Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons

. 2023 ; 14 () : 1089630. [epub] 20230307

Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic-ecollection

Typ dokumentu časopisecké články, přehledy

Perzistentní odkaz   https://www.medvik.cz/link/pmid36960281

In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.

Zobrazit více v PubMed

Acuna J. J., Marileo L. G., Araya M. A., Rilling J. I., Larama G. A., Mora M. L., et al. (2020). In situ cultivation approach to increase the culturable bacterial diversity in the rhizobiome of plants. J. Soil Sci. Plant Nutr. 20, 1411–1426. doi: 10.1007/s42729-020-00222-0 DOI

Adam D., Maciejewska M., Naômé A., Martinet L., Coppieters W., Karim L., et al. (2018). Isolation, characterization, and antibacterial activity of hard-to-culture PubMed DOI PMC

Adamberg K., Kask S., Laht T.-M., Paalme T. (2003). The effect of temperature and pH on the growth of lactic acid bacteria: a pH-auxostat study. Int. J. Food Microbiol. 85, 171–183. doi: 10.1016/S0168-1605(02)00537-8, PMID: PubMed DOI

Akselband Y., Cabral C., Castor T. P., Chikarmane H. M., McGrath P. (2006). Enrichment of slow-growing marine microorganisms from mixed cultures using gel microdrop (GMD) growth assay and fluorescence-activated cell sorting. J. Exp. Mar. Biol. 329, 196–205. doi: 10.1016/j.jembe.2005.08.018 DOI

Alkayyali T., Pope E., Wheatley S. K., Cartmell C., Haltli B., Kerr R. G., et al. (2021). Development of a microbe domestication pod (MD pod) for in situ cultivation of micro-encapsulated marine bacteria. Biotechnol. Bioeng. 118, 1166–1176. doi: 10.1002/bit.27633, PMID: PubMed DOI

Almeida M., Pop M., Le Chatelier E., Prifti E., Pons N., Ghozlane A., et al. (2016). Capturing the most wanted taxa through cross-sample correlations. ISME J. 10, 2459–2467. doi: 10.1038/ismej.2016.35, PMID: PubMed DOI PMC

Anderson C. R., Peterson M. E., Frampton R. A., Bulman S. R., Keenan S., Curtin D. (2018). Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from the Firmicutes phylum. PeerJ 6:e6090. doi: 10.7717/peerj.6090, PMID: PubMed DOI PMC

Aoi Y., Kinoshita T., Hata T., Ohta H., Obokata H., Tsuneda S. (2009). Hollow-fiber membrane chamber as a device for in situ environmental cultivation. Appl. Environ. Microbiol. 75, 3826–3833. doi: 10.1128/AEM.02542-08, PMID: PubMed DOI PMC

Asker D., Awad T. S., Beppu T., Ueda K. (2012). “Isolation, characterization, and diversity of novel radiotolerant carotenoid-producing bacteria” in Microbial carotenoids from bacteria and microalgae: methods and protocols, methods in molecular biology. eds. Barredo and José-Luis (Springer), 21–60. PubMed

Avhad D. N., Rathod V. K. (2015). Ultrasound assisted production of a fibrinolytic enzyme in a bioreactor. Ultrason. Sonochem. 22, 257–264. doi: 10.1016/j.ultsonch.2014.04.020, PMID: PubMed DOI

Ayrapetyan M., Williams T. C., Oliver J. D. (2015). Bridging the gap between viable but non-culturable and antibiotic persistent bacteria. Trends Microbiol. 23, 7–13. doi: 10.1016/j.tim.2014.09.004, PMID: PubMed DOI

Bahram M., Hildebrand F., Forslund S. K., Anderson J. L., Soudzilovskaia N. A., Bodegom P. M., et al. (2018). Structure and function of the global topsoil microbiome. Nature 560, 233–237. doi: 10.1038/s41586-018-0386-6, PMID: PubMed DOI

Bai Y., Weibull E., Joensson H. N., Andersson-Svahn H. (2014). Interfacing picoliter droplet microfluidics with addressable microliter compartments using fluorescence activated cell sorting. Sens Actuators B Chem. 194, 249–254. doi: 10.1016/j.snb.2013.12.089 DOI

Baker R. M., Singleton F. L., Hood M. A. (1983). Effects of nutrient deprivation on PubMed DOI PMC

Balaban N. (2011). Persistence: mechanisms for triggering and enhancing phenotypic variability. Curr. Opin. Genet. Dev. 21, 768–775. doi: 10.1016/j.gde.2011.10.001, PMID: PubMed DOI

Bartelme R. P., Custer J. M., Dupont C. L., Espinoza J. L., Torralba M., Khalili B., et al. (2020). Influence of substrate concentration on the culturability of heterotrophic soil microbes isolated by high-throughput dilution-to-extinction cultivation. mSphere 5, e00024–e00020. doi: 10.1128/mSphere.00024-20 PubMed DOI PMC

Batchelor S. E., Cooper M., Chhabra S. R., Glover L. A., Stewart G. S., Williams P., et al. (1997). Cell density-regulated recovery of starved biofilm populations of ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 63, 2281–2286. doi: 10.1128/aem.63.6.2281-2286.1997, PMID: PubMed DOI PMC

Behera H. T., Mojumdar A., Ray L. (2022). “Chapter 9 – biology, genetic aspects and oxidative stress response of actinobacteria and strategies for bioremediation of toxic metals” in Microbial biodegradation and bioremediation. eds. Das S., Dash H. R. 2nd ed (Amsterdam: Elsevier; ), 181–192.

Bender K. E., Glover K., Archey A., Barton H. A. (2020). The impact of sample processing and media chemistry on the culturable diversity of bacteria isolated from a cave. Int. J. Speleol. 49, 209–220. doi: 10.5038/1827-806X.49.3.2337 DOI

Ben-Dov E., Kramarsky-Winter E., Kushmaro A. (2009). An in situ method for cultivating microorganisms using a double encapsulation technique. FEMS Microbiol. 68, 363–371. doi: 10.1111/j.1574-6941.2009.00682.x, PMID: PubMed DOI

Berdy B., Spoering A. L., Ling L. L., Epstein S. S. (2017). In situ cultivation of previously uncultivable microorganisms using the ichip. Nat. Protoc. 12, 2232–2242. doi: 10.1038/nprot.2017.074, PMID: PubMed DOI

Bhuiyan M. N. I., Takai R., Mitsuhashi S., Shigetomi K., Tanaka Y., Kamagata Y., et al. (2016). Zincmethylphyrins and coproporphyrins, novel growth factors released by PubMed DOI

Bigger J. (1944). Treatment of staphyloeoeeal infections with penicillin by intermittent sterilisation. Lancet. 244, 497–500. doi: 10.1016/S0140-6736(00)74210-3, PMID: DOI

Biosca E. G., Amaro C., Marco-Noales E., Oliver J. D. (1996). Effect of low temperature on starvation-survival of the eel pathogen PubMed DOI PMC

Bochu W., Lanchun S., Jing Z., Yuanyuan Y., Yanhong Y. (2003). The influence of Ca DOI

Bogosian G., Aardema N. D., Bourneuf E. V., Morris P. J., O'Neil J. P. (2000). Recovery of hydrogen peroxide-sensitive culturable cells of PubMed DOI PMC

Boilattabi N., Barrassi L., Bouanane-Darenfed A., La Scola B. (2021). Isolation and identification of PubMed DOI

Bollmann A., Lewis K., Epstein S. S. (2007). Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Appl. Environ. Microbiol. 73, 6386–6390. doi: 10.1128/AEM.01309-07, PMID: PubMed DOI PMC

Bomar L., Maltz M., Colston S., Graf J. (2011). Directed culturing of microorganisms using metatranscriptomics. MBio 2, e00012–e00011. doi: 10.1128/mBio.00012-11, PMID: PubMed DOI PMC

Börner R. A., Aliaga M. T. A., Mattiasson B. (2013). Microcultivation of anaerobic bacteria single cells entrapped in alginate microbeads. Biotechnol. Lett. 35, 397–405. doi: 10.1007/s10529-012-1094-1, PMID: PubMed DOI

Brock T. D. (1967). Life at high temperatures: evolutionary, ecological, and biochemical significance of organisms living in hot springs is discussed. Science 158, 1012–1019. doi: 10.1126/science.158.3804.1012, PMID: PubMed DOI

Brock T. D., Freeze H. (1969). PubMed DOI PMC

Bruns A., Cypionka H., Overmann J. (2002). Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the Central Baltic Sea. Appl. Environ. Microbiol. 68, 3978–3987. doi: 10.1128/AEM.68.8.3978-3987.2002, PMID: PubMed DOI PMC

