Novel cultivation strategies for environmentally important microorganisms

Geomicrobiology: Molecular and Environmental Perspective

Volumn , Issue , 2010, Pages 69-89

  Overmann, Jörg ^a,b  

^a LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^b UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84870554346     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-90-481-9204-5_3     Document Type: Chapter

References (48)

1. Angle JS, McGrath SP, Chaney RL (1991) New culture medium containing ionic concentrations of nutrients similar to concentrations found in the soil solution. Appl Environ Microbiol 57:3674-3676
2. Balch WE, Wolfe RS (1976) New approach to the cultivation of methanogenic bacteria: 2-mercaptoethane sulfonic acid (HS-CoM)-dependent growth of Methanobacterium ruminantium in a pressurized atmosphere. Appl Environ Microbiol 32:781-791
3. Bartscht K, Cypionka H, Overmann J (1999) Evaluation of cell activity and of methods for the cultivation of bacteria from a natural lake community. FEMS Microbiol Ecol 28:249-259
4. Bast E (2001) Mikrobiologische methoden, 2nd edn. Gustav Fischer, Stuttgart, 429 pp
5. Bond DR, Holmes DE, Tender LM, Lovley DR (2002) Electrode-reducing microorganisms that harvest energy from marine sediments. Science 295:483-485
6. Bruns A, Hoffelner H, Overmann J (2003a) A novel approach for high throughput cultivation assays and the isolation of planktonic bacteria. FEMS Microbiol Ecol 45:161-171
7. Bruns A, Nübel U, Cypionka H, Overmann J (2003b) Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton. Appl Environ Microbiol 69:1980-1989
8. Button DK, Schut F, Quang P, Martin R, Robertson BR (1993) Viability and isolation of marine bacteria by dilution culture: theory, procedures, and initial results. Appl Environ Microbiol 59:881-891
9. Cho J-C, Giovannoni SJ (2004) Cultivation and growth characteristics of a diverse group of oligotrophic marine Gammaproteobacteria. Appl Environ Microbiol 70:432-440
10. Connon SA, Giovannoni SJ (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68:3878-3885
11. Coolen MJL, Overmann J (2000) Functional exoenzymes as indicators of metabolicallly active bacteria in 124, 000-year-old sapropel layers of the eastern Mediterranean sea. Appl Environ Microbiol 66:2589-2598
12. Eilers H, Pernthaler J, Peplies J, Glöckner FO, 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
13. Ferrari BC, Binnerup SJ, Gillings M (2005) Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria. Appl Environ Microbiol 71:8714-8720
14. Fröhlich J, König H (1999) Rapid isolation of single microbial cells from mixed natural and laboratory populations with the aid of a micromanipulator. System Appl Microbiol 22:249-257
15. Gans J, Wolinsky M, Dunbar J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309:1387-1390
16. Hahn MW, Stadler P, Wu QL, Pöckl M (2004) The filtration- acclimatization method for isolation of an important fraction of the not readily cultivable bacteria. J Microbiol Meth 57:379-390
17. 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
18. Hungate RE (1950) The anaerobic mesophilic cellulolytic bacteria. Bacteriol Rev 14:1-49
19. Hungate RE (1966) The rumen and its microbes. Academic, New York
20. Jannasch HW, Wirsen CO, Doherty KW (1996) A pressurized chemostat for the study of marine barophilic and oligotrophic bacteria. Appl Environ Microbiol 62:1593-1596
21. Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M (2002) Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol 68:2391-2396
22. Kaeberlein T, Lewis K, Epstein SS (2002) Isolating " uncultivable" microorganisms in pure culture in a simulated natural environment. Science 296:1127-1128
23. Leadbetter JR, Schmidt TM, Graber JR, Breznak JA (1999) Acetogenesis from H2 plus CO2 by spirochetes from termite guts. Science 283:686-689
24. Mukamolova GV, Murzin AG, Salina EG, Kell DB, Kaprelyants AS, Young M (2006) Muralytic activity of Micrococcus luteus Rpf and its relationship to physiological activity in promoting bacterial growth and resuscitation. Mol Microbiol 59:84-98
