cho B. C. (2011). Nitratireductor aquimarinus sp. nov., isolated from a culture of the diatom Skeletonema costatum, and emended description of the genus Nitratireductor. Int. J. Syst. Evol. Microbiol. 61 2676–2681. 10.1099/ijs.0.028373-0 PubMed DOI

Jarvis B. D. W., Van Berkum P., Chen W. X., Nour S. M., Fernandez M. P., Cleyet-Marel J. C., et al. (1997). Transfer of Rhizobium loti, Rhizobium huakuii, Rhizobium ciceri, Rhizobium mediterraneum, and Rhizobium tianshanense to Mesorhizobium gen. nov. Int. J. Syst. Bacteriol. 47 895–898. 10.1099/00207713-47-3-895 DOI

Jean W. D., Huang S. P., Chen J. S., Shieh W. Y. (2016). Tagaea marina gen. nov., sp. nov., a marine bacterium isolated from shallow coastal water. Int. J. Syst. Evol. Microbiol. 66 592–597. 10.1099/ijsem.0.000756 PubMed DOI

Jeffroy O., Brinkmann H., Delsuc F., Philippe H. (2006). Phylogenomics: the beginning of incongruence? Trends Genet. 22 225–231. 10.1016/j.tig.2006.02.003 PubMed DOI

Jeong H. I., Jin H. M., Jeon C. O. (2015). Confluentimicrobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from sea-tidal-flat sediment, and emended description of the genus Confluentimicrobium Park et al. 2015. Int. J. Syst. Evol. Microbiol. 65 4191–4195. 10.1099/ijsem.0.000561 PubMed DOI

Jia X., Kim H. R., Jia B., Jeon H. H., Baek K., Choi S. H., et al. (2017). Roseovarius confluentis sp. nov., isolated from estuary sediment. Int. J. Syst. Evol. Microbiol. 67 346–351. 10.1099/ijsem.0.001630 PubMed DOI

Jiang C.-Y., Dai X., Wang B.-J., Zhou Y.-G., Liu S.-J. (2006). Roseomonas lacus sp. nov., isolated from freshwater lake sediment. Int. J. Syst. Evol. Microbiol. 56 25–28. 10.1099/ijs.0.63938-0 PubMed DOI

Jiang L., Xu H., Shao Z., Long M. (2014). Defluviimonas indica sp. nov., a marine bacterium isolated from a deep-sea hydrothermal vent environment. Int. J. Syst. Evol. Microbiol. 64 2084–2088. 10.1099/ijs.0.061614-0 PubMed DOI

Jiao Y. S., Yan H., Ji Z. J., Liu Y. H., Sui X. H., Zhang X. X., et al. (2015). Phyllobacterium sophorae sp. nov., a symbiotic bacterium isolated from root nodules of Sophora flavescens. Int. J. Syst. Evol. Microbiol. 65 399–406. 10.1099/ijs.0.067017-0 PubMed DOI

Jin H. M., Lee H. J., Kim J. M., Park M. S., Lee K., Jeon C. O. (2011). Litorimicrobium taeanense gen. nov., sp. nov., isolated from a sandy beach. Int. J. Syst. Evol. Microbiol. 61 1392–1396. 10.1099/ijs.0.025007-0 PubMed DOI

Jindal S., Dua A., Lal R. (2013). Sphingopyxis indica sp. nov., isolated from a high dose point hexachlorocyclohexane (HCH)-contaminated dumpsite. Int. J. Syst. Evol. Microbiol. 63 2186–2191. 10.1099/ijs.0.040840-0 PubMed DOI

Jogler M., Chen H., Simon J., Rohde M., Busse H.-J., Klenk H.-P., et al. (2013). Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen. nov. Int. J. Syst. Evol. Microbiol. 63 1342–1349. 10.1099/ijs.0.043133-0 PubMed DOI

Johnson R. C., Burgdorfer W., Lane R. S., Barbour A. G., Hayes Stanley F., Hyde F. W. (1987). Borrelia coriaceae sp. nov.: putative agent of epizootic bovine abortion. Int. J. Syst. Bacteriol. 37 72–74. 10.1099/00207713-37-1-72 DOI

Jojima Y., Mihara Y., Suzuki S., Yokozeki K., Yamanaka S., Fudou R. (2004). Saccharibacter floricola gen. nov, sp. nov., a novel osmophilic acetic acid bacterium isolated from pollen. Int. J. Syst. Evol. Microbiol. 54 2263–2267. 10.1099/ijs.0.02911-0 PubMed DOI

Jordan D. C. (1982). Transfer of Rhizobium japonicum Buchanan 1980 to Bradyrhizobium gen. nov., a genus of slow-growing, root nodule bacteria from leguminous plants. Int. J. Syst. Bacteriol. 32 136–139. 10.1099/00207713-32-1-136 DOI

Jordan E. M., Thompson F. L., Zhang X. H., Li Y., Vancanneyt M., Kroppenstedt R. M., et al. (2007). Sneathiella chinensis gen. nov., sp. nov., a novel marine alphaproteobacterium isolated from coastal sediment in Qingdao. China. Int. J. Syst. Evol. Microbiol. 57 114–121. 10.1099/ijs.0.64478-0 PubMed DOI

Jourand P., Giraud E., Béna G., Sy A., Willems A., Gillis M., et al. (2004). Methylobacterium nodulans sp. nov., for a group of aerobic, facultatively methylotrophic, legume root-nodule-forming and nitrogen-fixing bacteria. Int. J. Syst. Evol. Microbiol. 54 2269–2273. 10.1099/ijs.0.02902-0 PubMed DOI

Jung J. Y., Kim J. M., Jin H. M., Kim S. Y., Park W., Jeon C. O. (2011). Litorimonas taeanensis gen. nov., sp. nov., isolated from a sandy beach. Int. J. Syst. Evol. Microbiol. 61 1534–1538. 10.1099/ijs.0.022129-0 PubMed DOI

Jung M.-Y., Shin K.-S., Kim S., Kim S.-J., Park S.-J., Kim J.-G., et al. (2013). Hoeflea halophila sp. nov., a novel bacterium isolated from marine sediment of the East Sea. Korea. Antonie Van Leeuwenhoek 103 971–978. 10.1007/s10482-013-9876-6 PubMed DOI

Jung Y.-T., Kim B.-H., Oh T.-K., Yoon J.-H. (2010). Pseudoruegeria lutimaris sp. nov., isolated from a tidal flat sediment, and emended description of the genus Pseudoruegeria. Int. J. Syst. Evol. Microbiol. 60 1177–1181. 10.1099/ijs.0.015073-0 PubMed DOI

Jung Y.-T., Lee J.-S., Yoon J.-H. (2014a). Roseivivax jejudonensis sp. nov., isolated from the junction between the ocean and a freshwater spring at Jeju island. South Korea Antonie Van Leeuwenhoek 106 959–967. 10.1007/s10482-014-0265-6 PubMed DOI

Jung Y. T., Lee J. S., Yoon J. H. (2016). Maliponia aquimaris gen. nov., sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol. 66 2271–2277. 10.1099/ijsem.0.001021 PubMed DOI

Jung Y.-T., Oh K.-H., Oh T.-K., Yoon J.-H. (2012a). Pseudorhodobacter aquimaris sp. nov., isolated from seawater, and emended description of the genus Pseudorhodobacter Uchino et al., 2002. Int. J. Syst. Evol. Microbiol. 62 100–105. 10.1099/ijs.0.029769-0 PubMed DOI

Jung Y. T., Park S., Lee J. S., Yoon J. H. (2014b). Defluviimonas aquaemixtae sp. nov., isolated from the junction between a freshwater spring and the ocean. Int. J. Syst. Evol. Microbiol. 64 4191–4197. 10.1099/ijs.0.068767-0 PubMed DOI

Jung Y.-T., Park S., Oh T.-K., Yoon J.-H. (2012b). Erythrobacter marinus sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol. 62 2050–2055. 10.1099/ijs.0.034702-0 PubMed DOI

Jung Y.-T., Yoon J.-H. (2014). Jannaschia faecimaris sp. nov., isolated from a tidal flat sediment. Int. J. Syst. Evol. Microbiol. 64 945–951. 10.1099/ijs.0.057984-0 PubMed DOI

Jung Y. T., Yoon J. H., Park S., Lee J.-S., Oh T.-K. (2012c). Pseudahrensia aquimaris gen. nov., sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol. 62 2056–2061. PubMed

Kaiya S., Rubaba O., Yoshida N., Yamada T., Hiraishi A. (2012). Characterization of Rhizobium naphthalenivorans sp. nov. with special emphasis on aromatic compound degradation and multilocus sequence analysis of housekeeping genes. J. Gen. Appl. Microbiol. 58 211–224. 10.2323/jgam.58.211 PubMed DOI

Kämpfer P., Arun A. B., Busse H.-J., Zhang Z.-L., Young C.-C., Glaeser S. P. (2015a). Chelativorans intermedius sp. nov. and proposal to reclassify Thermovum composti as Chelativorans composti comb. nov. Int. J. Syst. Evol. Microbiol. 65 1646–1652. 10.1099/ijs.0.000155 PubMed DOI

Kämpfer P., Arun A. B., Rekha P. D., Busse H.-J., Young C.-C., Glaeser S. P. (2013a). Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring. Int. J. Syst. Evol. Microbiol. 63 2538–2544. 10.1099/ijs.0.047910-0 PubMed DOI

Kämpfer P., Aurass P., Karste S., Flieger A., Glaeser S. P. (2016). Paracoccus contaminans sp. nov., isolated from a contaminated water microcosm. Int. J. Syst. Evol. Microbiol. 66 5101–5105. 10.1099/ijsem.0.001478 PubMed DOI

Kämpfer P., Buczolits S., Albrecht A., Busse H.-J., Stackebrandt E. (2003). Towards a standardized format for the description of a novel species (of an established genus): Ochrobactrum gallinifaecis sp. nov. Int. J. Syst. Evol. Microbiol. 53 893–896. 10.1099/ijs.0.02710-0 PubMed DOI

Kämpfer P., Busse H.-J., Rosséllo-Mora R., Kjellin E., Falsen E. (2004). Rhodovarius lipocyclicus gen. nov. sp. nov., a new genus of the α-1 subclass of the Proteobacteria. Syst. Appl Microbiol 27 511–516. 10.1078/0723202041748235 PubMed DOI

Kämpfer P., Glaeser S., Busse H. J., Eisenberg T., Scholz H. (2013b). Falsochrobactrum ovis gen. nov., sp. nov., isolated from a sheep. Int. J. Syst. Evol. Microbiol. 63 3841–3847. 10.1099/ijs.0.049627-0 PubMed DOI

Kämpfer P., Glaeser S. P. (2012). Prokaryotic taxonomy in the sequencing era – the polyphasic approach revisited. Environ. Microbiol. 14 291–317. 10.1111/j.1462-2920.2011.02615.x PubMed DOI

Kämpfer P., Huber B., Busse H.-J., Scholz H. C., Tomaso H., Hotzel H., et al. (2011). Ochrobactrum pecoris sp. nov., isolated from farm animals. Int. J. Syst. Evol. Microbiol. 61 2278–2283. 10.1099/ijs.0.027631-0 PubMed DOI

Kämpfer P., Huber B., Lodders N., Warfolomeow I., Busse H. J., Scholz H. C. (2009a). Pseudochrobactrum lubricantis sp. nov., isolated from a metal-working fluid. Int. J. Syst. Evol. Microbiol. 59 2464–2467. 10.1099/ijs.0.008540-0 PubMed DOI

Kämpfer P., Jerzak L., Wilharm G., Golke J., Busse H.-J., Glaeser S. P. (2015b). Gemmobacter intermedius sp. nov., isolated from a white stork (Ciconia ciconia). Int. J. Syst. Evol. Microbiol. 65 778–783. 10.1099/ijs.0.000012 PubMed DOI

Kämpfer P., Martin E., Lodders N., Jäckel U. (2009b). Transfer of Defluvibacter lusatiensis to the genus Aquamicrobium as Aquamicrobium lusatiense comb. nov. and description of Aquamicrobium aerolatum sp. nov. Int. J. Syst. Evol. Microbiol. 59 2468–2470. 10.1099/ijs.0.008730-0 PubMed DOI

Kämpfer P., Martin E., Lodders N., Jäckel U., Huber B. E., Schumann P., et al. (2010a). Paenochrobactrum gallinarii gen. nov., sp. nov., isolated from air of a duck barn, and reclassification of Pseudochrobactrum glaciei as Paenochrobactrum glaciei comb. nov. Int. J. Syst. Evol. Microbiol. 60 1493–1498. 10.1099/ijs.0.015842-0 PubMed DOI

Kämpfer P., Müller C., Mau M., Neef A., Auling G., Busse H.-J., et al. (1999). Description of Pseudaminobacter gen. nov. with two new species, Pseudarninobacter salicylatoxidans sp. nov. and Pseudaminobacter defluvii sp. nov. Int. J. Syst. Bacteriol. 49 887–897. 10.1099/00207713-49-2-887 PubMed DOI

Kämpfer P., Neef A., Salkinoja-Salonen M. S., Busse H.-J. (2002a). Chelatobacter heintzii (Auling et al., 1993) is a later subjective synonym of Aminobacter aminovorans (Urakami et al., 1992). Int. J. Syst. Evol. Microbiol. 52 835–839. 10.1099/ijs.0.01897-0 PubMed DOI

Kämpfer P., Poppel M. T., Wilharm G., Glaeser S. P., Busse H. J. (2014). Paenochrobactrum pullorum sp. nov. isolated from a chicken. Int. J. Syst. Evol. Microbiol. 64 1724–1728. 10.1099/ijs.0.061101-0 PubMed DOI

Kämpfer P., Scholz H. C., Huber B., Falsen E., Busse H.-J. (2007a). Ochrobactrum haematophilum sp. nov. and Ochrobactrum pseudogrignonense sp. nov., isolated from human clinical specimens. Int. J. Syst. Evol. Microbiol. 57 2513–2518. 10.1099/ijs.0.65066-0 PubMed DOI

Kämpfer P., Scholz H., Huber B., Thummes K., Busse H. J., Maas E. W., et al. (2007b). Description of Pseudochrobactrum kiredjianiae sp. nov. Int. J. Syst. Evol. Microbiol. 57 755–760. 10.1099/ijs.0.64714-0 PubMed DOI

Kämpfer P., Scholz H. C., Langer S., Wernery U., Wernery R., Johnson B., et al. (2010b). Camelimonas lactis gen. nov., sp. nov., isolated from the milk of camels. Int. J. Syst. Evol. Microbiol. 60 2382–2386. 10.1099/ijs.0.017806-0 PubMed DOI

Kämpfer P., Sessitsch A., Schloter M., Huber B., Busse H.-J., Scholz H. C. (2008). Ochrobactrum rhizosphaerae sp. nov. and Ochrobactrum thiophenivorans sp. nov., isolated from the environment. Int. J. Syst. Evol. Microbiol. 58 1426–1431. 10.1099/ijs.0.65407-0 PubMed DOI

Kämpfer P., Witzenberger R., Denner E. B. M., Busse H.-J., Neef A. (2002b). Sphingopyxis witflariensis sp. nov., isolated from activated sludge. Int. J. Syst. Evol. Microbiol. 52 2029–2034. 10.1099/ijs.0.02217-0 PubMed DOI

Kämpfer P., Young C. C., Arun A. B., Shen F. T., Jäckel U., Rosselló-Mora R., et al. (2006). Pseudolabrys taiwanensis gen. nov., sp. nov., an alphaproteobacterium isolated from soil. Int. J. Syst. Evol. Microbiol. 56 2469–2472. 10.1099/ijs.0.64124-0 PubMed DOI

Kang H. S., Lee S. D. (2009). Ponticaulis koreensis gen. nov., sp. nov., a new member of the family Hyphomonadaceae isolated from seawater. Int. J. Syst. Evol. Microbiol. 59 2951–2955. 10.1099/ijs.0.011114-0 PubMed DOI

Kang J. Y., Kim M.-J., Chun J., Son K. P., Jahng Y. (2017). Gemmobacter straminiformis sp. nov., isolated from an artificial fountain. Class Quantum Gravity 67 5019–5025. 10.1099/ijsem.0.002403 PubMed DOI

Kang Y.-S., Kim J., Shin H.-D., Nam Y.-D., Bae J.-W., Jeon C. O., et al. (2007). Methylobacterium platani sp. nov., isolated from a leaf of the tree Platanus orientalis. Int. J. Syst. Evol. Microbiol. 57 2849–2853. 10.1099/ijs.0.65262-0 PubMed DOI

Kanso S., Patel B. K. C. (2003). Microvirga subterranea gen. nov., sp. nov., a moderate thermophile from a deep subsurface Australian thermal aquifer. Int. J. Syst. Evol. Microbiol. 53 401–406. 10.1099/ijs.0.02348-0 PubMed DOI

Kathiravan R., Jegan S., Ganga V., Prabavathy V. R., Tushar L., Sasikala C., et al. (2013). Ciceribacter lividus gen. nov., sp. nov., isolated from rhizosphere soil of chick pea (Cicer arietinum L.). Int. J. Syst. Evol. Microbiol. 63 4484–4488. 10.1099/ijs.0.049726-0 PubMed DOI

Kato Y., Asahara M., Goto K., Kasai H., Yokota A. (2008). Methylobacterium persicinum sp. nov., Methylobacterium komagatae sp. nov., Methylobacterium brachiatum sp. nov., Methylobacterium tardum sp. nov. and Methylobacterium gregans sp. nov., isolated from freshwater. Int. J. Syst. Evol. Microbiol. 58 1134–1141. 10.1099/ijs.0.65583-0 PubMed DOI

Katoh K., Kuma K., Miyata T., Toh H. (2005). Improvement in the accuracy of multiple sequence alignment program MAFFT. Genome Inf. 16 22–33. PubMed

Katsura K., Yamada Y., Uchimura T., Komagata K. (2002). Gluconobacter asaii Mason and Claus, 1989 is a junior subjective synonym of Gluconobacter cerinus Yamada and Akita 1984. Int. J. Syst. Evol. Microbiol. 52 1635–1640. 10.1099/ijs.0.02093-0 PubMed DOI

Kaur J., Kaur J., Niharika N., Lal R. (2012). Sphingomonas laterariae sp. nov., isolated from a hexachlorocyclohexane-contaminated dump site. Int. J. Syst. Evol. Microbiol. 62 2891–2896. 10.1099/ijs.0.034686-0 PubMed DOI

Kaur J., Moskalikova H., Niharika N., Sedlackova M., Hampl A., Damborsky J., et al. (2013). Sphingobium baderi sp. nov., isolated from a hexachlorocyclohexane dump site. Int. J. Syst. Evol. Microbiol. 63 673–678. 10.1099/ijs.0.039834-0 PubMed DOI

Kawasaki H., Hoshino Y., Hirata A., Yamasato K. (1993). Is intracytoplasmic membrane structure a generc criterion? It does not coincide with phylogenetic interrelationships among phototrophic purple nonsulfur bacteria. Arch. Microbiol. 160 358–362. PubMed

Kelly D. P., McDonald I. R., Wood A. P. (2000). Proposal for the reclassification of Thiobacillus novellus as Starkeya novella gen. nov., comb. nov., in the α-subclass of the Proteobacteria. Int. J. Syst. Evol. Microbiol. 50 1797–1802. 10.1099/00207713-50-5-1797 PubMed DOI

Khammas K. M., Ageron E., Grimont P. A. D., Kaiser P. (1989). Azospirillum irakense sp. nov., a nitrogen-fixing bacterium associated with rice roots and rhizosphere soil. Res. Microbiol. 140 679–693. 10.1016/0923-2508(89)90199-x PubMed DOI

Khan I. U., Hussain F., Habib N., Wadaan M. A. M., Ahmed I., Im W. T., et al. (2017). Phenylobacterium deserti sp. nov., isolated from desert soil. Int. J. Syst. Evol. Microbiol. 67 4722–4727. 10.1099/ijsem.0.002366 PubMed DOI

Kim B.-Y., Yoo S.-H., Weon H.-Y., Jeon Y.-A., Hong S.-B., Go S.-J., et al. (2008). Jannaschia pohangensis sp. nov., isolated from seashore sand in Korea. Int. J. Syst. Evol. Microbiol. 58 496–499. 10.1099/ijs.0.65167-0 PubMed DOI

Kim D., Kang K., Ahn T. Y. (2017). Chthonobacter albigriseus gen. nov., sp. nov., isolated from grass-field soil. Int. J. Syst. Evol. Microbiol. 67 883–888. 10.1099/ijsem.0.001695 PubMed DOI

Kim H. S., Srinivasan S., Lee S. S. (2016). Methyloterrigena soli gen. nov., sp. nov., a methanol-utilizing bacterium isolated from chloroethylene-contaminated soil. Int. J. Syst. Evol. Microbiol. 66 101–106. 10.1099/ijsem.0.000680 PubMed DOI

Kim J. H., Konkit M., Yoon J. H., Kim W. (2015). Limibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium in the family Rhodospirillaceae isolated from reclaimed land. Int. J. Syst. Evol. Microbiol. 65 3155–3161. 10.1099/ijs.0.000346 PubMed DOI

Kim J. M., Jung J. Y., Chae H. B., Park W., Jeon C. O. (2010). Hwanghaeicola aestuarii gen. nov., sp. nov., a moderately halophilic bacterium isolated from a tidal flat of the Yellow Sea. Int. J. Syst. Evol. Microbiol. 60 2877–2881. 10.1099/ijs.0.021048-0 PubMed DOI

Kim K. H., Cho G. Y., Chun B. H., Weckx S., Moon J. Y., Yeo S. H., et al. (2018). Acetobacter oryzifermentans sp. nov., isolated from Korean traditional vinegar and reclassification of the type strains of Acetobacter pasteurianus subsp. ascendens (Henneberg 1898) and Acetobacter pasteurianus subsp. paradoxus (Frateur 1950) as Acetobact. Syst. Appl. Microbiol. 41 324–332. 10.1016/j.syapm.2018.03.003 PubMed DOI

Kim K. K., Lee J.-S., Lee K. C., Oh H.-M., Kim S.-G. (2010). Pontibaca methylaminivorans gen. nov., sp. nov., a member of the family Rhodobacteraceae. Int. J. Syst. Evol. Microbiol. 60 2170–2175. 10.1099/ijs.0.020172-0 PubMed DOI

Kim K. K., Lee K. C., Eom M. K., Kim J.-S., Kim D.-S., Ko S.-H., et al. (2014). Variibacter gotjawalensis gen. nov., sp. nov., isolated from soil of a lava forest. Antonie Van Leeuwenhoek 105 915–924. 10.1007/s10482-014-0146-z PubMed DOI

Kim M., Chun J. (2014). 16S rRNA gene based identification of bacteria and Archaea using the EzTaxon server. Meth. Microbiol. 41 61–74. 10.1016/bs.mim.2014.08.001 PubMed DOI

Kim M. C., Kang O. C., Zhang Y., Ren L., Chang X., Jiang F., et al. (2016). Sphingoaurantiacus polygranulatus gen. nov., sp. nov., isolated from high-Arctic tundra soil, and emended descriptions of the genera Sandarakinorhabdus, Polymorphobacter and Rhizorhabdus and the species Sandarakinorhabdus limnophila, Rhizorhabdus argentea and Sphingomonas wittichii. Int. J. Syst. Evol. Microbiol. 66 91–100. 10.1099/ijsem.0.000677 PubMed DOI

Kim M. K., Im W.-T., Ohta H., Lee M., Lee S.-T. (2005). Sphingopyxis granuli sp. nov., a β-glucosidase-producing bacterium in the family Sphingomonadaceae in α-4 subclass of the Proteobacteria. J. Microbiol. 43 152–157. PubMed

Kim S. J., Ahn J. H., Lee T. H., Weon H. Y., Hong S. B., Seok S. J., et al. (2013). Reyranella soli sp. nov., isolated from forest soil, and emended description of the genus Reyranella Pagnier et al., 2011. Int. J. Syst. Evol. Microbiol. 63 3164–3167. 10.1099/ijs.0.045922-0 PubMed DOI

Kim Y.-G., Hwang C. Y., Cho B. C. (2008). Pelagicola litoralis gen. nov., sp. nov., isolated from coastal water in Korea. Int. J. Syst. Evol. Microbiol. 58 2102–2106. 10.1099/ijs.0.65820-0 PubMed DOI

Kim Y. O., Park I. S., Park S., Nam B. H., Park J. M., Kim D. G., et al. (2016a). Octadecabacter ascidiaceicola sp. nov., isolated from a sea squirt (Halocynthia roretzi). Int. J. Syst. Evol. Microbiol. 66 296–301. 10.1099/ijsem.0.000715 PubMed DOI

Kim Y.-O., Park S., Nam B.-H., Kang S.-J., Hur Y.-B., Kim D.-G., et al. (2012a). Description of Litoreibacter meonggei sp. nov., isolated from the sea squirt Halocynthia roretzi, reclassification of Thalassobacter arenae as Litoreibacter arenae comb. nov. and emended description of the genus Litoreibacter Romanenko et al. 2011. Int. J. Syst. Evol. Microbiol. 62 1825–1831. 10.1099/ijs.0.035113-0 PubMed DOI

Kim Y.-O., Park S., Nam B.-H., Kang S.-J., Hur Y. B., Lee S.-J., et al. (2012b). Ruegeria halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi. Int. J. Syst. Evol. Microbiol. 62 925–930. 10.1099/ijs.0.031609-0 PubMed DOI

Kim Y. O., Park S., Nam B. H., Park J. M., Kim D. G., Yoon J. H. (2016b). Ascidiaceihabitans donghaensis gen. nov., sp. nov., isolated from the golden sea squirt Halocynthia aurantium. Int. J. Syst. Evol. Microbiol. 64 3970–3975. 10.1099/ijsem.0.000849 PubMed DOI

Kimes N. E., López-Pérez M., Flores-Félix J. D., Ramírez-Bahena M.-H., Igual J. M., Peix A., et al. (2015). Pseudorhizobium pelagicum gen. nov., sp. nov. isolated from a pelagic Mediterranean zone. Syst. Appl. Microbiol. 38 293–299. 10.1016/j.syapm.2015.05.003 PubMed DOI

Kishimoto N., Kosako Y., Wakao N., Tano T., Hiraishi A. (1995). Transfer of Acidiphilium facilis and Acidiphilium aminolytica to the genus Acidocella gen. nov., and emendation of the genus Acidiphilium. Syst. Appl. Microbiol. 18 85–91. 10.1016/S0723-2020(11)80453-4 DOI

Klenk H.-P., Göker M. (2010). En route to a genome-based classification of Archaea and Bacteria? Syst. Appl. Microbiol. 33 175–182. 10.1016/j.syapm.2010.03.003 PubMed DOI

Klotz F., Brinkhoff T., Freese H. M., Wietz M., Teske A., Simon M., et al. (2018). Tritonibacter horizontis gen. nov., sp. nov., a member of the rhodobacteraceae, isolated from the Deepwater Horizon oil spill. Int. J. Syst. Evol. Microbiol. 68 736–744. 10.1099/ijsem.0.002573 PubMed DOI

Kluyver B., van Niel C. B. (1936). Prospects for a natural system of classification of bacteria. Zentralblatt fur Bakteriol. Parasitenkunde, Infekt. und Hyg. 94 369–403.

