Skip to main content
Log in

Safeguarding bacterial resources promotes biotechnological innovation

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

Abstract

Environmental research delivers valuable bacterial resources for biotechnology. We believe that systematic long-term preservation of bacteria will promote future biotechnological innovations, by safeguarding the accessibility of bacteria already recognized to have interesting features and providing a “pool” of bacterial resources for novel applied research. To this end, we want to advocate the incorporation of preservation tests in environmental or applied microbiological research. This paper introduces non-specialists to different preservation methods for bacteria. Several parameters that influence long-term storage of bacterial resources are explained and practical tips and guidelines are formulated. Also, the vital role of public culture collections is highlighted and the state-of-the-art of preservation of non-pure cultures is described.

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

Access this article

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

Instant access to the full article PDF.

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Abma W, Schultz C, Mulder J-W, Van Loosdrecht M, Van Der Star W, Strous M, Tokutoimi T (2007) The advance of Anammox. Water 21:36–37

    Google Scholar 

  • Adams G (2007) The principles of freeze-drying. In: Day JG, Stacey GN (eds) Cryopreservation and freeze-drying protocols. Humana Press, Totowa, NJ, pp 15–38

    Chapter  Google Scholar 

  • Alvarez GS, Foglia ML, Copello GJ, Desimone MF, Diaz LE (2009) Effect of various parameters on viability and growth of bacteria immobilized in solgel-derived silica matrices. Appl Microbiol Biotechnol 82:639–646

    Article  CAS  Google Scholar 

  • Bell T, Newman JA, Silverman BW, Turner SL, Lilley AK (2005) The contribution of species richness and composition to bacterial services. Nature 436:1157–1160

    Article  CAS  Google Scholar 

  • Bjerketorp J, Hakansson S, Belkin S, Jansson JK (2006) Advances in preservation methods: keeping biosensor microorganisms alive and active. Curr Opin Biotechnol 17:43–49

    Article  CAS  Google Scholar 

  • Bowman J (2006) The methanotrophs—the families Methylococcaceae and Methylocystaceae. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) Prokaryotes, 3rd edn. Springer, New York, pp 266–289

    Chapter  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 

  • Bryukhanov AL, Netrusov AI (2006) Long-term storage of obligate anaerobic microorganisms in glycerol. Appl Biochem Microbiol 42:177–180

    Article  CAS  Google Scholar 

  • Davey HM (2011) Life, death, and in-between: meanings and methods in microbiology. Appl Environ Microbiol 77:5571–5576

    Article  CAS  Google Scholar 

  • de las Heras A, de Lorenzo V (2011) In situ detection of aromatic compounds with biosensor Pseudomonas putida cells perserved and delivered to soil in water-soluble gelatine capsules. Anal Bioanal Chem 400:1093–1104

    Article  Google Scholar 

  • Dedeurwaerdere T (2010) Global microbial commons: institutional challenges for the global exchange and distribution of microorganisms in the life sciences. Res Microbiol 161:414–421

    Article  Google Scholar 

  • Dijkshoorn L, Vos PD, Dedeurwaerdere T (2010) Understanding patterns of use and scientific opportunities in the emerging global microbial commons. Res Microbiol 16:407–413

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Freiwald A, Sauer S (2009) Phylogenetic classification and identification of bacteria by mass spectrometry. Nat Protoc 4:732–742

    Article  CAS  Google Scholar 

  • Fuller BJ (2004) Cryoprotectants: the essential antifreezes to protect life in the frozen state. CryoLetters 25:375–388

    CAS  Google Scholar 

  • Furman JL, Stern S (2006) Climbing Atop the Shoulders of Giants: The Impact of Institutions on Cumulative Research. NBER Working Paper No. 12523:http://www.nber.org/papers/w12523.pdf

  • Gilbert JA, Hill PJ, Dodd CER, Laybourn-Parry J (2004) Demonstration of antifreeze protein activity in Antarctic lake bacteria. Microbiology 150:171–180

    Article  CAS  Google Scholar 

  • Giugni D, Giugni V (2010) Intellectual property: a powerful tool to develop biotech research. Microb Biotechnol 3:493–506

    Article  Google Scholar 

  • Gorman R, Adley CC (2004) An evaluation of five preservation techniques and conventional freezing temperatures of −20°C and −85°C for long-term preservation of Campylobacter jejuni. Lett Appl Microbiol 38:306–310

    Article  CAS  Google Scholar 

  • Green PN, Woodfor SK (1992) Preservation studies on some obligately methanotrophic bacteria. Lett Appl Microbiol 14:158–162

    Article  Google Scholar 

  • Hays HCW, PAM T, Jones JK, Rayner-Brandes MH (2005) A novel and convenient self-drying system for bacterial preservation. J Microbiol Methods 63:29–35

