Cultivation gives context to the microbial ecologist

FEMS Microbiology Ecology

Volumn 60, Issue 3, 2007, Pages 351-357

  Nichols, Dominica ^a  

^a NORTHEASTERN UNIVERSITY   (United States)

Author keywords

'great plate count anomaly'; Cultivation strategies; Genome assembly; Metagenomics; Uncultivable bacteria

Indexed keywords

DNA;

BACTERIUM; COMMUNITY STRUCTURE; CULTIVATION; GENOME; MICROBIAL ECOLOGY;

COMMUNITY; ECOLOGY; GENE SEQUENCE; GENOME; MICROORGANISM; NONHUMAN; PRIORITY JOURNAL; PROCHLOROCOCCUS; REVIEW;

BACTERIA; CULTURE TECHNIQUES; ECOSYSTEM; ENVIRONMENTAL MICROBIOLOGY; GENOME, BACTERIAL; GENOMICS;

EID: 34249112197     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2007.00332.x     Document Type: Review

References (55)

1. Abulencia CB, Wyborski DL, Garcia JA et al 2006) Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl Environ Microbiol 72: 3291 3301.
2. Beja O, Spudich EN, Spudich JL, Leclerc M DeLong EF (2001) Proteorhodopsin phototrophy in the ocean. Nature 411: 786 789.
3. 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.
4. Bruns A, Nubel 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.
5. 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.
6. Cho JC Giovannoni SJ (2004) Cultivation and growth characteristics of a diverse group of oligotrophic marine gammaproteobacteria. Appl Environ Microbiol 70: 432 440.
7. Connon S Giovannoni S (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68: 3878 3885.
8. Davelos Baines AL, Xiao K Kinkel LL (2007) Lack of correspondence between genetic and phenotypic groups amongst soil-borne streptomycetes. FEMS Microb Ecol 59: 564 575.
9. 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 Microbiol 71: 826 834.
10. DeLong EF (2005) Microbial community genomics in the ocean. Nat Rev Microbiol 3: 459 469.
11. DeLong EF Karl DM (2005) Genomic perspectives in microbial oceanography. Nature 437: 336 342.
12. Ellis RJ, Morgan P, Weightman AJ Fry JC (2003) Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Appl Environ Microbiol 69: 3223 3230.
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. Fry JC (2000) Bacterial diversity and 'unculturables'. Microbiol Today 27: 186 189.
15. Furrie E (2006) A molecular revolution in the study of intestinal microflora. Gut 55: 141 143.
16. Giovannoni SJ, Bibbs L, Cho JC et al 2005) Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438: 82 85.
17. Green BD Keller M (2006) Capturing the uncultivated majority. Curr Opin Biotechnol 17: 236 240.
18. Hahn MW Pockl M (2005) Ecotypes of planktonic actinobacteria with identical 16S rRNA genes adapted to thermal niches in temperate, subtropical, and tropical freshwater habitats. Appl Environ Microbiol 71: 766 773.
19. Hahn M, Stadler P, Wu Q Pockl M (2004) The filtration-acclimatization method for isolation of an important fraction of the not readily cultivable bacteria. J Microbiol Methods 57: 379 390.
20. Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68: 669 685.
21. Handelsman J, Rondon MR, Brady SF, Clardy J Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5: R245 R249.
22. Hutchison CA III. Venter JC (2006) Single-cell genomics. Nat Biotechnol 24: 657 658.
23. Janssen PH, Schuhmann A, Morschel E Rainey FA (1997) Novel anaerobic ultramicrobacteria belonging to the Verrucomicrobiales lineage of bacterial descent isolated by dilution culture from anoxic rice paddy soil. Appl Environ Microbiol 63: 1382 1388.
24. Joseph S, Hugenholtz P, Sangwan P, Osborne C Janssen P (2003) Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69: 7210 7215.
25. Kaeberlein T, Lewis K Epstein SS (2002) Isolating " uncultivable" microorganisms in pure culture in a simulated natural environment. Science 296: 1127 1129.
26. Kopke 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.
27. Kvist T, Ahring BK, Lasken RS Westermann P (2007) Specific single-cell isolation and genomic amplification of uncultured microorganisms. Appl Microbiol Biotechnol 74: 926 935.
