Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution.

Centre Algatech Institute of Microbiology Czech Academy of Sciences Novohradská 237 379 81 Třeboň Czech Republic

Department of Ecosystem Biology Faculty of Science University of South Bohemia Branišovská 1760 37005 České Budějovice Czech Republic

National Marine Fisheries Research Institute Kołłątaja 1 81 332 Gdynia Poland

Zobrazit více v PubMed

Woese C.R. Bacterial evolution. Microbiol. Rev. 1987;51:221–271. doi: 10.1128/mr.51.2.221-271.1987. PubMed DOI PMC

Hug L.A., Baker B.J., Anantharaman K., Brown C.T., Probst A.J., Castelle C.J., Butterfield C.N., Hernsdorf A.W., Amano Y., Ise K., et al. A new view of the tree of life. Nat. Microbiol. 2016;1:16048. doi: 10.1038/nmicrobiol.2016.48. PubMed DOI

Parks D.H., Rinke C., Chuvochina M., Chaumeil P.A., Woodcroft B.J., Evans P.N., Hugenholtz P., Tyson G.W. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol. 2017;2:1533–1542. doi: 10.1038/s41564-017-0012-7. PubMed DOI

Hugenholtz P., Tyson G.W., Webb R.I., Wagner A.M., Blackall L.L. Investigation of candidate division tm7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives. Appl. Environ. Microbiol. 2001;67:411–419. doi: 10.1128/AEM.67.1.411-419.2001. PubMed DOI PMC

Mummey D.L., Stahl P.D. Candidate Division BD: Phylogeny, Distribution and abundance in soil ecosystems. Syst. Appl. Microbiol. 2003;26:228–235. doi: 10.1078/072320203322346074. PubMed DOI

Li L., Kato C., Horikoshi K. Bacterial diversity in deep-sea sediments from different depths. Biodivers. Conserv. 1999;8:659–677. doi: 10.1023/A:1008848203739. DOI

Madrid V.M., Aller J.Y., Aller R.C., Chistoserdov A.Y. High prokaryote diversity and analysis of community structure in mobile mud deposits off French Guiana: Identification of two new bacterial candidate divisions. FEMS Microbiol. Ecol. 2001;37:197–209. doi: 10.1111/j.1574-6941.2001.tb00867.x. DOI

Zhang H., Sekiguchi Y., Hanada S., Hugenholtz P., Kim H., Kamagata Y., Nakamura K. Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Int. J. Syst. Evol. Microbiol. 2003;53:1155–1163. doi: 10.1099/ijs.0.02520-0. PubMed DOI

Zeng Y., Feng F., Medová H., Dean J., Koblížek M. Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes. Proc. Natl. Acad. Sci. USA. 2014;111:7795–7800. doi: 10.1073/pnas.1400295111. PubMed DOI PMC

Ward L.M., Cardona T., Holland-Moritz H. Evolutionary Implications of Anoxygenic Phototrophy in the Bacterial Phylum Candidatus Eremiobacterota (WPS-2) Front. Microbiol. 2019;10:1658. doi: 10.3389/fmicb.2019.01658. PubMed DOI PMC

Cardona T. Thinking twice about the evolution of photosynthesis. Open Biol. 2019;9:180246. doi: 10.1098/rsob.180246. PubMed DOI PMC

Mendler K., Chen H., Parks D.H., Lobb B., Hug L.A., Doxey A.C. AnnoTree: Visualization and exploration of a functionally annotated microbial tree of life. Nucleic Acids Res. 2019;47:4442–4448. doi: 10.1093/nar/gkz246. PubMed DOI PMC

Parks D.H., Chuvochina M., Rinke C., Mussig A.J., Chaumeil P.-A., Hugenholtz P. GTDB: An ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res. 2021;50:785–794. doi: 10.1093/nar/gkab776. PubMed DOI PMC

Parks D.H., Chuvochina M., Waite D.W., Rinke C., Skarshewski A., Chaumeil P.A., Hugenholtz P. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 2018;36:996–1004. doi: 10.1038/nbt.4229. PubMed DOI

Zeng Y., Selyanin V., Lukeš M., Dean J., Kaftan D., Feng F., Koblížek M. Characterization of the microaerophilic, bacteriochlorophyll a-containing bacterium Gemmatimonas phototrophica sp. nov., and emended descriptions of the genus Gemmatimonas and Gemmatimonas aurantiaca. Int. J. Syst. Evol. Microbiol. 2015;65:2410–2419. doi: 10.1099/ijs.0.000272. PubMed DOI

Zeng Y., Nupur, Wu N., Madsen A.M., Chen X., Gardiner A.T., Koblížek M. Gemmatimonas groenlandica sp. nov. Is an Aerobic Anoxygenic Phototroph in the Phylum Gemmatimonadetes. Front. Microbiol. 2021;11:606612. doi: 10.3389/fmicb.2020.606612. PubMed DOI PMC