Bruns A., Nübel U., Cypionka H., Overmann J. (2003). Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton. Appl. Environ. Microbiol. 69, 1980–1989. doi: 10.1128/AEM.69.4.1980-1989.2003, PMID: PubMed DOI PMC

Buerger S., Spoering A., Gavrish E., Leslin C., Ling L., Epstein S. S. (2012). Microbial scout hypothesis, stochastic exit from dormancy, and the nature of slow growers. Appl. Environ. Microbiol. 78, 3221–3228. doi: 10.1128/AEM.07307-11, PMID: PubMed DOI PMC

Burmeister A., Hilgers F., Langner A., Westerwalbesloh C., Kerkhoff Y., Tenhaef N., et al. (2019). A microfluidic co-cultivation platform to investigate microbial interactions at defined microenvironments. Lab Chip 19, 98–110. doi: 10.1039/C8LC00977E, PMID: PubMed DOI

Carini P., Steindler L., Beszteri S., Giovannoni S. J. (2013). Nutrient requirements for growth of the extreme oligotroph ‘ PubMed DOI PMC

Carvalho G., Balestrino D., Forestier C., Mathias J.-D. (2018). How do environment-dependent switching rates between susceptible and persister cells affect the dynamics of biofilms faced with antibiotics? NPJ Biofilms Microbiomes 4:6. doi: 10.1038/s41522-018-0049-2, PMID: PubMed DOI PMC

Castelle C. J., Banfield J. F. (2018). Major new microbial groups expand diversity and alter our understanding of the tree of life. Cells 172, 1181–1197. doi: 10.1016/j.cell.2018.02.016, PMID: PubMed DOI

Chang C. B., Wilking J. N., Kim S. H., Shum H. C., Weitz D. A. (2015). Monodisperse emulsion drop microenvironments for bacterial biofilm growth. Small 11, 3954–3961. doi: 10.1002/smll.201403125, PMID: PubMed DOI

Chaudhary D. K., Khulan A., Kim J. (2019). Development of a novel cultivation technique for uncultured soil bacteria. Sci. Rep. 9:6666. doi: 10.1038/s41598-019-43182-x, PMID: PubMed DOI PMC

Chaudhary D. K., Kim J. (2019). Experimental setup for a diffusion bioreactor to isolate unculturable soil bacteria. Bio Protoc. 9:e3388. doi: 10.21769/BioProtoc.3388, PMID: PubMed DOI PMC

Cho J.-C., Giovannoni S. J. (2004). Cultivation and growth characteristics of a diverse group of oligotrophic marine PubMed DOI PMC

Christensen B. T. (1992). “Physical fractionation of soil and organic matter in primary particle size and density separates” in Advances in soil science. ed. B. A. Stewart (New York, NY: Springer), 1–90.

Christensen B. T. (2001). Physical fractionation of soil and structural and functional complexity in organic matter turnover. Eur. J. Soil Sci. 52, 345–353. doi: 10.1046/j.1365-2389.2001.00417.x DOI

Cohen-Gonsaud M., Barthe P., Bagnéris C., Henderson B., Ward J., Roumestand C., et al. (2005). The structure of a resuscitation-promoting factor domain from PubMed DOI

Combet-Blanc Y., Kalamba K. K., Kergoat P. Y. (1995). Effect of pH on PubMed DOI PMC

Connon S. A., Giovannoni S. J. (2002). High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl. Environ. Microbiol. 68, 3878–3885. doi: 10.1128/AEM.68.8.3878-3885.2002, PMID: PubMed DOI PMC

Costa O. Y. A., Oguejiofor C., Zühlke D., Barreto C. C., Wünsche C., Riedel K., et al. (2020). Impact of different trace elements on the growth and proteome of two strains of PubMed DOI PMC

Crane K. W., Grover J. P. (2010). Coexistence of mixotrophs, autotrophs, and heterotrophs in planktonic microbial communities. J. Theor. Biol. 262, 517–527. doi: 10.1016/j.jtbi.2009.10.027, PMID: PubMed DOI

Cross K. L., Campbell J. H., Balachandran M., Campbell A. G., Cooper C. J., Griffen A., et al. (2019). Targeted isolation and cultivation of uncultivated bacteria by reverse genomics. Nat. Biotechnol. 37, 1314–1321. doi: 10.1038/s41587-019-0260-6, PMID: PubMed DOI PMC

Das N., Triparthi N., Basu S., Bose C., Maitra S., Khurana S. (2015). Progress in the development of gelling agents for improved culturability of microorganisms. Front. Microbiol. 6:698. doi: 10.3389/fmicb.2015.00698, PMID: PubMed DOI PMC

Davis K. E., Joseph S. J., Janssen P. H. (2005). Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl. Environ. Microbiol. 71, 826–834. doi: 10.1128/AEM.71.2.826-834.2005, PMID: PubMed DOI PMC

del Mar L. M., Pierobon S., Tafi M. C., Signoretto C., Canepari P. (2000). mRNA detection by reverse transcription-PCR for monitoring viability over time in an PubMed DOI PMC

Dellagnezze B. M., Vasconcellos S. P., Melo I. S., Santos Neto E. V., Oliveira V. M. (2016). Evaluation of bacterial diversity recovered from petroleum samples using different physical matrices. Braz. J. Microbiol. 47, 712–723. doi: 10.1016/j.bjm.2016.04.004, PMID: PubMed DOI PMC

Dong L., Chen D.-W., Liu S.-J., Du W. (2016). Automated chemotactic sorting and single-cell cultivation of microbes using droplet microfluidics. Sci. Rep. 6:24192. doi: 10.1038/srep24192, PMID: PubMed DOI PMC

Dorofeev A. G., Grigor’eva N. V., Kozlov M. N., Kevbrina M. V., Aseeva V. G., Nikolaev Y. A. (2014). Approaches to cultivation of “nonculturable” bacteria: cyclic cultures. Microbiology 83, 450–461. doi: 10.1134/S0026261714050087, PMID: DOI

Dorofeev A. G., Nikolaev Y. A., Mardanov A. V., Pimenov N. V. (2019). Cyclic metabolism as a mode of microbial existence. Microbiology 88, 402–415. doi: 10.1134/S0026261719040052, PMID: DOI

Droce A., Sørensen J. L., Giese H., Sondergaard T. E. (2013). Glass bead cultivation of fungi: combining the best of liquid and agar media. J. Microbiol. Methods 94, 343–346. doi: 10.1016/j.mimet.2013.07.005, PMID: PubMed DOI

Du M., Chen J., Zhang X., Li A., Li Y., Wang Y. (2007). Retention of virulence in a viable but nonculturable PubMed DOI PMC

Dworkin J., Shah I. M. (2010). Exit from dormancy in microbial organisms. Nat. Rev. Microbiol. 8, 890–896. doi: 10.1038/nrmicro2453, PMID: PubMed DOI

Eichorst S. A., Kuske C. R., Schmidt T. M. (2011). Influence of plant polymers on the distribution and cultivation of bacteria in the phylum PubMed DOI PMC

Eilers H., Pernthaler J., Peplies J., Glöckner F. O., Gerdts G., Amann R. (2001). Isolation of novel pelagic bacteria from the German bight and their seasonal contributions to surface picoplankton. Appl. Environ. Microbiol. 67, 5134–5142. doi: 10.1128/AEM.67.11.5134-5142.2001, PMID: PubMed DOI PMC

Epstein S. S. (2009). Microbial awakenings. Nature 457:1083. doi: 10.1038/4571083a PubMed DOI

Epstein S. S. (2013). The phenomenon of microbial uncultivability. Curr. Opin. Microbiol. 16, 636–642. doi: 10.1016/j.mib.2013.08.003, PMID: PubMed DOI

Espina L. (2020). An approach to increase the success rate of cultivation of soil bacteria based on fluorescence-activated cell sorting. PLoS One 15:e0237748. doi: 10.1371/journal.pone.0237748, PMID: PubMed DOI PMC

Esposito F. P., Ingham C. J., Hurtado-Ortiz R., Bizet C., Tasdemir D., de Pascale D. (2018). Isolation by miniaturized culture chip of an Antarctic bacterium PubMed DOI PMC

Estevinho L. M., Combarros-Fuertes P., Paula V. B. (2020). Recent advances in applied microbiology: editorial. Microorganisms 8:1364. doi: 10.3390/microorganisms8091364 PubMed DOI PMC