28. Maldonado A, Jimenez-Diaz R Ruiz-Barba JL (2004) Induction of plantaricin production in Lactobacillus plantarum NC8 after coculture with specific gram-positive bacteria is mediated by an autoinduction mechanism. J Bacteriol 186: 1556 1564.
29. Meyerdierks A, Kube M, Lombardot T, Knittel K, Bauer M, Glockner FO, Reinhardt R Amann R (2005) Insights into the genomes of archaea mediating the anaerobic oxidation of methane. Environ Microbiol 7: 1937 1951.
30. Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40: 337 365.
31. Parro V Moreno-Paz M (2003) Gene function analysis in environmental isolates: the nif regulon of the strict iron oxidizing bacterium Leptospirillum ferrooxidans. Proc Natl Acad Sci USA 100: 7883 7888.
32. Podar M Reysenbach AL (2006) New opportunities revealed by biotechnological explorations of extremophiles. Curr Opin Biotechnol 17: 250 255.
33. Raghunathan A, Ferguson HR Jr., Bornarth CJ, Song W, Driscoll M Lasken RS (2005) Genomic DNA amplification from a single bacterium. Appl Environ Microbiol 71: 3342 3347.
34. Rothschild L (2006) A microbiologist explodes the myth of the unculturables. Nature 443: 249.
35. Rusch DB, Halpern AL, Sutton G et al 2007) The sorcerer II global ocean sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5: e77.
36. Sait M, Hugenholtz P Janssen PH (2002) Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol 4: 654 666.
37. Schering A, Kanigan T, Hartke Quiett T, Lewis K Epstein SS (2006) New platform technology for high-throughput cultivation of novel microorganisms. In 11th International Symposium on Microbial Ecology, Vienna.
38. Schloss PD Handelsman J (2005) Metagenomics for studying unculturable microorganisms: cutting the gordian knot. Genome Biol 6: 229.
39. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD Church GM (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309: 1728 1732.
40. Staley J Konopka A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39: 321 346.
41. Stevenson B, Eichorst S, Wertz J, Schmidt T Breznak J (2004) New strategies for cultivation and detection of previously uncultured microbes. Appl Environ Microbiol 70: 4748 4755.
42. Sudo Y Spudich JL (2006) Three strategically placed hydrogen-bonding residues convert a proton pump into a sensory receptor. Proc Natl Acad Sci USA 103: 16129 16134.
43. Tringe SG Rubin EM (2005) Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 6: 805 814.
44. Tyson GW Banfield JF (2005) Cultivating the uncultivated: a community genomics perspective. Trends Microbiol 13: 411 415.
45. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37 43.
46. Tyson GW, Lo I, Baker BJ, Allen EE, Hugenholtz P Banfield JF (2005) Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community. Appl Environ Microbiol 71: 6319 6324.
47. Venter JC, Remington K Heidelberg JF (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66 74.
48. Welch RA, Burland V, Plunkett G III. et al 2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA 99: 17020 17024.
49. Wilmes P Bond PL (2006) Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol 14: 92 97.
50. Xavier KB Bassler BL (2005) Interference with AI-2-mediated bacterial cell-cell communication. Nature 437: 750 753.
51. Yooseph S, Sutton G, Rusch DB et al 2007) The sorcerer II global ocean sampling expedition: expanding the universe of protein families. PLoS Biol 5: e16.
52. Young P (1997) Major microbial diversity initiative recommended. ASM News 63: 417 421.
53. 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.
54. Zengler K, Walcher M, Clark G, Haller I, Toledo G, Holland T, Mathur EJ, Woodnutt G, Short JM Keller M (2005) High-throughput cultivation of microorganisms using microcapsules. Methods Enzymol 397: 124 130.
55. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW Church GM (2006) Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol 24: 680 686.