    Article  Google Scholar 

  • Hottot A, Vessot S, Andrieu J (2007) Freeze drying of pharmaceuticals in vials: influence of freezing protocol and sample configuration on ice morphology and freeze-dried cake texture. Chem Eng Process 46:666–674

    Article  CAS  Google Scholar 

  • Hsia T-H, Feng Y-J, Ho C-M, Chou W-P, Tseng S-K (2008) PVA-alginate immobilized cells for anaerobic ammonium oxidation (anammox) process. J Ind Microbiol Biotechnol 35:721–727

    Article  CAS  Google Scholar 

  • Hubàlek Z (2003) Protectants used in the cryopreservation of microorganisms. Cryobiology 46:205–229

    Article  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 16:422–429

    Article  Google Scholar 

  • Joint I, Mühling M, Querellou J (2010) Culturing marine bacteria—an essential prerequisite for biodiscovery. Microb Biotechnol 3:564–575

    Article  CAS  Google Scholar 

  • Joux F, Lebaron P (2000) Use of fluorescent probes to assess physiological functions of bacteria at single-cell level. Microbes Infect 2:1523–1535

    Article  CAS  Google Scholar 

  • Jules M, Guillou V, Francois J, Parrou J-L (2004) Two distinct pathways for trehalose assimilation in the yeast Saccharomyces cerevisiae. Appl Environ Microbiol 70:2771–2778

    Article  CAS  Google Scholar 

  • Kartal B, Kuenen JG, Loosdrecht MCMv (2010) Sewage treatment with anammox. Science 328:702–703

    Article  CAS  Google Scholar 

  • Khan MMT, Pyle BH, Camper AK (2010) Specific and rapid enumeration of viable but nonculturable and viable-culturable gram-negative bacteria by using flow cytometry. Appl Environ Microbiol 76:5088–5096

    Article  CAS  Google Scholar 

  • Krumnow AA, Sorokulova IB, Olsen E, Globa L, Barbaree JM, Vodyanoy VJ (2009) Preservation of bacteria in natural polymers. J Microbiol Methods 78:189–194

    Article  CAS  Google Scholar 

  • Kuppardt A, Chatzinotas A, Breuer U, Meer JRvd, Harms H (2009) Optimization of preservation conditions of As(III) bioreporter bacteria. Appl Microbiol Biotechnol 82:785–792

    Article  CAS  Google Scholar 

  • Laurin V, Labbe N, Juteau P, Parent S, Villemur R (2006) Long-term storage conditions for carriers with denitrifying biomass of the fluidized, methanol-fed denitrification reactor of the Montreal Biodome, and the impact on denitrifying activity and bacterial population. Water Res 40:1836–1840

    Article  CAS  Google Scholar 

  • Liolios K, Chen I-MA, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC (2010) The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 38:346–354

    Article  Google Scholar 

  • Mazur P (1984) Freezing of living cells: mechanisms and implications. Am J Physiol 247:125–142

    Google Scholar 

  • Miyamoto-Shinohara Y, Sukenobe J, Imaizumi T, Nakahara T (2008) Survival of freeze-dried bacteria. J Gen Appl Microbiol 1:9–24

    Article  Google Scholar 

  • Morgan CA, Herman N, White PA, Vesey G (2006) Preservation of micro-organisms by drying: a review. J Microbiol Methods 66:183–193

    Article  CAS  Google Scholar 

  • Mulder A, van de Graaf AA, Robertson LA, Kuenen JG (1995) Anaerobic ammonium oxidation discovered in a denitrifying fluidized bed reactor. FEMS Microbiol Ecol 16:177–184

    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 Microbiol 74:4889–4897

    Article  CAS  Google Scholar 

  • Oetjen G (1999) Industrial freeze-drying for pharmaceutical applications. In: Rey L, May JC (eds) Freeze-drying/lyophilization of pharmaceutical and biological products. Marcel Dekker, New York, pp 267–335

    Google Scholar 

  • Pegg DE (2007) Principles of cryopreservation. In: Day JG, Stacey GN (eds) Cryopreservation and freeze-drying protocols. Humana Press, Totowa, NJ, pp 39–58

    Chapter  Google Scholar 

  • Roslev P, King GM (1995) Aerobic and anaerobic starvation metabolism in methanotrophic bacteria. Appl Environ Microbiol 61:1563–1570

    CAS  Google Scholar 

  • Rothrock MJ, Vanotti MB, Szögi AA, Gonzalez MCG, Fuji T (2011) Long-term preservation of anammox bacteria. Appl Microbiol Biotechnol 92:147–157

    Article  CAS  Google Scholar 

  • Safronavo VI, Nokinova NI (1996) Comparison of two methods for root nodule bacteria preservation: lyophilisation and liquid nitrogen freezing. J Microbiol Methods 24:231–237