Eun Y. J., Utada A. S., Copeland M. F., Takeuchi S., Weibel D. B. (2011). Encapsulating bacteria in agarose microparticles using microfluidics for high-throughput cell analysis and isolation. ACS Chem. Biol. 6, 260–266. doi: 10.1021/cb100336p, PMID: PubMed DOI PMC

Faust K., Raes J. (2012). Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538–550. doi: 10.1038/nrmicro2832, PMID: PubMed DOI

Feng Y., Grogan P., Caporaso J. G., Zhang H., Lin X., Knight R., et al. (2014). pH is a good predictor of the distribution of anoxygenic purple phototrophic bacteria in Arctic soils. Soil Biol. Biochem. 74, 193–200. doi: 10.1016/j.soilbio.2014.03.014 DOI

Ferrari B. C., Binnerup S. J., Gillings M. (2005). Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria. Appl. Environ. Microbiol. 71, 8714–8720. doi: 10.1128/AEM.71.12.8714-8720.2005, PMID: PubMed DOI PMC

Fierer N., Nemergut D., Knight R., Craine J. M. (2010). Changes through time: integrating microorganisms into the study of succession. Res. Microbiol. 161, 635–642. doi: 10.1016/j.resmic.2010.06.002, PMID: PubMed DOI

Filiatrault M. J. (2011). Progress in prokaryotic transcriptomics. Curr. Opin. Microbiol. 14, 579–586. doi: 10.1016/j.mib.2011.07.023, PMID: PubMed DOI

Flemming H.-C., Wingender J. (2010). The biofilm matrix. Nat. Rev. Microbiol. 8, 623–633. doi: 10.1038/nrmicro2415, PMID: PubMed DOI

Frimat J.-P., Becker M., Chiang Y.-Y., Marggraf U., Janasek D., Hengstler J. G., et al. (2011). A microfluidic array with cellular valving for single cell co-culture. Lab Chip 11, 231–237. doi: 10.1039/C0LC00172D, PMID: PubMed DOI

Gao W., Navarroli D., Naimark J., Zhang W., Chao S.-h., Meldrum D. R. (2013). Microbe observation and cultivation array (MOCA) for cultivating and analyzing environmental microbiota. Microbiome 1:4. doi: 10.1186/2049-2618-1-4, PMID: PubMed DOI PMC

Gavrish E., Bollmann A., Epstein S., Lewis K. (2008). A trap for in situ cultivation of filamentous actinobacteria. J. Microbiol. Methods 72, 257–262. doi: 10.1016/j.mimet.2007.12.009, PMID: PubMed DOI PMC

Ge Z., Girguis P. R., Buie C. R. (2016). Nanoporous microscale microbial incubators. Lab Chip 16, 480–488. doi: 10.1039/C5LC00978B, PMID: PubMed DOI

Gerna D., Clara D., Allwardt D., Mitter B., Roach T. (2022). Tailored media are key to unlocking the diversity of endophytic bacteria in distinct compartments of germinating seeds. Microbiol. Spectr. 10, e00172–e00122. doi: 10.1128/spectrum.00172-22 PubMed DOI PMC

Giagnoni L., Arenella M., Galardi E., Nannipieri P., Renella G. (2018). Bacterial culturability and the viable but non-culturable (VBNC) state studied by a proteomic approach using an artificial soil. Soil Biol. Biochem. 118, 51–58. doi: 10.1016/j.soilbio.2017.12.004 DOI

Gich F., Janys M. A., König M., Overmann J. (2012). Enrichment of previously uncultured bacteria from natural complex communities by adhesion to solid surfaces. Environ. Microbiol. 14, 2984–2997. doi: 10.1111/j.1462-2920.2012.02868.x, PMID: PubMed DOI

Gilbert J. A., Blaser M. J., Caporaso J. G., Jansson J. K., Lynch S. V., Knight R. (2018). Current understanding of the human microbiome. Nat. Med. 24, 392–400. doi: 10.1038/nm.4517, PMID: PubMed DOI PMC

Goers L., Freemont P., Polizzi K. M. (2014). Co-culture systems and technologies: taking synthetic biology to the next level. J. R. Soc. Interface 11:20140065. doi: 10.1098/rsif.2014.0065, PMID: PubMed DOI PMC

Graham E. B., Knelman J. E., Schindlbacher A., Siciliano S., Breulmann M., Yannarell A., et al. (2016). Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes? Front. Microbiol. 7:214. doi: 10.3389/fmicb.2016.00214, PMID: PubMed DOI PMC

Greub G. (2012). Culturomics: a new approach to study the human microbiome. Clin. Microbiol. Infect. 18, 1157–1159. doi: 10.1111/1469-0691.12032, PMID: PubMed DOI

Grover S. C., Skirtach A. G., Gauthier R. C., Grover C. P. (2001). Automated single-cell sorting system based on optical trapping. J. Biomed. Opt. 6, 14–22. doi: 10.1117/1.1333676, PMID: PubMed DOI

Gurusinghe S., Brooks T. L., Barrow R. A., Zhu X., Thotagamuwa A., Dennis P. G., et al. (2019). Technologies for the selection, culture and metabolic profiling of unique rhizosphere microorganisms for natural product discovery. Molecules 24:1955. doi: 10.3390/molecules24101955, PMID: PubMed DOI PMC

Gutierrez T., Biddle J. F., Teske A., Aitken M. D. (2015). Cultivation-dependent and cultivation-independent characterization of hydrocarbon-degrading bacteria in Guaymas Basin sediments. Front. Microbiol. 6:695. doi: 10.3389/fmicb.2015.00695, PMID: PubMed DOI PMC

Gutierrez T., Singleton D. R., Berry D., Yang T., Aitken M. D., Teske A. (2013). Hydrocarbon-degrading bacteria enriched by the Deepwater horizon oil spill identified by cultivation and DNA-SIP. ISME J. 7, 2091–2104. doi: 10.1038/ismej.2013.98, PMID: PubMed DOI PMC

Gutleben J., Loureiro C., Ramírez Romero L. A., Shetty S., Wijffels R. H., Smidt H., et al. (2020). Cultivation of bacteria from PubMed DOI PMC

Handelsman J., Rondon M. R., Brady S. F., Clardy J., Goodman R. M. (1998). Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5, R245–R249. doi: 10.1016/S1074-5521(98)90108-9, PMID: PubMed DOI

Harriott M. M. (2019). “Biofilms and antibiotics” in Reference module in biomedical sciences (Elsevier; ), 1–11.

Hedlund B. P., Chuvochina M., Hugenholtz P., Konstantinidis K. T., Murray A. E., Palmer M., et al. (2022). SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nat. Microbiol. 7, 1702–1708. doi: 10.1038/s41564-022-01214-9, PMID: PubMed DOI PMC

Hemkemeyer M., Dohrmann A. B., Christensen B. T., Tebbe C. C. (2018). Bacterial preferences for specific soil particle size fractions revealed by community analyses. Front. Microbiol. 9:149. doi: 10.3389/fmicb.2018.00149, PMID: PubMed DOI PMC

Hemme C. L., Deng Y., Gentry T. J., Fields M. W., Wu L., Barua S., et al. (2010). Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J. 4, 660–672. doi: 10.1038/ismej.2009.154, PMID: PubMed DOI

Hett E. C., Chao M. C., Deng L. L., Rubin E. J. (2008). A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor. PLoS Pathog. 4:e1000001. doi: 10.1371/journal.ppat.1000001, PMID: PubMed DOI PMC

Ho A., Di Lonardo D. P., Bodelier P. L. (2017). Revisiting life strategy concepts in environmental microbial ecology. FEMS Microbiol. 93:fix006. doi: 10.1093/femsec/fix006 PubMed DOI

Hobby G. L., Meyer K., Chaffee E. (1942). Observations on the mechanism of action of penicillin. Proc. Soc. Exp. Biol. Med. 50, 281–285. doi: 10.3181/00379727-50-13773, PMID: DOI

Hu B., Xu B., Yun J., Wang J., Xie B., Li C., et al. (2020). High-throughput single-cell cultivation reveals the underexplored rare biosphere in deep-sea sediments along the southwest Indian ridge. Lab Chip 20, 363–372. doi: 10.1039/C9LC00761J, PMID: PubMed DOI

Huang G., Chen S., Dai C., Sun L., Sun W., Tang Y., et al. (2017). Effects of ultrasound on microbial growth and enzyme activity. Ultrason. Sonochem. 37, 144–149. doi: 10.1016/j.ultsonch.2016.12.018, PMID: PubMed DOI