Knösel D. H. (1984). “Genus IV, Phyllobacterium,” in Bergey’s Manual of Systematic Bacteriology, Vol. 1 eds Krieg N. R., Holt J. G. (Baltimore, MD: The Williams and Wilkins Co.), 254–256.

Koelschbach J. S., Mouttaki H., Pickl C., Heipieper H. J., Rache R., Lawson P. A., et al. (2017). Rectinema cohabitans gen. nov., sp. nov., a rod-shaped spirochaete isolated from an anaerobic naphthalene-degrading enrichment culture. Int. J. Syst. Evol. Microbiol. 67 1288–1295. 10.1099/ijsem.0.001799 PubMed DOI

Kommanee J., Tanasupawat S., Yukphan P., Malimas T., Muramatsu Y., Nakagawa Y., et al. (2011). Gluconobacter nephelii sp. nov., an acetic acid bacterium in the class Alphaproteobacteria. Int. J. Syst. Evol. Microbiol. 61 2117–2122. 10.1099/ijs.0.026385-0 PubMed DOI

Kordick D. L., Swaminathan B., Greene C. E., Wilson K. H., Whitney A. M., Connor S. O., et al. (1996). Bartonella vinsonii subsp. berkhofii subsp. nov., isolated from dogs; Bartonella vinsonii subsp. vinsonii; and emended description of Bartonella vinsonii. Int. J. Syst. Bacteriol. 46 704–709. 10.1099/00207713-46-3-704 PubMed DOI

Kosako Y., Yabuuchi E. (2005). “Order IV, Sphingomonadales ord. nov,” in Bergey’s Manual of Systematic Bacteriology Part C, Vol. 2 eds Brenner D. J., Krieg N. R., Staley J. T. (Boston, MA: Springer; ), 230–233. 10.1007/0-387-29298-5 DOI

Kosako Y., Yabuuchi E., Naka T., Fujiwara N., Kobayashi K. (2000). Proposal of Sphingomonadaceae fam. nov., consisting of Sphingomonas Yabuuchi et al., 1990, Erythrobacter Shiba and Shimidu 1982, Erythromicrobium Yurkov et al., 1994, Porphyrobacter Fuerst et al., 1993, Zymomonas Kluyver and van Niel, 1936, and Sandaracinobacter Yurkov et al. 1997, with the type genus Sphingomonas Yabuuchi et al., 1990. Microbiol. Immunol. 44 563–575. 10.1111/j.1348-0421.2000.tb02535.x PubMed DOI

Kulichevskaya I. S., Danilova O. V., Tereshina V. M., Kevbrin V. V., Dedysh S. N. (2014). Descriptions of Roseiarcus fermentans gen. nov., sp. nov., a bacteriochlorophyll α-containing fermentative bacterium related phylogenetically to alphaproteobacterial methanotrophs, and of the family Roseiarcaceae fam. nov. Int. J. Syst. Evol. Microbiol. 64 2558–2565. 10.1099/ijs.0.064576-0 PubMed DOI

Kulichevskaya I. S., Guzev V. S., Gorlenko V. M., Liesack W., Dedysh S. N. (2006). Rhodoblastus sphagnicola sp. nov., a novel acidophilic purple non-sulfur bacterium form Sphagnum peat bog. Int. J. Syst. Evol. Microbiol. 56 1397–1402. 10.1099/ijs.0.63962-0 PubMed DOI

Kumar B. V., Ramprasad E. V. V., Sasikala C., Ramana C. V. (2013). Rhodopseudomonas pentothenatexigens sp. nov. and Rhodopseudomonas thermotolerans sp. nov., isolated from paddy soils. Int. J. Syst. Evol. Microbiol. 63 200–207. 10.1099/ijs.0.038620-0 PubMed DOI

Kumar M., Verma M., Lal R. (2008). Devosia chinhatensis sp. nov., isolated from a hexachlorocyclohexane (HCH) dump site in India. Int. J. Syst. Evol. Microbiol. 58 861–865. 10.1099/ijs.0.65574-0 PubMed DOI

Kumari H., Gupta S. K., Jindal S., Katoch P., Lal R. (2009). Sphingobium lactosutens sp. nov., isolated from a hexachlorocyclohexane dump site and Sphingobium abikonense sp. nov., isolated from oil-contaminated soil. Int. J. Syst. Evol. Microbiol. 59 2291–2296. 10.1099/ijs.0.004739-0 PubMed DOI

Kurahashi M., Fukunaga Y., Harayama S., Yokota A. (2008). Sneathiella glossodoripedis sp. nov., a marine alphaproteobacterium isolated from the nudibranch Glossodoris cincta, and proposal of Sneathiellales ord. nov. and Sneathiellaceae fam. nov. Int. J. Syst. Evol. Microbiol. 58 548–552. 10.1099/ijs.0.65328-0 PubMed DOI

Kurtti T. J., Felsheim R. F., Burkhardt N. Y., Oliver J. D., Heu C. C., Munderloh U. G. (2015). Rickettsia buchneri sp. nov., a rickettsial endosymbiont of the blacklegged tick Ixodes scapularis. Int. J. Syst. Evol. Microbiol. 65 965–970. 10.1099/ijs.0.000047 PubMed DOI PMC

Kuykendall L. D. (2005). “Order VI, Rhizobiales ord. nov,” in Bergey’s Manual of Systematic Bacteriology: The Proteobacteria, (Part C), Vol. 2 eds Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. (New York, NY: Springer; ), 324.

Kuykendall L. D., Saxena B., Devine T. E., Udell S. E. (1992). Genetic diversity in Bradyrhizobium japonicum Jordan, 1982 and a proposal for Bradyrhizobium elkanii sp. nov. Can. J. Microbiol. 38 501–505. 10.1139/m92-082 DOI

Kwon K. K., Lee H. S., Yang S. H., Kim S. J. (2005). Kordiimonas gwangyangenis gen. nov., sp. nov., a marine bacterium isolated from marine sediments that forms a distinct lieage (Kordiimonadales ord. nov.) in the “Alphaproteobacteria.”. Int. J. Syst. Evol. Microbiol. 55 2033–2037. 10.1099/ijs.0.63684-0 PubMed DOI

Kwon K. K., Woo J.-H., Yang S.-H., Kang J.-H., Kang S. G., Kim S.-J., et al. (2007). Altererythrobacter epoxidivorans gen. nov., sp. nov., an epoxide hydrolase-active, mesophilic marine bacterium isolated from cold-seep sediment, and reclassification of Erythrobacter luteolus Yoon et al. 2005 as Altererythrobacter luteolus comb. nov. Int. J. Syst. Evol. Microbiol. 57 2207–2211. 10.1099/ijs.0.64863-0 PubMed DOI

La Scola B., Mallet M.-N., Grimont P. A. D., Raoult D. (2002). Description of Afipia birgiae sp. nov. and Afipia massiliensis sp. nov. and recognition of Afipia felis genospecies A. Int. J. Syst. Evol. Microbiol. 52 1773–1782. 10.1099/ijs.0.02149-0 PubMed DOI

La Scola B., Mallet M.-N., Grimont P. A. D., Raoult D. (2003). Bosea eneae sp. nov., Bosea massiliensis sp. nov. and Bosea vestrisii sp. nov., isolated from hospital water supplies, and emendation of the genus Bosea (Das et al., 1996). Int. J. Syst. Evol. Microbiol. 53 15–20. 10.1099/ijs.0.02127-0 PubMed DOI

Labbé N., Parent S., Villemur R. (2004). Nitratireductor aquibiodomus gen. nov., sp. nov., a novel α-proteobacterium from the marine denitrification system of the Montreal Biodome (Canada). Int. J. Syst. Evol. Microbiol. 54 269–273. 10.1099/ijs.0.02793-0 PubMed DOI

Labrenz M., Collins M. D., Lawson P. A., Tindall B. J., Schumann P., Hirsch P. (1999). Roseovarius tolerans gen. nov., sp. nov., a budding bacterium with variable bacteriochlorophyll α production from hypersaline Ekho Lake. Int. J. Syst. Bacteriol. 49 137–147. 10.1099/00207713-49-1-137 PubMed DOI

Labrenz M., Lawson P. A., Tindall B. J., Collins M. D., Hirsch P. (2005). Roseisalinus antarcticus gen. nov., sp. nov., a novel aerobic bacteriochlorophyll α-producing α-proteobacterium isolated from hypersaline Ekho Lake. Antarctica. Int. J. Syst. Evol. Microbiol. 55 41–47. 10.1099/ijs.0.63230-0 PubMed DOI

Lagesen K., Hallin P., Rødland E. A., Stærfeldt H.-H., Rognes T., Ussery D. W. (2007). RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35 3100–3108. 10.1093/nar/gkm160 PubMed DOI PMC

Lai Q., Cao J., Yuan J., Li F., Shao Z. (2014). Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov. Int. J. Syst. Evol. Microbiol. 64 4160–4167. 10.1099/ijs.0.069039-0 PubMed DOI

Lai Q., Fu Y., Wang J., Chen S., Zhong H., Sun F., et al. (2011a). Citreicella marina sp. nov., isolated from deep-sea sediment. Int. J. Syst. Evol. Microbiol. 61 728–731. 10.1099/ijs.0.022376-0 PubMed DOI

Lai Q., Li G., Liu X., Du Y., Sun F., Shao Z. (2015). Pseudooceanicola atlanticus gen. nov. sp. nov., isolated from surface seawater of the Atlantic Ocean and reclassification of Oceanicola batsensis, Oceanicola marinus, Oceanicola nitratireducens, Oceanicola nanhaiensis, Oceanicola antarcticus and Oceanicola flagellatus, as Pseudooceanicola batsensis comb. nov., Pseudooceanicola marinus comb. nov., Pseudooceanicola nitratireducens comb. nov., Pseudooceanicola nanhaiensis comb. nov., Pseudooceanicola antarcticus comb. nov., and Pseudooceanicola flagellatus comb. nov. Antonie Van Leeuwenhoek 107 1065–1074. 10.1007/s10482-015-0398-2 PubMed DOI

Lai Q., Yu Z., Wang J., Zhong H., Sun F., Wang L., et al. (2011b). Nitratireductor pacificus sp. nov., isolated from a pyrene-degrading consortium. Int. J. Syst. Evol. Microbiol. 61 1386–1391. 10.1099/ijs.0.024356-0 PubMed DOI

Lai Q., Yu Z., Yuan J., Sun F., Shao Z. (2011c). Nitratireductor indicus sp. nov., isolated from deep-sea water. Int. J. Syst. Evol. Microbiol. 61 295–298. 10.1099/ijs.0.022962-0 PubMed DOI

Lai Q., Yuan J., Wu C., Shao Z. (2009). Oceanibaculum indicum gen. nov., sp. nov., isolated from deep seawater of the Indian Ocean. Int. J. Syst. Evol. Microbiol. 59 1733–1737. 10.1099/ijs.0.004341-0 PubMed DOI

Lake J. A., Rivera M. C. (2004). Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction. Mol. Biol. Evol. 21 681–690. 10.1093/molbev/msh061 PubMed DOI

Lakshmi K. V. N. S., Divyasree B., Ramprasad E. V. V., Sasikala C., Ramana C. V. (2014). Reclassification of Rhodospirillum photometricum Molisch, 1907, Rhodospirillum sulfurexigens Kumar et al., 2008 and Rhodospirillum oryzae Lakshmi et al. 2013 in a new genus, Pararhodospirillum gen. nov., as Pararhodospirillum photometricum comb. nov., Pararhodospirillum sulfurexigens comb. nov. and Pararhodospirillum oryzae comb. nov., respectively, and emended description of the genus Rhodospirillum. Int. J. Syst. Evol. Microbiol. 64 1154–1159. 10.1099/ijs.0.059147-0 PubMed DOI

Lakshmi K. V. N. S., Sasikala C., Takaichi S., Ramana C. V. (2011). Phaeospirillum oryzae sp. nov., a spheroplast-forming, phototrophic alphaproteobacterium from a paddy soil. Int. J. Syst. Evol. Microbiol. 61 1656–1661. 10.1099/ijs.0.025544-0 PubMed DOI

Lassalle F., Périan S., Bataillon T., Nesme X., Duret L., Daubin V. (2015). GC-content evolution in bacterial genomes: the biased gene conversion hypothesis expands. PLoS Genet. 11:e1004941. 10.1371/journal.pgen.1004941 PubMed DOI PMC

Lau S. C. K., Tsoi M. M. Y., Li X., Plakhotnikova I., Wu M., Wong P.-K., et al. (2004). Loktanella hongkongensis sp. nov., a novel member of the α-Proteobacteria originating from marine biofilms in Hong Kong waters. Int. J. Syst. Evol. Microbiol. 54 2281–2284. 10.1099/ijs.0.63294-0 PubMed DOI

Lavrinenko K., Chernousova E., Gridneva E., Dubinina G., Akimov V., Kuever J., et al. (2010). Azospirillum thiophilum sp. nov., a diazotrophic bacterium isolated from a sulfide spring. Int. J. Syst. Evol. Microbiol. 60 2832–2837. 10.1099/ijs.0.018853-0 PubMed DOI

Lawson P. A., Collins M. (1996). Description of Bartonella clarridgeiae sp. nov. isolated from the cat of a patient with Bartonella henselae septicemia. Med. Microbiol. Lett. 5 64–73.

Le Quesne W. J. (1974). The uniquely evolved character concept and its cladistic application. Syst. Biol. 23 513–517. 10.1093/sysbio/23.4.513 DOI

Lebuhn M., Achouak W., Schloter M., Berge O., Meier H., Barakat M., et al. (2000). Taxonomic characterization of Ochrobactrum sp. isolates from soil samples and wheat roots and description of Ochrobactrum tritici sp. nov. and Ochrobactrum grignonense sp. nov. Int. J. Syst. Evol. Microbiol. 50 2207–2223. 10.1099/00207713-50-6-2207 PubMed DOI

Lee H., Kim D.-U., Lee S., Park S., Yoon J.-H., Seong C. N., et al. (2017). Reyranella terrae sp. nov., isolated from an agricultural soil, and emended description of the genus Reyranella. Int. J. Syst. Evol. Microbiol. 67 2031–2035. 10.1099/ijsem.0.001913 PubMed DOI

Lee H.-W., Yu H.-S., Liu Q.-M., Jung H.-M., An D.-S., Im W.-T., et al. (2007a). Kaistia granuli sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor. Int. J. Syst. Evol. Microbiol. 57 2280–2283. 10.1099/ijs.0.65023-0 PubMed DOI

Lee K., Choo Y.-J., Giovannoni S. J., Cho J.-C. (2007b). Maritimibacter alkaliphilus gen. nov., sp. nov., a genome-sequenced marine bacterium of the Roseobacter clade in the order Rhodobacterales. Int. J. Syst. Evol. Microbiol. 57 1653–1658. 10.1099/ijs.0.64960-0 PubMed DOI

Lee K., Choo Y.-J., Giovannoni S. J., Cho J.-C. (2007c). Ruegeria pelagia sp. nov., isolated from the Sargasso Sea, Atlantic Ocean. Int. J. Syst. Evol. Microbiol. 57 1815–1818. 10.1099/ijs.0.65032-0 PubMed DOI

Lee K., Lee H. K., Choi T.-H., Cho J.-C. (2007d). Robiginitomaculum antarcticum gen. nov., sp. nov., a member of the family Hyphomonadaceae, from Antarctic seawater. Int. J. Syst. Evol. Microbiol. 57 2595–2599. 10.1099/ijs.0.65274-0 PubMed DOI

Lee K.-B., Liu C.-T., Anzai Y., Kim H., Aono T., Oyaizu H. (2005). The hierarchical system of the ‘Alphaproteobacteria’: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov. Int. J. Syst. Evol. Microbiol. 55 1907–1919. 10.1099/ijs.0.63663-0 PubMed DOI

Lee M.-H., Lee S.-Y., Jung Y.-T., Park S., Yoon J.-H. (2013). Pseudorhodobacter wandonensis sp. nov., isolated from wood falls, and emended description of the genus Pseudorhodobacter. Int. J. Syst. Evol. Microbiol. 63 1479–1484. 10.1099/ijs.0.042879-0 PubMed DOI

Lee S. D. (2012). Loktanella tamlensis sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol. 62 586–590. 10.1099/ijs.0.029462-0 PubMed DOI

Lee S. D., Joung Y., Cho J. C. (2017). Phreatobacter stygius sp. nov., isolated from pieces of wood in a lava cave and emended description of the genus phreatobacter. Int. J. Syst. Evol. Microbiol. 67 3296–3300. 10.1099/ijsem.0.002106 PubMed DOI

Lee S. H., Shim J. K., Kim J. M., Choi H.-K., Jeon C. O. (2011). Henriciella litoralis sp. nov., isolated from a tidal flat, transfer of Maribaculum marinum Lai et al., 2009 to the genus Henriciella as Henriciella aquimarina nom. nov. and emended description of the genus Henriciella. Int. J. Syst. Evol. Microbiol. 61 722–727. 10.1099/ijs.0.020396-0 PubMed DOI

Lee S.-Y., Park S., Oh T.-K., Yoon J.-H. (2012). Celeribacter baekdonensis sp. nov., isolated from seawater, and emended description of the genus Celeribacter Ivanova et al., 2010. Int. J. Syst. Evol. Microbiol. 62 1359–1364. 10.1099/ijs.0.032227-0 PubMed DOI

Lee Y. M., Yang J. Y., Baek K., Han S. J., Shin S. C., Hwang C. Y., et al. (2016). Pseudorhodobacter psychrotolerans sp. nov., a psychrotolerant bacterium isolated from terrestrial soil, and emended description of the genus Pseudorhodobacter. Int. J. Syst. Evol. Microbiol. 66 1068–1073. 10.1099/ijsem.0.000841 PubMed DOI

Lee Y. S., Lee D.-H., Kahng H.-Y., Kim E. M., Jung J. S. (2010). Erythrobacter gangjinensis sp. nov., a marine bacterium isolated from seawater. Int. J. Syst. Evol. Microbiol. 60 1413–1417. 10.1099/ijs.0.015743-0 PubMed DOI

Lefort V., Desper R., Gascuel O. (2015). FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol. Biol. Evol. 32 2798–2800. 10.1093/molbev/msv150 PubMed DOI PMC

Lei X., Zhang H., Chen Y., Li Y., Chen Z., Lai Q., et al. (2015). Erythrobacter luteus sp. nov., isolated from mangrove sediment. Int. J. Syst. Evol. Microbiol. 65 2472–2478. 10.1099/ijs.0.000283 PubMed DOI

León-Barrios M., Ramírez-Bahena M. H., Igual J. M., Peix Á, Velázquez E. (2018). Phyllobacterium salinisoli sp. nov., isolated from a lotus lancerottensis root nodule in saline soil from lanzarote. Int. J. Syst. Evol. Microbiol. 68 1085–1089. 10.1099/ijsem.0.002628 PubMed DOI

Letunic I., Bork P. (2019). Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 47 W256–W259. 10.1093/nar/gkz239 PubMed DOI PMC

Levett P. N., Morey R. E., Galloway R., Steigerwalt A. G., Ellis W. A. (2005). Reclassification of Leptospira parva Hovind-Hougen et al. 1982 as Turneriella parva gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 55 1497–1499. 10.1099/ijs.0.63088-0 PubMed DOI

Li A.-H., Liu H.-C., Hou W.-G., Zhou Y.-G. (2016). Pseudorhodobacter sinensis sp. nov. and Pseudorhodobacer aquaticus sp. nov., isolated from crater lakes. Int. J. Syst. Evol. Microbiol. 66 2819–2824. 10.1099/ijsem.0.001061 PubMed DOI

Li A.-H., Zhou Y.-G. (2015). Frigidibacter albus gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from lake water. Int. J. Syst. Evol. Microbiol. 65 1199–1206. 10.1099/ijs.0.000080 PubMed DOI

Li G.-W., Zhang X.-Y., Wang C.-S., Zhang Y.-J., Xu X.-W., Liu C., et al. (2013). Albimonas pacifica sp. nov., isolated from seawater of the Pacific, and emended description of the genus Albimonas. Int. J. Syst. Evol. Microbiol. 63 3597–3601. 10.1099/ijs.0.049742-0 PubMed DOI

Li L., Li Y.-Q., Jiang Z., Gao R., Nimaichand S., Duan Y.-Q., et al. (2016). Ochrobactrum endophyticum sp. nov., isolated from roots of Glycyrrhiza uralensis. Arch. Microbiol. 198 171–179. 10.1007/s00203-015-1170-8 PubMed DOI

Li L., Stoeckert C. J., Roos D. S. (2003). OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13 2178–2189. 10.1101/gr.1224503 PubMed DOI PMC

Li Q. Q., Wang E. T., Chang Y. L., Zhang Y. Z., Zhang Y. M., Sui X. H., et al. (2011). Ensifer sojae sp. nov., isolated from root nodules of Glycine max grown in saline-alkaline soils. Int. J. Syst. Evol. Microbiol. 61 1981–1988. 10.1099/ijs.0.025049-0 PubMed DOI

Li Z., Qu Z., Zhang X., Zhang X.-H. (2012). Lentibacter algarum gen. nov., sp. nov., isolated from coastal water during a massive green algae bloom. Int. J. Syst. Evol. Microbiol. 62 1042–1047. 10.1099/ijs.0.029868-0 PubMed DOI

Li Z., Zhao R., Ji S., Shi X., Zhang X.-H. (2013). Roseovarius marisflavi sp. nov., isolated from an amphioxus breeding zone in the coastal region of the Yellow Sea, China. Antonie Van Leeuwenhoek 104 413–421. 10.1007/s10482-013-9965-6 PubMed DOI

Liang J., Zhang Z., Liu Y., Wang M., Zhang X.-H. (2015). Loktanella sediminum sp. nov., isolated from marine surface sediment. Int. J. Syst. Evol. Microbiol. 65 686–691. 10.1099/ijs.0.070680-0 PubMed DOI

Liao H., Li Y., Lin X., Lai Q., Tian Y. (2018). Zhengella mangrovi gen. nov., sp. nov., a novel member of family phyllobacteriaceae isolated from mangrove sediment. Int. J. Syst. Evol. Microbiol. 68 2819–2825. 10.1099/ijsem.0.002900 PubMed DOI

Lienau K. E., DeSalle R. (2009). Evidence, content and corroboration and the tree of life. Acta Biotheor. 57 187–199. 10.1007/s10441-008-9066-5 PubMed DOI PMC

Lin S.-Y., Hameed A., Shen F.-T., Liu Y.-C., Hsu Y.-H., Shahina M., et al. (2014). Description of Niveispirillum fermenti gen. nov., sp. nov., isolated from a fermentor in Taiwan, transfer of Azospirillum irakense (1989) as Niveispirillum irakense comb. nov., and reclassification of Azospirillum amazonense (1983) as Nitrospirillum amazonense gen. nov. Antonie Van Leeuwenhoek 105 1149–1162. 10.1007/s10482-014-0176-6 PubMed DOI

Lin S. Y., Hameed A., Young C. C., Liu Y. C., Hsu Y. H., Chung W. C., et al. (2015). Thalassocola ureilytica gen. nov., sp. nov., of the family Phyllobacteriaceae isolated from seawater. Int. J. Syst. Evol. Microbiol. 65 4100–4106. 10.1099/ijsem.0.000544 PubMed DOI