Zeng Y., Baumbach J., Barbosa E.G.V., Azevedo V., Zhang C., Koblížek M. Metagenomic evidence for the presence of phototrophic Gemmatimonadetes bacteria in diverse environments. Environ. Microbiol. Rep. 2016;8:139–149. doi: 10.1111/1758-2229.12363. PubMed DOI

Mujakić I., Andrei A.-Ş., Shabarova T., Fecskeová L.K., Salcher M.M., Piwosz K., Ghai R., Koblížek M. Common Presence of Phototrophic Gemmatimonadota in Temperate Freshwater Lakes. mSystems. 2021;6:e01241-20. doi: 10.1128/mSystems.01241-20. PubMed DOI PMC

Vavourakis C., Mehrshad M., Balkema C., Van Hall R., Andrei A.-Ş., Ghai R., Sorokin D.Y., Muyzer G. Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake. BMC Biol. 2019;17:69. doi: 10.1186/s12915-019-0688-7. PubMed DOI PMC

Koblížek M., Dachev M., Bína D., Nupur, Piwosz K., Kaftan D. Utilization of light energy in phototrophic Gemmatimonadetes. J. Photochem. Photobiol. B Biol. 2020;213:112085. doi: 10.1016/j.jphotobiol.2020.112085. PubMed DOI

DeBruyn J.M., Fawaz M.N., Peacock A.D., Dunlap J.R., Nixon L.T., Cooper K.E., Radosevich M. Gemmatirosa kalamazoonesis gen. nov., sp. nov., a member of the rarely-cultivated bacterial phylum Gemmatimonadetes. J. Gen. Appl. Microbiol. 2013;59:305–312. doi: 10.2323/jgam.59.305. PubMed DOI

Pascual J., Foesel B.U., Geppert A., Huber K.J., Boedeker C., Luckner M., Wanner G., Overmann J. Roseisolibacter agri gen. nov., sp. nov., a novel slow-growing member of the under-represented phylum Gemmatimonadetes. Int. J. Syst. Evol. Microbiol. 2018;68:1028–1036. doi: 10.1099/ijsem.0.002619. PubMed DOI

Pascual J., García-López M., Bills G.F., Genilloud O. Longimicrobium terrae gen. nov., sp. nov., an oligotrophic bacterium of the under-represented phylum Gemmatimonadetes isolated through a system of miniaturized diffusion chambers. Int. J. Syst. Evol. Microbiol. 2016;66:1976–1985. doi: 10.1099/ijsem.0.000974. PubMed DOI

Park D., Kim H., Yoon S. Nitrous oxide reduction by an obligate. Appl. Environ. Microbiol. 2017;83:1–12. doi: 10.1128/AEM.00502-17. PubMed DOI PMC

Chee-Sanford J., Tian D., Sanford R. Consumption of N2O and other N-cycle intermediates by Gemmatimonas aurantiaca strain T-27. Microbiology. 2019;165:1345–1354. doi: 10.1099/mic.0.000847. PubMed DOI

Hohmann-Marriott M.F., Blankenship R.E. Evolution of Photosynthesis. Annu. Rev. Plant Biol. 2011;62:515–548. doi: 10.1146/annurev-arplant-042110-103811. PubMed DOI

Nagashima S., Nagashima K.V.P. Advances in Botanical Research. Volume 66. Elsevier; Amsterdam, The Netherlands: 2013. Comparison of Photosynthesis Gene Clusters Retrieved from Total Genome Sequences of Purple Bacteria; pp. 151–178.

Zhaxybayeva O., Gogarten J.P., Charlebois R.L., Doolittle W.F., Papke R.T. Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events. Genome Res. 2006;16:1099–1108. doi: 10.1101/gr.5322306. PubMed DOI PMC

Sousa F.L., Shavit-Grievink L., Allen J.F., Martin W.F. Chlorophyll Biosynthesis Gene Evolution Indicates Photosystem Gene Duplication, Not Photosystem Merger, at the Origin of Oxygenic Photosynthesis. Genome Biol. Evol. 2013;5:200–216. doi: 10.1093/gbe/evs127. PubMed DOI PMC

Igarashi N., Harada J., Nagashima S., Matsuura K., Shimada K., Nagashima K.V.P. Horizontal Transfer of the Photosynthesis Gene Cluster and Operon Rearrangement in Purple Bacteria. J. Mol. Evol. 2001;52:333–341. doi: 10.1007/s002390010163. PubMed DOI

