Skip to main content
SpringerLink
Log in

Microbial cultivation and the role of microbial resource centers in the omics era

  • Mini-Review
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

Despite tremendous advances in microbial ecology over the past two decades, traditional cultivation methods have failed to grow ecologically more relevant microorganisms in the laboratory, leading to a predominance of weed-like species in the world’s culture collections. In this review, we highlight the gap between culture-based and culture-independent methods of microbial diversity analysis, especially in investigations of slow growers, oligotrophs, and fastidious and recalcitrant microorganisms. Furthermore, we emphasize the importance of microbial cultivation and the acquisition of the cultivation-based phenotypic data for the testing of hypotheses arising from genomics and proteomics approaches. Technical difficulties in cultivating novel microorganisms and how modern approaches have helped to overcome these limitations are highlighted. After cultivation, adequate preservation without changes in genotypic and phenotypic features of these microorganisms is necessary for future research and training. Hence, the contribution of microbial resource centers in the handling, preservation, and distribution of this novel diversity is discussed. Finally, we explore the concept of microbial patenting and requisite guidelines of the “Budapest Treaty” for establishment of an International Depositary Authority.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Alain K, Querellou J (2009) Cultivating the uncultured: limits, advances and future challenges. Extremophiles 13:583–594

    Article  Google Scholar 

  • Amann R (2000) Who is out there? Microbial aspects of diversity. Syst Appl Microbiol 23:1–8

    Article  CAS  Google Scholar 

  • Arrigo K (2005) Marine microorganisms and global nutrient cycles. Nature 437:349–355

    Article  CAS  Google Scholar 

  • Bent SJ, Forney LJ (2008) The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. ISME J 2:689–695

    Article  CAS  Google Scholar 

  • Bouzas TD, Barros-Velazquez J, Villa TG (2006) Industrial applications of hyperthermophilic enzymes: a review. Prot Pept Lett 13:445–451

    Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Cardenas E, Tiedje JM (2008) New tools for discovering and characterizing microbial diversity. Curr Opin Biotechnol 19:544–549

    Article  CAS  Google Scholar 

  • Challis G, Hopwood DA (2003) Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species. Proc Natl Acad Sci U S A 2:14555–14561

    Article  Google Scholar 

  • Chen GQ, Wu Q (2005) The application of polyhydroxyalkanoates as tissue engineering materials. Biomaterials 26:6565–6578

    Article  CAS  Google Scholar 

  • Coenye T, Vandamme P (2004) Bacterial whole-genome sequences: minimal information and strain availability. Microbiology 150:2017–2018

    Article  CAS  Google Scholar 

  • Colwell RR (1997) Microbial diversity: the importance of exploration and conservation. J Ind Microbiol Biotechnol 18:302–307

    Article  CAS  Google Scholar 

  • Connon SA, Giovannoni SJ (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new many isolates. Appl Environ Microbiol 68:3878–3885

    Google Scholar 

  • Cypess R (2003) Biological resource centers: from concept to reality. American Type Culture Collection, Manassas, VA.

  • Davis KE, Joseph SJ, Janssen PH (2005) Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl Environ Microb 71:826–834

    Article  CAS  Google Scholar 

  • Donachie SP, Foster JS, Brown MV (2007) Culture clash: challenging the dogma of microbial diversity. ISME J 1:97–99

    Article  Google Scholar 

  • Dorit R (2008) All things small and great. Am Sci 96:284–286

    Article  Google Scholar 

  • Emerson D, Wilson W (2009) Giving microbial diversity a home. Nat Rev Microbiol 7:758

    Article  CAS  Google Scholar 

  • Endy D (2005) Foundations for engineering biology. Nature 438:449–453

    Article  CAS  Google Scholar 

  • Ferrari B, Gillings MR (2009) Cultivation of fastidious bacteria by viability staining and micromanipulation in a soil substrate membrane system. Appl Environ Microbiol 75:3352–3354