Lin S.-Y., Shen F.-T., Young L.-S., Zhu Z.-L., Chen W.-M., Young C.-C. (2012). Azospirillum formosense sp. nov., a diazotroph from agricultural soil. Int. J. Syst. Evol. Microbiol. 62 1185–1190. 10.1099/ijs.0.030585-0 PubMed DOI

Lin S.-Y., Young C.-C., Hameed A., Liu Y.-C., Hsu Y.-H., Chung W.-C., et al. (2016). Actibacterium ureilyticum sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol. 66 2769–2773. 10.1099/ijsem.0.001052 PubMed DOI

Lingens F., Blecher R., Blecher H., Blobel F., Eberspächer J., Fröhner C., et al. (1985). Phenylobacterium immobile gen. nov., sp. nov., a gran-negative bacterium that degrades the herbicide chloridazon. Int. J. Syst. Bacteriol. 35 26–39. 10.1099/00207713-35-1-26 DOI

Lipski A., Kämpfer P. (2012). Aquamicrobium ahrensii sp. nov. and Aquamicrobium segne sp. nov., isolated from experimental biofilters. Int. J. Syst. Evol. Microbiol. 62 2511–2516. 10.1099/ijs.0.038224-0 PubMed DOI

Lipski A., Reichert K., Reuter B., Spröer C., Altendorf K. (1998). ldentif ication of bacterial isolates from biofilters as Paracoccus alkenifer sp. nov. and Paracoccus solventivorans with emended description of Paracoccus solventivorans. Int. J. Syst. Bacteriol. 48 529–536. 10.1099/00207713-48-2-529 PubMed DOI

Lisdiyanti P., Kawasaki H., Seki T., Yamada Y., Uchimura T., Kazuo K. (2000). Systematic study of the genus Acetobacter with descriptions of Acetobacter indonesiensis sp. nov., Acetobacter tropicalis sp. nov., Acetobacter orleanensis (Henneberg 1906) comb. nov., Acetobacter lovaniensis (Frateur 1950) comb. nov., and Acetobacter estunensis (Carr 1958) comb. nov. J. Gen. Appl. Microbiol. 46 147–165. 10.2323/jgam.46.147 PubMed DOI

Lisdiyanti P., Kawasaki H., Seki T., Yamada Y., Uchimura T., Komagata K. (2001). Identification of Acetobacter strains isolated from Indonesian sources, and proposals of Acetobacter syzygii sp. nov., Acetobacter cibinongensis sp. nov., and Acetobacter orientalis sp. nov. J. Gen. Appl. Microbiol. 47 119–131. 10.1016/S1043-2760(97)84344-5 PubMed DOI

Liu B. B., Wang H. F., Li Q. L., Zhou X. K., Zhang Y. G., Xiao M., et al. (2016). Aurantimonas endophytica sp. nov., a novel endophytic bacterium isolated from roots of Anabasis elatior (C. A. Mey.) Schischk. Int. J. Syst. Evol. Microbiol. 66 4112–4117. 10.1099/ijsem.0.001320 PubMed DOI

Liu C., Wu Y., Li L., Ma Y., Shao Z. (2007). Thalassospira xiamenensis sp. nov. and Thalassospira profundimaris sp. nov. Int. J. Syst. Evol. Microbiol. 57 316–320. 10.1099/ijs.0.64544-0 PubMed DOI

Liu J., Wang Y., Liu Y., Zhang X.-H. (2016). Ahrensia marina sp. nov., a dimethylsulfoniopropionate-cleaving bacterium isolated from seawater, and emended descriptions of the genus Ahrensia and Ahrensia kielensis. Int. J. Syst. Evol. Microbiol. 66 874–880. 10.1099/ijsem.0.000805 PubMed DOI

Liu J., Wang Y., Yang X., Sun Z., Ren Q., Zhang Y., et al. (2017). Roseibium sediminis sp. nov., isolated from sea surface sediment. Int. J. Syst. Evol. Microbiol. 67 2862–2867. 10.1099/ijsem.0.002034 PubMed DOI

Liu J.-H., Wang Y.-X., Zhang X.-X., Wang Z.-G., Chen Y.-G., Wen M.-L., et al. (2010). Salinarimonas rosea gen. nov., sp. nov., a new member of the α-2 subgroup of the Proteobacteria. Int. J. Syst. Evol. Microbiol. 60 55–60. 10.1099/ijs.0.006981-0 PubMed DOI

Liu J.-J., Zhang X.-Q., Chi F.-T., Pan J., Sun C., Wu M. (2014). Gemmobacter megaterium sp. nov., isolated from coastal planktonic seaweeds. Int. J. Syst. Evol. Microbiol. 64 66–71. 10.1099/ijs.0.050955-0 PubMed DOI

Liu K., Li S., Jiao N., Tang K. (2014). Pacificamonas flava gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from the Southeastern Pacific. Curr. Microbiol. 69 96–101. 10.1007/s00284-014-0560-5 PubMed DOI

Liu M., Dai J., Liu Y., Cai F., Wang Y., Rahman E., et al. (2011). Desertibacter roseus gen. nov., sp. nov., a gamma radiation-resistant bacterium in the family Rhodospirillaceae, isolated from desert sand. Int. J. Syst. Evol. Microbiol. 61 1109–1113. 10.1099/ijs.0.021246-0 PubMed DOI

Liu X.-Z., Wang Q.-M., Göker M., Groenewald M., Kachalkin A. V., Lumbsch H. T., et al. (2015). Towards an integrated phylogenetic classification of the Tremellomycetes. Stud. Mycol. 81 85–147. 10.1016/j.simyco.2015.12.001 PubMed DOI PMC

Liu Y., Jin J. H., Liu Y. H., Zhou Y. G., Liu Z. P. (2010). Dongia mobilis gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from a sequencing batch reactor for treatment of malachite green effluent. Int. J. Syst. Evol. Microbiol. 60 2780–2785. 10.1099/ijs.0.020347-0 PubMed DOI

Liu Y., Wang R.-P., Ren C., Lai Q.-L., Zeng R.-Y. (2015). Rhizobium marinum sp. nov., a malachite-green-tolerant bacterium isolated from seawater. Int. J. Syst. Evol. Microbiol. 65 4449–4454. 10.1099/ijsem.0.000593 PubMed DOI

Liu Y., Zhang X., Lai Q., Shao Z. (2018). Reclassification of Mameliella phaeodactyli, Mameliella atlantica, Ponticoccus lacteus and Alkalimicrobium pacificum as later heterotypic synonyms of Mameliella alba and an emended description of Mameliella alba. Int. J. Syst. Evol. Microbiol. 68 1047–1051. 10.1099/ijsem.0.002617 PubMed DOI

Liu Z.-P., Wang B.-J., Liu X.-Y., Dai X., Liu Y.-H., Liu S.-J. (2008). Paracoccus halophilus sp. nov., isolated from marine sediment of the South China Sea, China, and emended description of genus Paracoccus Davis 1969. Int. J. Syst. Evol. Microbiol. 58 257–261. 10.1099/ijs.0.65237-0 PubMed DOI

López-López A., Pujalte M. J., Benlloch S., Mata-Roig M., Roselló-Mora R., Garay E., et al. (2002). Thalassospira lucentensis gen. nov., sp. nov., a new marine member of the α-Proteobacteria. Int. J. Syst. Evol. Microbiol. 52 1277–1283. 10.1099/ijs.0.01928-0 PubMed DOI

Lucena T., Ruvira M. A., Garay E., Macián M. C., Arahal D. R., Pujalte M. J. (2012). Actibacterium mucosum gen. nov., sp. nov., a marine alphaproteobacterium from Mediterranean seawater. Int. J. Syst. Evol. Microbiol. 62 2858–2864. 10.1099/ijs.0.038026-0 PubMed DOI

Ludwig W., Mittenhuber G., Friedrich C. G. (1993). Transfer of Thiosphaera pantotropha to Paracoccus denitrificans. Int. J. Syst. Bacteriol. 43 363–367. 10.1099/00207713-43-2-363 PubMed DOI

Luis-Pantoja M., Ramos-González P. L., Naranjo M., Hernández-Rodríguez L., Rodríguez J., Pérez-López E. (2015). Rickettsia-related bacteria associated with papaya plants showing bunchy top disease in Cuba. J. Gen. Plant. Pathol. 81 166–168. 10.1007/s10327-014-0571-x DOI

Luo G., Shi Z., Wang H., Wang G. (2012). Skermanella stibiiresistens sp. nov., a highly antimony-resistant bacterium isolated from coal-mining soil, and emended description of the genus Skermanella. Int. J. Syst. Evol. Microbiol. 62 1271–1276. 10.1099/ijs.0.033746-0 PubMed DOI

Lv H., Masuda S., Fujitani Y., Sahin N., Tani A. (2017). Oharaeibacter diazotrophicus gen. nov., sp. nov., a diazotrophic and facultatively methylotrophic bacterium, isolated from rice rhizosphere. Int. J. Syst. Evol. Microbiol. 67 576–582. 10.1099/ijsem.0.001660 PubMed DOI

Lv X.-L., Xie B.-S., Cai M., Geng S., Tang Y.-Q., Wang Y.-N., et al. (2014). Glycocaulis albus sp. nov., a moderately halophilic dimorphic prosthecate bacterium isolated from petroleum-contaminated saline soil. Int. J. Syst. Evol. Microbiol. 64 3181–3187. 10.1099/ijs.0.063537-0 PubMed DOI

Macián M. C., Arahal D. R., Garay E., Ludwig W., Schleifer K. H., Pujalte M. J. (2005). Jannaschia rubra sp. nov., a red-pigmented bacterium isolated from sea water. Int. J. Syst. Evol. Microbiol. 55 649–653. 10.1099/ijs.0.63412-0 PubMed DOI

Madhaiyan M., Jin T. Y., Roy J. J., Kim S. J., Weon H. Y., Kwon S. W., et al. (2013). Pleomorphomonas diazotrophica sp. nov., an endophytic N-fixing bacterium isolated from root tissue of Jatropha curcas L. Int. J. Syst. Evol. Microbiol. 63 2477–2483. 10.1099/ijs.0.044461-0 PubMed DOI

Madhaiyan M., Kim B.-Y., Poonguzhali S., Kwon S.-W., Song M.-H., Ryu J.-H., et al. (2007). Methylobacterium oryzae sp. nov., and aerobic, pink-pigmented, facultatively methylotrophic, 1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from rice. Int. J. Syst. Evol. Microbiol. 57 326–331. 10.1099/ijs.0.64603-0 PubMed DOI

Madhaiyan M., Poonguzhali S. (2014). Methylobacterium pseudosasicola sp. nov. and Methylobacterium phyllostachyos sp. nov., isolated from bamboo leaf surfaces. Int. J. Syst. Evol. Microbiol. 64 2376–2384. 10.1099/ijs.0.057232-0 PubMed DOI

Madhaiyan M., Poonguzhali S., Kwon S.-W., Sa T.-M. (2009). Methylobacterium phyllosphaerae sp. nov., a pink-pigmented, facultative methylotroph from the phyllosphere of rice. Int. J. Syst. Evol. Microbiol. 59 22–27. 10.1099/ijs.0.001693-0 PubMed DOI

Madhaiyan M., Poonguzhali S., Senthilkumar M., Lee J.-S., Lee K.-C. (2012). Methylobacterium gossipiicola sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the cotton phyllosphere. Int. J. Syst. Evol. Microbiol. 62 162–167. 10.1099/ijs.0.030148-0 PubMed DOI

Maina A. N., Fogarty C., Krueger L., Macaluso K. R., Odhiambo A., Nguyen K., et al. (2016). Rickettsial infections among Ctenocephalides felis and host animals during a flea-borne rickettsioses outbreak in Orange County, California. PLoS One 11:e0160604. 10.1371/journal.pone.0160604 PubMed DOI PMC

Malimas T., Yukphan P., Takahashi M., Kaneyasu M., Potacharoen W., Tanasupawat S., et al. (2007). Gluconobacter kondonii sp. nov., an acetic acid bacterium in the a-Proteobacteria. J. Gen. Appl. Microbiol. 53 301–307. 10.2323/jgam.53.301 PubMed DOI

Mann S., Chen Y.-P. P. (2010). Bacterial genomic G + C composition-eliciting environmental adaptation. Genomics 95 7–15. 10.1016/j.ygeno.2009.09.002 PubMed DOI

Mantelin S., Fischer-Le Saux M., Zakhia F., Béna G., Bonneau S., Jeder H., et al. (2006). Emended description of the genus Phyllobacterium and description of four novel species associated with plant roots: Phyllobacterium bourgognense sp. nov., Phyllobacterium ifriqiyense sp. nov., Phyllobacterium leguminum sp. nov. and Phyllobacterium brassicacearum sp. nov. Int. J. Syst. Evol. Microbiol. 56 827–839. 10.1099/ijs.0.63911-0 PubMed DOI

Margesin R., Zhang D.-C. (2013). Humitalea rosea gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium of the family Acetobacteraceae isolated from soil. Int. J. Syst. Evol. Microbiol. 63 1411–1416. 10.1099/ijs.0.043018-0 PubMed DOI

Margos G., Lane R. S., Fedorova N., Koloczek J., Piesman J., Hojgaard A., et al. (2016). Borrelia bissettiae sp. nov. and Borrelia californiensis sp. nov. prevail in diverse enzootic transmission cycles. Int. J. Syst. Evol. Microbiol. 66 1447–1452. 10.1099/ijsem.0.000897 PubMed DOI PMC

Margos G., Wilske B., Sing A., Hizo-Teufel C., Cao W. C., Chu C., et al. (2013). Borrelia bavariensis sp. nov. is widely distributed in Europe and Asia. Int. J. Syst. Evol. Microbiol. 63 4284–4288. 10.1099/ijs.0.052001-0 PubMed DOI

Martens M., Dawyndt P., Coopman R., Gillis M., De Vos P., Willems A. (2008). Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium). Int. J. Syst. Evol. Microbiol. 58 200–214. 10.1099/ijs.0.65392-0 PubMed DOI

Martens T., Heidorn T., Pukall R., Simon M., Tindall B. J., Brinkhoff T. (2006). Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinov. Int. J. Syst. Evol. Microbiol. 56 1293–1304. 10.1099/ijs.0.63724-0 PubMed DOI

Martínez-Cánovas M. J., Quesada E., Martínez-Checa F., del Moral A., Béjar V. (2004). Salipiger mucescens gen. nov., sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium isolated from hypersaline soil, belonging to the α-Proteobacteria. Int. J. Syst. Evol. Microbiol. 54 1735–1740. 10.1099/ijs.0.63166-0 PubMed DOI

Martínez-Hidalgo P., Ramírez-Bahena M. H., Flores-Félix J. D., Rivas R., Igual J. M., Mateos P. F., et al. (2015). Revision of the taxonomic status of type strains of Mesorhizobium loti and reclassification of strain USDA 3471T as the type strain of Mesorhizobium erdmanii sp. nov. and ATCC 33669T as the type strain of Mesorhizobium jarvisii sp. nov. Int. J. Syst. Evol. Microbiol. 65 1703–1708. 10.1099/ijs.0.000164 PubMed DOI

Martínez-Romero E., Segovia L., Mercante F. M., Franco A. A., Graham P., Pardo M. A. (1991). Rhizobium tropici, a novel species nodulating Phaseolus vulgaris L. Beans and Leucaena sp. trees. Int. J. Syst. Bacteriol. 41 417–426. PubMed

Maruyama T., Park H.-D., Ozawa K., Tanaka Y., Sumino T., Hamana K., et al. (2006). Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. Int. J. Syst. Evol. Microbiol. 56 85–89. 10.1099/ijs.0.63789-0 PubMed DOI

Mason L. M., Claus G. W. (1989). Phenotypic characteristics correlated with deoxyribonucleic acid sequence similarities for three species of Gluconobacter: G. oxydans (Henneberg 1897) De Ley 1961. G. frateurii sp. nov., and G. asaii sp. nov. Int. J. Syst. Bacteriol. 39 174–184. 10.1099/00207713-39-2-174 DOI

Maszenan A. M., Seviour R. J., Patel B. K. C., Janssen P. H., Wanner J. (2005). Defluvicoccus vanus gen. nov., sp. nov., a novel Gram-negative coccus/coccobacillus in the “Alphaproteobacteria” from activated sludge. Int. J. Syst. Evol. Microbiol. 55 2105–2111. 10.1099/ijs.0.02332-0 PubMed DOI

Math R. K., Jin H. M., Jeong S. H., Jeon C. O. (2013). Defluviimonas aestuarii sp. nov., a marine bacterium isolated from a tidal flat, and emended description of the genus Defluviimonas Foesel et al., 2011. Int. J. Syst. Evol. Microbiol. 63 2895–2900. 10.1099/ijs.0.048389-0 PubMed DOI

Matsumoto M., Iwama D., Arakaki A., Tanaka A., Tanaka T., Miyashita H., et al. (2011). Altererythrobacter ishigakiensis sp. nov., an astaxanthin-producing bacterium isolated from a marine sediment. Int. J. Syst. Evol. Microbiol. 61 2956–2961. 10.1099/ijs.0.024729-0 PubMed DOI

Matthias M. A., Ricaldi J. N., Cespedes M., Diaz M. M., Galloway R. L., Saito M., et al. (2008). Human Leptospirosis caused by a new, antigenically unique Leptospira associated with a Rattus species reservoir in the Peruvian Amazon. PLoS Neglected Top. Dis. 2:e213. 10.1371/journal.pntd.0000213 PubMed DOI PMC

Mavromatis K., Land M. L., Brettin T. S., Quest D. J., Copeland A., Clum A., et al. (2012). The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. PLoS One 7:e48837. 10.1371/journal.pone.0048837 PubMed DOI PMC

McCutcheon J. P., McDonald B. R., Moran N. A. (2009). Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont. PLoS Genet. 5:e1000565. 10.1371/journal.pgen.1000565 PubMed DOI PMC

McDonald I. R., Doronina N. V., Trotsenko Y. A., McAnulla C., Murrell J. C. (2001). Hyphomicrobium chloromethanicum sp. nov. and Methylobacterium chloromethanicum sp. nov., chloromethane-utilizing bacteria isolated from a polluted environment. Int. J. Syst. Evol. Microbiol. 51 119–122. 10.1099/00207713-51-1-119 PubMed DOI

Mediannikov O., Matsumoto K., Samoylenko I., Drancourt M., Roux V., Rydkina E., et al. (2008). Rickettsia raoultii sp. nov., a spotted fever group rickettsia associated with Dermacentor ticks in Europe and Russia. Int. J. Syst. Evol. Microbiol. 58 1635–1639. 10.1099/ijs.0.64952-0 PubMed DOI

Meier-Kolthoff J. P., Auch A. F., Klenk H.-P., Göker M. (2013a). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60. 10.1186/1471-2105-14-60 PubMed DOI PMC

Meier-Kolthoff J. P., Auch A. F., Klenk H.-P., Göker M. (2014a). Highly parallelized inference of large genome-based phylogenies. Concurr. Comput. Pract. Exp. 26 1715–1729. 10.1002/cpe.3112 DOI

Meier-Kolthoff J. P., Göker M. (2019). TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat. Commun. 10:2182. 10.1038/s41467-019-10210-3 PubMed DOI PMC

Meier-Kolthoff J. P., Göker M., Spröer C., Klenk H.-P. (2013b). When should a DDH experiment be mandatory in microbial taxonomy? Arch. Microbiol. 195 413–418. 10.1007/s00203-013-0888-4 PubMed DOI

Meier-Kolthoff J. P., Hahnke R. L., Petersen J., Scheuner C., Michael V., Fiebig A., et al. (2014b). Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand. Genomic Sci. 9:2. 10.1186/1944-3277-9-2 PubMed DOI PMC

Meier-Kolthoff J. P., Klenk H.-P., Göker M. (2014c). Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int. J. Syst. Evol. Microbiol. 64 352–356. 10.1099/ijs.0.056994-0 PubMed DOI

Meng Y., Liu H., Kang Y., Zhou Y., Cai M. (2017). Blastomonas marina sp. nov., a bacteriochlorophyll-containing bacterium isolated from seawater. Int. J. Syst. Evol. Microbiol. 67 3015–3019. 10.1099/ijsem.0.002070 PubMed DOI

Mergaert J., Swings J. (2005). “Family IV. Phyllobacteriaceae fam. nov,” in Bergey’s Manual of Systematic Bacteriology: The Proteobacteria, (Part C), Vol. 2 eds Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. (New York, NY: Springer; ), 393.

Mesbah M., Premachandran U., Whitman W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int. J. Syst. Bacteriol. 39 159–167. 10.1099/00207713-39-2-159 DOI

Meyer K. F., Shaw E. B. (1920). A comparison of the morphologic, cultural and biochemical characteristics of B. abortus and B. melitensis: studies on the genus Brucella nov. gen. I. J. Infect. Dis. 27 173–184. 10.1093/infdis/27.3.173 DOI

Meyer O., Stackebrandt E., Auling G. (1993). Reclassification of Ubiquinone Q-10 containing carboxidotrophic bacteria: transfer of “[Pseudomonas] carboxydovorans” OM5T to Oligotropha, gen. nov., as Oligotropha carboxidovorans, comb. nov., transfer of “[Alcaligenes] carboxydus” DSM 1086T to Carbophilus, gen. nov., as Carbophilus carboxidus, comb. nov., transfer of “[Pseudomonas] compransoris” DSM 1231T to Zavarzinia, gen. nov., as Zavarzinia compransoris, comb. nov., and Amended Descriptions of the New Genera. Syst. Appl. Microbiol. 16 390–395. 10.1016/S0723-2020(11)80271-7 DOI

Miyazaki M., Sakai S., Ritalahti K. M., Saito Y., Yamanaka Y., Saito Y., et al. (2014a). Sphaerochaeta multiformis sp. nov., an anaerobic, psychrophilic bacterium isolated from subseafloor sediment, and emended description of the genus Sphaerochaeta. Int. J. Syst. Evol. Microbiol. 64 4147–4154. 10.1099/ijs.0.068148-0 PubMed DOI

Miyazaki M., Sakai S., Yamanaka Y., Saito Y., Takai K., Imachi H. (2014b). Spirochaeta psychrophila sp. nov., a psychrophilic spirochaete isolated from subseafloor sediment offshore Shimokita, Japan, and emended description of the genus Spirochaeta. Int. J. Syst. Evol. Microbiol. 64(Pt 8) 2798–2804. 10.1099/ijs.0.062463-0 PubMed DOI

Mohd Nor M. N., Sabaratnam V., Annie Tan G. Y. (2017). Devosia elaeis sp. nov., isolated from oil palm rhizospheric soil. Int. J. Syst. Evol. Microbiol. 67 851–855. 10.1099/ijsem.0.001683 PubMed DOI

Molisch H. (1907). Die Purpurbakterien Nach Neuen Untersuchungen. Jena: G. Fischer; 1–95.

Montero-Calasanz M., del C., Meier-Kolthoff J. P., Zhang D. F., Yaramis A., Rohde M., et al. (2017). Genome-scale data call for a taxonomic rearrangement of Geodermatophilaceae. Front. Microbiol. 8:2501. 10.3389/fmicb.2017.02501 PubMed DOI PMC

Moon Y. G., Seo S. H., Lee S. D., Heo M. S. (2010). Loktanella pyoseonensis sp. nov., isolated from beach sand, and emended description of the genus Loktanella. Int. J. Syst. Evol. Microbiol. 60 785–789. 10.1099/ijs.0.011072-0 PubMed DOI

Moore R. L., Weiner R. M., Gebers R. (1984). Genus Hyphomonas Pongratz 1957 nom. rev. emend., Hyphomonas polymorpha Pongratz 1957 nom. rev. emend., and Hyphomonas neptunium (Leifson 1964) comb. nov. emend. (Hyphomicrobium neptunium). Int. J. Syst. Bacteriol. 34 71–73. 10.1099/00207713-34-1-71 DOI

Moreira A. P. B., Pereira N., Thompson F. L., Pereira N., Jr., Thompson F. L. (2011). Usefulness of a real-time PCR platform for G+C content and DNA-DNA hybridization estimations in vibrios. Int. J. Syst. Evol. Microbiol. 61 2379–2383. 10.1099/ijs.0.023606-0 PubMed DOI

Moreira F. M., de S., Cruz L., de Faria S. M., Marsh T., Martínez-Romero E., et al. (2006). Azorhizobium doebereinerae sp. nov. microsymbiont of Sesbania virgata (caz.) pers. Syst. Appl. Microbiol. 29 197–206. 10.1016/j.syapm.2005.09.004 PubMed DOI

Moshkovski S. D. (1945). Cytotropic inducers of infection and the classification of the Rickettsiae within Chlamydozoa (original title in russian). Adv. Mod. Biol. 19 1–44.