Ward L.M., Hemp J., Shih P.M., McGlynn S.E., Fischer W.W. Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer. Front. Microbiol. 2018;9:260. doi: 10.3389/fmicb.2018.00260. PubMed DOI PMC

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

Cardona T. Origin of Bacteriochlorophyll a and the Early Diversification of Photosynthesis. PLoS ONE. 2016;11:e0151250. doi: 10.1371/journal.pone.0151250. PubMed DOI PMC

Dachev M., Bína D., Sobotka R., Moravcová L., Gardian Z., Kaftan D., Šlouf V., Fuciman M., Polívka T., Koblížek M. Unique double concentric ring organization of light harvesting complexes in Gemmatimonas phototrophica. PLoS Biol. 2017;15:1–16. doi: 10.1371/journal.pbio.2003943. PubMed DOI PMC

Yurkov V.V., Beatty J.T. Aerobic Anoxygenic Phototrophic Bacteria. Microbiol. Mol. Biol. Rev. 1998;62:695–724. doi: 10.1128/MMBR.62.3.695-724.1998. PubMed DOI PMC

Takaichi S., Maoka T., Takasaki K., Hanada S. Carotenoids of Gemmatimonas aurantiaca (Gemmatimonadetes): Identification of a novel carotenoid, deoxyoscillol 2-rhamnoside, and proposed biosynthetic pathway of oscillol 2,2′-dirhamnoside. Microbiology. 2010;156:757–763. doi: 10.1099/mic.0.034249-0. PubMed DOI

Yurkov V., Csotonyi J.T. Advances in Photosynthesis and Respiration. Springer; Berlin/Heidelberg, Germany: 2009. New Light on Aerobic Anoxygenic Phototrophs; pp. 31–55.

Nupur, Kuzma M., Hájek J., Hrouzek P., Gardiner A.T., Lukeš M., Moos M., Šimek P., Koblížek M. Structure elucidation of the novel carotenoid gemmatoxanthin from the photosynthetic complex of Gemmatimonas phototrophica AP64. Sci. Rep. 2021;11:15964. doi: 10.1038/s41598-021-95254-6. PubMed DOI PMC

Janssen P.H. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 2006;72:1719–1728. doi: 10.1128/AEM.72.3.1719-1728.2006. PubMed DOI PMC

DeBruyn J.M., Nixon L.T., Fawaz M.N., Johnson A.M., Radosevich M. Global Biogeography and Quantitative Seasonal Dynamics of Gemmatimonadetes in Soil. Appl. Environ. Microbiol. 2011;77:6295–6300. doi: 10.1128/AEM.05005-11. PubMed DOI PMC

Delgado-Baquerizo M., Oliverio A.M., Brewer T.E., Benavent-González A., Eldridge D.J., Bardgett R.D., Maestre F.T., Singh B.K., Fierer N. A global atlas of the dominant bacteria found in soil. Science. 2018;359:320–325. doi: 10.1126/science.aap9516. PubMed DOI

Ren C., Chen J., Lu X., Doughty R., Zhao F., Zhong Z., Han X., Yang G., Feng Y., Ren G. Responses of soil total microbial biomass and community compositions to rainfall reductions. Soil Biol. Biochem. 2018;116:4–10. doi: 10.1016/j.soilbio.2017.09.028. DOI

Bakermans C., Skidmore M.L., Douglas S., McKay C.P. Molecular characterization of bacteria from permafrost of the Taylor Valley, Antarctica. FEMS Microbiol. Ecol. 2014;89:331–346. doi: 10.1111/1574-6941.12310. PubMed DOI

Frey B., Rime T., Phillips M., Stierli B., Hajdas I., Widmer F., Hartmann M. Microbial diversity in European alpine permafrost and active layers. FEMS Microbiol. Ecol. 2016;92:fiw018. doi: 10.1093/femsec/fiw018. PubMed DOI

Tuorto S.J., Darias P., McGuinness L.R., Panikov N., Zhang T., Häggblom M.M., Kerkhof L.J. Bacterial genome replication at subzero temperatures in permafrost. ISME J. 2014;8:139–149. doi: 10.1038/ismej.2013.140. PubMed DOI PMC

Cary S.C., McDonald I.R., Barrett J.E., Cowan D.A. On the rocks: The microbiology of Antarctic Dry Valley soils. Nat. Rev. Microbiol. 2010;8:129–138. doi: 10.1038/nrmicro2281. PubMed DOI

Breidenbach B., Pump J., Dumont M.G. Microbial Community Structure in the Rhizosphere of Rice Plants. Front. Microbiol. 2016;6:1537. doi: 10.3389/fmicb.2015.01537. PubMed DOI PMC