Huang X., Li P., Zhou M., Li Y., Ou X., Chen P., et al. (2021). A high-throughput ultrasonic spraying inoculation method promotes colony cultivation of rare microbial species. Environ. Microbiol. 23, 1275–1285. doi: 10.1111/1462-2920.15386, PMID: PubMed DOI

Hugenholtz P., Pitulle C., Hershberger K. L., Pace N. R. (1998). Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180, 366–376. doi: 10.1128/JB.180.2.366-376.1998, PMID: PubMed DOI PMC

Imachi H., Nobu M. K., Nakahara N., Morono Y., Ogawara M., Takaki Y., et al. (2020). Isolation of an archaeon at the prokaryote–eukaryote interface. Nature 577, 519–525. doi: 10.1038/s41586-019-1916-6, PMID: PubMed DOI PMC

Imazaki I., Kobori Y. (2010). Improving the culturability of freshwater bacteria using FW70, a low-nutrient solid medium amended with sodium pyruvate. Can. J. Microbiol. 56, 333–341. doi: 10.1139/W10-019, PMID: PubMed DOI

Ingham C. J., Sprenkels A., Bomer J., Molenaar D., van den Berg A., van Hylckama Vlieg J. E., et al. (2007). The micro-petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms. Proc. Natl. Acad. Sci. U. S. A. 104, 18217–18222. doi: 10.1073/pnas.0701693104, PMID: PubMed DOI PMC

Inglis T. J. J., Sagripanti J.-L. (2006). Environmental factors that affect the survival and persistence of PubMed DOI PMC

Jacoby R., Peukert M., Succurro A., Koprivova A., Kopriva S. (2017). The role of soil microorganisms in plant mineral nutrition-current knowledge and future directions. Front. Plant Sci. 8:1617. doi: 10.3389/fpls.2017.01617, PMID: PubMed DOI PMC

Janssen P. H., Yates P. S., Grinton B. E., Taylor P. M., Sait M. (2002). Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions PubMed DOI PMC

Jeon C. O., Park W., Ghiorse W. C., Madsen E. L. (2004). PubMed DOI

Jeon C. O., Park W., Padmanabhan P., DeRito C., Snape J. R., Madsen E. L. (2003). Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment. Proc. Natl. Acad. Sci. U. S. A. 100, 13591–13596. doi: 10.1073/pnas.1735529100, PMID: PubMed DOI PMC

Ji S., Zhao R., Yin Q., Zhao Y., Liu C., Xiao T., et al. (2012). Gel microbead cultivation with a subenrichment procedure can yield better bacterial cultivability from a seawater sample than standard plating method. J. Ocean Univ. China 11, 45–51. doi: 10.1007/s11802-012-1869-y DOI

Jian X., Guo X., Wang J., Tan Z. L., Xing X., Wang L., et al. (2020). Microbial microdroplet culture system (MMC): an integrated platform for automated, high-throughput microbial cultivation and adaptive evolution. Biotechnol. Bioeng. 117, 1724–1737. doi: 10.1002/bit.27327, PMID: PubMed DOI

Jiang C.-Y., Dong L., Zhao J.-K., Hu X., Shen C., Qiao Y., et al. (2016). High throughput single-cell cultivation on microfluidic streak plates. Appl. Environ. Microbiol. 85, 2210–2218. doi: 10.1128/AEM.03588-15 PubMed DOI PMC

Jin Q., Kirk M. F. (2018). pH as a primary control in environmental microbiology: 1 Thermodynamic perspective. Front. Environ. Sci. 6:21. doi: 10.3389/fenvs.2018.00021 DOI

Jin Z., Nie M., Hu R., Zhao T., Xu J., Chen D., et al. (2018). Dynamic sessile-droplet habitats for controllable cultivation of bacterial biofilm. Small 14:e1800658. doi: 10.1002/smll.201800658, PMID: PubMed DOI

Jung D., Aoi Y., Epstein S. S. (2016). PubMed DOI PMC

Jung D., Seo E.-Y., Epstein S. S., Joung Y., Yim J. H., Lee H. K., et al. (2013). A new method for microbial cultivation and its application to bacterial community analysis in Buus Nuur, Mongolia. Fundam. Appl. Limnol. 182, 171–181. doi: 10.1127/1863-9135/2013/0391 DOI

Jung D., Seo E. Y., Owen J. S., Aoi Y., Yong S., Lavrentyeva E. V., et al. (2018). Application of the filter plate microbial trap (FPMT), for cultivating thermophilic bacteria from thermal springs in Barguzin area, eastern Baikal, Russia. Biosci. Biotechnol. Biochem. 82, 1624–1632. doi: 10.1080/09168451.2018.1482194, PMID: PubMed DOI

Kaeberlein T., Lewis K., Epstein S. S. (2002). Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science 296, 1127–1129. doi: 10.1126/science.1070633, PMID: PubMed DOI

Kakumanu M. L., Williams M. A. (2012). Soil diffusion system enriches the growth of diverse and previously uncultivated bacterial taxa. Soil Sci. Soc. Am. J. 76, 463–474. doi: 10.2136/sssaj2011.0227 DOI

Kapinusova G., Jani K., Smrhova T., Pajer P., Jarosova I., Suman J., et al. (2022). Culturomics of bacteria from radon-saturated water of the world’s oldest radium mine. Microbiol. Spectr. 10, e01995–e01922. doi: 10.1128/spectrum.01995-22 PubMed DOI PMC

Kaprelyants A. S., Mukamolova G. V., Kell D. B. (1994). Estimation of dormant DOI

Karimi E., Keller-Costa T., Slaby B. M., Cox C. J., da Rocha U. N., Hentschel U., et al. (2019). Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant and cultivatable PubMed DOI PMC

Karnachuk O. V., Lukina A. P., Kadnikov V. V., Sherbakova V. A., Beletsky A. V., Mardanov A. V., et al. (2020). Targeted isolation based on metagenome-assembled genomes reveals a phylogenetically distinct group of thermophilic spirochetes from deep biosphere. Environ. Microbiol. 23, 3585–3598. doi: 10.1111/1462-2920.15218 PubMed DOI

Kato S., Terashima M., Yama A., Sato M., Kitagawa W., Kawasaki K., et al. (2020). Improved isolation of uncultured anaerobic bacteria using medium prepared with separate sterilization of agar and phosphate. Microbes Environ. 35:n/a. doi: 10.1264/jsme2.ME19060, PMID: PubMed DOI PMC

Kato S., Yamagishi A., Daimon S., Kawasaki K., Tamaki H., Kitagawa W., et al. (2018). Isolation of previously uncultured slow-growing bacteria by using a simple modification in the preparation of agar media. Appl. Environ. Microbiol. 84, e00807–e00818. doi: 10.1128/AEM.00807-18 PubMed DOI PMC

Keep N. H., Ward J. M., Cohen-Gonsaud M., Henderson B. (2006). Wake up! Peptidoglycan lysis and bacterial non-growth states. Trends Microbiol. 14, 271–276. doi: 10.1016/j.tim.2006.04.003, PMID: PubMed DOI

Kell D. B., Kaprelyants A. S., Weichart D. H., Harwood C. R., Barer M. R. (1998). Viability and activity in readily culturable bacteria: a review and discussion of the practical issues. Antonie Van Leeuwenhoek 73, 169–187. doi: 10.1023/A:1000664013047, PMID: PubMed DOI

Knobloch S., Jóhannsson R., Marteinsson V. (2019). Co-cultivation of the marine sponge PubMed DOI PMC

Koch A. L. (1971). “The adaptive responses of Escherichia coli to a feast and famine existence” in Advances in microbial physiology. eds. Rose A. H., Wilkinson J. F., vol. 6 (Academic Press; ), 147–217. PubMed

Koch A. L. (2001). Oligotrophs versus copiotrophs. BioEssays 23, 657–661. doi: 10.1002/bies.1091, PMID: PubMed DOI

Konopka A. (2009). What is microbial community ecology? ISME J. 3, 1223–1230. doi: 10.1038/ismej.2009.88, PMID: PubMed DOI

Lagier J. C., Dubourg G., Million M., Cadoret F., Bilen M., Fenollar F., et al. (2018). Culturing the human microbiota and culturomics. Nat. Rev. Microbiol. 16, 540–550. doi: 10.1038/s41579-018-0041-0, PMID: PubMed DOI

Lane D. J., Pace B., Olsen G. J., Stahl D. A., Sogin M. L., Pace N. R. (1985). Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. U. S. A. 82, 6955–6959. doi: 10.1073/pnas.82.20.6955, PMID: PubMed DOI PMC