Mousavi S. A., Österman J., Wahlberg N., Nesme X., Lavire C., Vial L., et al. (2014). Phylogeny of the Rhizobium–Allorhizobium–Agrobacterium clade supports the delineation of Neorhizobium gen. nov. Syst. Appl. Microbiol. 37 208–215. 10.1016/j.syapm.2013.12.007 PubMed DOI

Mousavi S. A., Willems A., Nesme X., de Lajudie P., Lindström K. (2015). Revised phylogeny of Rhizobiaceae: proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations. Syst. Appl. Microbiol. 38 84–90. 10.1016/j.syapm.2014.12.003 PubMed DOI

Mu Y., Zhou L., Zeng X. C., Liu L., Pan Y., Chen X., et al. (2016). Arsenicitalea aurantiaca gen. nov., sp. nov., a new member of the family Hyphomicrobiaceae, isolated from high-arsenic sediment. Int. J. Syst. Evol. Microbiol. 66 5478–5484. 10.1099/ijsem.0.001543 PubMed DOI

Mukherjee S., Seshadri R., Varghese N. J., Eloe-Fadrosh E. A., Meier-Kolthoff J. P., Göker M., et al. (2017). 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nat. Biotechnol. 35 676–685. 10.1038/nbt.3886 PubMed DOI

Muramatsu Y., Uchino Y., Kasai H., Suzuki K., Nakagawa Y. (2007). Ruegeria mobilis sp. nov., a member of the Alphaproteobacteria isolated in Japan and Palau. Int. J. Syst. Evol. Microbiol. 57 1304–1309. 10.1099/ijs.0.64572-0 PubMed DOI

Nakagawa Y., Yokotat A. (1996). Transfer of “Pseudomonas riboflavina” (Foster 1944), a Gram-negative, motile rod with long-chain 3-hydroxy fatty acids, to Devosia riboflavina gen. nov., sp. nov., nom. rev. Int. J. Syst. Bacteriol 46 16–22. 10.1099/00207713-46-1-16 PubMed DOI

Nedashkovskaya O. I., Kukhlevskiy A. D., Zhukova N. V., Kim S.-J., Rhee S.-K. (2013). Litorimonas cladophorae sp. nov., a new Alphaproteobacterium isolated from the Pacific green alga Cladophora stimpsoni, and emended descriptions of the genus Litorimonas and Litorimonas taeaensis. Antonie Van Leeuwenhoek 103 1263–1269. 10.1007/s10482-013-9906-4 PubMed DOI

Nguyen T. M., Pham V. H. T., Kim J. (2015). Mesorhizobium soli sp. nov., a novel species isolated from the rhizosphere of Robinia pseudoacacia L. in South Korea by using a modified culture method. Antonie Van Leeuwenhoek 108 301–310. 10.1007/s10482-015-0481-8 PubMed DOI

Nigam A., Jit S., Lal R. (2010). Sphingomonas histidinilytica sp. nov., isolated from a hexachlorocyclohexane dump site. Int. J. Syst. Evol. Microbiol. 60 1038–1043. 10.1099/ijs.0.008995-0 PubMed DOI

Niharika N., Jindal S., Kaur J., Lal R. (2012). Sphingomonas indica sp. nov., isolated from hexachlorocyclohexane (HCH)-contaminated soil. Int. J. Syst. Evol. Microbiol. 62 2997–3002. 10.1099/ijs.0.033845-0 PubMed DOI

Niharika N., Moskalikova H., Kaur J., Khan F., Sedlackova M., Hampl A., et al. (2013a). Sphingobium czechense sp. nov., isolated from a hexachlorocyclohexane dump site. Int. J. Syst. Evol. Microbiol. 63 723–728. 10.1099/ijs.0.039396-0 PubMed DOI

Niharika N., Moskalikova H., Kaur J., Sedlackova M., Hampl A., Damborsky J., et al. (2013b). Novosphingobium barchaimii sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int. J. Syst. Evol. Microbiol. 63 667–672. 10.1099/ijs.0.039826-0 PubMed DOI

Nikoh N., Hosokawa T., Moriyama M., Oshima K., Hattori M., Fukatsu T. (2014). Evolutionary origin of insect – Wolbachia nutritional mutualism. Proc. Natl. Acad. Sci. U.S.A. 111 10257–10262. 10.1073/pnas.1409284111 PubMed DOI PMC

Nogi Y., Mori K., Makita H., Hatada Y. (2016). Thalassobius abyssi sp. nov., a marine bacterium isolated from cold-seep sediment. Int. J. Syst. Evol. Microbiol. 66 574–579. 10.1099/ijsem.0.000758 PubMed DOI

Nogi Y., Yoshizumi M., Miyazaki M. (2014). Thalassospira povalilytica sp. nov., a polyvinyl-alcohol-degrading marine bacterium. Int. J. Syst. Evol. Microbiol. 64 1149–1153. 10.1099/ijs.0.058321-0 PubMed DOI

Nordhoff M., Taras D., Macha M., Tedin K., Busse H.-J., Wieler L. H. (2005). Treponema berlinense sp. nov. and Treponema porcinum sp. nov., novel spirochaetes isolated from porcine faeces. Int. J. Syst. Evol. Microbiol. 55 1675–1680. 10.1099/ijs.0.63388-0 PubMed DOI

Nouioui I., Carro L., García-López M., Meier-Kolthoff J. P., Woyke T., Kyrpides N. C., et al. (2018). Genome-based taxonomic classification of the phylum actinobacteria. Front. Microbiol. 9:2007 10.3389/fmicb.2018.02007 PubMed DOI PMC

Nupur P., Srinivas T.N.R., Takaichi S., AnilKumar P. (2015). Phaeobacterium nitratireducens gen. nov., sp. nov., a phototrophic gammaproteobacterium isolated from a mangrove forest sediment sample. Int. J. Syst. Evol. Microbiol. 65 2357–2364. 10.1099/ijs.0.000263 PubMed DOI

Ochiai S., Adachi Y., Mori K. (1997). Unification of the genera serpulina and Brachyspira, and proposals of Brachyspira hyodysenteriae comb. nov., Brachyspira innocens comb. nov. and Brachyspira pilosicoli comb. nov. Microbiol. Immunol. 41 445–452. 10.1111/j.1348-0421.1997.tb01877.x PubMed DOI

Oh K.-H., Choi W.-C., Jung Y.-T., Kang S.-J., Oh T.-K., Yoon J.-H. (2012). Tropicimonas aquimaris sp. nov., isolated from seawater, and emended description of the genus Tropicimonas Harwati et al. 2009. Int. J. Syst. Evol. Microbiol. 62 688–692. 10.1099/ijs.0.029371-0 PubMed DOI

Oh K.-H., Jung Y.-T., Oh T.-K., Yoon J.-H. (2011). Ruegeria faecimaris sp. nov., isolated from a tidal flat sediment. Int. J. Syst. Evol. Microbiol. 61 1182–1188. 10.1099/ijs.0.025999-0 PubMed DOI

Oh M., Kim J.-H., Kim W. (2016). Tropicimonas arenosa sp. nov., isolated from marine sand. Int. J. Syst. Evol. Microbiol. 66 5514–5518. 10.1099/ijsem.0.001549 PubMed DOI

Oh Y.-S., Lim H.-J., Cha I.-T., Im W.-T., Yoo J.-S., Kang U. G., et al. (2009). Roseovarius halotolerans sp. nov., isolated from deep seawater. Int. J. Syst. Evol. Microbiol. 59 2718–2723. 10.1099/ijs.0.002576-0 PubMed DOI

Oren A. (2017a). A plea for linguistic accuracy – also for Candidatus taxa. Int. J. Syst. Evol. Microbiol. 67 1085–1094. 10.1099/ijsem.0.001715 PubMed DOI

Oren A. (2017b). On names of genera of prokaryotes that are later homonyms of generic names with standing in the zoological or the botanical nomenclature. proposal of Neomegalonema gen. nov. and Neomegalonema perideroedes comb. nov. as replacements for the prokaryotic generic name Meganema and the species name Meganema perideroedes. Int. J. Syst. Evol. Microbiol. 67 4276–4278. 10.1099/ijsem.0.002349 PubMed DOI

Pagnier I., Raoult D., La Scola B. (2011). Isolation and characterization of Reyranella massiliensis gen. nov., sp. nov. from freshwater samples by using an amoeba co-culture procedure. Int. J. Syst. Evol. Microbiol. 61 2151–2154. 10.1099/ijs.0.025775-0 PubMed DOI

Pal R., Bala S., Dadhwal M., Kumar M., Dhingra G., Prakash O., et al. (2005). Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov. Int. J. Syst. Evol. Microbiol. 55 1965–1972. 10.1099/ijs.0.63201-0 PubMed DOI

Pan J., Sun C., Zhang X.-Q., Huo Y.-Y., Zhu X.-F., Wu M. (2014). Paracoccus sediminis sp. nov., isolated from Pacific Ocean marine sediment. Int. J. Syst. Evol. Microbiol. 64 2512–2516. 10.1099/ijs.0.051318-0 PubMed DOI

Pan X.-C., Geng S., Lv X.-L., Mei R., Jiangyang J.-H., Wang Y.-N., et al. (2015). Defluviimonas alba sp. nov., isolated from an oilfield. Int. J. Syst. Evol. Microbiol. 65 1805–1811. 10.1099/ijs.0.000181 PubMed DOI

Panday D., Das S. K. (2010). Chelatococcus sambhunathii sp. nov., a moderately thermophilic alphaproteobacterium isolated from hot spring sediment. Int. J. Syst. Evol. Microbiol. 60 861–865. 10.1099/ijs.0.013466-0 PubMed DOI

Paramasivam N., Ben-Dov E., Arotsker L., Kushmaro A. (2013). Eilatimonas milleporae gen. nov., sp. nov., a marine bacterium isolated from the hydrocoral Millepora dichotoma. Int. J. Syst. Evol. Microbiol. 63 1880–1884. 10.1099/ijs.0.043976-0 PubMed DOI

Park J. R., Bae J.-W., Nam Y.-D., Chang H.-W., Kwon H.-Y., Quan Z.-X., et al. (2007). Sulfitobacter litoralis sp. nov., a marine bacterium isolated from the East Sea, Korea. Int. J. Syst. Evol. Microbiol. 57 692–695. 10.1099/ijs.0.64267-0 PubMed DOI

Park M. S., Chung B.-S., Lee H. J., Jin H. M., Lee S.-S., Oh Y. K., et al. (2011). Citreicella aestuarii sp. nov., isolated from a tidal flat. Int. J. Syst. Evol. Microbiol. 61 2595–2599. 10.1099/ijs.0.028332-0 PubMed DOI

Park S., Jung Y.-T., Won S.-M., Yoon J.-H. (2014a). Pseudoruegeria sabulilitoris sp. nov., isolated from seashore sand. Int. J. Syst. Evol. Microbiol. 64 3276–3281. 10.1099/ijs.0.066258-0 PubMed DOI

Park S., Jung Y.-T., Yoon J.-H. (2013a). Pelagicola litorisediminis sp. nov., a novel alphaproteobacterium isolated from tidal flat sediment. Antonie Van Leeuwenhoek 104 103–110. 10.1007/s10482-013-9930-4 PubMed DOI

Park S., Jung Y.-T., Yoon J.-H. (2014b). Wenxinia saemankumensis sp. nov., isolated from a tidal flat sediment. Int. J. Syst. Evol. Microbiol. 64 1958–1963. 10.1099/ijs.0.062190-0 PubMed DOI

Park S., Kang C.-H., Park J.-M., Yoon J.-H. (2014c). Aquimixticola soesokkakensis gen. nov., sp. nov., a novel lipolytic alphaproteobacterium isolated from the junction between the ocean and a freshwater spring, and reclassification of Roseovarius marinus as Pacificibacter marinus comb. nov. and emended description of the genus Pacificibacter. Antonie Van Leeuwenhoek 106 647–655. 10.1007/s10482-014-0235-z PubMed DOI

Park S., Kang S.-J., Oh T.-K., Yoon J.-H. (2010). Roseivivax lentus sp. nov., isolated from a tidal flat sediment, and emended description of the genus Roseivivax Suzuki et al. 1999. Int. J. Syst. Evol. Microbiol. 60 1113–1117. 10.1099/ijs.0.014795-0 PubMed DOI

Park S., Lee J.-S., Lee K.-C., Yoon J.-H. (2013b). Lentilitoribacter donghaensis gen. nov., sp. nov., a slowly-growing alphaproteobacterium isolated from coastal seawater. Antonie Van Leeuwenhoek 103 457–464. 10.1007/s10482-012-9825-9 PubMed DOI

Park S., Lee M.-H., Yoon J.-H. (2013c). Oceanicola litoreus sp. nov., an alphaproteobacterium isolated from the seashore sediment. Antonie Van Leeuwenhoek 103 859–866. 10.1007/s10482-012-9867-z PubMed DOI

Park S., Park J.-M., Jung Y.-T., Won S.-M., Yoon J.-H. (2015a). Primorskyibacter insulae sp. nov., isolated from the junction between the ocean and a freshwater spring. Int. J. Syst. Evol. Microbiol. 65 3971–3976. 10.1099/ijsem.0.000522 PubMed DOI

Park S., Park J. M., Kang C. H., Kim S. G., Yoon J. H. (2015b). Pseudoseohaeicola caenipelagi gen. nov., sp. nov., isolated from a tidal flat. Int. J. Syst. Evol. Microbiol. 65 1819–1824. 10.1099/ijs.0.000182 PubMed DOI

Park S., Park J. M., Kang C. H., Yoon J.-H. (2014d). Aestuariispira insulae gen. nov., sp. nov., a lipolytic bacterium isolated from a tidal flat. Int. J. Syst. Evol. Microbiol. 64 1841–1846. 10.1099/ijs.0.062406-0 PubMed DOI

Park S., Park J.-M., Kang C.-H., Yoon J.-H. (2014e). Confluentimicrobium lipolyticum gen. nov., sp. nov., a novel lipolytic alphaproteobacterium isolated from the junction between the ocean and a freshwater spring, and emended description of Actibacterium mucosum Lucena et al., 2012. Antonie Van Leeuwenhoek 106 969–977. 10.1007/s10482-014-0266-5 PubMed DOI

Park S., Park J. M., Kang C. H., Yoon J. H. (2015c). Aliiroseovarius pelagivivens gen. nov., sp. nov., isolated from seawater, and reclassification of three species of the genus Roseovarius as Aliiroseovarius crassostreae comb. nov., Aliiroseovarius halocynthiae comb. nov. and Aliiroseovarius sediminilitori. Int. J. Syst. Evol. Microbiol. 65 2646–2652. 10.1099/ijs.0.000315 PubMed DOI

Park S., Won S. M., Kim H., Park D. S., Yoon J. H. (2014f). Aestuariivita boseongensis gen. nov., sp. nov., isolated from a tidal flat sediment. Int. J. Syst. Evol. Microbiol. 64 2969–2974. 10.1099/ijs.0.062406-0 PubMed DOI

Park S. C., Baik K. S., Choe H. N., Lim C. H., Kim H. J., Ka J.-O., et al. (2011). Altererythrobacter namhicola sp. nov. and Altererythrobacter aestuarii sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol. 61 709–715. 10.1099/ijs.0.021196-0 PubMed DOI

Parker C. T., Tindall B. J., Garrity G. M. (2019). International code of nomenclature of prokaryotes. Int. J. Syst. Evol. Microbiol. 69 S1–S111. PubMed

Patt T. E., Cole G. C., Hanson R. S. (1976). Methylobacterium, a new genus of facultatively methyotrophic bacteria. Int. J. Syst. Bacteriol. 26 226–229. 10.1099/00207713-26-2-226 DOI

Patwardhan S., Vetriani C. (2016). Varunaivibrio sulfuroxidans gen. nov., sp. nov., a facultatively chemolithoautotrophic, mesophilic alphaproteobacterium from a shallow-water gas vent at Tor Caldara, Tyrrhenian Sea. Int. J. Syst. Evol. Microbiol. 66 3579–3584. 10.1099/ijsem.0.001235 PubMed DOI

Peix A., Rivas R., Trujillo M. E., Vancanneyt M., Velázquez E., Willems A. (2005). Reclassification of Agrobacterium ferrugineum LMG 128 as Hoeflea marina gen. nov., sp. nov. Int. J. Syst. Evol. Microbiol. 55 1163–1166. 10.1099/ijs.0.63291-0 PubMed DOI

Penesyan A., Breider S., Schumann P., Tindall B. J., Egan S., Brinkhoff T. (2013). Epibacterium ulvae gen. nov., sp. nov., epibiotic bacteria isolated from the surface of a marine alga. Int. J. Syst. Evol. Microbiol. 63 1589–1596. 10.1099/ijs.0.042838-0 PubMed DOI

Perolat P., Chappel R. J., Adler B., Baranton G., Bulacht D. M., Billinghurst M. L., et al. (1998). Leptospira fainei sp. nov., isolated from pigs in Australia. Int. J. Syst. Bacteriol. 48 851–858. 10.1099/00207713-48-3-851 PubMed DOI

Pfennig N., Lünsdorf H., Süling J., Imhoff J. F. (1997). Rhodospira trueperi gen. nov., spec. nov., a new phototrophic Proteobacterium of the alpha group. Arch. Microbiol. 168 39–45. 10.1007/s002030050467 PubMed DOI

Pfennig N., Trüper H. G. (1971). Higher taxa of the phototrophic bacteria. Int. J. Syst. Bacteriol. 21 17–18. 10.1099/00207713-21-1-17 DOI

Philip C. B. (1943). Nomenclature of the pathogenic rickettsiae. Am. J. Hyg. 37 301–309.

Philip C. B. (1950). “Miscellaneous human rickettsioses,” in Communicable Diseases, ed. Pullen R. L. (Philadelphia, PA: Lea and Febiger Co.), 781–788.

Philip C. B. (1957). ““Family IV. anaplasmataceae philip, fam. nov,” in Bergey’s Manual of Systematic Bacteriology, 7th Edn, eds Breed R. S., Murray E. G. D., Smith N. R. (Baltimore, MD: The Williams and Wilkins Co.), 980–984.

Philip R. N., Casper E. A., Anacker R. L., Cory J., Hayes S. F., Burgdorfer W., et al. (1983). Rickettsia bellii sp. nov.: a tick-borne Rickettsia, widely distributed in the United States, that is distinct from the spotted fever and typhus biogroups. Int. J. Syst. Bacteriol. 33 94–106. 10.1099/00207713-33-1-94 DOI

Pikuta E. V., Hoover R. B., Bej A. K., Marsic D., Whitman W. B., Krader P. (2009). Spirochaeta dissipatitropha sp. nov., an alkaliphilic, obligately anaerobic bacterium, and emended description of the genus Spirochaeta Ehrenberg 1835. Int. J. Syst. Evol. Microbiol. 59 1798–1804. 10.1099/ijs.0.016733-0 PubMed DOI

Pini F., Galardini M., Bazzicalupo M., Mengoni A. (2011). Plant-bacteria association and symbiosis: are there common genomic traits in Alphaproteobacteria? Genes (Basel) 2 1017–1032. 10.3390/genes2041017 PubMed DOI PMC

Poindexter J. S. (1964). Biological properties and classification of the Caulobacter group. Bacteriol. Rev. 28 231–295. 10.1128/mmbr.28.3.231-295.1964 PubMed DOI PMC

Poroshina M. N., Trotsenko Y. A., Doronina N. V. (2015). Metylobrevis pamukkalensis gen. nov., sp. nov., a halotolerant restricted facultative methylotroph isolated from saline water. Int. J. Syst. Evol. Microbiol. 65 1321–1327. 10.1099/ijs.0.000105 PubMed DOI

Prakash O., Lal R. (2006). Description of Sphingobium fuliginis sp. nov., a phenanthrene-degrading bacterium from a fly ash dumping site, and reclassification of Sphingomonas cloacae as Sphingobium cloacae comb. nov. Int. J. Syst. Evol. Microbiol. 56 2147–2152. 10.1099/ijs.0.64080-0 PubMed DOI

Pritt B. S., Respicio-Kingry L. B., Sloan L. M., Schriefer M. E., Replogle A. J., Bjork J., et al. (2016). Borrelia mayonii sp. nov., a member of the Borrelia burgdorferi sensu lato complex, detected in patients and ticks in the upper midwestern United States. Int. J. Syst. Evol. Microbiol. 66 4878–4880. 10.1099/ijsem.0.001445 PubMed DOI PMC

Proença D. N., Whitman W. B., Varghese N., Shapiro N., Woyke T., Kyrpides N. C., et al. (2018). Arboriscoccus pini gen. nov., sp. nov., an endophyte from a pine tree of the class Alphaproteobacteria, emended description of Geminicoccus roseus, and proposal of Geminicoccaceae fam. nov. Syst. Appl. Microbiol. 41 94–100. 10.1016/j.syapm.2017.11.006 PubMed DOI

Pujalte M. J., Lucena T., Rodrigo-Torres L., Arahal D. R. (2018). Comparative genomics of Thalassobius including the description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov. Front. Microbiol. 8:2645. 10.3389/fmicb.2017.02645 PubMed DOI PMC

Pujalte M. J., Macián M. C., Arahal D. R., Ludwig W., Schleifer K. H., Garay E. (2005). Nereida ignava gen. nov., sp. nov., a novel aerobic marine α-proteobacterium that is closely related to uncultured prionitis (alga) gall symbionts. Int. J. Syst. Evol. Microbiol. 55 631–636. 10.1099/ijs.0.63442-0 PubMed DOI

Pukall R., Laroche M., Kroppenstedt R. M., Schumann P., Stackebrandt E., Ulber R. (2003). Paracoccus seriniphilus sp. nov., an L-serine-dehydratase-producing coccus isolated from the marine bryozoan Bugula plumosa. Int. J. Syst. Evol. Microbiol. 53 443–447. 10.1099/ijs.0.02352-0 PubMed DOI

Qu L., Lai Q., Zhu F., Hong X., Sun X., Shao Z. (2011). Cohaesibacter marisflavi sp. nov., isolated from sediment of a seawater pond used for sea cucumber culture, and emended description of the genus Cohaesibacter. Int. J. Syst. Evol. Microbiol. 61 762–766. 10.1099/ijs.0.021972-0 PubMed DOI

Quan Z.-X., Zeng D.-N., Xiao Y.-P., Roh S. W., Nam Y.-D., Chang H.-W., et al. (2009). Henriciella marina gen. nov., sp. nov., a novel member of the family Hyphomonadaceae isolated form the East Sea. J. Microbiol. 47 156–161. 10.1007/s12275-008-0290-0 PubMed DOI

Radl V., Simôes-Araújo J. L., Leite J., Ribeiro Passos S., Vieira Martins L. M., Ribeiro Xavier G., et al. (2014). Microvirga vignae sp. nov., a root nodule symbiotic bacterium isolated from cowpea grown in semi-arid Brazil. Int. J. Syst. Evol. Microbiol. 64 725–730. 10.1099/ijs.0.053082-0 PubMed DOI

Rahalkar M., Bahulikar R. A., Deutzmann J. S., Kroth P. G., Schink B. (2012). Elstera litoralis gen. nov., sp. nov., isolated from stone biofilms of lake constance, Germany. Int. J. Syst. Evol. Microbiol. 62 1750–1754. 10.1099/ijs.0.026609-0 PubMed DOI

Rahul K., Azmatunnisa M., Sasikala C., Ramana C. V. (2015). Hoeflea olei sp. nov., a diesel-oil-degrading, anoxygenic, phototrophic bacterium isolated from backwaters and emended description of the genus Hoeflea. Int. J. Syst. Evol. Microbiol. 65 2403–2409. 10.1099/ijs.0.000277 PubMed DOI

Rainey F. A., Kelly D. P., Stackebrandt E., Burghardt J., Hiraishi A., Katayama Y., et al. (1999). A re-evaluation of the taxonomy of Paracoccus denitrificans and a proposal for the combination Paracoccus pantotrophus comb. nov. Int. J. Syst. Bacteriol. 49 645–651. 10.1099/00207713-49-2-645 PubMed DOI

Rainey F. A., Silva J., Nobre M. F., Silva M. T., da Costa M. S. (2003). Porphyrobacter cryptus sp. nov., a novel slightly thermophilic, aerobic, bacteriochlorophyll α-containing species. Int. J. Syst. Evol. Microbiol. 53 35–41. 10.1099/ijs.0.02308-0 PubMed DOI

Raj H. D. (1983). Proposal of Ancylobacter gen. nov. as a substitute for the bacterial genus microcyclus Ørskov 1928. Int. J. Syst. Bacteriol. 33 397–398. 10.1099/00207713-33-2-397 DOI

Raj P. S., Chakravarthy S. K., Ramaprasad E. V. V., Sasikala C., Ramana C. V. (2012). Phaeospirillum tilakii sp. nov., a phototrophic Alphaproteobacterium isolated from aquatic sediments. Int. J. Syst. Evol. Microbiol. 62 1069–1074. 10.1099/ijs.0.032250-0 PubMed DOI

Rajasabapathy R., Mohandass C., Dastager S. G., Liu Q., Khieu T.-N., Son C. K., et al. (2014). Roseovarius azorensis sp. nov., isolated from seawater at Espalamaca, Azores. Antonie Van Leeuwenhoek 105 571–578. 10.1007/s10482-013-0109-9 PubMed DOI

Ramadass P., Jarvis B. D. W., Corner R. J., Penny D., Marshall R. B. (1992). Genetic characterization of pathogenic Leptospira apecies by DNA hybridization. Int. J. Syst. Bacteriol. 42 215–219. 10.1099/00207713-42-2-215 PubMed DOI