Yang Y., Wang N., Guo X., Zhang Y., Ye B. Comparative analysis of bacterial community structure in the rhizosphere of maize by high-throughput pyrosequencing. PLoS ONE. 2017;12:e0178425. doi: 10.1371/journal.pone.0178425. PubMed DOI PMC

Gkarmiri K., Mahmood S., Ekblad A., Alström S., Högberg N., Finlay R. Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape. Appl. Environ. Microbiol. 2017;83:e01938-17. doi: 10.1128/AEM.01938-17. PubMed DOI PMC

Ren N., Wang Y., Ye Y., Zhao Y., Huang Y., Fu W., Chu X. Effects of Continuous Nitrogen Fertilizer Application on the Diversity and Composition of Rhizosphere Soil Bacteria. Front. Microbiol. 2020;11:1948. doi: 10.3389/fmicb.2020.01948. PubMed DOI PMC

Rodriguez M.T.F., Valverde N.B., Lagurara P., Revale S., De Souza J.A.M., Vilaro M.D.R. Soil and Rhizosphere Bacterial Diversity in Maize Agro- Ecosystem. Sustain. Agric. Res. 2017;6:35. doi: 10.5539/sar.v6n3p35. DOI

Na X., Xu T., Li M., Zhou Z., Ma S., Wang J., He J., Jiao B., Ma F. Variations of Bacterial Community Diversity Within the Rhizosphere of Three Phylogenetically Related Perennial Shrub Plant Species Across Environmental Gradients. Front. Microbiol. 2018;9:709. doi: 10.3389/fmicb.2018.00709. PubMed DOI PMC

Gugliandolo C., Michaud L., Giudice A.L., Lentini V., Rochera C., Camacho A., Maugeri T.L. Prokaryotic Community in Lacustrine Sediments of Byers Peninsula (Livingston Island, Maritime Antarctica) Microb. Ecol. 2016;71:387–400. doi: 10.1007/s00248-015-0666-8. PubMed DOI

Sheng P., Yu Y., Zhang G., Huang J., He L., Ding J. Bacterial diversity and distribution in seven different estuarine sediments of Poyang Lake, China. Environ. Earth Sci. 2016;75:479. doi: 10.1007/s12665-016-5346-6. DOI

Röske K., Sachse R., Scheerer C., Röske I. Microbial diversity and composition of the sediment in the drinking water reservoir Saidenbach (Saxonia, Germany) Syst. Appl. Microbiol. 2012;35:35–44. doi: 10.1016/j.syapm.2011.09.002. PubMed DOI

Song H., Li Z., Du B., Wang G., Ding Y. Bacterial communities in sediments of the shallow Lake Dongping in China. J. Appl. Microbiol. 2012;112:79–89. doi: 10.1111/j.1365-2672.2011.05187.x. PubMed DOI

Liu Y., Zhang J., Zhao L., Zhang X., Xie S. Spatial distribution of bacterial communities in high-altitude freshwater wetland sediment. Limnology. 2014;15:249–256. doi: 10.1007/s10201-014-0429-0. DOI

Zhang J., Yang Y., Yuzhao L., Li Y., Xie S., Liu Y. Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes. Appl. Microbiol. Biotechnol. 2015;99:3291–3302. doi: 10.1007/s00253-014-6262-x. PubMed DOI

Hanada S., Sekiguchi Y. The Prokaryotes. 4th ed. Volume 11. Springer; Berlin/Heidelberg, Germany: 2014. The phylum Gemmatimonadetes; pp. 677–681.

Qin H., Ji B., Zhang S., Kong Z. Study on the bacterial and archaeal community structure and diversity of activated sludge from three wastewater treatment plants. Mar. Pollut. Bull. 2018;135:801–807. doi: 10.1016/j.marpolbul.2018.08.010. PubMed DOI

Durbin A.M., Teske A. Microbial diversity and stratification of South Pacific abyssal marine sediments. Environ. Microbiol. 2011;13:3219–3234. doi: 10.1111/j.1462-2920.2011.02544.x. PubMed DOI

Cerqueira T., Pinho D., Egas C., Froufe H., Altermark B., Candeias C., Santos R.S., Bettencourt R. Microbial diversity in deep-sea sediments from the Menez Gwen hydrothermal vent system of the Mid-Atlantic Ridge. Mar. Genom. 2015;24:343–355. doi: 10.1016/j.margen.2015.09.001. PubMed DOI

Zhang J., Sun Q.-L., Zeng Z.-G., Chen S., Sun L. Microbial diversity in the deep-sea sediments of Iheya North and Iheya Ridge, Okinawa Trough. Microbiol. Res. 2015;177:43–52. doi: 10.1016/j.micres.2015.05.006. PubMed DOI

Zhang L., Kang M., Xu J., Xu J., Shuai Y., Zhou X., Yang Z., Ma K. Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge. Sci. Rep. 2016;6:25982. doi: 10.1038/srep25982. PubMed DOI PMC