Larke-Mejía N. L., Crombie A. T., Pratscher J., McGenity T. J., Murrell J. C. (2019). Novel isoprene-degrading PubMed DOI PMC

Lauber C. L., Hamady M., Knight R., Fierer N. (2009). Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75, 5111–5120. doi: 10.1128/AEM.00335-09, PMID: PubMed DOI PMC

Lee K. C., Dunfield P. F., Morgan X. C., Crowe M. A., Houghton K. M., Vyssotski M., et al. (2011). PubMed DOI

Lewis K. (2010). Persister cells. Annu. Rev. Microbiol. 64, 357–372. doi: 10.1146/annurev.micro.112408.134306, PMID: PubMed DOI

Lewis K., Epstein S., D'Onofrio A., Ling L. L. (2010). Uncultured microorganisms as a source of secondary metabolites. J. Antibiot. 63, 468–476. doi: 10.1038/ja.2010.87, PMID: PubMed DOI

Li Y., Chen J., Wang Y., Ma D., Rui W. (2020). The effects of the recombinant YeaZ of PubMed DOI PMC

Li J., Luo C., Zhang D., Cai X., Jiang L., Zhang G. (2019). Stable-isotope probing-enabled cultivation of the indigenous bacterium PubMed DOI PMC

Li L., Mendis N., Trigui H., Oliver J. D., Faucher S. P. (2014). The importance of the viable but non-culturable state in human bacterial pathogens. Front. Microbiol. 5:258. doi: 10.3389/fmicb.2014.00258, PMID: PubMed DOI PMC

Li B., Yang Y., Ma L., Ju F., Guo F., Tiedje J. M., et al. (2015). Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. ISME J. 9, 2490–2502. doi: 10.1038/ismej.2015.59, PMID: PubMed DOI PMC

Ling L. L., Schneider T., Peoples A. J., Spoering A. L., Engels I., Conlon B. P., et al. (2015). A new antibiotic kills pathogens without detectable resistance. Nature 517, 455–459. doi: 10.1038/nature14098, PMID: PubMed DOI PMC

Liu S., Moon C. D., Zheng N., Huws S., Zhao S., Wang J. (2022). Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation. Microbiome 10:76. doi: 10.1186/s40168-022-01272-5, PMID: PubMed DOI PMC

Liu X., Wang M., Nie Y., Wu X. L. (2021). Isolation chip increases culturable bacterial diversity and reduces cultivation bias. Curr. Microbiol. 78, 2025–2032. doi: 10.1007/s00284-021-02474-0, PMID: PubMed DOI

Lloyd K. G., Steen A. D., Ladau J., Yin J., Crosby L., Neufeld J. D. (2018). Phylogenetically novel uncultured microbial cells dominate earth microbiomes. mSystems 3, e00055–e00018. doi: 10.1128/mSystems.00055-18 PubMed DOI PMC

Lopez Marin M. A., Strejcek M., Junkova P., Suman J., Santrucek J., Uhlik O. (2021). Exploring the potential of PubMed DOI PMC

Lopez Marin M. A., Suman J., Jani K., Ulbrich P., Cajthaml T., Filipova A., et al. (2023). Solicola gregarius gen. nov., sp. nov., a soil actinobacterium isolated after enhanced cultivation with Micrococcus luteus culture supernatant. Int J Syst Evol Microbiol. 73. doi: PubMed

Lopez Marin M. A., Suman J., Jani K., Ulbrich P., Cajthaml T., Pajer P., et al. (2022). PubMed DOI

Louca S., Mazel F., Doebeli M., Parfrey L. W. (2019). A census-based estimate of Earth's bacterial and archaeal diversity. PLoS Biol. 17:e3000106. doi: 10.1371/journal.pbio.3000106, PMID: PubMed DOI PMC

Lynch M. D., Bartram A. K., Neufeld J. D. (2012). Targeted recovery of novel phylogenetic diversity from next-generation sequence data. ISME J. 6:2067. doi: 10.1038/ismej.2012.50, PMID: PubMed DOI PMC

Ma L., Datta S. S., Karymov M. A., Pan Q., Begolo S., Ismagilov R. F. (2014). Individually addressable arrays of replica microbial cultures enabled by splitting SlipChips. Integr. Biol. (Camb) 6, 796–805. doi: 10.1039/C4IB00109E, PMID: PubMed DOI PMC

Manivasagan P., Kang K. H., Sivakumar K., Li-Chan E. C., Oh H. M., Kim S. K. (2014). Marine actinobacteria: an important source of bioactive natural products. Environ. Toxicol. Pharmacol. 38, 172–188. doi: 10.1016/j.etap.2014.05.014, PMID: PubMed DOI

Marchesi J. R., Ravel J. (2015). The vocabulary of microbiome research: a proposal. Microbiome 3:31. doi: 10.1186/s40168-015-0094-5, PMID: PubMed DOI PMC

Maza F., Maldonado J., Vásquez-Dean J., Mandakovic D., Gaete A., Cambiazo V., et al. (2019). Soil bacterial communities from the Chilean Andean highlands: taxonomic composition and culturability. Front. Bioeng. Biotechnol. 7:10. doi: 10.3389/fbioe.2019.00010, PMID: PubMed DOI PMC

McLain J. E., Cytryn E., Durso L. M., Young S. (2016). Culture-based methods for detection of antibiotic resistance in agroecosystems: advantages, challenges, and gaps in knowledge. J. Environ. Qual. 45, 432–440. doi: 10.2134/jeq2015.06.0317, PMID: PubMed DOI

Mehetre G., Shah M., Dastager S. G., Dharne M. S. (2018). Untapped bacterial diversity and metabolic potential within Unkeshwar hot springs, India. Arch. Microbiol. 200, 753–770. doi: 10.1007/s00203-018-1484-4 PubMed DOI

Meyer O. (1994). “Functional groups of microorganisms” in Biodiversity and ecosystem function. eds. Schulze, Ernst-Detlef, Mooney and A. Harold (Berlin, Heidelberg: Springer), 67–96.

Miller C. N., Khan M., Ahmed S. A., Kota K., Panchal R. G., Hale M. L. (2020). Development of a PubMed DOI

Mills A. L. (2003). Keeping in touch: microbial life on soil particle surfaces. Adv. Agron. 78, 2–45. doi: 10.1016/S0065-2113(02)78001-2 DOI

Mirzaie A., Mehrabadi J. F., Amirmozafari N., Nejadsattari T. (2015). Isolation and characterization of a new gamma and UV radiation resistant bacterium from soil samples of an Iranian radioactive site and analysis of its pigment. Microbiology 84, 449–452. doi: 10.1134/S0026261715030133 DOI

Mishamandani S., Gutierrez T., Aitken M. D. (2014). DNA-based stable isotope probing coupled with cultivation methods implicates PubMed DOI PMC

Molina-Menor E., Gimeno-Valero H., Pascual J., Peretó J., Porcar M. (2021). High culturable bacterial diversity from a european desert: the Tabernas desert. Front. Microbiol. 11:583120. doi: 10.3389/fmicb.2020.583120, PMID: PubMed DOI PMC

Moran N. A., Bennett G. M. (2014). The tiniest tiny genomes. Annu. Rev. Microbiol. 68, 195–215. doi: 10.1146/annurev-micro-091213-112901, PMID: PubMed DOI

Mori K., Sunamura M., Yanagawa K., Ishibashi J.-i., Miyoshi Y., Iino T., et al. (2008). First cultivation and ecological investigation of a bacterium affiliated with the candidate phylum OP5 from hot springs. Appl. Environ. Microbiol. 74, 6223–6229. doi: 10.1128/AEM.01351-08, PMID: PubMed DOI PMC

Morrison E. W., Rettger L. F. (1930). Bacterial spores I. a study in heat resistance and dormancy. J. Bacteriol. 20, 299–311. doi: 10.1128/jb.20.5.299-311.1930, PMID: PubMed DOI PMC

Mukamolova G. V., Kaprelyants A. S., Kell D. B., Young M. (2003). Adoption of the transiently non-culturable state-a bacterial survival strategy? Adv. Microb. Physiol. 47, 66–131. doi: 10.1016/S0065-2911(03)47002-1 PubMed DOI

Mukamolova G. V., Kaprelyants A. S., Young D. I., Young M., Kell D. B. (1998). A bacterial cytokine. Proc. Natl. Acad. Sci. U. S. A. 95, 8916–8921. doi: 10.1073/pnas.95.15.8916, PMID: PubMed DOI PMC