Ramana C. V., Parag B., Girija K. R., Ram B. R., Ramana V. V., Sasikala C. (2013). Rhizobium subbaraonis sp. nov., an endolithic bacterium isolated from beach sand. Int. J. Syst. Evol. Microbiol. 63 581–585. 10.1099/ijs.0.041442-0 PubMed DOI

Ramana V. V., Raj P. S., Tushar L., Sasikala C., Ramana C. V. (2013). Rhodomicrobium udaipurense sp. nov., a psychrotolerant, phototrophic Alphaproteobacterium isolated from a freshwater stream. Int. J. Syst. Evol. Microbiol. 63 2684–2689. 10.1099/ijs.0.046409-0 PubMed DOI

Ramírez-Bahena M. H., García-Fraile P., Peix A., Valverde A., Rivas R., Mateos P. F., et al. (2008). Revision of the taxonomic status of the species Rhizobium leguminosarum (Frank 1879) Frank, 1889 AL, Rhizobium phaseoli Dangeard 1926AL and Rhizobium trifolii Dangeard 1926AL. R. trifolii is a later synonym of R. leguminosarum. Reclassification of the stra. Int. J. Syst. Evol. Microbiol. 58 2484–2490. 10.1099/ijs.0.65621-0 PubMed DOI

Ramírez-Bahena M. H., Peix A., Rivas R., Camacho M., Rodríguez-Navarro D. N., Mateos P. F., et al. (2009). Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus. Int. J. Syst. Evol. Microbiol. 59 1929–1934. 10.1099/ijs.0.006320-0 PubMed DOI

Rathsack K., Reitner J., Stackebrandt E., Tindall B. J. (2011). Reclassification of Aurantimonas altamirensis (Jurado et al. 2006), Aurantimonas ureilytica (Weon et al., 2007) and Aurantimonas frigidaquae (Kim Y.-G. et al., 2008) as members of a new genus, Aureimonas gen. nov., as Aureimonas altamirensis gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 61 2722–2728. 10.1099/ijs.0.027029-0 PubMed DOI

Reddy G. S. N., Garcia-Pichel F. (2007). Sphingomonas mucosissima sp. nov. and Sphingomonas desiccabilis sp. nov., from biological soil crusts in the Colorado Plateau, USA. Int. J. Syst. Evol. Microbiol. 57(Pt 5) 1028–1034. 10.1099/ijs.0.64331-0 PubMed DOI

Reddy G. S. N., Nagy M., Garcia-Pichel F. (2006). Belnapia moabensis en. nov., sp. nov., an Alphaproteobacterium from biological soil crusts in the Colorado Plateau, USA. Int. J. Syst. Evol. Microbiol. 56 51–58. 10.1099/ijs.0.63764-0 PubMed DOI

Rekha P. D., Young C.-C., Kämpfer P., Martin K., Arun A. B., Chen W.-M., et al. (2011). Jhaorihella thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring. Int. J. Syst. Evol. Microbiol. 61 1544–1548. 10.1099/ijs.0.025817-0 PubMed DOI

Ren D. W., Chen W. F., Sui X. H., Wang E. T., Chen W. X. (2011). Rhizobium vignae sp. nov., a symbiotic bacterium isolated from multiple legume species. Int. J. Syst. Evol. Microbiol. 61 580–586. 10.1099/ijs.0.023143-0 PubMed DOI

Ren F., Zhang L., Song L., Xu S., Xi L., Huang L., et al. (2014). Fulvimarina manganoxydans sp. nov., isolated from a deep-sea hydrothermal plume in the south-west Indian Ocean. Int. J. Syst. Evol. Microbiol. 64 2920–2925. 10.1099/ijs.0.060558-0 PubMed DOI

Ribeiro R. A., Rogel M. A., López-López A., Ormeño-Orillo E., Barcellos F. G., Martínez J., et al. (2012). Reclassification of Rhizobium tropici type A strains as Rhizobium leucaenae sp. nov. Int. J. Syst. Evol. Microbiol. 62 1179–1184. 10.1099/ijs.0.032912-0 PubMed DOI

Rihs J. D., Brenner D. J., Weaver R. E., Steigerwalt A. G., Hollis D. G., Yu V. L. (1993). Roseomonas, a new genus associated with bacteremia and other human infections. J. Clin. 31 3275–3283. 10.1128/jcm.31.12.3275-3283.1993 PubMed DOI PMC

Rincón-Rosales R., Villalobos-Escobedo J. M., Rogel M. A., Martinez J., Ormeño-Orrillo E., Martínez-Romero E. (2013). Rhizobium calliandrae sp. nov., Rhizobium mayense sp. nov. and Rhizobium jaguaris sp. nov., rhizobial species nodulating the medicinal legume Calliandra grandiflora. Int. J. Syst. Evol. Microbiol. 63 3423–3429. 10.1099/ijs.0.048249-0 PubMed DOI

Ritalahti K. M., Justicia-Leon S. D., Cusick K. D., Ramos-Hernandez N., Rubin M., Dornbush J., et al. (2012). Sphaerochaeta globosa gen. nov., sp. nov. and Sphaerochaeta pleomorpha sp. nov., free-living, spherical spirochaetes. Int. J. Syst. Evol. Microbiol. 62 210–216. 10.1099/ijs.0.023986-0 PubMed DOI

Ritika C., Suresh K., Anil Kumar P. (2012). Caenispirillum salinarum sp. nov., a member of the family Rhodospirillaceae isolated from a solar saltern. Int. J. Syst. Evol. Microbiol. 62 1698–1702. 10.1099/ijs.0.035287-0 PubMed DOI

Rivas R., Abril A., Trujillo M. E., Velázquez E. (2004). Sphingomonas phyllosphaerae sp. nov., from the phyllosphere of Acacia caven in Argentina. Int. J. Syst. Evol. Microbiol. 54 2147–2150. 10.1099/ijs.0.63102-0 PubMed DOI

Rivas R., Martens M., de Lajudie P., Willems A. (2009). Multilocus sequence analysis of the genus Bradyrhizobium. Syst. Appl. Microbiol. 32 101–110. 10.1016/j.syapm.2008.12.005 PubMed DOI

Rivas R., Sánchez-Márquez S., Mateos P. F., Martínez-Molina E., Velázquez E. (2005). Martelella mediterranea gen. nov., sp. nov., a novel α-proteobacterium isolated from a subterranean saline lake. Int. J. Syst. Evol. Microbiol. 55 955–959. 10.1099/ijs.0.63438-0 PubMed DOI

Rivas R., Willems A., Subba-Rao N. S., Mateos P. F., Dazzo F. B., Kroppenstedt R. M., et al. (2003). Description of Devosia neptuniae sp. nov. that nodulates and fixes nitrogen in symbiosis with Neptunia natans, an aquatic legume from India. Syst. Appl. Microbiol. 26 47–53. 10.1078/072320203322337308 PubMed DOI

Robinson G. H. (1948). “Order V. Spirochaetales buchanan,” in Bergey’s Manual of Determinative Bacteriology, eds Breed R. S., Murray E. G. D., Hitchens A. P. (Baltimore, MD: The Williams & Wilkins Co.), 1051–1058.

Rocha E. P. C., Danchin A. (2002). Base composition bias might result from competition for metabolic resources. Trends Genet. 18 291–294. 10.1016/S0168-9525(02)02690-2 PubMed DOI

Roh S. W., Kim K.-H., Nam Y.-D., Chang H.-W., Kim M.-S., Oh H.-M., et al. (2009). Sphingomonas aestuarii sp. nov., isolated from tidal flat sediment. Int. J. Syst. Evol. Microbiol. 59 1359–1363. 10.1099/ijs.0.65528-0 PubMed DOI

Romanenko L. A., Tanaka N., Frolova G. M., Mikhailov V. V. (2008). Pseudochrobactrum glaciei sp. nov., isolated from sea ice collected from Peter the great bay of the sea of Japan. Int. J. Syst. Evol. Microbiol. 58 2454–2458. 10.1099/ijs.0.65828-0 PubMed DOI

Romanenko L. A., Tanaka N., Frolova G. M., Svetashev V. I., Mikhailov V. V. (2011a). Litoreibacter albidus gen. nov., sp. nov. and Litoreibacter janthinus sp. nov., members of the class Alphaproteobacteria isolated from the seashore. Int. J. Syst. Evol. Microbiol. 61 148–154. 10.1099/ijs.0.019513-0 PubMed DOI

Romanenko L. A., Tanaka N., Svetashev V. I., Mikhailov V. V. (2011b). Primorskyibacter sedentarius gen. nov., sp. nov., a novel member of the class Alphaproteobacteria from shallow marine sediments. Int. J. Syst. Evol. Microbiol. 61 1572–1578. 10.1099/ijs.0.025551-0 PubMed DOI

Romanenko L. A., Tanaka N., Svetashev V. I., Mikhailov V. V. (2011c). Vadicella arenosi gen. nov., sp. nov., a novel member of the class Alphaproteobacteria isolated from sandy sediments from the Sea of Japan seashore. Curr. Microbiol. 62 795–801. 10.1007/s00284-010-9780-5 PubMed DOI

Romanenko L. A., Tanaka N., Svetashev V. I. (2013). Devosia submarina sp. nov., isolated from deepsea surface sediments. Int. J. Syst. Evol. Microbiol. 63 3079–3085. 10.1099/ijs.0.046607-0 PubMed DOI

Rosselló-Mora R., Amann R. (2001). The species concept for prokaryotes. FEMS Microbiol. Rev. 25 39–67. 10.1016/S0168-6445(00)00040-1 PubMed DOI

Rothe B., Fischer A., Hirsch P., Sittig M., Stackebrandt E. (1987). The phylogenetic position of the budding bacteria Blastobacter aggregatus and Gemmobacter aquatilis gen., nov. sp. nov. Arch. Microbiol. 147 92–99. 10.1007/bf00492911 DOI

Rüger H.-J., Höfle M. G. (1992). Marine star-shaped-sggregate-forming bacteria: Agrobacterium atlanticum sp. nov.; Agrobacterium meteori sp. nov.; Agrobacterium ferrugineum sp. nov., nom. rev.; Agrobacterium gelatinovorum sp. nov., nom. rev.; and Agrobacterium stellulatum sp. nov., nom. Int. J. Syst. Bacteriol. 42 133–143. 10.1099/00207713-42-1-133 PubMed DOI

Ryu S. H., Chung B. S., Le N. T., Jang H. H., Yun P.-Y., Park W., et al. (2008). Devosia geojensis sp. nov., isolated from diesel-contaminated soil in Korea. Int. J. Syst. Evol. Microbiol. 58 633–636. 10.1099/ijs.0.65481-0 PubMed DOI

Ryu S. H., Park M., Lee J. R., Yun P.-Y., Jeon C. O. (2007). Brevundimonas aveniformis sp. nov., a stalked species isolated from activated sludge. Int. J. Syst. Evol. Microbiol. 57 1561–1565. 10.1099/ijs.0.64737-0 PubMed DOI

Sánchez-Porro C., Gallego V., Busse H.-J., Kämpfer P., Ventosa A. (2009). Transfer of Teichococcus ludipueritiae and Muricoccus roseus to the genus Roseomonas, as Roseomonas ludipueritiae comb. nov. and Roseomonas rosea comb. nov., respectively, and emended description of the genus Roseomonas. Int. J. Syst. Evol. Microbiol. 59 1193–1198. 10.1099/ijs.0.004820-0 PubMed DOI

Satomi M., Kimura B., Hamada T., Harayama S., Fujii T. (2002). Phylogenetic study of the genus Oceanospirillum based on 16S rRNA and gyrB genes : emended description of the genus Oceanospirillum, description of Pseudospirillum gen. nov., Oceanobacter gen. nov. and Terasakiella gen. nov. and transfer of Oceanospirillum jannaschii and Pseudomonas stanieri to Marinobacterium as Marinobacterium jannaschii comb. nov. and Marinobacterium stanieri comb. nov. Int. J. Syst. Evol. Microbiol. 52 739–747. 10.1099/ijs.0.01427-0 PubMed DOI

Sawada H., Ieki H., Oyaizu H., Matsumoto S. (1993). Proposal for rejection of Agrobacterium tumefaciens and revised descriptions for the genus Agrobacterium and for Agrobacterium radiobacter and Agrobacterium rhizogenes. Int. J. Syst. Bacteriol. 43 694–702. 10.1099/00207713-43-4-694 PubMed DOI

Saxena A., Anand S., Dua A., Sangwan N., Khan F., Lal R. (2013). Novosphingobium lindaniclasticum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite. Int. J. Syst. Evol. Microbiol. 63 2160–2167. 10.1099/ijs.0.045443-0 PubMed DOI

Schaudinn F. (1905). Korrespondenzen. Dtsch. Med. Wochenschr. 31:1728.

Schiaffino R., Sánchez L., Gerea M., Unrein F., Balagué V., Gasol J. M., et al. (2016). Distribution patterns of the abundance of major bacterial and archaeal groups in Patagonian lakes. J. Plankton Res. 38 64–82. 10.1093/plankt/fbv105 DOI

Schleheck D., Tindall B. J., Roselló-Mora R., Cook A. M. (2004). Parvibaculum lavamentivorans gen. nov., sp. nov., a novel heterotroph that initiates catabolism of linear alkylbenzenesulfonate. Int. J. Syst. Evol. Microbiol. 54 1489–1497. 10.1099/ijs.0.03020-0 PubMed DOI

Schleifer H. K., Schüler D., Spring S., Weizenegger M., Amann R., Ludwig W., et al. (1991). The genus Magnetospirillum gen. nov. description of Magnetospirillum gryphiswaldense sp. nov. and transfer of Aquaspirillum magnetotacticum to Magnetospirillum magnetotacticum comb. nov. Syst. Appl. Microbiol. 14 379–385. 10.1016/S0723-2020(11)80313-9 DOI

Scholz H. C., Hubalek Z., Sedláèek I., Vergnaud G., Tomaso H., Al Dahouk S., et al. (2008). Brucella microti sp. nov., isolated from the common vole Microtus arvalis. Int. J. Syst. Evol. Microbiol. 58 375–382. 10.1099/ijs.0.65356-0 PubMed DOI

Scholz H. C., Nöckler K., Göllner C., Bahn P., Vergnaud G., Tomaso H., et al. (2010). Brucella inopinata sp. nov., isolated from a breast implant infection. Int. J. Syst. Evol. Microbiol. 60 801–808. 10.1099/ijs.0.011148-0 PubMed DOI

Schrank K., Choi B.-K., Grund S., Moter A., Heuner K., Nattermann H., et al. (1999). Treponema brennaborense sp. nov., a novel spirochaete isolated from a diary cow suffering from digital dermatitis. Int. J. Syst. Bacteriol. 49 43–50. 10.1099/00207713-49-1-43 PubMed DOI

Schüller G., Hertel C., Hammes W. P. (2000). Gluconacetobacter entanii sp. nov., isolated from submerged high-acid industrial vinegar fermentations. Int. J. Syst. Evol. Microbiol. 50 2013–2020. 10.1099/00207713-50-6-2013 PubMed DOI

Segers P., Vancanneyt M., Pot B., Torck U., Hoste B., Dewettinck D., et al. (1994). Classification of Pseudomonas diminuta Leifson and Hugh 1954 and Pseudomonas vesicularis Büsing, Döll, and Freytag 1953 in Brevundimonas gen. nov. as Brevundimonas diminuta comb. nov. and Brevundimonas vesicularis comb. nov., respectively. Int. J. Syst. Bacteriol. 44 499–510. 10.1099/00207713-44-3-499 PubMed DOI

Segovia L., Young J. P. W., Martínez-Romero E. (1993). Reclassification of American Rhizobium leguminosarum biovar phaseoli type I strains as Rhizobium etli sp. nov. Int. J. Syst. Bacteriol. 43 374–377. 10.1099/00207713-43-2-374 PubMed DOI

Sekeyová Z., Roux V., Xu W., Øeháèek J., Raoultl D. (1998). Rickettsia slovaca sp. nov., a member of the spotted fever group rickettsiae. Int. J. Syst. Bacteriol. 48 1455–1462. 10.1099/00207713-48-4-1455 PubMed DOI

Seo S. H., Lee S. D. (2010). Altererythrobacter marensis sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol. 60 307–311. 10.1099/ijs.0.011031-0 PubMed DOI

Sha S., Zhong J., Chen B., Lin L., Luan T. (2017). Novosphingobium guangzhouense sp. nov., with the ability to degrade 1-methylphenanthrene. Int. J. Syst. Evol. Microbiol. 67 489–497. 10.1099/ijsem.0.001669 PubMed DOI

Shalem Raj P., Ramaprasad E. V. V., Vaseef S., Sasikala C., Ramana C. V. (2013). Rhodobacter viridis sp. nov., a phototrophic bacterium isolated from mud of a stream. Int. J. Syst. Evol. Microbiol. 63 181–186. 10.1099/ijs.0.038471-0 PubMed DOI

Sharma P., Verma M., Bala K., Nigam A., Lal R. (2010). Sphingopyxis ummariensis sp. nov., isolated from a hexachlorocyclohexane dump site. Int. J. Syst. Evol. Microbiol. 60 780–784. 10.1099/ijs.0.008805-0 PubMed DOI

Shen X., Li Y., Zhao Z., Han Y. F., Zhang W. W., Yu X. Y., et al. (2018). Polyphasic taxonomic characterisation of a novel strain as Pararhizobium haloflavum sp. nov., isolated from soil samples near a sewage treatment tank. Antonie van Leeuwenhoek 111 485–491. 10.1007/s10482-017-0969-5 PubMed DOI

Sheu S. Y., Chen Y. L., Young C. C., Chen W. M. (2013). Lacibacterium aquatile gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from a freshwater lake. Int. J. Syst. Evol. Microbiol. 63 4797–4804. 10.1099/ijs.0.055145-0 PubMed DOI

Shi B.-H., Arunpairojana V., Palakawong S., Yokota A. (2002). Tistrella mobilis gen. nov., sp. nov., a novel polyhydroxyalkanoate-producing bacterium belonging to.ALPHA.-Proteobacteria. J. Gen. Appl. Microbiol. 48 335–343. 10.2323/jgam.48.335 PubMed DOI

Shi X., Li C., Zhao L., Si M., Zhu L., Xin K., et al. (2016). Rhizobium gei sp. nov., A bacterial endophyte of Geum aleppicum. Int. J. Syst. Evol. Microbiol. 66 4282–4288. 10.1099/ijsem.0.001348 PubMed DOI

Shiba T. (1991). Roseobacter litoralis gen. nov., sp. nov., and Roseobacter denitrificans sp. nov., aerobic pink-pigmented bacteria which contain bacteriochlorophyll α. Syst. Appl. Microbiol. 14 140–145. 10.1016/s0723-2020(11)80292-4 DOI

Shiba T., Smidu U. (1982). Erythrobacter longus gen. nov., sp. nov., an aerobic bacterium which contains bacteriochlorophyll α. Int. J. Syst. Bacteriol. 32 211–217. 10.1099/00207713-32-2-211 DOI

Shieh W. Y., Lin Y.-T., Jean W. D. (2004). Pseudovibrio denitrificans gen. nov., sp. nov., a marine, facultatively anaerobic, fermentative bacterium capable of denitrification. Int. J. Syst. Evol. Microbiol. 54 2307–2312. 10.1099/ijs.0.63107-0 PubMed DOI

Shin N.-R., Roh S. W., Kim M.-S., Yun B., Whon T. W., Kim Y.-O., et al. (2012). Tropicimonas sediminicola sp. nov., isolated from marine sediment. Int. J. Syst. Evol. Microbiol. 62 2424–2429. 10.1099/ijs.0.037929-0 PubMed DOI

Shivani Y., Subhash Y., Sasikala C., Ramana C. V. (2016). Description of ‘Candidatus Marispirochaeta associata’ and reclassification of Spirochaeta bajacaliforniensis, Spirochaeta smaragdinae and Spirochaeta sinaica to a new genus Sediminispirochaeta gen. nov. as Sediminispirochaeta bajacalidorniensis comb. nov. Int. J. Syst. Evol. Microbiol. 66 5485–5492. 10.1099/ijsem.0.001545 PubMed DOI

Shivani Y., Subhash Y., Tushar L., Sasikala C., Ramana C. V. (2015). Spirochaeta lutea sp. nov., isolated from marine habitats and emended description of the genus Spirochaeta. Syst. Appl. Microbiol. 38 110–114. 10.1016/j.syapm.2014.11.002 PubMed DOI

Siddall M. E. (2010). Unringing a bell: metazoan phylogenomics and the partition bootstrap. Cladistics 26 444–452. 10.1111/j.1096-0031.2009.00295.x PubMed DOI

Siddavattam D., Karegoudar T. B., Mudde S. K., Kumar N., Baddam R., Avasthi T. S., et al. (2011). Genome of a novel isolate of Paracoccus denitrificans capable of degrading N,N-dimethylformamide. J. Bacteriol. 193 5598–5599. 10.1128/JB.05667-11 PubMed DOI PMC

Simon M., Scheuner C., Meier-Kolthoff J. P., Brinkhoff T., Wagner-Döbler I., Ulbrich M., et al. (2017). Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. ISME J. 11 1483–1499. 10.1038/ismej.2016.198 PubMed DOI PMC

Singh A., Lal R. (2009). Sphingobium ummariense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium, isolated from HCH-contaminated soil. Int. J. Syst. Evol. Microbiol. 59 162–166. 10.1099/ijs.0.65712-0 PubMed DOI

Singh P., Kim Y.-J., Hoang V.-A., Farh M. E.-A., Yang D.-C. (2016). Erratum to: Sphingomonas panacis sp. nov., isolated from rhizosphere of rusty ginseng. Antonie Van Leeuwenhoek 109 735–736. 10.1007/s10482-016-0662-0 PubMed DOI

Sizova M. V., Panikov N. S., Spiridonova E. M., Slobodova N. V., Tourova T. P. (2007). Novel facultative anaerobic acidotolerant Telmatospirillum siberiense gen. nov. sp. nov. isolated from mesotrophic fen. Syst. Appl. Microbiol. 30 213–220. 10.1016/j.syapm.2006.06.003 PubMed DOI

Skerman V. B. D., McGowan V., Sneath P. H. A. (1980). Approved lists of bacterial names. Int. J. Syst. Bacteriol. 30 225–420. 10.1099/00207713-30-1-225 DOI

Slack A. T., Kalambaheti T., Symonds M. L., Dohnt M. F., Galloway R. L., Steigerwalt A. G., et al. (2008). Leptospira wolffii sp. nov., isolated from a human with suspected leptospirosis in Thailand. Int. J. Syst. Evol. Microbiol. 58 2305–2308. 10.1099/ijs.0.64947-0 PubMed DOI

Slack A. T., Khairani-Bejo S., Symonds M. L., Dohnt M. F., Galloway R. L., Steigerwalt A. G., et al. (2009). Leptospira kmetyi sp. nov., isolated from an environmental source in Malaysia. Int. J. Syst. Evol. Microbiol. 59 705–708. 10.1099/ijs.0.002766-0 PubMed DOI

Sly L. I., Cahill M. M. (1997). Transfer of Blastobacter natatorius (Sly 1985) to the genus Blastomonas gen. nov. as Blastomonas natatoria comb. nov. Int. J. Syst. Bacteriol. 47 566–568. 10.1099/00207713-47-2-566 PubMed DOI

Sly L. I., Stackebrandt E. (1999). Description of Skermanella parooensis gen. nov., sp. nov. to accommodate Conglomeromonas largomobilis subsp. parooensis following the transfer of Conglomeromonas largomobilis subsp. largomobilis to the genus Azospirillum. Int. J. Syst. Bacteriol. 49 541–544. 10.1099/00207713-49-2-541 DOI

Smibert R. M., Johnson J. L., Ranney R. R. (1984). Treponema socranskii sp. nov., Treponema socranskii subsp. socranskii subsp. nov., Treponema socranskii subsp. buccale subsp. nov., and Treponema socranskii subsp. paredis subsp. nov. Isolated from the human periodontia. Int. J. Syst. Evol. Microbiol. 34 457–462. 10.1099/00207713-34-4-457 DOI

Smythe L., Adler B., Hartskeerl R. A., Galloway R. L., Turenne C. Y., Levett P. N. (2013). Classification of Leptospira genomospecies 1, 3, 4 and 5 as Leptospira alstonii sp. nov., Leptospira vanthielii sp. nov., Leptospira terpstrae sp. nov. and Leptospira yanagawae sp. nov., respectively. Int. J. Syst. Evol. Microbiol. 63 1859–1862. 10.1099/ijs.0.047324-0 PubMed DOI

Sohn J. H., Kwon K. K., Kang J.-H., Jung H.-B., Kim S.-J. (2004). Novosphingobium pentaromativorans sp. nov. a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int. J. Syst. Evol. Microbiol. 54 1483–1487. 10.1099/ijs.0.02945-0 PubMed DOI

Sorokin D. Y. (1995). Sulfitobacter pontiacus gen. nov., sp. nov. a new heterotrophic bacterium from the Black Sea, specialized on sulfite oxidation. Microbiology 64 354–365.