    Article  CAS  Google Scholar 

  • Ferrari B, Winsley T, Gillings M, Binnerup S (2008) Cultivating previously uncultured soil bacteria using a soil substrate membrane system. Nat Protoc 3:1261–1269

    Article  CAS  Google Scholar 

  • Field D, Hughes J (2005) Cataloguing our current genome collection. Microbiology 151:1016–1019

    Article  Google Scholar 

  • Fritze D (1994) Patent aspects of the convention at the microbial level. In: Kirsop B, Hawksworth DL (eds) The biodiversity of micro-organisms and the role of microbial resource centres. World Federation of Culture Collections, Braunschweig, pp 37–43

    Google Scholar 

  • Frohlich J, Konig H (2000) New techniques for isolation of single prokaryotic cells. FEMS Microbiol Rev 24:567–572

    Article  CAS  Google Scholar 

  • Fry J (2000) Bacterial diversity and unculturables. Microbiol Today 27:186–188

    Google Scholar 

  • Gest H (2001) Evolution of knowledge encapsulated in scientific definitions. Persp Biol Med 44:556–564

    Article  CAS  Google Scholar 

  • Gest H (2008; posting date). The modern myth of “unculturable” bacteria/scotoma of contemporary microbiology. http://hdl.handle.net/2022/3149

  • Giovannoni S, Stingl U (2007) The importance of culturing bacterioplankton in the “omics” age. Nat Rev Microbiol 5:820–826

    Article  CAS  Google Scholar 

  • Giovannoni SJ, Foster RA, Rappe MS, Epstein S (2007) New cultivation strategies bring more microbial plankton species into the laboratory. Oceanography 20:62–69

    Article  Google Scholar 

  • Gírio FM, Fonseca C, Carvalheiro F, Duarte LC, Marques S, Bogel-Łukasik R (2010) Hemicelluloses for fuel ethanol: a review. Bioresour Technol 13:4775–4800

    Article  Google Scholar 

  • Gordon RF, Stein MA, Diedrich DI (1993) Heat shock induced axenic growth of Bdellovibrio bacteriovorus. J Bacteriol 175:2157–2161

    CAS  Google Scholar 

  • Green SJ, Prakash O, Akob DM, Gihring TM, Jardin P, Watson DB, Kostka JE (2010) Denitrifying bacteria isolated from terrestrial subsurface sediment exposed to mixed contamination. Appl Environ Microbiol 76:3244–3254

    Article  CAS  Google Scholar 

  • Gupta R, Beg QK, Lorenz P (2002) Bacterial alkaline proteases: molecular approaches and industrial applications. Appl Microbiol Biotechnol 59:15–32

    Article  CAS  Google Scholar 

  • Hahn MW, Stadler P, Wu QL, Pockl M (2004) The filtration-acclimatization method for isolation of an important fraction of the not readily cultivable bacteria. J Microbiol Meth 57:379–390

    Article  CAS  Google Scholar 

  • Heylen K, Hoefman S, Vekeman B, Peiren J, De Vos P (2012) Safeguarding bacterial resources promotes biotechnological innovation. Appl Microbiol Biotechnol 94:565–574

    Article  CAS  Google Scholar 

  • Huber R, Burggraf S, Mayer T, Barns SM, Rossnagel P, Stetter KO (1995) Isolation of a hyperthermophilic archaeum predicted by in situ RNA analysis. Nature 376:57–58

    Article  CAS  Google Scholar 

  • Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO (2002) A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nat 417:27–28

    Google Scholar 

  • Hughes DT, Sperandio V (2008) Inter-kingdom signaling: communication between bacteria and their hosts. Nat Rev Microbiol 6:111–120

    Article  CAS  Google Scholar 

  • Ingham CJ, Sprenkels A, Bomer J, Molenaar D, van den Berg A, van Hylckama Vlieg JE, de Vos WM (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