Kamke J., Taylor M.W., Schmitt S. Activity profiles for marine sponge-associated bacteria obtained by 16S rRNA vs 16S rRNA gene comparisons. ISME J. 2010;4:498–508. doi: 10.1038/ismej.2009.143. PubMed DOI

Montalvo N.F., Hill R.T. Sponge-Associated Bacteria Are Strictly Maintained in Two Closely Related but Geographically Distant Sponge Hosts. Appl. Environ. Microbiol. 2011;77:7207–7216. doi: 10.1128/AEM.05285-11. PubMed DOI PMC

Souza D.T., Genuário D.B., Silva F.S.P., Pansa C.C., Kavamura V.N., Moraes F.C., Taketani R.G., Melo I.S. Analysis of bacterial composition in marine sponges reveals the influence of host phylogeny and environment. FEMS Microbiol. Ecol. 2017;93:fiw204. doi: 10.1093/femsec/fiw204. PubMed DOI

Kennedy J., Flemer B., Jackson S.A., Morrissey J.P., O’Gara F., Dobson A.D.W. Evidence of a Putative Deep Sea Specific Microbiome in Marine Sponges. PLoS ONE. 2014;9:e91092. doi: 10.1371/journal.pone.0091092. PubMed DOI PMC

Gołębiewski M., Całkiewicz J., Creer S., Piwosz K. Tideless estuaries in brackish seas as possible freshwater-marine transition zones for bacteria: The case study of the Vistula river estuary. Environ. Microbiol. Rep. 2017;9:129–143. doi: 10.1111/1758-2229.12509. PubMed DOI

Hentschel U., Hopke J., Horn M., Friedrich A.B., Wagner M., Hacker J., Moore B.S. Molecular evidence for a uniform microbial community in sponges from different oceans. Appl. Environ. Microbiol. 2002;68:4431–4440. doi: 10.1128/AEM.68.9.4431-4440.2002. PubMed DOI PMC

Dunbar J., Barns S.M., Ticknor L.O., Kuske C.R. Empirical and theoretical bacterial diversity in four arizona soils. Appl. Environ. Microbiol. 2002;68:3035–3045. doi: 10.1128/AEM.68.6.3035-3045.2002. PubMed DOI PMC

Trifinopoulos J., Nguyen L.T., von Haeseler A., Minh B.Q. W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 2016;44:W232–W235. doi: 10.1093/nar/gkw256. PubMed DOI PMC

Nguyen L.-T., Schmidt H.A., Von Haeseler A., Minh B.Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 2015;32:268–274. doi: 10.1093/molbev/msu300. PubMed DOI PMC

Kalyaanamoorthy S., Minh B.Q., Wong T.K.F., Von Haeseler A., Jermiin L.S. Model Finder: Fast model selection for accurate phylogenetic estimates. Nat. Methods. 2017;14:587–589. doi: 10.1038/nmeth.4285. PubMed DOI PMC

Letunic I., Bork P. Interactive Tree Of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49:W293–W296. doi: 10.1093/nar/gkab301. PubMed DOI PMC

Bajerski F., Wagner D. Bacterial succession in Antarctic soils of two glacier forefields on Larsemann Hills, East Antarctica. FEMS Microbiol. Ecol. 2013;85:128–142. doi: 10.1111/1574-6941.12105. PubMed DOI

Niederberger T.D., McDonald I.R., Hacker A.L., Soo R.M., Barrett J.E., Wall D.H., Cary S.C. Microbial community composition in soils of Northern Victoria Land, Antarctica. Environ. Microbiol. 2008;10:1713–1724. doi: 10.1111/j.1462-2920.2008.01593.x. PubMed DOI

Acosta-Martínez V., Dowd S., Sun Y., Allen V. Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol. Biochem. 2008;40:2762–2770. doi: 10.1016/j.soilbio.2008.07.022. DOI

Kim J.-S., Dungan R.S., Crowley D. Microarray analysis of bacterial diversity and distribution in aggregates from a desert agricultural soil. Biol. Fertil. Soils. 2008;44:1003–1011. doi: 10.1007/s00374-008-0291-5. DOI

Ahmed V., Verma M.K., Gupta S., Mandhan V., Chauhan N.S. Metagenomic Profiling of Soil Microbes to Mine Salt Stress Tolerance Genes. Front. Microbiol. 2018;9:159. doi: 10.3389/fmicb.2018.00159. PubMed DOI PMC

Zhao S., Liu J.J., Banerjee S., Zhou N., Zhao Z.Y., Zhang K., Hu M.F., Tian C.Y. Biogeographical distribution of bacterial communities in saline agricultural soil. Geoderma. 2020;361:114095. doi: 10.1016/j.geoderma.2019.114095. DOI

