About this Journal Submit a Manuscript Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 958719, 15 pages
http://dx.doi.org/10.1155/2013/958719
Review Article

Microbial Diversity in the Era of Omic Technologies

Department of Environmental and Natural Resources Management, University of Patras, 2 Seferi Street, 30100 Agrinio, Greece

Received 30 April 2013; Revised 26 August 2013; Accepted 26 August 2013

Academic Editor: Dimitrios Karpouzas

Copyright © 2013 Sofia Nikolaki and George Tsiamis. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. J. C. Venter, K. Remington, J. F. Heidelberg et al., “Environmental genome shotgun sequencing of the Sargasso Sea,” Science, vol. 304, no. 5667, pp. 66–74, 2004. View at Publisher · View at Google Scholar · View at Scopus
  2. National Research Council (US) Committee on Metagenomics: Challenges and Functional Applications, The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet, National Academies Press, Washington, DC, USA, 2007.
  3. J. Handelsman, “Metagenomics: application of genomics to uncultured microorganisms,” Microbiology and Molecular Biology Reviews, vol. 68, no. 4, pp. 669–685, 2004. View at Publisher · View at Google Scholar · View at Scopus
  4. C. R. Woese and G. E. Fox, “Phylogenetic structure of the prokaryotic domain: the primary kingdoms,” Proceedings of the National Academy of Sciences of the United States of America, vol. 74, no. 11, pp. 5088–5090, 1977. View at Scopus
  5. C. R. Woese, O. Kandler, and M. L. Wheelis, “Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya,” Proceedings of the National Academy of Sciences of the United States of America, vol. 87, no. 12, pp. 4576–4579, 1990. View at Publisher · View at Google Scholar · View at Scopus
  6. J. Rajendhran and P. Gunasekaran, “Microbial phylogeny and diversity: small subunit ribosomal RNA sequence analysis and beyond,” Microbiological Research, vol. 166, no. 2, pp. 99–110, 2011. View at Publisher · View at Google Scholar · View at Scopus
  7. J. A. Gilbert and C. L. Dupont, “Microbial metagenomics: beyond the genome,” Annual Review of Marine Science, vol. 3, pp. 347–371, 2011. View at Publisher · View at Google Scholar · View at Scopus
  8. D. Wu, P. Hugenholtz, K. Mavromatis et al., “A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea,” Nature, vol. 462, no. 7276, pp. 1056–1060, 2009. View at Publisher · View at Google Scholar · View at Scopus
  9. N. C. Kyrpides, “Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream,” Nature Biotechnology, vol. 27, no. 7, pp. 627–632, 2009. View at Publisher · View at Google Scholar · View at Scopus
  10. D. J. Lane, B. Pace, and G. J. Olsen, “Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses,” Proceedings of the National Academy of Sciences of the United States of America, vol. 82, no. 20, pp. 6955–6959, 1985. View at Scopus
  11. J. L. Stein, T. L. Marsh, K. Y. Wu, H. Shizuya, and E. F. Delong, “Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon,” Journal of Bacteriology, vol. 178, no. 3, pp. 591–599, 1996. View at Scopus
  12. S. G. Tringe and P. Hugenholtz, “A renaissance for the pioneering 16S rRNA gene,” Current Opinion in Microbiology, vol. 11, no. 5, pp. 442–446, 2008. View at Publisher · View at Google Scholar · View at Scopus
  13. D. B. Rusch, A. L. Halpern, G. Sutton et al., “The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific,” PLoS Biology, vol. 5, no. 3, article e77, 2007. View at Publisher · View at Google Scholar · View at Scopus
  14. R. Drmanac, A. B. Sparks, M. J. Callow et al., “Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays,” Science, vol. 327, no. 5961, pp. 78–81, 2010. View at Publisher · View at Google Scholar · View at Scopus
  15. E. R. Mardis, “The impact of next-generation sequencing technology on genetics,” Trends in Genetics, vol. 24, no. 3, pp. 133–141, 2008. View at Publisher · View at Google Scholar · View at Scopus
  16. M. L. Metzker, “Sequencing technologies the next generation,” Nature Reviews Genetics, vol. 11, no. 1, pp. 31–46, 2010. View at Publisher · View at Google Scholar · View at Scopus
  17. J. Handelsman, M. R. Rondon, S. F. Brady, J. Clardy, and R. M. Goodman, “Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products,” Chemistry and Biology, vol. 5, no. 10, pp. R245–R249, 1998. View at Scopus
  18. G. W. Tyson, J. Chapman, P. Hugenholtz et al., “Community structure and metabolism through reconstruction of microbial genomes from the environment,” Nature, vol. 428, no. 6978, pp. 37–43, 2004. View at Publisher · View at Google Scholar · View at Scopus
  19. D. Chivian, E. L. Brodie, E. J. Alm et al., “Environmental genomics reveals a single-species ecosystem deep within earth,” Science, vol. 322, no. 5899, pp. 275–278, 2008. View at Publisher · View at Google Scholar · View at Scopus
  20. T. Woyke, H. Teeling, N. N. Ivanova et al., “Symbiosis insights through metagenomic analysis of a microbial consortium,” Nature, vol. 443, no. 7114, pp. 950–955, 2006. View at Publisher · View at Google Scholar · View at Scopus
  21. F. B. Dean, J. R. Nelson, T. L. Giesler, and R. S. Lasken, “Rapid amplification of plasmid and phage DNA using Phi29 DNA polymerase and multiply-primed rolling circle amplification,” Genome Research, vol. 11, no. 6, pp. 1095–1099, 2001. View at Publisher · View at Google Scholar · View at Scopus