    Article  Google Scholar 

  • Santivarangkna C, Kulozik U, Foerst P (2007) Alternative drying processes for the industrial preservation of lactic acid starter cultures. Biotechnol Prog 23:302–315

    Article  CAS  Google Scholar 

  • Shi L, Günther S, Hübschmann T, Wick LY, Harms H, Müller S (2007) Limits of propidium iodide as a cell viability indicator for environmental bacteria. Cytometry Part A 71A:592–598

    Article  Google Scholar 

  • Siaterlis A, Deepika G, Charalampopoulos D (2009) Effect of culture medium and cryoprotectants on the growth and survival of probiotic lactobacilli during freeze drying. Lett Appl Microbiol 48:295–301

    Article  CAS  Google Scholar 

  • Siddiqui KS, Cavicchioli R (2006) Cold-adapted enzymes. Annu Rev Biochem 75:403–433

    Article  CAS  Google Scholar 

  • Siegele DA, Kolter R (1992) Life after log. J Bacteriol 174:345–348

    CAS  Google Scholar 

  • Smith D (2003) Culture collections over the world. Int Microbiol 6:95–100

    Article  Google Scholar 

  • Smith D, Ryan MJ (2008) The impact of OECD best practices on the validation of cryopreservation techniques for microorganisms. CryoLetters 29:63–72

    CAS  Google Scholar 

  • Stacey GN, Day JG (2007) Long-term ex situ conservation of biological resources and the role of biological resource centers. In: Day JG, Stacey GN (eds) Cryopreservation and Freeze-drying protocols, 2nd edn. Humana Press, Totowa, NJ, pp 1–14

    Chapter  Google Scholar 

  • Stackebrandt E (2010) Diversification and focusing: strategies of microbial culture collections. Trends Microbiol 18:283–287

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  • Stahl DA, Wagner M (2006) The knowledge explosion in environmental microbiology offers new opportunities in biotechnology. Curr Opin Biotechnol 17:227–228

    Article  CAS  Google Scholar 

  • Staley JT, FitzGerald K, Fuerst JA, Dijkshoorn L (2010) Microbiological material exchanges among scientists. Res Microbiol 161:446–452

    Article  Google Scholar 

  • Streeter JG (2003) Effect of trehalose on survival of Bradyrhizobium japonicum during desiccation. J Appl Bacteriol 95:384–491

    Google Scholar 

  • Strous M, Fuerst JA, Kramer EHM, Logemann S, Muyzer G, van de Pas-Schoonen K, Webb R, Kuenen JG, Jetten MSM (1999) Missing lithotroph identified as new planctomycete. Nature 400:446–449

    Article  CAS  Google Scholar 

  • Tindall BJ (2007) Vacuum-drying and cryopreservation of prokaryotes. In: Day JG, Stacey GN (eds) Cryopreservation and freeze-drying protocols. Humana Press, Totowa, NJ, pp 73–98

    Chapter  Google Scholar 

  • Vandamme P, Pot B, Gillis M, Vos PD, Kerstens K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438

    CAS  Google Scholar 

  • Vartoukian SR, Palmer RM, Wade WG (2010) Strategies for culture of ‘unculturable’ bacteria. FEMS Microbiol Lett 309:1–7

    CAS  Google Scholar 

  • Vogelsang C, Gollenbiewski K, Ostgaard K (1999) Effect of preservation techniques on the regeneration of gel entrapped nitrifying sludge. Water Res 33:164–168

    Article  CAS  Google Scholar 

  • Wang Y, Claeys L, Dvd H, Verstraete W, Boon N (2010) Effects of chemically and electrochemically dosed chlorine on Escherichia coli and Legionella beliardensis assessed by flow cytometry. Appl Microbiol Biotechnol 87:331–341

    Article  CAS  Google Scholar 

  • Wittebolle L, Marzorati M, Clement L, Balloi A, Daffonchio D, Heylen K, De Vos P, Verstraete W, Boon N (2009) Initial community evenness favours functionality under selective stress. Nature 458:623–626

    Article  CAS  Google Scholar 

  • Zeigler DR (2003) Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53:1893–1900

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was funded by the Geconcerteerde Onderzoeksactie (GOA) of Ghent University (BOF09/GOA/005). The authors are grateful to Dr. Eva Spieck and Dr. Andreas Pömmerening-Roeser (Hamburg University, Germany) for providing nitrite- and ammonia-oxidizing strains which were used in unpublished preservation research.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Kim Heylen.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Heylen, K., Hoefman, S., Vekeman, B. et al. Safeguarding bacterial resources promotes biotechnological innovation. Appl Microbiol Biotechnol 94, 565–574 (2012). https://doi.org/10.1007/s00253-011-3797-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-011-3797-y

Keywords

Navigation