Neilson J.W., Califf K., Cardona C., Copeland A., van Treuren W., Josephson K.L., Knight R., Gilbert J.A., Quade J., Caporaso J.G., et al. Significant Impacts of Increasing Aridity on the Arid Soil Microbiome. mSystems. 2017;2:1–15. doi: 10.1128/mSystems.00195-16. PubMed DOI PMC

Mummey D., Holben W., Six J., Stahl P. Spatial Stratification of Soil Bacterial Populations in Aggregates of Diverse Soils. Microb. Ecol. 2006;51:404–411. doi: 10.1007/s00248-006-9020-5. PubMed DOI

Lauber C.L., Strickland M.S., Bradford M.A., Fierer N. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol. Biochem. 2008;40:2407–2415. doi: 10.1016/j.soilbio.2008.05.021. DOI

Mendez M.O., Neilson J.W., Maier R.M. Characterization of a Bacterial Community in an Abandoned Semiarid Lead-Zinc Mine Tailing Site. Appl. Environ. Microbiol. 2008;74:3899–3907. doi: 10.1128/AEM.02883-07. PubMed DOI PMC

Malard L.A., Anwar M.Z., Jacobsen C.S., Pearce D.A. Biogeographical patterns in soil bacterial communities across the Arctic region. FEMS Microbiol. Ecol. 2019;95:fiz128. doi: 10.1093/femsec/fiz128. PubMed DOI PMC

Guan Y., Jiang N., Wu Y., Yang Z., Bello A., Yang W. Disentangling the role of salinity-sodicity in shaping soil microbiome along a natural saline-sodic gradient. Sci. Total Environ. 2021;765:142738. doi: 10.1016/j.scitotenv.2020.142738. PubMed DOI

Liu M., Li X., Zhu R., Chen N., Ding L., Chen C. Vegetation richness, species identity and soil nutrients drive the shifts in soil bacterial communities during restoration process. Environ. Microbiol. Rep. 2021;13:1758–2229. doi: 10.1111/1758-2229.12913. PubMed DOI

Deng J., Bai X., Zhou Y., Zhu W., Yin Y. Variations of soil microbial communities accompanied by different vegetation restoration in an open-cut iron mining area. Sci. Total Environ. 2020;704:135243. doi: 10.1016/j.scitotenv.2019.135243. PubMed DOI

Ye W., Liu X., Lin S., Tan J., Pan J., Li D., Yang H. The vertical distribution of bacterial and archaeal communities in the water and sediment of Lake Taihu. FEMS Microbiol. Ecol. 2009;70:263–276. doi: 10.1111/j.1574-6941.2009.00761.x. PubMed DOI

Traving S.J., Rowe O., Jakobsen N.M., Sørensen H., Dinasquet J., Stedmon C.A., Andersson A., Riemann L. The Effect of Increased Loads of Dissolved Organic Matter on Estuarine Microbial Community Composition and Function. Front. Microbiol. 2017;8:1–15. doi: 10.3389/fmicb.2017.00351. PubMed DOI PMC

Morrison J.M., Baker K.D., Zamor R.M., Nikolai S., Elshahed M.S., Youssef N.H. Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA) PLoS ONE. 2017;12:e0177488. doi: 10.1371/journal.pone.0177488. PubMed DOI PMC

Cabello-Yeves P.J., Zemskaya T., Rosselli R., Coutinho F.H., Zakharenko A.S., Blinov V.V., Rodriguez-Valera F. Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal. Appl. Environ. Microbiol. 2018;84:e02132-17. doi: 10.1128/AEM.02132-17. PubMed DOI PMC

Shia L., Cai Y., Wang X., Li P., Yu Y., Kong F. Community Structure of Bacteria Associated withMicrocystisColonies from Cyanobacterial Blooms. J. Freshw. Ecol. 2010;25:193–203. doi: 10.1080/02705060.2010.9665068. DOI

Vavourakis C.D., Andrei A.S., Mehrshad M., Ghai R., Sorokin D.Y., Muyzer G. A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments 06 Biological Sciences 0605 Microbiology 06 Biological Sciences 0604 Genetics. Microbiome. 2018;6:168. doi: 10.1186/s40168-018-0548-7. PubMed DOI PMC

Çınar S., Mutlu M.B. Prokaryotic community compositions of the hypersaline sediments of tuz lake demonstrated by cloning and high-throughput sequencing. Microbiology. 2020;89:756–768. doi: 10.1134/S0026261720060028. DOI

Cui G., Li J., Gao Z., Wang Y. Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep. PeerJ. 2019;7:e6961. doi: 10.7717/peerj.6961. PubMed DOI PMC