Mukamolova G. V., Murzin A. G., Salina E. G., Demina G. R., Kell D. B., Kaprelyants A. S., et al. (2006). Muralytic activity of PubMed DOI

Mukamolova G. V., Turapov O. A., Young D. I., Kaprelyants A. S., Kell D. B., Young M. (2002). A family of autocrine growth factors in PubMed DOI

Nguyen L. D., Kalachová L., Novotná J., Holub M., Kofroňová O., Benada O., et al. (2005). Cultivation system using glass beads immersed in liquid medium facilitates studies of PubMed DOI PMC

Nichols D. (2007). Cultivation gives context to the microbial ecologist. FEMS Microbiol 60, 351–357. doi: 10.1111/j.1574-6941.2007.00332.x, PMID: PubMed DOI

Nichols D., Cahoon N., Trakhtenberg E. M., Pham L., Mehta A., Belanger A., et al. (2010). Use of ichip for high-throughput in situ cultivation of “uncultivable” microbial species. Appl. Environ. Microbiol. 76, 2445–2450. doi: 10.1128/AEM.01754-09, PMID: PubMed DOI PMC

Nichols D., Lewis K., Orjala J., Mo S., Ortenberg R., O'Connor P., et al. (2008). Short peptide induces an “uncultivable” microorganism to grow in vitro. Appl. Environ. Microbiol. 74, 4889–4897. doi: 10.1128/AEM.00393-08, PMID: PubMed DOI PMC

Nikitushkin V. D., Demina G. R., Kaprelyants A. S. (2016). Rpf proteins are the factors of reactivation of the dormant forms of Actinobacteria. Biochem. Mosc. 81, 1719–1734. doi: 10.1134/S0006297916130095, PMID: PubMed DOI

Nowrotek M., Jałowiecki Ł., Harnisz M., Płaza G. A. (2019). Culturomics and metagenomics: in understanding of environmental resistome. Front. Environ. Sci. Eng. 13:40. doi: 10.1007/s11783-019-1121-8 DOI

Ohan J., Pelle B., Nath P., Huang J.-H., Hovde B., Vuyisich M., et al. (2019). High-throughput phenotyping of cell-to-cell interactions in gel microdroplet pico-cultures. BioTechniques 66, 218–224. doi: 10.2144/btn-2018-0124, PMID: PubMed DOI

Omsland A., Cockrell D. C., Howe D., Fischer E. R., Virtaneva K., Sturdevant D. E., et al. (2009). Host cell-free growth of the Q fever bacterium PubMed DOI PMC

Ota Y., Saito K., Takagi T., Matsukura S., Morita M., Tsuneda S., et al. (2019). Fluorescent nucleic acid probe in droplets for bacterial sorting (FNAP-sort) as a high-throughput screening method for environmental bacteria with various growth rates. PLoS One 14:e0214533. doi: 10.1371/journal.pone.0214533, PMID: PubMed DOI PMC

Palmer M., Sutcliffe I., Venter S. N., Hedlund B. P. (2022). It is time for a new type of type to facilitate naming the microbial world. New Microbes New Infect. 47:100991. doi: 10.1016/j.nmni.2022.100991, PMID: PubMed DOI PMC

Panda A. K., Bisht S. S., Rana M., De Mandal S., Kumar N. S. (2018). “Biotechnological potential of thermophilic

Pande S., Kost C. (2017). Bacterial unculturability and the formation of intercellular metabolic networks. Trends Microbiol. 25, 349–361. doi: 10.1016/j.tim.2017.02.015, PMID: PubMed DOI

Papik J., Folkmanova M., Polivkova M., Suman J., Uhlik O. (2020). The invisible life inside plants: deciphering the riddles of endophytic bacterial diversity. Biotechnol. Adv. 44:107614. doi: 10.1016/j.biotechadv.2020.107614, PMID: PubMed DOI

Parte A. C., Carbasse J. S., Meier-Kolthoff J. P., Reimer L. C., Göker M. (2020). List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int. J. Syst. Evol. Microbiol. 70, 5607–5612. doi: 10.1099/ijsem.0.004332, PMID: PubMed DOI PMC

Pascoal F., Magalhães C., Costa R. (2020). The link between the ecology of the prokaryotic rare biosphere and its biotechnological potential. Front. Microbiol. 11:231. doi: 10.3389/fmicb.2020.00231 PubMed DOI PMC

Pascual J., García-López M., Carmona C., Sousa Tda S., de Pedro N., Cautain B., et al. (2014). PubMed DOI

Pascual J., García-López M., González I., Genilloud O. (2017). PubMed DOI

Pathak A., Jaswal R., Xu X., White J. R., Edwards B., 3rd, Hunt J., et al. (2020). Characterization of bacterial and fungal assemblages from historically contaminated metalliferous soils using metagenomics coupled with diffusion chambers and microbial traps. Front. Microbiol. 11:1024. doi: 10.3389/fmicb.2020.01024, PMID: PubMed DOI PMC

Pernthaler J., Pernthaler A., Amann R. (2003). Automated enumeration of groups of marine picoplankton after fluorescence in situ hybridization. Appl. Environ. Microbiol. 69, 2631–2637. doi: 10.1128/AEM.69.5.2631-2637.2003, PMID: PubMed DOI PMC

Pinto D., Almeida V., Almeida Santos M., Chambel L. (2011). Resuscitation of PubMed DOI

Pinto D., Santos M. A., Chambel L. (2015). Thirty years of viable but nonculturable state research: unsolved molecular mechanisms. Crit. Rev. Microbiol. 41, 61–76. doi: 10.3109/1040841X.2013.794127, PMID: PubMed DOI

Pinto D., São-José C., Santos M. A., Chambel L. (2013). Characterization of two resuscitation promoting factors of PubMed DOI

Power J. F., Carere C. R., Lee C. K., Wakerley G. L. J., Evans D. W., Button M., et al. (2018). Microbial biogeography of 925 geothermal springs in New Zealand. Nat. Commun. 9:2876. doi: 10.1038/s41467-018-05020-y, PMID: PubMed DOI PMC

Pudasaini S., Wilson J., Ji M., van Dorst J., Snape I., Palmer A. S., et al. (2017). Microbial diversity of Browning peninsula, eastern Antarctica revealed using molecular and cultivation methods. Front. Microbiol. 8:591. doi: 10.3389/fmicb.2017.00591, PMID: PubMed DOI PMC

Pulschen A. A., Bendia A. G., Fricker A. D., Pellizari V. H., Galante D., Rodrigues F. (2017). Isolation of uncultured bacteria from Antarctica using long incubation periods and low nutritional media. Front. Microbiol. 8:1346. doi: 10.3389/fmicb.2017.01346, PMID: PubMed DOI PMC

Puspita I. D., Kamagata Y., Tanaka M., Asano K., Nakatsu C. H. (2012). Are uncultivated bacteria really uncultivable? Microbes Environ. 27, 356–366. doi: 10.1264/jsme2.ME12092, PMID: PubMed DOI PMC

Rahman I., Shahamat M., Kirchman P., Russek-Cohen E., Colwell R. (1994). Methionine uptake and cytopathogenicity of viable but nonculturable PubMed DOI PMC

Rappé M. S., Connon S. A., Vergin K. L., Giovannoni S. J. (2002). Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630. doi: 10.1038/nature00917, PMID: PubMed DOI

Ratzke C., Gore J. (2018). Modifying and reacting to the environmental pH can drive bacterial interactions. PLoS Biol. 16:e2004248. doi: 10.1371/journal.pbio.2004248, PMID: PubMed DOI PMC

Remenár M., Karelová E., Harichová J., Zámocký M., Kamlárová A., Ferianc P. (2015). Isolation of previously uncultivable bacteria from a nickel contaminated soil using a diffusion-chamber-based approach. Appl. Soil Ecol. 95, 115–127. doi: 10.1016/j.apsoil.2015.06.013 DOI

Ren B., Hu Y., Chen B., Zhang Y., Thiele J., Shi R., et al. (2018). Soil pH and plant diversity shape soil bacterial community structure in the active layer across the latitudinal gradients in continuous permafrost region of northeastern China. Sci. Rep. 8:5619. doi: 10.1038/s41598-018-24040-8, PMID: PubMed DOI PMC

Ren L., Jeppesen E., He D., Wang J., Liboriussen L., Xing P., et al. (2015). pH influences the importance of niche-related and neutral processes in lacustrine bacterioplankton assembly. Appl. Environ. Microbiol. 81, 3104–3114. doi: 10.1128/AEM.04042-14, PMID: PubMed DOI PMC