Sorokin D. Y., Tourova T. P., Kuznetsov B. B., Bryantseva I. A., Gorlenko V. M. (2000). Roseinatronobacter thiooxidans gen. nov., sp. nov., a new alkaliphilic aerobic bacteriochlorophyll α-containing bacterium isolated from a Soda Lake. Microbiology 69 75–82. 10.1007/bf02757261 PubMed DOI

Sorokin D. Y., Tourova T. P., Muyzer G. (2005a). Citreicella thiooxidans gen. nov., sp. nov., a novel lithoheterotrophic sulfur-oxidizing bacterium from the Black Sea. Syst. Appl. Microbiol. 28 679–687. 10.1016/j.syapm.2005.05.006 PubMed DOI

Sorokin D. Y., Tourova T. P., Spiridonova E. M., Rainey F. A., Muyzer G. (2005b). Thioclava pacifica gen. nov., sp. nov., a novel facultatively autotrophic, marine, sulfur-oxidizing bacterium from a near-shore sulfidic hydrothermal area. Int. J. Syst. Evol. Microbiol. 55 1069–1075. 10.1099/ijs.0.63415-0 PubMed DOI

Sorokina A. Y., Chernousova E. Y., Dubinina G. A. (2012). Ferrovibrio denitrificans gen. nov., sp. nov., a novel neutrophilic facultative anaerobic Fe(II)-oxidizing bacterium. FEMS Microbiol. Lett. 335 19–25. 10.1111/j.1574-6968.2012.02631.x PubMed DOI

Sravanthi T., Tushar L., Sasikala C., Ramana C. V. (2016). Alkalispirochaeta cellulosivorans gen. nov., sp. nov., a cellulose-hydrolysing, alkaliphilic, halotolerant bacterium isolated from the gut of a wood-eating cockroach (Cryptocercus punctulatus), and reclassification of four species of Spirochaeta as new combinations within Alkalispirochaeta gen. nov. Int. J. Syst. Evol. Microbiol. 66 1612–1619. 10.1099/ijsem.0.000865 PubMed DOI

Srinivas A., Vinay Kumar B., Divya Sree B., Tushar L., Sasikala C., Ramana C. V. (2014). Rhodovulum salis sp. nov. and Rhodovulum viride sp. nov., phototrophic Alphaproteobacteria isolated from marine habitats. Int. J. Syst. Evol. Microbiol. 64(Pt 3) 957–962. 10.1099/ijs.0.058974-0 PubMed DOI

Srinivas T. N. R., Anil Kumar P., Sasikala C., Ramana C. V. (2007a). Rhodovulum imhoffii sp. nov. Int. J. Syst. Evol. Microbiol. 57 228–232. 10.1099/ijs.0.64470-0 PubMed DOI

Srinivas T. N. R., Kumar P. A., Sasikala C., Ramana C. V., Imhoff J. F. (2007b). Rhodobacter vinaykumarii sp. nov., a marine phototrophic Alphaproteobacterium from tidal waters, and emended description of the genus Rhodobacter. Int. J. Syst. Evol. Microbiol. 57 1984–1987. 10.1099/ijs.0.65077-0 PubMed DOI

Srinivas T. N. R., Kumar P. A., Sasikala C., Ramana C. V., Süling J., Imhoff J. F. (2006). Rhodovulum marinum sp. nov., a novel phototrophic purple non-sulfur alphaproteobacterium from marine tides of Visakhapatnam, India. Int. J. Syst. Evol. Microbiol. 56 1651–1656. 10.1099/ijs.0.64005-0 PubMed DOI

Srinivas T. N. R., Kumar P. A., Sasikala C., Spröer C., Ramana C. V. (2008). Rhodobacter ovatus sp. nov., a phototrophic Alphaproteobacterium isolated from a polluted pond. Int. J. Syst. Evol. Microbiol. 58 1379–1383. 10.1099/ijs.0.65619-0 PubMed DOI

Stackebrandt E. (1992). “Unifying phylogeny and phenotypic diversity,” in The Prokaryotes, eds Balows A., Trueper H. G., Dworkin M., Harder W., Schleifer K. H. (New York, NY: Springer; ), 19–47.

Staley J. T. (1968). Prosthecomicrobium and Ancalomicrobiutm: new prosthecate freshwater bacteria. J. Bacteriol. 95 1921–1942. 10.1128/jb.95.5.1921-1942.1968 PubMed DOI PMC

Staley J. T. (1984). Prosthecomicrobium hirschii, a new species in a redefined genus. Int. J. Syst. Bacteriol. 34 304–308. 10.1099/00207713-34-3-304 DOI

Stamatakis A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30 1312–1313. 10.1093/bioinformatics/btu033 PubMed DOI PMC

Stanton T. B., Postic D., Jensenl N. S. (1998). Serpulina alvinipulli sp. nov., a new Serpulina species that is enteropathogenic for chickens. Int. J. Syst. Bacteriol. 48 669–676. 10.1099/00207713-48-3-669 PubMed DOI

Stenos J., Roux V., Walker D., Raoult D. (1998). Rickettsia honei sp. nov., the aetiological agent of Flinders Island spotted fever in Australia. Int. J. Syst. Bacteriol. 48 1399–1404. 10.1099/00207713-48-4-1399 PubMed DOI

Stoenner H. G., Lackman D. B. (1957). A new species of Brucella isolated fromde desert wook rat, Neotoma lepida Thomas. Am. J. Vet. Res. 69 947–951. PubMed

Strömpl C., Hold G. L., Lünsdorf H., Graham J., Gallacher S., Abraham W.-R., et al. (2003). Oceanicaulis alexandrii gen. nov., sp. nov., a novel stalked bacterium isolated from a culture of the dinoflagellate Alexandrium tamarense (Lebour) Balech. Int. J. Syst. Evol. Microbiol. 53 1901–1906. 10.1099/ijs.0.02635-0 PubMed DOI

Strong R. P., Tyzzer E. E., Sellards A. W. (1915). Oroya fever. Second report. J. Am. Med. Assoc. 64 806–808.

Stutzer A., Hartleb R. (1899). Untersuchungen über die bei der Bildung von Salpeter beobachteten Mikroorganismen. Breslau: Abhandlungen und Mitteilungen des Landwirtschaftlishen Instituts der Königlichen Universität.

Su Y., Han S., Wang R., Yu X., Fu G., Chen C., et al. (2017). Microbaculum marinum gen. nov., sp. nov., isolated from deep seawater. Int. J. Syst. Evol. Microbiol. 67 812–817. 10.1099/ijsem.0.001647 PubMed DOI

Suarez C., Ratering S., Geissler-Plaum R., Schnell S. (2014). Hartmannibacter diazotrophicus gen. nov., sp. nov., A phosphate-solubilizing and nitrogen-fixing alphaproteobacterium isolated from the rhizosphere of a natural salt-meadow plant. Int. J. Syst. Evol. Microbiol. 64 3160–3167. 10.1099/ijs.0.064154-0 PubMed DOI

Subhash Y., Tushar L., Sasikala C., Ramana C. V. (2013). Erythrobacter odishensis sp. nov. and Pontibacter odishensis sp. nov. isolated from dry soil of a solar saltern. Int. J. Syst. Evol. Microbiol. 63 4524–4532. 10.1099/ijs.0.052183-0 PubMed DOI

Sultanpuram V. R., Lodha T. D., Chintalapati V. R., Chintalapati S. (2013). Cohaesibacter haloalkalitolerans sp. nov., isolated from a soda lake, and emended description of the genus Cohaesibacter. Int. J. Syst. Evol. Microbiol. 63 4271–4276. 10.1099/ijs.0.050112-0 PubMed DOI

Sun C., Pan J., Zhang X.-Q., Su Y., Wu M. (2015). Pseudoroseovarius zhejiangensis gen. nov., sp. nov., a novel alpha-proteobacterium isolated from the chemical wastewater, and reclassification of Roseovarius crassostreae as Pseudoroseovarius crassostreae comb. nov., Roseovarius sediminilitoris as Pseudoroseovarius sediminilitoris comb. nov. and Roseovarius halocynthiae as Pseudoroseovarius halocynthiae comb. nov. Antonie Van Leeuwenhoek 108 291–299. 10.1007/s10482-015-0480-9 PubMed DOI

Sun C., Wang R., Su Y., Fu G., Zhao Z., Yu X., et al. (2017). Hyphobacterium vulgare gen. nov., sp. nov., a novel Alphaproteobacterium isolated from seawater. Int. J. Syst. Evol. Microbiol. 67 1169–1176. 10.1099/ijsem.0.001780 PubMed DOI

Sun L., Liu H., Chen W., Huang K., Lyu W., Gao X. (2018). Alsobacter soli sp. nov., a novel bacterium isolated from paddy soil, emended description of the genus Alsobacter and description of the family Alsobacteraceae fam. nov. Int. J. Syst. Evol. Microbiol. 68 3902–3907. 10.1099/ijsem.0.003088 PubMed DOI

Suresh G., Sasikala C., Ramana C. V. (2015). Reclassification of Gemmobacter changlensis to a new genus as Cereibacter changlensis gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 65 794–798. 10.1099/ijs.0.000016 PubMed DOI

Suzuki R., Zhang Y., Iino T., Kosako Y., Komagata K., Uchimura T. (2010). Asaia astilbes sp. nov., Asaia platycodi sp. nov. and Asaia prunellae sp. nov., novel acetic acid bacteria isolated from flowers in Japan. J. Gen. Appl. Microbiol. 56 339–346. 10.2323/jgam.56.339 PubMed DOI

Suzuki T., Mori Y., Nishimura Y. (2006). Roseibacterium elongatum gen. nov., sp. nov., sp. nov., an aerobic, bacteriochlorophyll-containing bacterium isolated from the west coast of Australia. Int. J. Syst. Evol. Microbiol. 56 417–421. 10.1099/ijs.0.02094-0 PubMed DOI

Suzuki T., Muroga Y., Takahama M., Nishimura Y. (1999a). Roseivivax holodurans gen. nov., sp. nov. and Roseivivax halotolerans sp. nov., aerobic bacteriochlorophyll-containing bacteria isolated from a saline lake. Int. J. Syst. Bacteriol. 49 629–634. 10.1099/00207713-49-2-629 PubMed DOI

Suzuki T., Muroga Y., Takahama M., Nishimura Y. (2000). Roseibium denhamense gen. nov., sp. nov. and Roseibium hamelinense sp. nov., aerobic bacteriochlorophyll-containing bacteria isolated from the east and west coasts of Australia. Int. J. Syst. Evol. Microbiol. 50 2151–2156. 10.1099/00207713-50-6-2151 PubMed DOI

Suzuki T., Muroga Y., Takahama M., Shiba T., Nishimura Y. (1999b). Rubrimonas cliftonensis gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium isolated from a saline lake. Int. J. Syst. Bacteriol. 49 201–205. 10.1099/00207713-49-1-201 PubMed DOI

Swellengrebel N. H. (1907). Sur la cytologie comparée des spirochètes et des spirilles. Ann. Institut Pasteur 21 562–586.

Takeuchi M., Hamana K., Hiraishi A. (2001). Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int. J. Syst. Evol. Microbiol. 51 1405–1417. 10.1099/00207713-51-4-1405 PubMed DOI

Takeuchi M., Katayama T., Yamagishi T., Hanada S., Tamaki H., Kamagata Y., et al. (2014). Methyloceanibacter caenitepidi gen. nov., sp. nov., a facultatively methylotrophic bacterium isolated from marine sediments near a hydrothermal vent. Int. J. Syst. Evol. Microbiol. 64 462–468. 10.1099/ijs.0.053397-0 PubMed DOI

Takeuchi M., Kawai F., Shimada Y., Yokota A. (1993). Taxonomic study of polyethylene glycol-utilizing bacteria: emended description of the genus Sphingomonas and new descriptions of Sphingomonas macrogoltabidus sp. nov., Sphingomonas sanguis sp. nov. and Sphingomonas terrae sp. nov. Syst. Appl. Microbiol. 16 227–238. 10.1016/S0723-2020(11)80473-X DOI

Takeuchi M., Sakane T., Yanagi M., Yamasato K., Hamana K., Yokota A. (1995). Taxonomic study of bacteria isolated from plants: proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov. Int. J. Syst. Bacteriol. 45 334–341. 10.1099/00207713-45-2-334 PubMed DOI

Takeuchi M., Yamagishi T., Kamagata Y., Oshima K., Hattori M., Katayama T., et al. (2015). Tepidicaulis marinus gen. nov., sp. nov., a marine bacterium that reduces nitrate to nitrous oxide under strictly microaerobic conditions. Int. J. Syst. Evol. Microbiol. 65 1749–1754. 10.1099/ijs.0.000167 PubMed DOI

Tamura A., Ohashi N., Urakami H., Miyamura S. (1995). Classification of Rickettsia tsutsugamushi in a new genus, Orientia gen. nov., as Orientia tsutsugamushi comb. nov. Int. J. Syst. Evol. Microbiol. 45 589–591. 10.1099/00207713-45-3-589 PubMed DOI

Tanaka N., Romanenko L. A., Kurilenko V. V., Svetashev V. I., Kalinovskaya N. I., Mikhailov V. V. (2014). Loktanella maritima sp. nov. isolated from shallow marine sediments. Int. J. Syst. Evol. Microbiol. 64 2370–2375. 10.1099/ijs.0.061747-0 PubMed DOI

Tanaka Y., Hanada S., Manome A., Tsuchida T., Kurane R., Nakamura K., et al. (2004). Catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus Sphingomonas for vigorous growth. Int. J. Syst. Evol. Microbiol. 54 955–959. 10.1099/ijs.0.02750-0 PubMed DOI

Tarhriz V., Thiel V., Nematzadeh G., Hejazi M. A., Imhoff J. F., Hejazi M. S. (2013). Tabrizicola aquatica gen. nov. sp. nov., a novel Alphaproteobacterium isolated from Qurugöl Lake nearby Tabriz city, Iran. Antonie Van Leeuwenhoek 104 1205–1215. 10.1007/s10482-013-0042-y PubMed DOI

Tarrand J., Krieg N., Döbereiner J. (1978). A taxonomic study of the Spirillum lipoferum group, with descriptions of a new genus, Azospirillum gen. nov. and two species, Azospirillum lipoferum (Beijerinck) comb. nov. and Azospirillum brasilense sp. nov. Can. J. Microbiol. 24 967–980. 10.1139/m78-160 PubMed DOI

Taylor D. J., Piel W. H. (2004). An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data. Mol. Biol. Evol. 21 1534–1537. 10.1093/molbev/msh156 PubMed DOI

Teixeira L., Ferreira Á, Ashburner M. (2008). The bacterial symbiont Wolbachia induces resistance to RNA viral infections in Drosophila melanogaster. PLoS Biol. 6:e1000002. 10.1371/journal.pbio.1000002 PubMed DOI PMC

Teramoto M., Nishijima M. (2014). Temperatibacter marinus gen. nov., sp. nov., a mesophilic bacterium isolated from surface seawater and description of Temperatibacteraceae fam. nov. in the class Alphaproteobacteria. Int. J. Syst. Evol. Microbiol. 64 3075–3080. 10.1099/ijs.0.063685-0 PubMed DOI

Teyssier C., Marchandin H., Jean-Pierre H., Masnou A., Dusart G., Jumas-Bilak E. (2007). Ochrobactrum pseudintermedium sp. nov., a novel member of the family Brucellaceae, isolated from human clinical samples. Int. J. Syst. Evol. Microbiol. 57 1007–1013. 10.1099/ijs.0.64416-0 PubMed DOI

Thomsen T. R., Blackall L. L., Aquino, de Muro, Marilena Nielsen J. L., Nielsen P. H. (2006). Meganema perideroedes gen. nov., sp. nov., a filamentous Alphaproteobacterium from activated sludge. Int. J. Syst. Evol. Microbiol. 56 1865–1868. 10.1099/ijs.0.02916-0 PubMed DOI

Tindall B. J. (2019a). The name Bradyrhizobiaceae Garrity et al. 2006 contains Nitrobacter Winogradsky, 1892 (Approved Lists 1980), the nomenclatural type of the family Nitrobacteraceae Buchanan, 1917 (Approved Lists 1980), is illegitimate and proposals to alter the wording of Rule 54 of the International Code of Nomenclature of Prokaryotes to clarify the fact that the family name Bradyrhizobiaceae Garrity et al. 2006 is replaced by the family name Nitrobacteraceae Buchanan, 1917 (Approved Lists 1980) the only correct name. Int. J. Syst. Evol. Microbiol. 69 2609–2611. 10.1099/ijsem.0.003253 PubMed DOI

Tindall B. J. (2019b). The role of incorrect citation of the international code of nomenclature of prokaryotes and subsequent misinterpretation in causing unnecessary nomenclatural confusion. Int. J. Syst. Evol. Microbiol. 69 2621–2625. 10.1099/ijsem.0.003529 PubMed DOI

Tirandaz H., Mehdi S. M. D., Amoozegar M. A., Shavandi M., de la Haba R. R., Ventosa A. (2015). Pseudorhodoplanes sinuspersici gen nov sp. nov isolated from oil-contaminated soil. Int. J. Syst. Evol. Microbiol. 65 4743–4748. 10.1099/ijsem.0.000643 PubMed DOI

To T. H., Jung M., Lycett S., Gascuel O. (2016). Fast dating using least-squares criteria and algorithms. Syst. Biol. 65 82–97. 10.1093/sysbio/syv068 PubMed DOI PMC

Tóth E. M., Vengring A., Homonnay Z. G., Kéki Z., Spröer C., Borsodi A. K., et al. (2014). Phreatobacter oligotrophus gen. nov., sp. nov., an Alphaproteobacterium isolated from ultrapure water of the water purification system of a power plant. Int. J. Syst. Evol. Microbiol. 64 839–845. 10.1099/ijs.0.053843-0 PubMed DOI

Tripathi A. K., Verma S. C., Chowdhury S. P., Lebuhn M., Gattinger A., Schloter M. (2006). Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in India. Int. J. Syst. Evol. Microbiol. 56 1677–1680. 10.1099/ijs.0.63934-0 PubMed DOI

Trujillo M. E., Willems A., Abril A., Luden D., Mateos P. F., Vela E. (2005). Nodulation of Lupinus albus by strains of Ochrobactrum lupini sp. nov. Society 71 1318–1327. 10.1128/AEM.71.3.1318 PubMed DOI PMC

Tsubouchi T., Ohta Y., Haga T., Usui K., Shimane Y., Mori K., et al. (2014). Thalassospira alkalitolerans sp. nov. and Thalassospira mesophila sp. nov., isolated from a decaying bamboo sunken in the marine environment, and emended description of the genus Thalassospira. Int. J. Syst. Evol. Microbiol. 64 107–115. 10.1099/ijs.0.056028-0 PubMed DOI

Tsubouchi T., Shimane Y., Mori K., Miyazaki M., Tame A., Uematsu K., et al. (2013). Loktanella cinnabarina sp. nov., isolated from a deep subseafloor sediment, and emended description of the genus Loktanella. Int. J. Syst. Evol. Microbiol. 63 1390–1395. 10.1099/ijs.0.043174-0 PubMed DOI

Uchida T., Uchiyama T., Kumano K., Walker D. H. (1992). Rickettsia japonica sp. nov., the etiological agent of spottedfever group rickettsiosis in Japan. Int. J. Syst. Bacteriol. 42 303–305. 10.1099/00207713-42-2-303 PubMed DOI

Uchino Y., Hamada T., Yokota A. (2002). Proposal of Pseudorhodobacter ferrugineus gen. nov., comb. nov., for a non-photosynthetic marine bacterium, Agrobacterium ferrugineum, related to the genus Rhodobacter. J. Gen. Appl. Microbiol. 48 309–319. 10.2323/jgam.48.309 PubMed DOI

Uchino Y., Hirata A., Yokota A., Sugiyama J. (1998). Reclassification of marine Agrobacterium species: proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev. J. Gen. Appl. Microbiol. 44 201–210. 10.2323/jgam.44.201 PubMed DOI

Ueki A., Kodama Y., Kaku N., Shiromura T., Satoh A., Watanabe K., et al. (2010). Rhizomicrobium palustre gen. nov., sp. nov., a facultatively anaerobic, fermentative stalked bacterium in the class Alphaproteobacteria isolated from rice plant roots. J. Gen. Appl. Microbiol. 56 193–203. 10.2323/jgam.56.193 PubMed DOI

Umemoto T., Nakazawa F., Hoshino E., Okada K., Fukunaga M., Namikawa I. (1997). Treponema medium sp. nov., isolated from human subgingival dental plaque. Int. J. Syst. Bacteriol. 47 67–72. 10.1099/00207713-47-1-67 PubMed DOI

Urakami T., Araki H., Oyanagi H., Suzuki K., Komagata K. (1992). Transfer of Pseudomonas aminovorans (den Dooren de Jong 1926) to Aminobacter gen. nov. as Arninobacter aminovorans comb. nov. and description of Aminobacter aganoensis sp. nov. and Aminobactev niigataensis sp. nov. Int. J. Syst. Bacteriol. 42 84–92. 10.1099/00207713-42-1-84 DOI

Urakami T., Komagata K. (1984). Protomonas, a new genus of facultatively methylotrophic bacteria. Int. J. Syst. Bacteriol. 34 188–201. 10.1099/00207713-34-2-188 DOI

Urakami T., Oyanagi H., Araki H., Suzuki K.-I., Komagata K. (1990). Recharacterization and emended description of the genus Mycoplana and description of two new species, Mycoplana ramosa and Mycoplana segnis. Int. J. Syst. Bacteriol. 40 434–442. 10.1099/00207713-40-4-434 PubMed DOI

Urakami T., Tamaoka J., Suzuki K.-I., Komagata K. (1989). Paracoccus alcaliphilus sp. nov., an alkaliphilic and facultatively methylotrophic bacterium. Int. J. Syst. Bacteriol. 39 116–121. 10.1099/00207713-39-2-116 DOI

Urbance J. W., Bratina B. J., Stoddard S. F., Schmidt T. M. (2001). Taxonomic characterization of Ketogulonigenium vulgare gen. nov., sp. nov. and Ketogulonigenium robustum sp. nov., which oxidize L-sorbose to 2-keto-L-gulonic acid. Int. J. Syst. Evol. Microbiol. 51 1059–1070. 10.1099/00207713-51-3-1059 PubMed DOI

Urdiain M., López-López A., Gonzalo C., Busse H.-J., Langer S., Kämpfer P., et al. (2008). Reclassification of Rhodobium marinum and Rhodobium pfennigii as Afifella marina gen. nov. comb. nov. and Afifella pfennigii comb. nov., a new genus of photoheterotrophic Alphaproteobacteria and emended descriptions of Rhodobium, Rhodobium orientis and Rhodobium gokarnense. Syst. Appl. Microbiol. 31 339–351. 10.1016/j.syapm.2008.07.002 PubMed DOI

Urios L., Michotey V., Intertaglia L., Lesongeur F., Lebaron P. (2010). Thalassobaculum salexigens sp. nov., a new member of the family Rhodospirillaceae from the NW Mediterranean Sea, and emended description of the genus Thalassobaculum. Int. J. Syst. Evol. Microbiol. 60 209–213. 10.1099/ijs.0.011460-0 PubMed DOI

Urios L., Michotey V., Intertalia L., Lesongeur F., Lebaron P. (2008). Nisaea denitrificans gen. nov., sp. nov. and Nisaea nitritireducens sp. nov., two novel members of the class Alphaproteobacteria from the Mediterranean Sea. Int. J. Syst. Evol. Microbiol. 58 2336–2341. 10.1099/ijs.0.64592-0 PubMed DOI

Ushiba Y., Takahara Y., Ohta H. (2003). Sphingobium amiense sp. nov., a novel nonylphenol-degrading bacterium isolated from a river sediment. Int. J. Syst. Evol. Microbiol. 53 2045–2048. 10.1099/ijs.0.02581-0 PubMed DOI

Vaas L. A. I., Sikorski J., Hofner B., Fiebig A., Buddruhs N., Klenk H.-P., et al. (2013). opm: an R package for analysing OmniLog§phenotype microarray data. Bioinformatics 29 1823–1824. 10.1093/bioinformatics/btt291 PubMed DOI

Valverde A., Igual J. M., Peix A., Cervantes E., Velázquez E. (2006). Rhizobium lusitanum sp. nov. a bacterium that nodulates Phaseolus vulgaris. Int. J. Syst. Evol. Microbiol. 56 2631–2637. 10.1099/ijs.0.64402-0 PubMed DOI

van Berkum P., Beyene D., Bao G., Campbell T. A., Eardly B. D. (1998). Rhizobium mongolense sp. nov. is one of three rhizobial genotypes identified which nodulate and form nitrogen-fixing symbioses with Medicago ruthenica [(L.) Ledebour]. Int. J. Syst. Bacteriol. 48 13–22. 10.1099/00207713-48-1-13 PubMed DOI

van Niel C. B. (1944). The culture, general physiology, morphology, and classification of the non-sulfur purple and brown bacteria. Bacteriol. Rev. 8 1–118. 10.1128/mmbr.8.1.1-118.1944 PubMed DOI PMC

Van Trappen S., Mergaert J., Swings J. (2004). Loktanella salsilacus gen. nov., sp. nov., Loktanella fryxellensis sp. nov. and Loktanella vestfoldensis sp. nov., new members of the Rhodobacter group, isolated from microbial mats in Antarctic lakes. Int. J. Syst. Evol. Microbiol. 54 1263–1269. 10.1099/ijs.0.03006-0 PubMed DOI