Peoples L.M., Grammatopoulou E., Pombrol M., Xu X., Osuntokun O., Blanton J.C., Allen E.E., Nunnally C.C., Drazen J., Mayor D.J., et al. Microbial Community Diversity Within Sediments from Two Geographically Separated Hadal Trenches. Front. Microbiol. 2019;10:347. doi: 10.3389/fmicb.2019.00347. PubMed DOI PMC

Kato S., Nakawake M., Kita J., Yamanaka T., Utsumi M., Okamura K., Ishibashi J.-I., Ohkuma M., Yamagishi A. Characteristics of Microbial Communities in Crustal Fluids in a Deep-Sea Hydrothermal Field of the Suiyo Seamount. Front. Microbiol. 2013;4:85. doi: 10.3389/fmicb.2013.00085. PubMed DOI PMC

Nunoura T., Nishizawa M., Hirai M., Shimamura S., Harnvoravongchai P., Koide O., Morono Y., Fukui T., Inagaki F., Miyazaki J., et al. Microbial Diversity in Sediments from the Bottom of the Challenger Deep, the Mariana Trench. Microbes Environ. 2018;33:186–194. doi: 10.1264/jsme2.ME17194. PubMed DOI PMC

Thiel V., Neulinger S.C., Staufenberger T., Schmaljohann R., Imhoff J.F. Spatial distribution of sponge-associated bacteria in the Mediterranean sponge Tethya aurantium. FEMS Microbiol. Ecol. 2007;59:47–63. doi: 10.1111/j.1574-6941.2006.00217.x. PubMed DOI

Slaby B.M., Hackl T., Horn H., Bayer K., Hentschel U. Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization. ISME J. 2017;11:2465–2478. doi: 10.1038/ismej.2017.101. PubMed DOI PMC

Alvarez-Yela A.C.A., Mosquera-Rendón J., Noreña-P A., Cristancho M., López-Alvarez D. Microbial Diversity Exploration of Marine Hosts at Serrana Bank, a Coral Atoll of the Seaflower Biosphere Reserve. Front. Mar. Sci. 2019;6:338. doi: 10.3389/fmars.2019.00338. DOI

Liu R., Wang Z., Wang L., Li Z., Fang J., Wei X., Wei W., Cao J., Wei Y., Xie Z. Bulk and Active Sediment Prokaryotic Communities in the Mariana and Mussau Trenches. Front. Microbiol. 2020;11:1521. doi: 10.3389/fmicb.2020.01521. PubMed DOI PMC

Vipindas P.V., Mujeeb R.K.M., Jabir T., Thasneem T.R., Mohamed Hatha A.A. Diversity of sediment bacterial communities in the South Eastern Arabian Sea. Reg. Stud. Mar. Sci. 2020;35:101153. doi: 10.1016/j.rsma.2020.101153. DOI

Herlemann D.P.R., Labrenz M., Jürgens K., Bertilsson S., Waniek J.J., Andersson A.F. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 2011;5:1571–1579. doi: 10.1038/ismej.2011.41. PubMed DOI PMC

Hu Y.O.O., Karlson B., Charvet S., Andersson A.F. Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea. Front. Microbiol. 2016;7:679. doi: 10.3389/fmicb.2016.00679. PubMed DOI PMC

Chen Y., Chen H., Chen Z., Hu H., Deng C., Wang X. The benefits of autotrophic nitrogen removal from high concentration of urea wastewater through a process of urea hydrolysis and partial nitritation in sequencing batch reactor. J. Environ. Manag. 2021;292:112762. doi: 10.1016/j.jenvman.2021.112762. PubMed DOI

Hu H., Deng C., Wang X., Chen Z., Zhong Z., Wang R. Performance and mechanism of urea hydrolysis in partial nitritation system based on SBR. Chemosphere. 2020;258:127228. doi: 10.1016/j.chemosphere.2020.127228. PubMed DOI

Chen L., Feng Q., Li C., Wei Y., Zhao Y., Feng Y., Zheng H., Li F., Li H. Impacts of aquaculture wastewater irrigation on soil microbial functional diversity and community structure in arid regions. Sci. Rep. 2017;7:11193. doi: 10.1038/s41598-017-11678-z. PubMed DOI PMC

Ziganshina E.E., Ibragimov E.M., Ilinskaya O.N., Ziganshin A.M. Bacterial communities inhabiting toxic industrial wastewater generated during nitrocellulose production. Biologia. 2016;71:70–78. doi: 10.1515/biolog-2016-0014. DOI

Correa-Galeote D., Roibás-Rozas A., Mosquera-Corral A., Juárez-Jiménez B., González-López J., Rodelas B. Revealing the dissimilar structure of microbial communities in different WWTPs that treat fish-canning wastewater with different NaCl content. J. Water Process. Eng. 2021;44:102328. doi: 10.1016/j.jwpe.2021.102328. DOI

