Microbial Ecology in the Age of Metagenomics

Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches

Volumn , Issue , 2011, Pages 111-122

  Xu, Jianping ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

Development and application of high throughput " omics" tools undergoing a renaissance; Metagenomics, its impact on microbial ecology broad sense metagenomics, four complementary fields; Microbial ecology in the age of metagenomics

Indexed keywords

EID: 84886188947     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781118010518.ch14     Document Type: Chapter

References (56)

1. Allen EE, Banfield JF. 2005. Community genomics in microbial ecology and evolution. Nat. Rev. Microbiol. 3:489-498.
2. Baker GC, Smith JJ, Cowan DA. 2003. Review and re-analysis of domain-specific 16S primers. J. Microbiol. Methods 55:541-555.
3. Beijerinck MW. 1888. The root-nodule bacteria. Bot. Zeitung 46: 725-804.
4. Beja O, Aravind L, Koonin EV, Suzuki MT, Hadd A, et al. 2000. Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. Science 289:1902-1906.
5. Beja O, Spudich EN, Spudich JL, Leclerc M, DeLong EF. 2001. Proteorhodopsin phototrophy in the ocean. Nature 411:786-789.
6. Benndorf D, Balcke GU, Harms H, von Bergen M. 2007. Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. The ISME J. 1:224-234.
7. Blochl E, Rachel R, Burggraf S, Hafenbradl D, Jannasch HW, Stetter KO. 1997. Pyrolobus fumarii, gen. and sp. nov., represents a novel group of archaea, extending the upper temperature limit for life to 113 degrees C. Extremophiles 1:14-21.
8. Bond AM, Scholz F. 2005. Electroanalytical Methods: Guide to Experiments and Applications. Berlin: Springer.
9. Cohan FM. 2004. Concepts of bacterial biodiversity for the age of genomics. In Fraser CM, Read TD, Nelson KE, eds. Microbial Genomics. Totowa, NJ: Humana Press, pp. 175-194.
10. Daniel R. 2005. The metagenomics of soil. Nat. Rev. Microbiol. 3:470-478.
11. Dawson SC, Pace NR. 2002. Novel kingdom-level eukaryotic diversity in anoxic environments. Proc. Natl. Acad. Sci. USA 99:8324-8329.
12. DeLong EF. 2005. Microbial community genomics in the ocean. Nat. Rev. Microbiol. 3:459-469.
13. Edwards RA, Rohwer F. 2005. Viral metagenomics. Nat. Rev. Microbiol 3:504-510.
14. Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, et al. 2006. Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7:e57.
15. Faith DP. 1992. Conservation evaluation and phylogenetic diversity. Biol. Conserv. 61:1-10.
16. Garrity GM, Libum TG, Bell JA. 2005. Bergey's Manual of Systematic Bacteriology, 2nd ed. New York: Springer-Verlag.
17. Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, et al. 2005. Re-evaluating prokaryotic species. Nat. Rev. Microbiol. 3:733-739.
18. Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I. 2008. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE 3:e3042.
19. Haeckel E. 1866. Generelle Morphologie der Organismen. Berlin: Reimer. Handelsman J, Rondon MR, Brady SF, Clardy J, and Goodman RM. 1998. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5:245-249.
20. Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO. 2002. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63-67.
21. Hugenholtz P, Goebel BM, Pace NR. 1998. Impact of cultureindependent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-4774.
22. Huson DH, Auch A, Qi J, Schuster SC. 2007. MEGAN: Analysis of metagenomic data. Genome Res. 17:377-386.
23. Karner MB, DeLong EF, Karl DM. 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409:507-510.
24. Kasting JF, Siefert JL. 2002. Life and the evolution of earth's atmosphere. Science 296:1066-1067.
25. Konstantinidis KT, Tiedje JM. 2005. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. USA 102:2567-2572.
26. Kvist T, Ahring BK, Lasken RS, Westernmann P. 2007. Specific single-cell isolation and genomic amplification of uncultured microorganisms. Appl. Microbiol. Biotech. 74:926-935.
27. Lehner A, Loy A, Behr T, Gaenge H, Ludwig W, Wagner M, Schleifer KH. 2005. Oligonucleotide microarray for identification of Enterococcus species. FEMS Microbiol. Lett. 246:133-142.