Vandamme P., Pot B., Gillis M., De Vos P., Kersters K., Swings J. (1996). Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60 407–438. 10.1128/mmbr.60.2.407-438.1996 PubMed DOI PMC

Vandecandelaere I., Nercessian O., Segaert E., Achouak W., Faimali M., Vandamme P. (2008a). Ruegeria scottomollicae sp. nov., isolated from a marine electroactive biofilm. Int. J. Syst. Evol. Microbiol. 58 2726–2733. 10.1099/ijs.0.65843-0 PubMed DOI

Vandecandelaere I., Nercessian O., Segaert E., Achouak W., Mollica A., Faimali M., et al. (2009). Nautella italica gen. nov., sp. nov., isolated from a marine electroactive biofilm. Int. J. Syst. Evol. Microbiol. 59 811–817. 10.1099/ijs.0.002683-0 PubMed DOI

Vandecandelaere I., Segaert E., Mollica A., Faimali M., Vandamme P. (2008b). Leisingera aquimarina sp. nov., isolated from a marine electroactive biofilm, and emended descriptions of Leisingera methylohalidivorans Schaefer et al. 2002, Phaeobacter daeponensis Yoon et al. 2007 and Phaeobacter inhibens Martens et al., 2006. Int. J. Syst. Evol. Microbiol. 58 2788–2793. 10.1099/ijs.0.65844-0 PubMed DOI

Vasil’eva L. V., Lafitskaya T. N., Namsaraev B. B. (1980). Angulomicrobium tetraedrale, a new genus of budding bacteria with radial cell symmetry. Mikrobiologiya 48 843–849. PubMed

Vasilyeva L. V. (1985). Stella, a new genus of soil prosthecobacteria, with proposals for Stella humosa sp. nov. and Stella vacuolata sp. nov. Int. J. Syst. Evol. Microbiol. 35 518–521. 10.1099/00207713-35-4-518 DOI

Vasilyeva L. V., Omelchenko M. V., Berestovskaya Y. Y., Lysenko A. M., Abraham W.-R., Dedysh S. N., et al. (2006). Asticcacaulis benevestitus sp. nov., a psychrotolerant, dimorphic, prosthecate bacterium from tundra wetland soil. Int. J. Syst. Evol. Microbiol. 56 2083–2088. 10.1099/ijs.0.64122-0 PubMed DOI

Vekeman B., Kerckhof F. M., Cremers G., de Vos P., Vandamme P., Boon N., et al. (2016). New methyloceanibacter diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase. Environ. Microbiol. 18 4523–4536. 10.1111/1462-2920.13485 PubMed DOI

Velasco J., Romero C., Leiva J., Diaz R., Moriyon I., Lopez-Goni I. (1998). Evaluation of the relatedness of Brucella spp. and Ochrobactrum anthropi and description of Ochrobactrum intermedium sp. nov., a new species with a closer relationship to Brucella spp. Int. J. Syst. Bacteriol. 48 759–768. 10.1099/00207713-48-3-759 PubMed DOI

Vences M., Guayasamin J. M., Miralles A., De La Riva I. (2013). To name or not to name: criteria to promote economy of change in Linnaean classification schemes. Zootaxa 3636 201–244. 10.11646/zootaxa.3636.2.1 PubMed DOI

Venkata Ramana V., Anil Kumar P., Srinivas T. N. R., Sasikala C., Ramana C. V. (2009). Rhodobacter aestuarii sp. nov., a phototrophic Alphaproteobacterium isolated an estuarine environment. Int. J. Syst. Evol. Microbiol. 59 1133–1136. 10.1099/ijs.0.004507-0 PubMed DOI

Venkata Ramana V., Chakravarthy S. K., Raj P. S., Kumar B. V., Shobha E., Ramaprasad E. V. V., et al. (2012). Descriptions of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov. and Rhodopseudomonas pseudopalustris sp. nov., and emended description of Rhodopseudomonas palustris. Int. J. Syst. Evol. Microbiol. 62 1790–1798. 10.1099/ijs.0.026815-0 PubMed DOI

Venkata Ramana V., Sasikala C., Ramana C. V. (2008). Rhodobacter maris sp. nov., a phototrophic Alphaproteobacterium isolated from a marine habitat of India. Int. J. Syst. Evol. Microbiol. 58 1719–1722. 10.1099/ijs.0.65638-0 PubMed DOI

Venkata Ramana V., Sasikala C., Takaichi S., Ramana C. V. (2010). Roseomonas aestuarii sp. nov., a bacteriochlorophyll-a containing alphaproteobacterium isolated from an estuarine habitat of India. Syt. Appl. Microbiol. 33 198–203. 10.1016/j.syapm.2009.09.004 PubMed DOI

Verger J.-M., Grimont F., Grimont P. A. D., Grayon M. (1985). Brucella, a monospecific genus as shown by deoxyribonucleic acid hybridization. Int. J. Syst. Bacteriol. 35 292–295. 10.1099/00207713-35-3-292 DOI

Verma M., Kumar M., Dadhwal M., Kaur J., Lal R. (2009). Devosia albogilva sp. nov. and Devosia crocina sp. nov., isolated from a hexachlorocyclohexane dump site. Int. J. Syst. Evol. Microbiol. 59 795–799. 10.1099/ijs.0.005447-0 PubMed DOI

Veyisoglu A., Camas M., Tatar D., Guven K., Sazak A., Sahin N. (2013). Methylobacterium tarhaniae sp. nov., isolated from arid soil. Int. J. Syst. Evol. Microbiol. 63 2823–2828. 10.1099/ijs.0.049551-0 PubMed DOI

Vidal C., Chantreuil C., Berge O., Mauré L., Escarré J., Béna G., et al. (2009). Mesorhizobium metallidurans sp. nov., a metal-resistant symbiont of Anthyllis vulneraria growing on metallicolous soil in Languedoc, France. Int. J. Syst. Evol. Microbiol. 59 850–855. 10.1099/ijs.0.003327-0 PubMed DOI

Visser’t Hooft F. (1925). Biochemische Onderzoekingen over het geslacht Acetobacter. Delft: Meinema.

Vorobev A. V., Baani M., Doronina N. V., Brady A. L., Liesack W., Dunfield P. F., et al. (2011). Methyloferula stellat gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase. Int. J. Syst. Evol. Microbiol. 61 2456–2463. 10.1099/ijs.0.028118-0 PubMed DOI

Wagner-Döbler I., Rheims H., Felske A., El-Ghezal A., Flade-Schröder D., Laatsch H., et al. (2004). Oceanibulbus indolifex gen. nov., sp. nov., a North Sea Alphaproteobacterium that produces bioactive metabolites. Int. J. Syst. Evol. Microbiol. 54 1177–1184. 10.1099/ijs.0.02850-0 PubMed DOI

Wakao N., Nagasawa N., Matsuura T., Matsukura H., Matsumoto T., Hiraishi A., et al. (1994). Acidiphilium multivorum sp. nov., an acidophilic chemoorganotrophic bacterium from pyritic acid mine drainage. J. Gen. Appl. Microbiol. 40 143–159. 10.2323/jgam.40.143 DOI

Wang B., Sun F., Lai Q., Du Y., Liu X., Li G., et al. (2010). Roseovarius nanhaiticus sp. nov., a member of the Roseobacter clade isolated from marine sediment. Int. J. Syst. Evol. Microbiol. 60 1289–1295. 10.1099/ijs.0.012930-0 PubMed DOI

Wang D., Liu H., Zheng S., Wang G. (2014). Paenirhodobacter enshiensis gen. nov., sp. nov., a non-photosynthetic bacterium isolated from soil, and emended descriptions of the genera Rhodobacter and Haematobacter. Int. J. Syst. Evol. Microbiol. 64 551–558. 10.1099/ijs.0.050351-0 PubMed DOI

Wang F. Q., Wang E. T., Liu J., Chen Q., Sui X. H., Chen W. F., et al. (2007). Mesorhizobium albiziae sp. nov., a novel bacterium that nodulates Albizia kalkora in a subtropical region of China. Int. J. Syst. Evol. Microbiol. 57 1192–1199. 10.1099/ijs.0.64363-0 PubMed DOI

Wang G., Tang M., Wu H., Dai S., Li T., Chen C., et al. (2016). Pyruvatibacter mobilis gen. nov., sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122. Int. J. Syst. Evol. Microbiol. 66 184–188. 10.1099/ijsem.0.000692 PubMed DOI

Wang G., van Dam A. P., Le Fleche A., Postic D., Peter O., Baranton G., et al. (1997). Genetic and phenotypic analysis of Bowelia valaisiana sp. nov. (Bowelia genomic groups VS116 and M19). Int. J. Syst. Bacteriol. 47 926–932. 10.1099/00207713-47-4-926 PubMed DOI

Wang G., Wang Y., Su H., Wu H., Li T., Liang J., et al. (2017). Butyratibacter algicola gen. nov., sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122. Int. J. Syst. Evol. Microbiol. 67 3209–3213. 10.1099/ijsem.0.002081 PubMed DOI

Wang J., Zhang J., Ding K., Xin Y., Pang H. (2012). Brevundimonas viscosa sp. nov., isolated from saline soil. Int. J. Syst. Evol. Microbiol. 62 2475–2479. 10.1099/ijs.0.035352-0 PubMed DOI

Wang L., Liu Y., Shi X., Wang Y., Zheng Y., Dai X., et al. (2016). Xuhuaishuia manganoxidans gen. nov., sp. nov., a manganese-oxidizing bacterium isolated from deep-sea sediments from the Pacific Polymetallic Nodule Province. Int. J. Syst. Evol. Microbiol. 66 1521–1526. 10.1099/ijsem.0.000912 PubMed DOI

Wang L., Liu Y., Wang Y., Dai X., Zhang X.-H. (2015). Celeribacter manganoxidans sp. nov., a manganese-oxidizing bacterium isolated from deep-sea sediment of a polymetallic nodule province. Int. J. Syst. Evol. Microbiol. 65 4180–4185. 10.1099/ijsem.0.000558 PubMed DOI

Wang R., Chang Y. L., Zheng W. T., Zhang D., Zhang X. X., Sui X. H., et al. (2013). Bradyrhizobium arachidis sp. nov., isolated from effective nodules of Arachis hypogaea grown in China. Syst. Appl. Microbiol. 36 101–105. 10.1016/j.syapm.2012.10.009 PubMed DOI

Wang Y., Tang S.-K., Lou K., Mao P.-H., Jin X., Jiang C.-L., et al. (2009). Paracoccus saliphilus sp. nov., a halophilic bacterium isolated from a saline soil. Int. J. Syst. Evol. Microbiol. 59 1924–1928. 10.1099/ijs.0.005918-0 PubMed DOI

Wang Y. C., Wang F., Hou B. C., Wang E. T., Chen W. F., Sui X. H., et al. (2013). Proposal of Ensifer psoraleae sp. nov., Ensifer sesbaniae sp. nov., Ensifer morelense comb. nov. and Ensifer americanum comb. nov. Syst. Appl. Microbiol. 36 467–473. 10.1016/j.syapm.2013.05.001 PubMed DOI

Wang Y. X., Huang F. Q., Nogi Y., Pang S. J., Wang P. K., Lv J. (2015). Youhaiella tibetensis gen. nov., sp. nov., isolated from subsurface sediment. Int. J. Syst. Evol. Microbiol. 65 2048–2055. 10.1099/ijs.0.000219 PubMed DOI

Wang Y.-X., Liu J.-H., Zhang X.-X., Chen Y.-G., Wang Z.-G., Chen Y., et al. (2009). Fodinicurvata sediminis gen. nov., sp. nov. and Fodinicurvata fenggangensis sp. nov., poly-β-hydroxybutyrate-producing bacteria in the family Rhodospirillaceae. Int. J. Syst. Evol. Microbiol. 59 2575–2581. 10.1099/ijs.0.009340-0 PubMed DOI

Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., et al. (1987). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37 463–464. 10.1099/00207713-37-4-463 DOI

Wei G. H., Tan Z. Y., Zhu M. E., Wang E. T., Han S. Z., Chen W. X. (2003). Characterization of rhizobia isolated from legume species within the genera Astragalus and Lespedeza grown in the Loess Plateau of China and description of Rhizobium loessense sp. nov. Int. J. Syst. Evol. Microbiol. 53 1575–1583. 10.1099/ijs.0.02031-0 PubMed DOI

Wei S., Wang T., Liu H., Zhang C., Guo J., Wang Q., et al. (2015). Sphingomonas hengshuiensis sp. nov., isolated from lake wetland. Int. J. Syst. Evol. Microbiol. 65 4644–4649. 10.1099/ijsem.0.000626 PubMed DOI

Weiner R. M., Devine R. A., Powell D. M., Dagasan L., Moore R. L. (1985). Hyphomonas oceanitis sp. nov., Hyphomonas hirschiana sp. nov., and Hyphomonas jannaschiana sp. nov. Int. J. Syst. Bacteriol. 35 237–243. 10.1007/s10482-014-0236-y PubMed DOI

Weiner R. M., Melick M., O’Neill K., Quintero E. (2000). Hyphomonas adhaerens sp. nov., Hyphomonas johnsonii sp. nov. and Hyphomonas rosenbergii sp. nov., marine budding and prosthecate bacteria. Int. J. Syst. Evol. Microbiol. 50 459–469. 10.1099/00207713-50-2-459 PubMed DOI

Welch D. F., Carroll K. C., Hofmeister E. K., Persing D. H., Robison D. A., Steigerwalt A. G., et al. (1999). Isolation of a new subspecies, Bartonella vinsonii subsp. arupensis, from a cattle rancher: identity with isolates found in conjunction with Borrelia burgdorferi and Babesia microti among naturally infected mice. J. Clin. Microbiol. 37 2598–2601. 10.1128/jcm.37.8.2598-2601.1999 PubMed DOI PMC

Weon H.-Y., Kim B.-Y., Hong S.-B., Joa J.-H., Nam S.-S., Lee K. H., et al. (2007). Skermanella aerolata sp. nov., isolated from air, and emended description of the genus Skermanella. Int. J. Syst. Evol. Microbiol. 57 1539–1542. 10.1099/ijs.0.64676-0 PubMed DOI

Weon H.-Y., Kim B.-Y., Kwon S.-W., Go S.-J., Koo B.-S., Stackebrandt E. (2008a). Phenylobacterium composti sp. nov., isolated from cotton waste compost in Korea. Int. J. Syst. Evol. Microbiol. 58 2301–2304. 10.1099/ijs.0.65530-0 PubMed DOI

Weon H.-Y., Kim B.-Y., Yoo S.-H., Kim J.-S., Kwon S.-W., Go S.-J., et al. (2006). Loktanella koreensis sp. nov., isolated from sea sand in Korea. Int. J. Syst. Evol. Microbiol. 56 2199–2202. 10.1099/ijs.0.64276-0 PubMed DOI

Weon H.-Y., Lee C.-M., Hong S.-B., Kim B.-Y., Yoo S.-H., Kwon S.-W., et al. (2008b). Kaistia soli sp. nov., isolated from a wetland in Korea. Int. J. Syst. Evol. Microbiol. 58 1522–1524. 10.1099/ijs.0.65366-0 PubMed DOI

Wichlacz P. L., Unz R. F., Langworthy T. A. (1986). Acidiphilium angustum sp. nov., Acidiphilium facilis sp. nov., and Acidiphilium rubrum sp. nov.: acidopilic heterotrophic bacteria isolated from acidic coal mine drainage. Int. J. Syst. Bacteriol. 36 197–201. 10.1099/00207713-36-2-197 DOI

Wiegel J., Wilke D., Baumgarten J., Opitz R., Schlegel H. G. (1978). Transfer of the nitrogen-fixing hydrogen bacterium Corynebacterium autotrophicum Baumgarten et al. to Xanthobacter gen. nov. Int. J. Syst. Evol. Microbiol. 28 573–581. 10.1099/00207713-28-4-573 DOI

Wiese J., Thiel V., Gärtner A., Schmaljohann R., Imhoff J. F. (2009). Kiloniella laminariae gen. nov., sp. nov., an Alphaproteobacterium from the marine macroalga Laminaria saccharina. Int. J. Syst. Evol. Microbiol. 59 350–356. 10.1099/ijs.0.001651-0 PubMed DOI

Wiley E. O., Lieberman B. S. (2011). Phylogenetics: Theory and Practice of Phylogenetic Systematics, 2nd Edn Hoboken, NJ: John Wiley & Sons, Inc.

Willems A. (2006). The taxonomy of rhizobia: an overview. Plant Soil 287 3–14. 10.1007/s11104-006-9058-7 PubMed DOI

Williams K. P., Sobral B. W., Dickerman A. W. (2007). A robust species tree for the Alphaproteobacteria. J. Bacteriol. 189 4578–4586. 10.1128/JB.00269-07 PubMed DOI PMC

Williams T. J., Lefèvre C. T., Zhao W., Beveridge T. J., Bazylinski D. A. (2012). Magnetospira thiophila gen. nov., sp. nov., a marine magnetotactic bacterium that represents a novel lineage within the Rhodospirillaceae (Alphaproteobacteria). Int. J. Syst. Evol. Microbiol. 62 2443–2450. 10.1099/ijs.0.037697-0 PubMed DOI

Winogradsky S. (1892). Contributions à la morphologie des organismes de la nitrification. Arkhiv Biol. Nauk 1 87–137.

Winslow C.-E. A., Broadhurst J., Buchanan R. E., Krumwiede C., Rogers L. A., Smith G. H. (1917). The families and genera of the bacteria: preliminary report of the committee of the society of american bacteriologist on characterization and classification of bacterial types. J. Bacteriol. 2 505–566. 10.1128/jb.2.5.505-566.1917 PubMed DOI PMC

Wirth J. S., Whitman W. B. (2018). Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal. Int. J. Syst. Evol. Microbiol. 68 2393–2411. 10.1099/ijsem.0.002833 PubMed DOI

Wolf Y. I., Rogozin I. B., Grishin N. V., Tatusov R. L., Koonin E. V. (2001). Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol 1:8. 10.1186/1471-2148-1-8 PubMed DOI PMC

Wolf Y. I., Rogozin I. B., Grishin N. V., Koonin E. V. (2002). Genome trees and the tree of life. Trends Genet. 18 472–479. 10.1016/S0168-9525(02)02744-0 PubMed DOI

Wong S. K., Yoshizawa S., Nakajima Y., Cuadra M. J., Nogi Y., Nakamura K., et al. (2018). Amylibacter kogurei sp. nov., a novel marine Alphaproteobacterium isolated from the coastal sea surface microlayer of a marine inlet. Int. J. Syst. Evol. Microbiol. 68 2872–2877. 10.1099/ijsem.0.002911 PubMed DOI

Woo S. G., Ten L. N., Park J., Lee M. (2011). Ochrobactrum daejeonense sp. nov., a nitrate-reducing bacterium isolated from sludge of a leachate treatment plant. Int. J. Syst. Evol. Microbiol. 61 2690–2696. 10.1099/ijs.0.025510-0 PubMed DOI

Wood S. (1994). Monophyly and comparison between trees. Cladistics 10 339–346. 10.1006/clad.1994.1024 DOI

Wu X.-L., Yu S.-L., Gu J., Zhao G.-F., Chi C.-Q. (2009). Filomicrobium insigne sp. nov., isolated from an oil-polluted saline soil. Int. J. Syst. Evol. Microbiol. 59 300–305. 10.1099/ijs.0.65758-0 PubMed DOI

Wu Y.-H., Jian S.-L., Meng F.-X., Maripatay, Tohty D., Wang C.-S., et al. (2016). Kordiimonas lipolytica sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol. 66 2198–2204. 10.1099/ijsem.0.001007 PubMed DOI

Wu Y.-H., Meng F.-X., Xu L., Zhang X.-Q., Wang C.-S., Oren A., et al. (2013). Roseivivax pacificus sp. nov., isolated from deep-sea sediment. Int. J. Syst. Evol. Microbiol. 63 4574–4579. 10.1099/ijs.0.052274-0 PubMed DOI

Wu Y.-H., Xu L., Meng F.-X., Zhang D.-S., Wang C.-S., Oren A., et al. (2014). Altererythrobacter atlanticus sp. nov., isolated from deep-sea sediment. Int. J. Syst. Evol. Microbiol. 64 116–121. 10.1099/ijs.0.052951-0 PubMed DOI

Wu Y.-H., Xu L., Zhou P., Wang C.-S., Oren A., Xu X.-W. (2015). Brevirhabdus pacifica gen. nov., sp. nov., isolated from deep-sea sediment in a hydrothermal vent field. Int. J. Syst. Evol. Microbiol. 65 3645–3651. 10.1099/ijsem.0.000469 PubMed DOI

Wu Z.-G., Wang F., Gu C.-G., Zhang Y.-P., Yang Z.-Z., Wu X.-W., et al. (2014). Aquamicrobium terrae sp. nov., isolated from the polluted soil near a chemical factory. Antonie Van Leeuwenhoek 105 1131–1137. 10.1007/s10482-014-0174-8 PubMed DOI

Wyss C., Choi B. K., Schüpbach P., Guggenheim B., Göbel U. B. (1996). Treponema maltophilum sp. nov., a small oral Spirochete isolated from human periodontal lesions. Int. J. Syst. Bacteriol. 46 745–752. 10.1099/00207713-46-3-745 PubMed DOI

Wyss C., Choi B.-K., Schüpbach P., Moter A., Guggenheim B., Göbel U. B. (1999). Treponema lecithinolyticum sp. nov., a small saccharolytic spirochaete with phospholipase A and C activities associated with periodontal diseases. Int. J. Syst. Bacteriol. 49 1329–1339. 10.1099/00207713-49-4-1329 PubMed DOI

Wyss C., Moter A., Choi B.-K., Dewhirst F. E., Xue Y., Schüpbach P., et al. (2004). Treponema putidum sp. nov., a medium-sized proteolytic spirochaete isolated from lesions of human periodontitis and acute necrotizing ulcerative gingivitis. Int. J. Syst. Evol. Microbiol. 54 1117–1122. 10.1099/ijs.0.02806-0 PubMed DOI

Xi J., Wang Y., Yang X., Tao Y., Shao Y., Feng F. (2017). Mongoliimonas terrestris gen. nov., sp. nov., isolated from desert soil. Int. J. Syst. Evol. Microbiol. 67 3010–3014. 10.1099/ijsem.0.002067 PubMed DOI

Xi X.-D., Dong W. -l, Zhang J., Huang Y., Cui Z. -l. (2013). Taonella mepensis gen. nov., sp. nov., a member of the family Rhodospirillaceae isolated from activated sludge. Int. J. Syst. Evol. Microbiol 63 2472–2476. 10.1099/ijs.0.047803-0 PubMed DOI

Xie C.-H., Yokota A. (2005). Pleomorphomonas oryzae gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from paddy soil of Oryza sativa. Int. J. Syst. Evol. Microbiol. 55 1233–1237. 10.1099/ijs.0.63406-0 PubMed DOI

Xie C.-H., Yokota A. (2006). Sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of Oryza sativa. Int. J. Syst. Evol. Microbiol. 56 889–893. 10.1099/ijs.0.64056-0 PubMed DOI

Xu H., Jiang L., Li S., Zeng X., Shao Z. (2015). Mameliella atlantica sp. nov., a marine bacterium of the Roseobacter clade isolated from deep-sea sediment of the South Atlantic Ocean. Int. J. Syst. Evol. Microbiol. 65 2255–2259. 10.1099/ijs.0.000248 PubMed DOI

Xu H. Y., Chen L. P., Fu S. Z., Fan H. X., Zhou Y. G., Liu S. J., et al. (2009). Zhangella mobilis gen. nov., sp. nov., a new member of the family Hyphomicrobiaceae isolated from coastal seawater. Int. J. Syst. Evol. Microbiol. 59 2297–2301. 10.1099/ijs.0.004366-0 PubMed DOI

Xu M., Xin Y., Yu Y., Zhang J., Zhou Y., Liu H., et al. (2010). Erythrobacter nanhaisediminis sp. nov., isolated from marine sediment of the South China Sea. Int. J. Syst. Evol. Microbiol. 60 2215–2220. 10.1099/ijs.0.014027-0 PubMed DOI

Xu X.-W., Huo Y.-Y., Wang C.-S., Oren A., Cui H.-L., Vedler E., et al. (2011). Pelagibacterium halotolerans gen. nov. sp. nov. and Pelagibacterium luteolum sp. nov., novel members of the family Hyphomicrobiaceae. Int. J. Syst. Evol. Microbiol. 61 1817–1822. 10.1099/ijs.0.023325-0 PubMed DOI

Xu X.-W., Wu M., Oren A. (2014). “The family kordiimonadaceae,” in The Prokaryotes, eds Rosenberg E., DeLong E. F., Lory S., Stackebrandt E., Thompson F. (Berlin: Springer Berlin Heidelberg; ), 307–312. 10.1007/978-3-642-30197-1_261 DOI

Xu X.-W., Wu Y.-H., Wang C.-S., Wang X.-G., Oren A., Wu M. (2009). Croceicoccus marinus gen. nov., sp. nov. a yellow-pigmented bacterium from deep-sea sediment, and emended description of the family Erythrobacteraceae. Int. J. Syst. Evol. Microbiol. 59 2247–2253. 10.1099/ijs.0.004267-0 PubMed DOI