    Article  CAS  Google Scholar 

  • Janssens D, Arahal DR, Bizet C, Garay E (2010) The role of public biological resource centers in providing a basic infrastructure for microbial research. Res Microbiol 161:422–429

    Article  Google Scholar 

  • Joseph S, Hugenholtz P, Sangwan P, Osborne CA, Janssen PH (2003) Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69:7210–7215

    Article  CAS  Google Scholar 

  • Kaeberlein T, Lewis K, Epstein SS (2002) Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296:1227–1229

    Article  Google Scholar 

  • Kamagata Y, Fulthorpe RR, Tamura K, Takami H, Forney LJ, Tiedje JM (1997) Pristine environments harbor a new group of oligotrophic 2,4-dichlorophenoxyacetic acid-degrading bacteria. Appl Environ Microbiol 63:2266–2272

    Google Scholar 

  • Kamagata Y, Tamaki H (2005) Cultivation of uncultured fastidious microbes. Microbes Environ 20:85–91

    Article  Google Scholar 

  • Keller M, Zengler K (2004) Tapping into microbial diversity. Nat Rev Microbiol 2:141–150

    Article  CAS  Google Scholar 

  • Kelley J, Smith D (1997) Depositing micro-organisms as part of the patenting process. Ballantyne Ross Ltd, London

    Google Scholar 

  • Kim JJ, Kim HN, Masui R, Kuramitsu S, Seo JH, Kim K, Sung MH (2008) Isolation of uncultivable anaerobic thermophiles of the family Clostridiaceae requiring growth-supporting factors. J Microbiol Biotechn 18:611–615

    CAS  Google Scholar 

  • Köpke B, Wilms R, Engelen B, Cypionka H, Sass H (2005) Microbial diversity in coastal subsurface sediments: a cultivation approach using various electron acceptors and substrate gradients. Appl Environ Microbiol 71:7819–7830

    Article  Google Scholar 

  • Kostka JE, Prakash O, Overholt W, Green S, Freyer G, Canion A, Delgardio J, Norton N, Huettel M (2011) Hydrocarbon-degrading bacteria and the bacterial community response in Gulf of Mexico beach sands impacted by the Deepwater Horizon oil spill. Appl Environ Microbiol 77:7962–7797

    Article  CAS  Google Scholar 

  • Kuske C, Ticknor LO, Miller ME, Dunbar JM, Davis JA, Barns SM, Belnap J (2002) Comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland. Appl Environ Microbiol 68:1854–1863

    Article  CAS  Google Scholar 

  • Labeda DP, Oren A (2008) International Committee on Systematics of Prokaryotes; XIth International (IUMS) Congress of Microbiology and Applied Bacteriology, Minutes of the meetings, 23, 24, 26 and 28 July 2005, San Francisco, CA, USA. Int J Syst Evol Microbiol (58):1746–1752

  • Lal R, Pandey G, Sharma P, Kumari K, Malhotra S, Pandey R, Raina V, Kohler HP, Holliger C, Jackson C, Oakeshott JG (2010) Biochemistry of microbial degradation of hexachlorocyclohexane and prospects for bioremediation. Microbiol Mol Biol Rev 74:58–80

    Article  CAS  Google Scholar 

  • Leadbetter JR (2003) Cultivation of recalcitrant microbes: cells are alive, well and revealing their secrets in the 21st century laboratory. Curr Opin Microbiol 6:274–281

    Article  CAS  Google Scholar 

  • Lewis N, Nagarajan H, Palsson BO (2012) Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol 10:291–305

    CAS  Google Scholar 

  • Lomax AR, Calder PC (2009) Prebiotics, immune function, infection and inflammation: a review of the evidence. Br J Nutr 101:633–658

    Article  CAS  Google Scholar 

  • Lovley DR (2006) Bug juice: harvesting electricity with microorganisms. Nat Rev Microbiol 4:497–508

