A Culture-Independent Approach to Unravel Uncultured Bacteria and Functional Genes in a Complex Microbial Community

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Wang, Yun ^a   Chen, Yin ^b   Zhou, Qian ^c   Huang, Shi ^c   Ning, Kang ^c   Xu, Jian ^c   Kalin, Robert M ^d   Rolfe, Stephen ^a   Huang, Wei E ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b UNIVERSITY OF WARWICK   (United Kingdom)

^c QINGDAO INSTITUTE OF BIOENERGY AND BIOPROCESS TECHNOLOGY   (China)

^d UNIVERSITY OF STRATHCLYDE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; GROUND WATER; NAPHTHALENE;

ACIDOVORAX; ARTICLE; BACTERIAL GENE; BACTERIUM; BACTERIUM CULTURE; BIODEGRADATION; BIOSENSOR; BIOSENSOR BASED GENETIC TRANSDUCER; CONTROLLED STUDY; DNA SEQUENCE; FRACTIONATION; GENE CLUSTER; GENE FUNCTION; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIAL DEGRADATION; MICROBIAL GENETICS; NAG GENE; NAG2 GENE; NAH GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; POLAROMONAS NAPHTHALENIVORANS; PSEUDOMONAS FLUORESCENS; PSEUDOMONAS PUTIDA; PYROSEQUENCING; RALSTONIA; SEQUENCE HOMOLOGY; WATER CONTAMINATION;

BACTERIA; BIODEGRADATION, ENVIRONMENTAL; BIOSENSING TECHNIQUES; CARBON ISOTOPES; CELL CULTURE TECHNIQUES; COMAMONADACEAE; CONJUGATION, GENETIC; DIOXYGENASES; DNA, BACTERIAL; GENES, BACTERIAL; ISOTOPE LABELING; LUMINESCENT MEASUREMENTS; METAGENOME; MULTIENZYME COMPLEXES; NAPHTHALENES; OPERON; PLASMIDS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; TEMPERATURE;

EID: 84867645614     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0047530     Document Type: Article

References (62)