Rettedal E. A., Gumpert H., Sommer M. O. A. (2014). Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria. Nat. Commun. 5:4714. doi: 10.1038/ncomms5714, PMID: PubMed DOI

Řezanka T., Gharwalová L., Nováková G., Kolouchová I., Uhlík O., Sigler K. (2019). PubMed DOI

Rice S. A., McDougald D., Kjelleberg S. (2000). PubMed DOI

Rosero-Chasoy G., Rodríguez-Jasso R. M., Aguilar C. N., Buitrón G., Chairez I., Ruiz H. A. (2021). Microbial co-culturing strategies for the production high value compounds, a reliable framework towards sustainable biorefinery implementation – an overview. Bioresour. Technol. 321:124458. doi: 10.1016/j.biortech.2020.124458, PMID: PubMed DOI

Rosselló-Móra R., Amann R. (2015). Past and future species definitions for PubMed DOI

Rousk J., Bååth E., Brookes P. C., Lauber C. L., Lozupone C., Caporaso J. G., et al. (2010). Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4, 1340–1351. doi: 10.1038/ismej.2010.58, PMID: PubMed DOI

Sangwan P., Kovac S., Davis K. E. R., Sait M., Janssen P. H. (2005). Detection and cultivation of soil PubMed DOI PMC

Schink B. (2002). Synergistic interactions in the microbial world. Antonie Van Leeuwenhoek 81, 257–261. doi: 10.1023/A:1020579004534, PMID: PubMed DOI

Schneider Y. K.-H., Ø Hansen K., Isaksson J., Ullsten S., H Hansen E., Hammer Andersen J. (2019). Anti-bacterial effect and cytotoxicity assessment of lipid 430 isolated from PubMed DOI PMC

Seeger S., Monajembashi S., Hutter K. J., Futterman G., Wolfrum J., Greulich K. (1991). Application of laser optical tweezers in immunology and molecular genetics. Cytom. J. Int. Soc. Anal. Cytol 12, 497–504. doi: 10.1002/cyto.990120606, PMID: PubMed DOI

Senoh M., Ghosh-Banerjee J., Ramamurthy T., Hamabata T., Kurakawa T., Takeda M., et al. (2010). Conversion of viable but nonculturable PubMed DOI

Sessitsch A., Weilharter A., Gerzabek M. H., Kirchmann H., Kandeler E. (2001). Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl. Environ. Microbiol. 67, 4215–4224. doi: 10.1128/AEM.67.9.4215-4224.2001, PMID: PubMed DOI PMC

Sexton D. L., St-Onge R. J., Haiser H. J., Yousef M. R., Brady L., Gao C., et al. (2015). Resuscitation-promoting factors are cell wall-lytic enzymes with important roles in the germination and growth of PubMed DOI PMC

Shah I. M., Dworkin J. (2010). Induction and regulation of a secreted peptidoglycan hydrolase by a membrane Ser/Thr kinase that detects muropeptides. Mol. Microbiol. 75, 1232–1243. doi: 10.1111/j.1365-2958.2010.07046.x, PMID: PubMed DOI

Shleeva M., Mukamolova G. V., Young M., Williams H. D., Kaprelyants A. S. (2004). Formation of ‘non-culturable’cells of PubMed DOI

Signoretto C., del Mar L. M., Tafi M. C., Canepari P. (2000). Cell wall chemical composition of PubMed DOI PMC

Smrhova T., Jani K., Pajer P., Kapinusova G., Vylita T., Suman J., et al. (2022). Prokaryotes of renowned Karlovy Vary (Carlsbad) thermal springs: phylogenetic and cultivation analysis. Environ. Microbiol. 17:48. doi: 10.1186/s40793-022-00440-2, PMID: PubMed DOI PMC

Song W., Kim M., Tripathi B. M., Kim H., Adams J. M. (2016). Predictable communities of soil bacteria in relation to nutrient concentration and successional stage in a laboratory culture experiment. Environ. Microbiol. 18, 1740–1753. doi: 10.1111/1462-2920.12879, PMID: PubMed DOI

Srikanth S., Dubey S. K., Javed A., Goel S. (2021). Droplet based microfluidics integrated with machine learning. Sens Actuator A Phys. 332:113096. doi: 10.1016/j.sna.2021.113096, PMID: DOI

Staley J. T., Konopka A. (1985). Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39, 321–346. doi: 10.1146/annurev.mi.39.100185.001541, PMID: PubMed DOI

Steele J. A., Countway P. D., Xia L., Vigil P. D., Beman J. M., Kim D. Y., et al. (2011). Marine bacterial, archaeal and protistan association networks reveal ecological linkages. ISME J. 5, 1414–1425. doi: 10.1038/ismej.2011.24, PMID: PubMed DOI PMC

Steiner P. A., Geijo J., Fadeev E., Obiol A., Sintes E., Rattei T., et al. (2020). Functional seasonality of free-living and particle-associated prokaryotic communities in the coastal Adriatic Sea. Front. Microbiol. 11:584222. doi: 10.3389/fmicb.2020.584222, PMID: PubMed DOI PMC

Stewart E. J. (2012). Growing unculturable bacteria. J. Bacteriol. 194, 4151–4160. doi: 10.1128/JB.00345-12, PMID: PubMed DOI PMC

Strejcek M., Smrhova T., Junkova P., Uhlik O. (2018). Whole-cell MALDI-TOF MS versus 16S rRNA gene analysis for identification and dereplication of recurrent bacterial isolates. Front. Microbiol. 9:1294. doi: 10.3389/fmicb.2018.01294, PMID: PubMed DOI PMC

Sturm A., Dworkin J. (2015). Phenotypic diversity as a mechanism to exit cellular dormancy. Curr. Biol. 25, 2272–2277. doi: 10.1016/j.cub.2015.07.018, PMID: PubMed DOI PMC

Su X., Li S., Xie M., Tao L., Zhou Y., Xiao Y., et al. (2021). Enhancement of polychlorinated biphenyl biodegradation by resuscitation promoting factor (Rpf) and Rpf-responsive bacterial community. Chemosphere 263:128283. doi: 10.1016/j.chemosphere.2020.128283, PMID: PubMed DOI

Su X., Shen H., Yao X., Ding L., Yu C., Shen C. (2013). A novel approach to stimulate the biphenyl-degrading potential of bacterial community from PCBs-contaminated soil of e-waste recycling sites. Bioresour. Technol. 146, 27–34. doi: 10.1016/j.biortech.2013.07.028, PMID: PubMed DOI

Su X., Wang Y., Xue B., Zhang Y., Mei R., Zhang Y., et al. (2018). Resuscitation of functional bacterial community for enhancing biodegradation of phenol under high salinity conditions based on Rpf. Bioresour. Technol. 261, 394–402. doi: 10.1016/j.biortech.2018.04.048, PMID: PubMed DOI

Su X., Zhang Q., Hu J., Hashmi M. Z., Ding L., Shen C. (2015). Enhanced degradation of biphenyl from PCB-contaminated sediments: the impact of extracellular organic matter from PubMed DOI

Suman J., Zubrova A., Rojikova K., Pechar R., Svec P., Cajthaml T., et al. (2019). PubMed DOI

Sun J., Guo J., Yang Q., Huang J. (2019). Diluted conventional media improve the microbial cultivability from aquarium seawater. J. Microbiol. 57, 759–768. doi: 10.1007/s12275-019-9175-7, PMID: PubMed DOI

Sussman A. S., Halvorson H. O. Spores: their dormancy and germination, New York and London: Harper & Row.; (1966) 356.