    Article  CAS  Google Scholar 

  • Lupp C (2007) Host–microbes interactions. Nature 449:830

    Article  Google Scholar 

  • Malik KA, Claus D (1987) Bacterial culture collections: their importance to biotechnology and microbiology. Biotechnol Genet Eng Rev 5:137–197

    CAS  Google Scholar 

  • Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31–46

    Article  CAS  Google Scholar 

  • Morales SE, Holben WE (2011) Linking bacterial identities and ecosystem processes: can ‘omic’ analyses be more than the sum of their parts? FEMS Microbiol Ecol 75:2–16

    Article  CAS  Google Scholar 

  • Nichols D, Lewis K, Orjala J, Mo S, Ortenberg R, O’Connor P, Zhao C, Vouros P, Kaeberlein T, Epstein SS (2008) Short peptide induces an ‘uncultivable’ microorganism to grow in vitro. Appl Environ Microb 74:4889–4897

    Article  CAS  Google Scholar 

  • Ogawa J, Shimizu S (2002) Industrial microbial enzymes: their discovery by screening and use in large-scale production of useful chemicals in Japan. Curr Opin Biotechno 13:367–375

    Article  CAS  Google Scholar 

  • Ohno M, Okano I, Watsuji T, Kakinuma T, Ueda K, Beppu T (1999) Establishing the independent culture of a strictly symbiotic bacterium Symbiobacterium thermophilum from its supporting Bacillus strain. Biosci Biotechnol Biochem 63:1083–1090

    Article  CAS  Google Scholar 

  • Overmann J (2006) Principal of enrichment, isolation, cultivation and preservation of prokaryotes. Prokaryotes 1:80–136

    Article  Google Scholar 

  • Palleroni NJ (1997) Prokaryotic diversity and the importance of culturing. Antonie Van Leeuwenhoek 72:3–19

    Article  CAS  Google Scholar 

  • Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic JM (2009) Pyrosequencing and microbial identification. Clin Chem 5:856–866

    Article  Google Scholar 

  • Pham VH, Kim J (2012) Cultivation of unculturable soil bacteria. Trends Biotechnol 30:475–484

    Article  CAS  Google Scholar 

  • Prakash O, Nimonkar Y, Shouche YS (2012) Practice and prospects of microbial preservation. FEMS Microbiol Lett. doi:10:1111/1574-6968

  • Rappe MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633

    Article  CAS  Google Scholar 

  • Rawlings DE, Silver S (1995) Mining with microbes. Nat Biotechnol 13:773–778

    Article  CAS  Google Scholar 

  • Saeki K, Ozaki K, Kobayashi T, Ito S (2007) Detergent alkaline proteases: enzymatic properties, genes, and crystal structures. J Biosci Bioeng 103:501–508

    Article  CAS  Google Scholar 

  • Sekar S, Kandavel D (2004) The future of patent deposition of microorganisms? Trends Biotechnol 22:213–218

    Article  CAS  Google Scholar 

  • Senni K, Pereira J, Gueniche F, Delbarre-Ladrat C, Sinquin C, Ratiskol J, Godeau G, Fischer AM, Helley D, Sylvia CJ (2011) Marine polysaccharides: a source of bioactive molecules for cell therapy and tissue engineering. Mar Drugs 9:1664–1681

    Article  CAS  Google Scholar 

  • Singh BK, Richard D, Smith BP, Reay DS (2010) Microorganisms and climate change: terrestrial feedbacks and mitigation options. Nat Rev Microbiol 8:779–790

    Article  CAS  Google Scholar 

  • Song J, Oh HM, Cho JC (2009) Improved culturability of SAR11 strains in dilution-to-extinction culturing from the East Sea, West Pacific Ocean. FEMS Microbiol Lett 295:141–147