Rampadarath S., Bandhoa K., Puchooa D., Jeewon R., Bal S. Early bacterial biofilm colonizers in the coastal waters of Mauritius. Electron. J. Biotechnol. 2017;29:13–21. doi: 10.1016/j.ejbt.2017.06.006. DOI

Besemer K., Hödl I., Singer G., Battin T.J. Architectural differentiation reflects bacterial community structure in stream biofilms. ISME J. 2009;3:1318–1324. doi: 10.1038/ismej.2009.73. PubMed DOI

Wu X., Pan J., Li M., Li Y., Bartlam M., Wang Y. Selective enrichment of bacterial pathogens by microplastic biofilm. Water Res. 2019;165:114979. doi: 10.1016/j.watres.2019.114979. PubMed DOI

Cardoso D.C., Cretoiu M.S., Stal L.J., Bolhuis H. Seasonal development of a coastal microbial mat. Sci. Rep. 2019;9:9035. doi: 10.1038/s41598-019-45490-8. PubMed DOI PMC

Yutin N., Suzuki M.T., Rosenberg M., Rotem D., Madigan M.T., Süling J., Imhoff J.F., Béjà O. BchY-Based Degenerate Primers Target All Types of Anoxygenic Photosynthetic Bacteria in a Single PCR. Appl. Environ. Microbiol. 2009;75:7556–7559. doi: 10.1128/AEM.01014-09. PubMed DOI PMC

Huang Y., Zeng Y., Lu H., Feng H., Zeng Y., Koblížek M. Novel acsF Gene Primers Revealed a Diverse Phototrophic Bacterial Population, Including Gemmatimonadetes, in Lake Taihu (China) Appl. Environ. Microbiol. 2016;82:5587–5594. doi: 10.1128/AEM.01063-16. PubMed DOI PMC

Boldareva-Nuianzina E.N., Bláhová Z., Sobotka R., Koblížek M. Distribution and Origin of Oxygen-Dependent and Oxygen-Independent Forms of Mg-Protoporphyrin Monomethylester Cyclase among Phototrophic Proteobacteria. Appl. Environ. Microbiol. 2013;79:2596–2604. doi: 10.1128/AEM.00104-13. PubMed DOI PMC

Fecskeová L.K., Piwosz K., Hanusová M., Nedoma J., Znachor P., Koblížek M. Diel changes and diversity of pufM expression in freshwater communities of anoxygenic phototrophic bacteria. Sci. Rep. 2019;9:18766. doi: 10.1038/s41598-019-55210-x. PubMed DOI PMC

Zorz J.K., Sharp C., Kleiner M., Gordon P.M.K., Pon R.T., Dong X., Strous M. A shared core microbiome in soda lakes separated by large distances. Nat. Commun. 2019;10:4230. doi: 10.1038/s41467-019-12195-5. PubMed DOI PMC

Ashida H., Saito Y., Kojima C., Kobayashi K., Ogasawara N., Yokota A. A Functional Link Between RuBisCO-like Protein of Bacillus and Photosynthetic RuBisCO. Science. 2003;302:286–290. doi: 10.1126/science.1086997. PubMed DOI

Ashida H., Danchin A., Yokota A. Was photosynthetic RuBisCO recruited by acquisitive evolution from RuBisCO-like proteins involved in sulfur metabolism? Res. Microbiol. 2005;156:611–618. doi: 10.1016/j.resmic.2005.01.014. PubMed DOI

Gudelj I., Weitz J.S., Ferenci T., Horner-Devine M., Marx C.J., Meyer J.R., Forde S.E. An integrative approach to understanding microbial diversity: From intracellular mechanisms to community structure. Ecol. Lett. 2010;13:1073–1084. doi: 10.1111/j.1461-0248.2010.01507.x. PubMed DOI PMC

Piwosz K., Shabarova T., Tomasch J., Šimek K., Kopejtka K., Kahl S., Pieper D.H., Koblížek M. Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS) ISME J. 2018;12:2640–2654. doi: 10.1038/s41396-018-0213-y. PubMed DOI PMC

On the evolution of chromosomal regions with high gene strand bias in bacteria

Untapped rich microbiota of mangroves of Pakistan: diversity and community compositions

Ecology of aerobic anoxygenic phototrophs on a fine-scale taxonomic resolution in Adriatic Sea unravelled by unsupervised neural network

Multi-environment ecogenomics analysis of the cosmopolitan phylum Gemmatimonadota

The Influence of Calcium on the Growth, Morphology and Gene Regulation in Gemmatimonas phototrophica