Sylvain F.-É., Cheaib B., Llewellyn M., Gabriel Correia T., Barros Fagundes D., Luis Val A., et al. (2016). pH drop impacts differentially skin and gut microbiota of the Amazonian fish tambaqui ( PubMed DOI PMC

Tahon G., Willems A. (2017). Isolation and characterization of aerobic anoxygenic phototrophs from exposed soils from the Sør Rondane Mountains, East Antarctica. Syst. Appl. Microbiol. 40, 357–369. doi: 10.1016/j.syapm.2017.05.007, PMID: PubMed DOI

Tamaki H., Tanaka Y., Matsuzawa H., Muramatsu M., Meng X. Y., Hanada S., et al. (2011). PubMed DOI

Tamames J., Rosselló-Móra R. (2012). On the fitness of microbial taxonomy. Trends Microbiol. 20, 514–516. doi: 10.1016/j.tim.2012.08.012, PMID: PubMed DOI

Tanaka T., Kawasaki K., Daimon S., Kitagawa W., Yamamoto K., Tamaki H., et al. (2014). A hidden pitfall in the preparation of agar media undermines microorganism cultivability. Appl. Environ. Microbiol. 80, 7659–7666. doi: 10.1128/AEM.02741-14, PMID: PubMed DOI PMC

Tandogan N., Abadian P. N., Epstein S., Aoi Y., Goluch E. D. (2014). Isolation of microorganisms using sub-micrometer constrictions. PLoS One 9:e101429. doi: 10.1371/journal.pone.0101429, PMID: PubMed DOI PMC

Tewari Kumar P., Decrop D., Safdar S., Passaris I., Kokalj T., Puers R., et al. (2020). Digital microfluidics for single bacteria capture and selective retrieval using optical tweezers. Micromachines 11:308. doi: 10.3390/mi11030308, PMID: PubMed DOI PMC

Thompson J. N. (2020). “Population ecology” in Encyclopedia Britannica. Available at: https://www.britannica.com/science/population-ecology (Accessed November 18, 2020).

Tripathi B. M., Stegen J. C., Kim M., Dong K., Adams J. M., Lee Y. K. (2018). Soil pH mediates the balance between stochastic and deterministic assembly of bacteria. ISME J. 12, 1072–1083. doi: 10.1038/s41396-018-0082-4, PMID: PubMed DOI PMC

Turnbaugh P. J., Ley R. E., Hamady M., Fraser-Liggett C. M., Knight R., Gordon J. I. (2007). The human microbiome project. Nature 449, 804–810. doi: 10.1038/nature06244, PMID: PubMed DOI PMC

Uhlik O., Leewis M.-C., Strejcek M., Musilova L., Mackova M., Leigh M. B., et al. (2013). Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation. Biotechnol. Adv. 31, 154–165. doi: 10.1016/j.biotechadv.2012.09.003, PMID: PubMed DOI PMC

Vallejo Esquerra E., Yang H., Sanchez S. E., Omsland A. (2017). Physicochemical and nutritional requirements for axenic replication suggest physiological basis for PubMed DOI PMC

van Dorst J. M., Hince G., Snape I., Ferrari B. C. (2016). Novel culturing techniques select for heterotrophs and hydrocarbon degraders in a subantarctic soil. Sci. Rep. 6:36724. doi: 10.1038/srep36724, PMID: PubMed DOI PMC

Versluis D., de J Bello González T., Zoetendal E. G., Passel M. W. J. V., Smidt H. (2019). High throughput cultivation-based screening on porous aluminum oxide chips allows targeted isolation of antibiotic resistant human gut bacteria. PLoS One 14:e0210970. doi: 10.1371/journal.pone.0210970, PMID: PubMed DOI PMC

Wang C., Bendle J., Yang Y., Yang H., Sun H., Huang J., et al. (2016). Impacts of pH and temperature on soil bacterial 3-hydroxy fatty acids: development of novel terrestrial proxies. Org. Geochem. 94, 21–31. doi: 10.1016/j.orggeochem.2016.01.010 DOI

Watterson W. J., Tanyeri M., Watson A. R., Cham C. M., Shan Y., Chang E. B., et al. (2020). Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes. eLife 9:e56998. doi: 10.7554/eLife.56998, PMID: PubMed DOI PMC

Watve M., Shejval V., Sonawane C., Rahalkar M., Matapurkar A., Shouche Y., et al. (2000). The 'K' selected oligophilic bacteria: a key to uncultured diversity? Curr. Sci. 78, 1535–1542.

Whitman W. B., Chuvochina M., Hedlund B. P., Hugenholtz P., Konstantinidis K. T., Murray A. E., et al. (2022). Development of the SeqCode: a proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type. Syst. Appl. Microbiol. 45:126305. doi: 10.1016/j.syapm.2022.126305, PMID: PubMed DOI PMC

Wilson L., Iqbal K. M., Simmons-Ehrhardt T., Bertino M. F., Shah M. R., Yadavalli V. K., et al. (2019). Customizable 3D printed diffusion chambers for studies of bacterial pathogen phenotypes in complex environments. J. Microbiol. Methods 162, 8–15. doi: 10.1016/j.mimet.2019.05.002, PMID: PubMed DOI

Wirth J. S., Whitman W. B. (2018). Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera PubMed DOI

Woese C. R. (1992). “Prokaryote systematics: the evolution of a science” in The Prokayotes. eds. A. Balows, H. G. Trüper, M. Dworkin, W. Harder and K-H. Schleifer (New York, NY: Springer), 3–18.

Wood T. K., Knabel S. J., Kwan B. W. (2013). Bacterial persister cell formation and dormancy. Appl. Environ. Microbiol. 79, 7116–7121. doi: 10.1128/AEM.02636-13, PMID: PubMed DOI PMC

Wu X., Spencer S., Gushgari-Doyle S., Yee M. O., Voriskova J., Li Y., et al. (2020). Culturing of “unculturable” subsurface microbes: natural organic carbon source fuels the growth of diverse and distinct bacteria from groundwater. Front. Microbiol. 11:610001. doi: 10.3389/fmicb.2020.610001, PMID: PubMed DOI PMC

Wurch L., Giannone R. J., Belisle B. S., Swift C., Utturkar S., Hettich R. L., et al. (2016). Genomics-informed isolation and characterization of a symbiotic PubMed DOI PMC

Xian W.-D., Salam N., Li M.-M., Zhou E.-M., Yin Y.-R., Liu Z.-T., et al. (2020). Network-directed efficient isolation of previously uncultivated PubMed DOI PMC

Xu B., Hu B., Wang J., Lan Y., Zhu Y., Dai X., et al. (2018). PubMed DOI

Xu H.-S., Roberts N., Singleton F. L., Attwell R. W., Grimes D. J., Colwell R. R. (1982). Survival and viability of nonculturable PubMed DOI

Xu R., Zhang K., Liu P., Han H., Zhao S., Kakade A., et al. (2018). Lignin depolymerization and utilization by bacteria. Bioresour. Technol. 269, 557–566. doi: 10.1016/j.biortech.2018.08.118, PMID: PubMed DOI

Yasumoto-Hirose M., Nishijima M., Ngirchechol M. K., Kanoh K., Shizuri Y., Miki W. (2006). Isolation of marine bacteria by in situ culture on media-supplemented polyurethane foam. Mar. Biotechnol. 8, 227–237. doi: 10.1007/s10126-005-5015-3, PMID: PubMed DOI

Zang E., Brandes S., Tovar M., Martin K., Mech F., Horbert P., et al. (2013). Real-time image processing for label-free enrichment of PubMed DOI

Zengler K., Toledo G., Rappé M., Elkins J., Mathur E. J., Short J. M., et al. (2002). Cultivating the uncultured. Proc. Natl. Acad. Sci. U. S. A. 99, 15681–15686. doi: 10.1073/pnas.252630999, PMID: PubMed DOI PMC

Zengler K., Walcher M., Clark G., Haller I., Toledo G., Holland T., et al. (2005). High-throughput cultivation of microorganisms using microcapsules. Methods Enzymol. 397, 124–130. doi: 10.1016/S0076-6879(05)97007-9, PMID: PubMed DOI

Zhang Y. (2014). Persisters, persistent infections and the Yin–Yang model. Emerg Microbes Infect 3, 1–10. doi: 10.1038/emi.2014.3 PubMed DOI PMC

Zhang X.-H., Ahmad W., Zhu X.-Y., Chen J., Austin B. (2021). Viable but nonculturable bacteria and their resuscitation: implications for cultivating uncultured marine microorganisms. Mar. Life Sci. Technol. 3, 189–203. doi: 10.1007/s42995-020-00041-3 PubMed DOI PMC

Zhang L., Chen P., Zhou Z., Hu Y., Sha Q., Zhang H., et al. (2019). Agarose-based microwell array chip for high-throughput screening of functional microorganisms. Talanta 191, 342–349. doi: 10.1016/j.talanta.2018.08.090, PMID: PubMed DOI

Zhang A., Sun H., Wang P., Han Y., Wang X. (2012). Modern analytical techniques in metabolomics analysis. Analyst 137, 293–300. doi: 10.1039/C1AN15605E, PMID: PubMed DOI

Zhou N., Sun Y. T., Chen D. W., Du W., Yang H., Liu S. J. (2019). Harnessing microfluidic streak plate technique to investigate the gut microbiome of PubMed DOI PMC

Najít záznam

Citační ukazatele

Pouze přihlášení uživatelé

Možnosti archivace

Nahrávání dat ...