    Article  CAS  Google Scholar 

  • Stackebrandt E (2011) Towards a strategy to enhance access to microbial diversity. Int J Syst Evol Microbiol 61:479–481

    Google Scholar 

  • Stern S (2004) Biological resource centers: knowledge hubs for the life sciences. Brookings Institution Press, Washington (DC)

    Google Scholar 

  • Stevenson BS, Eichorst SA, Wertz JT, Schmidt TM, Breznak JA (2004) New strategies for cultivation and detection of previously uncultured microbe. Appl Environ Microbiol 70:4748–4755

    Article  CAS  Google Scholar 

  • Stewart EJ (2012) Growing unculturable bacteria. J Bacteriol 194:4151–4160

    Article  CAS  Google Scholar 

  • Tripp HJ, Kitner JB, Schwalbach MS, Dacey JW, Wilhelm LJ, Giovannoni SJ (2008) SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452:741–744

    Article  CAS  Google Scholar 

  • Tyson GW, Banfield JF (2005) Cultivating the uncultivated: a community genomics perspective. Trends Microbiol 9:411–415

    Article  Google Scholar 

  • Unsworth LD, van der Oost J, Koutsopoulos S (2007) Hyperthermophilic enzymes—stability, activity and implementation strategies for high temperature applications. FEBS J 274:4044–4056

    Article  CAS  Google Scholar 

  • Verlindin RA, Hill DJ, Kenward MA, Williams CD, Radecka I (2007) Bacterial synthesis of biodegradable polyhydroxyalkanoates. J Appl Microbiol 102:1437–1449

    Article  Google Scholar 

  • Walker JCG (1980) The oxygen cycle in the natural environment and the biogeochemical cycles. Springer, Berlin

    Google Scholar 

  • Ward N, Eisen J, Fraser C, Stackebrandt E (2001) Sequenced strains must be saved from extinction. Nature 414:148

    Article  CAS  Google Scholar 

  • Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95:6578–6583

    Article  Google Scholar 

  • Zaidi A, Khan MS, Ahemad M, Oves M (2009) Plant growth promotion by phosphate solubilizing bacteria. Acta Microbiol Immunol Hung 56:263–284

    Article  CAS  Google Scholar 

  • Zengler K (2009) Central role of the cell in microbial ecology. Microbiol Mol Biol Rev 73:712–729

    Article  CAS  Google Scholar 

  • Zengler K, Palsson BO (2012) A road map for the development of community systems (CoSy) biology. Nat Rev Microbiol 10:366–372

    CAS  Google Scholar 

  • Zengler K, Toledo C, Rappe M, Elkins J, Mathur EJ, Short JM, Keller M (2002) Cultivating the uncultured. Proc Natl Acad Sci U S A 99:15681–15686

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported from the grant no. BT/PR/0054/NDB/52/94/2007 funded by Department of Biotechnology (DBT), Government of India, under the project “Establishment of microbial culture collection.” We are grateful to our colleagues, especially Kiran N. Mahale, and anonymous reviewers for critically reading the manuscript and providing valuable critics and comments for its improvement.

Author information

Authors and Affiliations

  1. Microbial Culture Collection, National Centre for Cell Science, NCCS Complex, Ganeshkhind, Pune, Maharashtra, 411007, India

    Om Prakash, Yogesh Shouche & Kamlesh Jangid

  2. Schools of Biology and Earth and Atmospheric Sciences, Georgia Institute of Technology Atlanta, Atlanta, GA, 30332-0230, USA

    Joel E. Kostka

Authors
  1. Om Prakash
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yogesh Shouche
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kamlesh Jangid
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Joel E. Kostka
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Om Prakash.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Prakash, O., Shouche, Y., Jangid, K. et al. Microbial cultivation and the role of microbial resource centers in the omics era. Appl Microbiol Biotechnol 97, 51–62 (2013). https://doi.org/10.1007/s00253-012-4533-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-012-4533-y

Keywords

Search

Navigation