25. Musat N, Halm H, Winterholler B, Hoppe P, Peduzzi S, Hillion F, Horreard F, Amann R, Jørgensen BB, Kuypers MMM (2008) A single-cell view on the ecophyisology of anaerobic phototrophic bacteria. Proc Natl Acad Sci USA 105:17861-17866
26. Nedoma J, Vrba J (2006) Specific activity of cell-surface acid phosphatase in different bacterioplankton morphotypes in an acidified mountain lake. Environ Microbiol 8:1271-1279
27. Ouverney CC, Fuhrman JA (1999) Combined microautoradiography - 16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ. Appl Environ Microbiol 65:1746-1752
28. Overmann J (2001) Phototrophic consortia: a tight cooperation between non-related eubacteria. In: Seckbach J (ed) Symbiosis: mechanisms and model systems. Kluwer, Dordrecht, The Netherlands, pp 239-255
29. Overmann J (2002) Principles of enrichment, isolation, cultivation, and preservation of bacteria. In: Dworkin M et al (eds) The prokaryotes: an evolving electronic resource for the microbiological community, 3rd edn (latest update release 3.11, September 2002). Springer, New York, 2000 (http://ep. springer-ny.com:6336/contents/or http://141.150.157.117:8080/prokPROD/index.htm)
30. Overmann J (2005) Chemotaxis and behavioural physiology of not-yet-cultivated microbes. Methods in enzymology, vol 397, Chapter II.8. Elsevier, San Diego, CA, pp 133-147
31. Overmann J, Pfennig N (1989) Pelodictyon phaeoclathratiforme sp. nov., a new brown-colored member of the Chlorobiaceae forming net-like colonies. Arch Microbiol 152:401-406
32. Pernthaler A, Pernthaler J, Schattenhofer M, Amann R (2002) Identification of DNA-synthesizing bacterial cells in coastal North Sea plankton. Appl Environ Microbiol 68:5728-5736
33. Pfennig N (1980) Syntrophic mixed cultures and symbiotic consortia with phototrophic bacteria: a review. In: Gottschalk G, Pfennig N, Werner H (eds) Anaerobes and anaerobic infections. Fischer, Stuttgart, pp 127-131
34. Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646-649
35. Rappé MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630-633
36. Schink B (1991) Syntrophism among prokaryotes. In: Balows A, Trüper HG, Dworkin M, Schleifer KH (eds) The prokaryotes, 2nd edn. Springer, Berlin/Heidelberg/New York, pp 276-299
37. Schink B, Friedrich M (2000) Phosphite oxidation by sulphate reduction. Nature 406:37
38. Schut F, Devries EJ, Gottschal JC, Robertson BR, Harder W, Prins RA, Button DK (1993) Isolation of typical marine bacteria by dilution culture: growth, maintenance, and characteristics of isolates under laboratory conditions. Appl Environ Microbiol 59:2150-2160
39. Schut F, Gottschal JC, Prins RA (1997) Isolation and characterization of the marine ultramicrobacterium Sphingomonas sp. strain RB2256. FEMS Microbiol Rev 20:363-369
40. Staley JT, Konopka A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Ann Rev Microbiol 39:321-346
41. Stevenson BS, Eichorst SA, Wertz JT, Schmidt TM, Breznak JA (2004) New strategies for cultivation and detection of previously uncultured microbes. Appl Environ Microbiol 70:4748-4755
42. Thauer RK, Jungermann K, Decker K (1977) Energy conservation in chemotrophic anaerobic bacteria. Bacteriol Rev 41:100-180
43. Vogl K, Glaeser J, Pfannes KR, Wanner G, Overmann J (2006) Chlorobium chlorochromatii sp. nov., a symbiotic green sulfur bacterium isolated from the phototrophic consortium "Chlorochromatium aggregatum". Arch Microbiol 185:363-372
44. Waterbury JB (1991) The cyanobacteria - isolation, purification, and identification. P.2058-2078. In: Balows A, Trüper HG, Dworkin M, Schleifer KH (eds) The prokaryotes, 2nd edn. Springer, Berlin/Heidelberg/New York, pp 149-196
45. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: The unseen majority. Proc Natl Acad Sci USA 95:6578-6583
46. Widdel F (1983) Methods for the enrichment and pure culture isolation of filamentous gliding sulfate-reducing bacteria. Arch Microbiol 134:282-285
47. Widdel F, Kohring G-W, Mayer F (1983) Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids. III. Characterization of the filamentous gliding Desulfonema limicola gen. nov. sp. nov., and Desulfonema magnum sp. nov. Arch Microbiol 134:296-294
48. Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, Short JM, Keller M (2002) Cultivating the uncultured. Proc Natl Acad Sci USA 99:15681-15686