28. Li M, Xu J. 2009. Molecular ecology of ectomycorrhizal fungi: molecular markers, genets and ecological importance. Acta Botanica Yunnanica 31:193-209.
29. Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer KH, Wagner M. 2002. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfatereducing prokaryotes in the environment. Appl. Environ. Microbiol. 68:5064-5081.
30. Loy A, Schulz C, Lucker S, Schopfer-Wendels A, Stoecker K, Baranyi C, Lehner A, Wagner M. 2005. 16S rRNA genebased oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales". Appl. Environ. Microbiol. 71:1373-1386.
31. Mashego MR, Rumbold K, De Mey M, Vandamme E, Soetaert W, Heijnen JJ. 2007. Microbial metabolomics: Past, present and future methodologies. Biotech. Lett. 29:1-16.
32. Mayden RL. 1997. A hierarchy of species concepts: The denouement in the saga of the species problem. In Claridge MF, Dawah HA, Wilson MR, eds. Species: The Unit of Biodiversity. London: Chapman and Hall, pp. 381-424.
33. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, et al. 2008. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:e0.
34. Nam Y-D, Chang H-W, Kim K-H, Roh S-W, Bae J-W. 2009. Metatranscriptome analysis of lactic acid bacteria during kimchi fermentation with genome-probing microarrays. Int. J. Food Microbiol. 130:140-146.
35. Nunez ME, Martin MO, Duong LK, Ly E, Spain EM. 2003. Investigations into the life cycle of the bacterial predator Bdellovibrio bacteriovorus 109J at an interface by atomic force microscopy. Biophys. J. 84:3379-3388.
36. Pace NR. 1991. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173:4371-4378.
37. Pace NR, Stahl DA, Olsen GJ, Lane DJ. 1985. Analyzing natural microbial populations by rRNA sequences. ASM News 51:4-12.
38. Ram RJ, Verberkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC 2nd, Shah M, Hettich RL, Banfield JF. 2005. Community proteomics of a natural microbial biofilm. Science 308:1915-1920.
39. Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, et al. 2000. Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66:2541-2547.
40. Rothschild LJ, Mancinelli RL. 2001. Life in extreme environments. Nature 409:1092-1101.
41. Schadt CW, Martin AP, Lipson DA, Schmidt SK. 2003. Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science 301:1359-1361.
42. Schopf JW. 1993. Microfossils of the Early Archean Apex chert: New evidence of the antiquity of life. Science 260:640-646.
43. Sibley CG, Comstock JA, Ahlquist JE. 1990. DNA hybridization evidence of hominoid phylogeny: A reanalysis of the data. J. Mol. Evol. 30:202-236.
44. Slonczewski JL, Foster JW. 2009. Microbiology: An Evolving Science. New York: W.W. Norton & Company.
45. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, et al. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43.
46. Vandenkoornhuyse P, Baldauf SL, Leyval C, Straczek J, Young JP. 2002. Extensive fungal diversity in plant roots. Science 295: 2051.
47. 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.
48. Voget S, Leggewie C, Uesbeck A, Raasch C, Jaeger KE, Streit WR. 2003. Prospecting for novel biocatalysts in a soil metagenome. Appl. Environ. Microbiol. 69:6235-6242.
49. Winogradsky SN 1887. Concerning sulfur bacteria. Bot. Zeitung 45:489-507.
50. Woese CR. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
51. Wu JR, Ma HC, Lü M, Han SF, Zhu, YY, Jin H, Liang JF, Liu L, Xu J. 2011. Rhizoctonia fungi enhance the growth of the endangered orchid Cymbidium goeringii. Botany 88:20-29.
52. Wu L, Thompson DK, Liu X, Fields MW, Bagwell CE, Tiedje JM, Zhou J. 2004. Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications. Environ. Sci. Technol. 38:6775-6782.
53. Xu J. 2005. Evolutionary Genetics of Fungi. UK: Horizon Scientific Press.
54. Xu J. 2006. Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol. Ecol. 15:1713-1731.
55. Xu J. In Press. Reproduction and sex in microorganisms. In Reproduction and Development Biology (Edited by Prof. Andre Pires da Silva). In Encyclopedia of Life Support Systems (EOLSS), Developed under the Auspices of the UNESCO, Eolss Publishers. Oxford: UK. [http://www.eolss.net].
56. Zhou J. 2003. Microarrays for bacterial detection and microbial community analysis. Curr. Opin. Microbiol. 6:288-294.