Xue H., Piao C., Guo M., Wang L., Fang W., Li Y. (2016). Description of Altererythrobacter aerius sp. nov., isolated from air, and emended description of the genus Altererythrobacter. Int. J. Syst. Evol. Microbiol. 66 4543–4548. 10.1099/ijsem.0.001388 PubMed DOI

Xue X., Zhang K., Cai F., Dai J., Wang Y., Rahman E., et al. (2012). Altererythrobacter xinjiangensis sp. nov., isolated from desert sand, and emended description of the genus Altererythrobacter. Int. J. Syst. Evol. Microbiol. 62 28–32. 10.1099/ijs.0.025437-0 PubMed DOI

Yabuuchi E., Kosako Y., Naka T., Suzuki S., Yano I. (1999). Proposal of Sphingomonas suberifaciens (van Bruggen, Jochimsen and Brown 1990) comb. nov., Sphingomonas natatoria (Sly 1985) comb. nov., and Emendation of the Genus Sphingomonas. Microbiol. Immunol. 43 339–349. 10.1111/j.1348-0421.1999.tb02414.x PubMed DOI

Yabuuchi E., Yamamoto H., Terakubo S., Okamura N., Naka T., Fujiwara N., et al. (2001). Proposal of Sphingomonas wittichii sp. nov. for strain RW1T, known as a dibenzo-p-dioxin metabolizer. Int. J. Syst. Evol. Microbiol. 51 281–292. 10.1099/00207713-51-2-281 PubMed DOI

Yabuuchi E., Yano I., Oyaizu H., Hashimoto Y., Ezaki T., Yamamoto H. (1990). Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomoas adhaesiva sp. nov., Sphingomonas capsulata comb. nov. and two genospecies of the genus Sphingomonas. Microbiol. Immunol. 34 99–119. 10.1111/j.1348-0421.1990.tb00996.x PubMed DOI

Yamada K., Fukuda W., Kondo Y., Miyoshi Y., Atomi H., Imanaka T. (2011). Constrictibacter antarcticus gen. nov., sp. nov., a cryptoendolithic micro-organism from Antarctic white rock. Int. J. Syst. Evol. Microbiol. 61 1973–1980. 10.1099/ijs.0.026625-0 PubMed DOI

Yamada Y., Hoshino K., Ishikawa T. (1997). The phylogeny of acetic acid bacteria based on the partial sequences of 16S ribosomal RNA: the elevation of the subgenus Gluconoacetobacter to the generic level. Biosci. Biotechnol. Biochem. 61 1244–1251. 10.1271/bbb.61.1244 PubMed DOI

Yamada Y., Yukphan P., Vu H. T. L., Muramatsu Y., Ochaikul D., Tanasupawat S., et al. (2012). Description of Komagataeibacter gen. nov., with proposals of new combinations (Acetobacteraceae). J. Gen. Appl. Microbiol. 58 397–404. 10.2323/jgam.58.397 PubMed DOI

Yamashita S. I., Uchimura T., Komagata K. (2004). Emendation of the genus Acidomonas Urakami, Tamaoka, Suzuki and Komagata 1989. Int. J. Syst. Evol. Microbiol. 54 865–870. 10.1099/ijs.0.02946-0 PubMed DOI

Yang D.-C., Im W.-T., Kim M. K., Ohta H., Lee S.-T. (2006). Sphingomonas soli sp. nov., a ß-glucosidase-producing bacterium in the family Sphingomonadaceae in the α-4 subgroup of the Proteobacteria. Int. J. Syst. Evol. Microbiol. 56 703–707. 10.1099/ijs.0.63839-0 PubMed DOI

Yang S., Doolittle R. F., Bourne P. E. (2005). Phylogeny determined by protein domain content. Proc. Natl. Acad. Sci. U.S.A. 102 373–378. 10.1073/pnas.0408810102 PubMed DOI PMC

Yang S.-H., Kim M.-R., Seo H.-S., Lee S. H., Lee J.-H., Kim S.-J., et al. (2013). Description of Kordiimonas aquimaris sp. nov., isolated from seawater, and emended descriptions of the genus Kordiimonas (Kwon et al., 2005 emend. Xu et al., 2011 and of its existing species. Int. J. Syst. Evol. Microbiol. 63 298–302. 10.1099/ijs.0.038893-0 PubMed DOI

Yang S.-H., Seo H.-S., Lee J.-H., Kim S.-J., Kwon K. K. (2015). Kiloniella spongiae sp. nov., isolated from a marine sponge and emended description of the genus Kiloniella Wiese et al., 2009 and Kiloniella laminariae. Int. J. Syst. Evol. Microbiol. 65 230–234. 10.1099/ijs.0.069773-0 PubMed DOI

Yang S.-Z., Xiong X., Feng G.-D., Li H.-P., Zhu H.-H. (2017). Reclassification of Sphingopyxis contaminans as Sphingorhabdus contaminans comb. nov. and emended description of the genus Sphingorhabdus. Int. J. Syst. Evol. Microbiol. 67 4328–4331. 10.1099/ijsem.0.002201 PubMed DOI

Yang Y., Sun J., Tang K., Lin D., Li C., Lin Y. (2015). Ponticoccus lacteus sp. nov. of the family Rhodobacteraceae, isolated from surface seawater. Int. J. Syst. Evol. Microbiol. 65 1247–1250. 10.1099/ijs.0.000086 PubMed DOI

Yao L., Zhang J. J., Yu L. L., Chen Q., Zhu J. C., He J., et al. (2016). Rhizorhabdus dicambivorans sp. nov., a dicamba-degrading bacterium isolated from compost. Int. J. Syst. Evol. Microbiol. 66 3317–3323. 10.1099/ijsem.0.001194 PubMed DOI

Yao L. J., Shen Y. Y., Zhan J. P., Xu W., Cui G. L., Wei G. H. (2012). Rhizobium taibaishanense sp. nov., isolated from a root nodule of Kummerowia striata. Int. J. Syst. Evol. Microbiol. 62 335–341. 10.1099/ijs.0.029108-0 PubMed DOI

Yarza P., Munoz R. (2014). The all-species living tree project. Meth. Microbiol. 41 45–59. 10.1016/bs.mim.2014.07.006 DOI

Yarza P., Spröer C., Swiderski J., Mrotzek N., Spring S., Tindall B. J., et al. (2013). Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names. Syst. Appl. Microbiol. 36 69–73. 10.1016/j.syapm.2012.12.006 PubMed DOI

Yarza P., Yilmaz P., Pruesse E., Glöckner F. O., Ludwig W., Schleifer K. H., et al. (2014). Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat. Rev. Microbiol. 12 635–645. 10.1038/nrmicro3330 PubMed DOI

Yasir M., Aslam Z., Song G. C., Jeon C. O., Chung Y. R. (2010). Sphingosinicella vermicomposti sp. nov., isolated from vermicompost, and emended description of the genus Sphingosinicella. Int. J. Syst. Evol. Microbiol. 60 580–584. 10.1099/ijs.0.010777-0 PubMed DOI

Yasuda P. H., Steigerwalt A. G., Sulzer K. R., Kaufmann A. F., Rogers F., Brenner D. J. (1987). Deoxyribonucleic acid relatedness between serogroups and serovars in the family leptospiraceae with proposals for seven new Leptospira species. Int. J. Syst. Bacteriol. 37 407–415. 10.1099/00207713-37-4-407 PubMed DOI

Yee B., Oertli G. E., Fuerst J. A., Staley J. T. (2010). Reclassification of the polyphyletic genus Prosthecomicrobium to form two novel genera, Vasilyevaea gen. nov. and Bauldia gen. nov. with four new combinations: Vasilyevaea enhydra comb. nov., Vasilyevaea mishustinii comb. nov., Bauldia consociata comb. nov. and Bauldia litoralis comb. nov. Int. J. Syst. Evol. Microbiol. 60 2960–2966. 10.1099/ijs.0.018234-0 PubMed DOI PMC

Yi H., Lim Y. W., Chun J. (2007). Taxonomic evaluation of the genera Ruegeria and Silicibacter: a proposal to transfer the genus Silicibacter Petursdottir and Kristjansson 1999 to the genus Ruegeria Uchino et al. 1999. Int. J. Syst. Evol. Microbiol. 57 815–819. 10.1099/ijs.0.64568-0 PubMed DOI

Yin D., Xiao J., Ao J., Ai C., Chen X. (2012). Albidovulum xiamenense sp. nov., a moderately thermophilic bacterium from a terrestrial hot spring. Int. J. Syst. Evol. Microbiol. 62 1609–1612. 10.1099/ijs.0.034454-0 PubMed DOI

Ying J.-Y., Wang B.-J., Dai X., Yang S.-S., Liu S.-J., Liu Z.-P. (2007). Wenxinia marina gen. nov., sp. nov., a novel member of the Roseobacter clade isolated from oilfield sediments of the South China Sea. Int. J. Syst. Evol. Microbiol. 57 1711–1716. 10.1099/ijs.0.64825-0 PubMed DOI

Yoo S.-H., Weon H.-Y., Kim B.-Y., Hong S.-B., Kwon S.-W., Cho Y.-H., et al. (2006). Devosia soli sp. nov., isolated from greenhouse soil in Korea. Int. J. Syst. Evol. Microbiol. 56 2689–2692. 10.1099/ijs.0.64214-0 PubMed DOI

Yoo S.-H., Weon H.-Y., Noh H.-J., Hong S.-B., Lee C.-M., Kim B.-Y., et al. (2008). Roseomonas aerilata sp. nov., isolated from an air sample. Int. J. Syst. Evol. Microbiol. 58 1482–1485. 10.1099/ijs.0.65385-0 PubMed DOI

Yoon J., Kang D.-H. (2018). Terasakiella salincola sp. nov., a marine Alphaproteobacterium isolated from seawater, and emended description of the genus Terasakiella. Int. J. Syst. Evol. Microbiol. 68 2048–2053. 10.1099/ijsem.0.002788 PubMed DOI

Yoon J.-H., Kang S.-J., Im W.-T., Lee S.-T., Oh T.-K. (2008). Chelatococcus daeguensis sp. nov., isolated from wastewater of a textile dye works, and emended description of the genus Chelatococcus. Int. J. Syst. Evol. Microbiol. 58 2224–2228. 10.1099/ijs.0.65291-0 PubMed DOI

Yoon J.-H., Kang S.-J., Lee J.-S., Oh T.-K. (2009). Lutimaribacter saemankumensis gen. nov., sp. nov., isolated from a tidal flat of the Yellow Sea. Int. J. Syst. Evol. Microbiol. 59 48–52. 10.1099/ijs.0.000109-0 PubMed DOI

Yoon J.-H., Kang S.-J., Lee M.-H., Oh T.-K. (2007a). Description of Sulfitobacter donghicola sp. nov., isolated from seawater of the East Sea in Korea, transfer of Staleya guttiformis Labrenz et al. 2000 to the genus Sulfitobacter as Sulfitobacter guttiformis comb. nov. and emended description of the genus. Int. J. Syst. Evol. Microbiol. 57 1788–1792. 10.1099/ijs.0.65071-0 PubMed DOI

Yoon J.-H., Kang S.-J., Lee S.-Y., Jung Y.-T., Lee J.-S., Oh T.-K. (2012). Marivita hallyeonensis sp. nov., isolated from seawater, reclassification of Gaetbulicola byunsanensis as Marivita byunsanensis comb. nov. and emended description of the genus Marivita Hwang et al. 2009. Int. J. Syst. Evol. Microbiol. 62 839–843. 10.1099/ijs.0.032086-0 PubMed DOI

Yoon J. H., Kang S. J., Park S., Lee S. Y., Oh T. K. (2007b). Reclassification of Aquaspirillum itersonii and Aquaspirillum peregrinum as Novispirillum itersonii gen. nov., comb. nov. and Insolitispirillum peregrinum gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 57 2830–2835. 10.1099/ijs.0.65340-0 PubMed DOI

Yoon J. H., Kang S. J., Park S., Oh T. K. (2007c). Devosia insulae sp. nov., isolated from soil, and emended description of the genus Devosia. Int. J. Syst. Evol. Microbiol. 57 1310–1314. 10.1099/ijs.0.65028-0 PubMed DOI

Yoon J.-H., Lee C.-H., Yeo S.-H., Oh T.-K. (2005a). Sphingopyxis baekryunenis sp. nov., an orange-pigmented bacterium isolated from sea water of the Yellow Sea in Korea. Int. J. Syst. Evol. Microbiol. 55 1223–1227. 10.1099/ijs.0.63495-0 PubMed DOI

Yoon J.-H., Oh T.-K., Park Y.-H. (2005b). Erythrobacter seohaensis sp. nov. and Erythrobacter gaetbuli sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int. J. Syst. Evol. Microbiol. 55 71–75. 10.1099/ijs.0.63233-0 PubMed DOI

Young J. M. (2003). The genus name Ensifer Casida, 1982 takes priority over Sinorhizobium Chen et al. 1988, and Sinorhizobium morelense Wang et al. 2002 is a later synonym of Ensifer adhaerens Casida, 1982. Is the combination “Sinorhizobium adhaerens” (Casida, 1982) Willems et. Int. J. Syst. Evol. Microbiol. 53 2107–2110. 10.1099/ijs.0.02665-0 PubMed DOI

Young J. M., Kuykendall L. D., Martínez-Romero E., Kerr A., Sawada H. (2001). A revision of Rhizobium Frank, 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn, 1942 and Allorhizobium undicola de Lajudie et al., 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis. Int. J. Syst. Evol. Microbiol. 51 89–103. PubMed

Young J. M., Kuykendall L. D., Martínez-Romero E., Kerr A., Sawada H. (2003). Classification and nomenclature of Agrobacterium and Rhizobium – A reply to Farrand et al. (2003). Int. J. Syst. Evol. Microbiol. 53 1689–1695. 10.1099/ijs.0.02762-0 PubMed DOI

Yu X., Cloutier S., Tambong J. T., Bromfield E. S. P. (2014). Bradyrhizobium ottawaense sp. nov., a symbiotic nitrogen fixing bacterium from root nodules of soybeans in Canada. Int. J. Syst. Evol. Microbiol. 64 3202–3207. 10.1099/ijs.0.065540-0 PubMed DOI PMC

Yu X. Y., Tao T. Y., Fu G. Y., Su Y., Han S. B., Wang R. J., et al. (2016). Marinibaculum pumilum gen. nov., sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol. 66 4844–4849. 10.1099/ijsem.0.001439 PubMed DOI

Yukphan P., Malimas T., Muramatsu Y., Potacharoen W., Tanasupawat S., Nakagawa Y., et al. (2011). Neokomagataea gen. nov., with descriptions of Neokomagataea thailandica sp. nov. and Neokomagataea tanensis sp. nov., osmotolerant acetic acid bacteria of the α-Proteobacteria. Biosci. Biotechnol. Biochem. 75 419–426. 10.1271/bbb.100344 PubMed DOI

Yukphan P., Malimas T., Muramatsu Y., Takahashi M., Kaneyasu M., Tanasupawat S., et al. (2008). Tanticharoenia sakaeratensis gen. nov., sp. nov., a new osmotolerant acetic acid bacterium in the α-Proteobacteria. Biosci. Biotechnol. Biochem. 72 672–676. 10.1271/bbb.70319 PubMed DOI

Yukphan P., Malimas T., Potacharoen W., Tanasupawat S., Tanticharoen M., Yamada Y. (2005). Neoasaia chiangmaiensis gen. nov., sp. nov., a novel osmotolerant acetic acid bacterium in the α-Proteobacteria. J. Gen. Appl. Microbiol. 51 301–311. 10.2323/jgam.51.301 PubMed DOI

Yurkov V., Stackebrandt E., Buss O., Vermegl A., Gorlenk V., Beattyl J. T. (2017). Reorganization of the Genus Eythromicrobium: description of “Eythromicrobium sibiricum” as Sandaracinobacter sibiricus gen. nov., sp. nov., and of “Erythromicrobium ursincola” as Erythromonas ursincola gen. nov., sp. nov. Int. J. Syst. Bacteriol. 47 1172–1178. 10.1099/00207713-47-4-1172 PubMed DOI

Yurkov V., Stackebrandt E., Holmes A., Fuerst J. A., Hugenholtz P., Golecki J., et al. (1994). Phylogenetic positions of novel aerobic, bacteriochlorophyll α-containing bacteria and description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov. Int. J. Syst. Bacteriol. 44 427–434. 10.1099/00207713-44-3-427 PubMed DOI

Zdrodovskii P. F. (1948). Rickettsiae and Rickettsioses. Moscow: Academy of Medical Sciences.

Zeevi Ben, Yosef D., Ben-Dov E., Kushmaro A. (2008). Amorphus coralli gen. nov., sp. nov., a marine bacterium isolated from coral mucus, belonging to the order Rhizobiales. Int. J. Syst. Evol. Microbiol. 58 2704–2709. 10.1099/ijs.0.65462-0 PubMed DOI

Zhang D.-C., Liu H.-C., Xin Y.-H., Zhou Y.-G., Schinner F., Margesin R. (2010). Sphingopyxis bauzanensis sp. nov., a psychrophilic bacterium isolated from soil. Int. J. Syst. Evol. Microbiol. 60 2618–2622. 10.1099/ijs.0.018218-0 PubMed DOI

Zhang D.-C., Neuner K., Wu J., Yao J., Margesin R. (2015). Puniceibacterium sediminis sp. nov., from intertidal sediment. Int. J. Syst. Evol. Microbiol. 65 1462–1466. 10.1099/ijs.0.000119 PubMed DOI

Zhang D. C., Redzic M., Liu H. C., Zhou Y. G., Schinner F., Margesin R. (2012). Devosia psychrophila sp. nov. and Devosia glacialis sp. nov., from alpine glacier cryoconite, and an emended description of the genus Devosia. Int. J. Syst. Evol. Microbiol. 62 710–715. 10.1099/ijs.0.023937-0 PubMed DOI

Zhang G., Yang Y., Wang S., Sun Z., Jiao K. (2015). Alkalimicrobium pacificum gen. nov., a marine bacterium in the family Rhodobacteraceae. Int. J. Syst. Evol. Microbiol. 65 2453–2458. 10.1099/ijs.0.000282 PubMed DOI

Zhang G. I., Hwang C. Y., Cho B. C. (2008). Thalassobaculum litoreum gen. nov., sp. nov., a member of the family Rhodospirillaceae isolated from coastal seawater. Int. J. Syst. Evol. Microbiol. 58 479–485. 10.1099/ijs.0.65344-0 PubMed DOI

Zhang J., Song F., Xin Y. H., Zhang J., Fang C. (2009). Microvirga guangxiensis sp. nov., a novel Alphaproteobacterium from soil, and emended description of the genus Microvirga. Int. J. Syst. Evol. Microbiol. 59 1997–2001. 10.1099/ijs.0.007997-0 PubMed DOI

Zhang J. J., Liu T. Y., Chen W. F., Wang E. T., Sui X. H., Zhang X. X., et al. (2012). Mesorhizobium muleiense sp. nov., nodulating with Cicer arietinum L. Int. J. Syst. Evol. Microbiol. 62 2737–2742. 10.1099/ijs.0.038265-0 PubMed DOI

Zhang L., Li X., Zhang F., Wang G. (2014a). Genomic analysis of Agrobacterium radiobacter DSM 30147T and emended description of A. radiobacter (Beijerinck and van Delden 1902) Conn, 1942 (Approved Lists 1980) emend. Sawada et al., 1993. Stand. Genom. Sci. 9 574–584. 10.4056/sig PubMed DOI PMC

Zhang L., Shi X., Si M., Li C., Zhu L., Zhao L., et al. (2014b). Rhizobium smilacinae sp. nov., an endophytic bacterium isolated from the leaf of Smilacina japonica. Antonie Van Leeuwenhoek 106 715–723. 10.1007/s10482-014-0241-1 PubMed DOI

Zhang L., Wang K. L., Yin Q., Liang J. Y., Xu Y. (2018). Ruegeria kandeliae sp. nov., isolated from the rhizosphere soil of a mangrove plant kandelia candel. Int. J. Syst. Evol. Microbiol. 68 2653–2658. 10.1099/ijsem.0.002894 PubMed DOI

Zhang S., Yang S., Chen W., Chen Y., Zhang M., Zhou X., et al. (2017). Rhizobium arenae sp. nov., isolated from the sand of Desert Mu Us, China. Int. J. Syst. Evol. Microbiol. 67 2098–2103. 10.1099/ijsem.0.001810 PubMed DOI

Zhang X.-Y., Li G.-W., Wang C.-S., Zhang Y.-J., Xu X.-W., Li H., et al. (2013). Marinicauda pacifica gen. nov., sp. nov., a prosthecate Alphaproteobacterium of the family Hyphomonadaceae isolated from deep seawater. Int. J. Syst. Evol. Microbiol. 63 2248–2253. 10.1099/ijs.0.046656-0 PubMed DOI

Zhang Y., Jiang F., Chang X., Qiu X., Ren L., Qu Z., et al. (2016). Pseudorhodobacter collinsensis sp. nov., isolated from a till sample of an icecap front. Int. J. Syst. Evol. Microbiol. 66 178–183. 10.1099/ijsem.0.000693 PubMed DOI

Zhang Y., Xu Y., Fang W., Wang X., Fang Z., Xiao Y. (2017). Pseudoruegeria marinistellae sp. nov., isolated from an unidentified starfish in Sanya, China. Antonie Van Leeuwenhoek 110 187–194. 10.1007/s10482-016-0789-z PubMed DOI

Zhang Y.-J., Liu X.-F., Kuang B.-Z., Zhang X.-Y., Zhou M.-Y., Chen S. (2018). Neptunicoccus sediminis gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from the Yellow Sea. Int. J. Syst. Evol. Microbiol. 68 1702–1706. 10.1099/ijsem.0.002728 PubMed DOI

Zhang Y.-Q., Lee J.-C., Park D.-J., Lu X.-X., Mou X.-Z., Kim C.-J. (2014c). Roseivivax roseus sp. nov., an Alphaproteobacterium isolated from a solar saltern soil sample. Int. J. Syst. Evol. Microbiol. 64 1743–1746. 10.1099/ijs.0.061630-0 PubMed DOI

Zhang Y.-Q., Yu L.-Y., Wang D., Liu H.-Y., Sun C.-H., Jiang W., et al. (2008). Roseomonas vinacea sp. nov., a Gram-negative coccobacillus isolated from a soil sample. Int. J. Syst. Evol. Microbiol. 58 2070–2074. 10.1099/ijs.0.65789-0 PubMed DOI

Zhao J.-J., Zhang J., Sun L., Zhang R.-J., Zhang C.-W., Yin H.-Q., et al. (2017). Rhizobium oryziradicis sp. nov., isolated from rice roots. Int. J. Syst. Evol. Microbiol. 67 963–968. 10.1099/ijsem.0.001724 PubMed DOI

Zheng Q., Chen C., Yan X.-J., Wang Y.-N., Zeng Y.-H., Hao L.-K., et al. (2010). Mameliella alba gen. nov., sp. nov., a marine bacterium of the Roseobacter clade in the order Rhodobacterales. Int. J. Syst. Evol. Microbiol. 60 953–957. 10.1099/ijs.0.011437-0 PubMed DOI

Zheng W. T., Li Y., Wang R., Sui X. H., Zhang X. X., Zhang J. J., et al. (2013). Mesorhizobium qingshengii sp. nov., isolated from effective nodules of Astragalus sinicus. Int. J. Syst. Evol. Microbiol. 63 2002–2007. 10.1099/ijs.0.044362-0 PubMed DOI

Zhilina T. N., Zavarzin G. A., Rainey F., Kevbrin V. V., Kostrikina N. A., Lysenko A. M. (1996). Spirochaeta alkalica sp. nov., Spirochaeta africana sp. nov., and Spirochaeta asiatica sp. nov., alkaliphilic anaerobes from the continental soda lakes in central Asia and the East African Rift. Int. J. Syst. Bacteriol. 46 305–312. 10.1099/00207713-46-1-305 PubMed DOI

Zhong Z.-P., Liu Y., Liu H.-C., Wang F., Zhou Y.-G., Liu Z.-P. (2014). Roseibium aquae sp. nov., isolated from a saline lake. Int. J. Syst. Evol. Microbiol. 64 2812–2818. 10.1099/ijs.0.065508-0 PubMed DOI

Zhu C., Delmont T. O., Vogel T. M., Bromberg Y. (2015). Functional basis of microorganism classification. PLoS Comput. Biol. 11:e1004472. 10.1371/journal.pcbi.1004472 PubMed DOI PMC

Zhuang L., Liu Y., Wang L., Wang W., Shao Z. (2015). Erythrobacter atlanticus sp. nov., a bacterium from ocean sediment able to degrade polycyclic aromatic hydrocarbons. Int. J. Syst. Evol. Microbiol. 65 3714–3719. 10.1099/ijsem.0.000481 PubMed DOI

Zurdo-Piñeiro J. L., Rivas R., Trujillo M. E., Vizcaíno N., Carrasco J. A., Chamber M., et al. (2007). Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain. Int. J. Syst. Evol. Microbiol. 57 784–788. 10.1099/ijs.0.64613-0 PubMed DOI

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