1. Whitman WB, Coleman DC, Wiebe WJ, (1998) Prokaryotes: the unseen majority. P Natl Acad Sci USA 95: 6578-6583.
2. Falkowski PG, Fenchel T, Delong EF, (2008) The microbial engines that drive Earth's biogeochemical cycles. Science 320: 1034-1039.
3. Whitfield J, (2005) Is Everything Everywhere? Science 310: 960-961.
4. Amann RI, Ludwig W, Schleifer KH, (1995) Phylogenetic identifacation and in-situ detection of individual microbial-cells without cultivation. Microbiol Rev 59: 143-169.
5. Head IM, Saunders JR, Pickup RW, (1998) Microbial evolution, diversity, and ecology: A decade of ribosomal RNA analysis of uncultivated microorganisms. Microb Ecol 35: 1-21.
6. Rappe MS, Giovannoni SJ, (2003) The uncultured microbial majority. Annu Rev Microbiol 57: 369-394.
7. Venter JC, (2003) Unleashing the power of genomics: understanding the environment and biological diversity. Scientist 17: 8-8.
8. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
9. Lorenz P, Eck J, (2005) Metagenomics and industrial applications. Nat Rev Microbiol 3: 510-516.
10. Bode HB, Muller R, (2005) The impact of bacterial genomics on natural product research. Angew Chem Int Edit 44: 6828-6846.
11. Fortman JL, Sherman DH, (2005) Utilizing the power of microbial genetics to bridge the gap between the promise and the application of marine natural products. Chembiochem 6: 960-978.
12. Galvao TC, Mohn WW, de Lorenzo V, (2005) Exploring the microbial biodegradation and biotransformation gene pool. Trends Biotechnol 23: 497-506.
13. Vieites JM, Guazzaroni ME, Beloqui A, Golyshin PN, Ferrer M, (2009) Metagenomics approaches in systems microbiology. FEMS Microbiol Rev 33: 236-255.
14. Raes J, Bork P, (2008) Systems microbiology- Timeline- Molecular eco-systems biology: towards an understanding of community function. Nat Rev Microbiol 6: 693-699.
15. Handelsman J, (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68: 669-685.
16. Schloss PD, Handelsman J, (2003) Biotechnological prospects from metagenomics. Curr Opin Biotech 14: 303-310.
17. Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, et al. (2009) Shotgun metaproteomics of the human distal gut microbiota. ISME J 3: 179-189.
18. MacLean D, Jones JDG, Studholme DJ, (2009) Application of 'next-generation' sequencing technologies to microbial genetics. Nat Rev Microbiol 7: 287-296.
19. Rothberg JM, Leamon JH, (2008) The development and impact of 454 sequencing. Nat Biotechnol 26: 1117-1124.
20. Shendure J, Ji HL, (2008) Next-generation DNA sequencing. Nat Biotechnol 26: 1135-1145.
21. Cardenas E, Tiedje JM, (2008) New tools for discovering and characterizing microbial diversity. Curr Opin Biotech 19: 544-549.
22. Ishoey T, Woyke T, Stepanauskas R, Novotny M, Lasken RS, (2008) Genomic sequencing of single microbial cells from environmental samples. Curr Opin Microbiol 11: 198-204.
23. Stepanauskas R, Sieracki ME, (2007) Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. P Natl Acad Sci USA 104: 9052-9057.
24. Schnoes AM, Brown SD, Dodevski I, Babbitt PC, (2009) Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies. PLoS Comput Biol 5: e1000605.
25. Chen Y, Murrell JC, (2010) When metagenomics meets stable-isotope probing: progress and perspectives. Trends Microbiol 18: 157-163.
26. Huang WE, Ferguson A, Singer A, Lawson K, Thompson IP, et al. (2009) Resolving genetic functions within microbial populations: in situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell raman-fluorescence in situ hybridization. Appl Environ Microbiol 75: 234-241.
27. Ferguson AS, Huang WE, Lawson KA, Doherty R, Gibert O, et al. (2007) Microbial analysis of soil and groundwater from a gasworks site and comparison with a sequenced biological reactive barrier remediation process. J Appl Microbiol 102: 1227-1238.
28. Huang WE, Wang H, Huang LF, Zheng HJ, Singer AC, et al. (2005) Chromosomally located gene fusions constructed in Acinetobacter sp ADP1 for the detection of salicylate. Environ Microbiol 7: 1339-1348.
29. Cane PA, Williams PA, (1982) The plasmid-coded metabolism of naphthalene and 2-methylnaphthalene in Pseudomonas strains: phenotypic changes correlated with structural modification of the plasmid pWW60-1. J Gen Microbiol 128: 2281-2290.
30. Cane PA, Williams PA, (1982) The plasmid-coded metabolism of naphthalene and 2-methylnaphthalene in Pseudomonas strains: phenotypic changes correlated with structural modification of the plasmid pWW60-1. J Gen Microbiol 128: 2281-2290.
31. Dennis JJ, Zylstra GJ, (2004) Complete sequence and genetic organization of pDTG1, the 83 kilobase naphthalene degradation plasmid from Pseudomonas putida strain NCIB 9816-4. J Mol Biol 341: 753-768.
32. Bosch R, Garcia-Valdes E, Moore ERB, (2000) Complete nucleotide sequence and evolutionary significance of a chromosomally encoded naphthalene-degradation lower pathway from Pseudomonas stutzeri AN10. Gene 245: 65-74.
33. Murrell JC, S WA (2011) Stable Isotope Probing and Related Technologies. Washington DC: ASM Press. 1-351 p.
34. Fuchs BM, Wallner G, Beisker W, Schwippl I, Ludwig W, et al. (1998) Flow cytometric analysis of the in situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probes. Appl Environ Microbiol 64: 4973-4982.
35. Zhou NY, Fuenmayor SL, Williams PA, (2001) nag genes of Ralstonia (formerly Pseudomonas) sp strain U2 encoding enzymes for gentisate catabolism. J Bacteriol 183: 700-708.
36. Jeon CO, Park M, Ro HS, Park W, Madsen EL, (2006) The naphthalene catabolic (nag) genes of Polaromonas naphthalenivorans CJ2: Evolutionary implications for two gene clusters and novel regulatory control. Appl Environ Microbiol 72: 1086-1095.
37. Hunger M, Schmucker R, Kishan V, Hillen W, (1990) Analysis and nucleotide-sequence of an origin of DNA-replication in Acinetobacter-calcoaceticus and its use for Escherichia-coli shuttle plasmids. Gene 87: 45-51.
38. Gillespie DE, Brady SF, Bettermann AD, Cianciotto NP, Liles MR, et al. (2002) Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl Environ Microbiol 68: 4301-4306.
39. Torres-Cortes GT-CG, Millan V, Ramirez-Saad HC, Nisa-Martinez R, Toro N, et al. (2011) Characterization of novel antibiotic resistance genes identified by functional metagenomics on soil samples. Environ Microbiol 13: 1101-1114.
40. Uchiyama T, Miyazaki K, (2010) Product-induced gene expression, a product-responsive reporter assay used to screen metagenomic libraries for enzyme-encoding genes. Appl Environ Microbiol 76: 7029-7035.
41. Uchiyama T, Abe T, Ikemura T, Watanabe K, (2005) Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat Biotechnol 23: 88-93.
42. Ferrer M, Beloqui A, Vieites JM, Guazzaroni ME, Berger I, et al. (2009) Interplay of metagenomics and in vitro compartmentalization. Microb Biotechnol 2: 31-39.
43. Williamson LL, Borlee BR, Schloss PD, Guan CH, Allen HK, et al. (2005) Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor. Appl Environ Microbiol 71: 6335-6344.
44. Carreño CA, de Lorenzo D (2010) Genetic traps for surveying new catalysts in (meta) genomic DNA. In: Timmis KN, editor. Handbook of Hydrocarbon and Lipid Microbiology. Berlin Heidelberg: Springer-Verlag. 4563-4579.
45. Dietrich JA, McKee AE, Keasling JD, (2010) High-throughput metabolic engineering: advances in small-molecule screening and selection. Annu Rev Biochem 79: 563-590.
46. Yen KM, Gunsalus IC, (1982) Plasmid gene organization- naphthalene salicylate oxidation. P Natl Acad Sci USA 79: 874-878.
47. Jones RM, Britt-Compton B, Williams PA, (2003) The naphthalene catabolic (nag) genes of Ralstonia sp strain U2 are an operon that is regulated by NagR, a LysR-type transcriptional regulator. J Bacteriol 185: 5847-5853.
48. Allen CCR, Boyd DR, Larkin MJ, Reid KA, Sharma ND, et al. (1997) Metabolism of naphthalene, 1-naphthol, indene, and indole by Rhodococcus sp strain NCIMB 12038. Appl Environ Microbiol 63: 151-155.
49. Grund E, Denecke B, Eichenlaub R, (1992) Naphthalene degradation via salicylate and gentisate by Rhodococcus sp strain B4. Appl Environ Microbiol 58: 1874-1877.
50. Huang WE, Singer AC, Spiers AJ, Preston GM, Whiteley AS, (2008) Characterizing the regulation of the Pu promoter in Acinetobacter baylyi ADP1. Environ Microbiol 10: 1668-1680.
51. Song YZ, Li GH, Thornton SF, Thompson IP, Banwart SA, et al. (2009) Optimization of bacterial whole cell bioreporters for toxicity assay of environmental samples. Environ Sci Technol 43: 7931-7938.
52. Zhang D, Fakhrullin RF, Özmen M, Wang H, Wang J, et al. (2011) Functionalization of whole-cell bacterial reporters with magnetic nanoparticles. Microbl Biotechnol 4: 89-97.
53. Zhang D, He Y, Wang Y, Wang H, Wu L, et al. (2012) Whole-cell bacterial bioreporter for actively searching and sensing of alkanes and oil spills. Microbl Biotechnol 5: 87-97.
54. Andam CP, Gogarten JP, (2011) Biased gene transfer in microbial evolution. Nat Rev Microbiol 9: 543-555.
55. Bauchop T, Elsden SR, (1960) The growth of micro-organisms in relation to their energy supply. J Gen Microbiol 23: 457-469.
56. Neufeld JD, Vohra J, Dumont MG, Lueders T, Manefield M, et al. (2007) DNA stable-isotope probing. Nat Protoc 2: 860-866.
57. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual: Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
58. Griffiths RI, Whiteley AS, O'Donnell AG, Bailey MJ, (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microbiol 66: 5488-5491.
59. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
60. Manefield M, Whiteley AS, Griffiths RI, Bailey MJ, (2002) RNA stable isotope probing, a novel means of linking microbial community function to Phylogeny. Appl Environ Microbiol 68: 5367-5373.
61. Moser R, Stahl U, (2001) Insights into the genetic diversity of initial dioxygenases from PAH-degrading bacteria. Appl Microbiol Biotechnol 55: 609-618.
62. Juni E, Janik A, (1969) Transformation of Acinetobacter calcoaceticus(Bacterium anitratum). J Bacteriol 98: 281-288.