  22. R. S. Lasken, “Single-cell genomic sequencing using multiple displacement amplification,” Current Opinion in Microbiology, vol. 10, no. 5, pp. 510–516, 2007. View at Publisher · View at Google Scholar · View at Scopus
  23. T. C. Hazen, E. A. Dubinsky, T. Z. DeSantis et al., “Deep-sea oil plume enriches indigenous oil-degrading bacteria,” Science, vol. 330, no. 6001, pp. 204–208, 2010. View at Publisher · View at Google Scholar · View at Scopus
  24. Z. He, Y. Deng, J. D. Van Nostrand et al., “GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity,” ISME Journal, vol. 4, no. 9, pp. 1167–1179, 2010. View at Publisher · View at Google Scholar · View at Scopus
  25. C. A. Kellogg, Y. M. Piceno, L. M. Tom, T. Z. DeSantis, D. G. Zawada, and G. L. Andersen, “PhyloChip microarray comparison of sampling methods used for coral microbial ecology,” Journal of Microbiological Methods, vol. 88, no. 1, pp. 103–109, 2012. View at Publisher · View at Google Scholar · View at Scopus
  26. T. Z. DeSantis, I. Dubosarskiy, S. R. Murray, and G. L. Andersen, “Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA,” Bioinformatics, vol. 19, no. 12, pp. 1461–1468, 2003. View at Publisher · View at Google Scholar · View at Scopus
  27. L. Wu, D. K. Thompson, G. Li, R. A. Hurt, J. M. Tiedje, and J. Zhou, “Development and evaluation of functional gene arrays for detection of selected genes in the environment,” Applied and Environmental Microbiology, vol. 67, no. 12, pp. 5780–5790, 2001. View at Publisher · View at Google Scholar · View at Scopus
  28. J. Adamczyk, M. Hesselsoe, N. Iversen et al., “The isotope array, a new tool that employs substrate-mediated labeling of rrna for determination of microbial community structure and function,” Applied and Environmental Microbiology, vol. 69, no. 11, pp. 6875–6887, 2003. View at Publisher · View at Google Scholar · View at Scopus
  29. P. Dennis, E. A. Edwards, S. N. Liss, and R. Fulthorpe, “Monitoring gene expression in mixed microbial communities by using DNA microarrays,” Applied and Environmental Microbiology, vol. 69, no. 2, pp. 769–778, 2003. View at Publisher · View at Google Scholar · View at Scopus
  30. L. Bodrossy and A. Sessitsch, “Oligonucleotide microarrays in microbial diagnostics,” Current Opinion in Microbiology, vol. 7, no. 3, pp. 245–254, 2004. View at Publisher · View at Google Scholar · View at Scopus
  31. T. Majtán, G. Bukovská, and J. Timko, “DNA microarrays—techniques and applications in microbial systems,” Folia Microbiologica, vol. 49, no. 6, pp. 635–664, 2004. View at Scopus
  32. V. Torsvik and L. Øvreås, “Microbial diversity and function in soil: from genes to ecosystems,” Current Opinion in Microbiology, vol. 5, no. 3, pp. 240–245, 2002. View at Publisher · View at Google Scholar · View at Scopus
  33. P. Hugenholtz and N. C. Kyrpides, “A changing of the guard: genomics update,” Environmental Microbiology, vol. 11, no. 3, pp. 551–553, 2009. View at Publisher · View at Google Scholar · View at Scopus
  34. E. L. Brodie, T. Z. DeSantis, J. P. Moberg Parker, I. X. Zubietta, Y. M. Piceno, and G. L. Andersen, “Urban aerosols harbor diverse and dynamic bacterial populations,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 1, pp. 299–304, 2007. View at Publisher · View at Google Scholar · View at Scopus
  35. G. Tsiamis, K. Katsaveli, S. Ntougias et al., “Prokaryotic community profiles at different operational stages of a Greek solar saltern,” Research in Microbiology, vol. 159, no. 9-10, pp. 609–627, 2008. View at Publisher · View at Google Scholar · View at Scopus
  36. G. Tsiamis, G. Tzagkaraki, A. Chamalaki et al., “Olive-mill wastewater bacterial communities display a cultivar specific profile,” Current Microbiology, vol. 64, no. 2, pp. 197–203, 2012. View at Publisher · View at Google Scholar · View at Scopus
  37. E. L. Brodie, T. Z. DeSantis, D. C. Joyner et al., “Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation,” Applied and Environmental Microbiology, vol. 72, no. 9, pp. 6288–6298, 2006. View at Publisher · View at Google Scholar · View at Scopus
  38. D.-Y. Lee, K. Shannon, and L. A. Beaudette, “Detection of bacterial pathogens in municipal wastewater using an oligonucleotide microarray and real-time quantitative PCR,” Journal of Microbiological Methods, vol. 65, no. 3, pp. 453–467, 2006. View at Publisher · View at Google Scholar · View at Scopus
  39. K. Katsaveli, D. Vayenas, G. Tsiamis, and K. Bourtzis, “Bacterial diversity in Cr(VI) and Cr(III)-contaminated industrial wastewaters,” Extremophiles, vol. 16, no. 2, pp. 285–296, 2012. View at Publisher · View at Google Scholar · View at Scopus
  40. T. Z. DeSantis, E. L. Brodie, J. P. Moberg, I. X. Zubieta, Y. M. Piceno, and G. L. Andersen, “High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment,” Microbial Ecology, vol. 53, no. 3, pp. 371–383, 2007. View at Publisher · View at Google Scholar · View at Scopus
  41. T. M. Korves, Y. M. Piceno, L. M. Tom et al., “Bacterial communities in commercial aircraft high-efficiency particulate air (HEPA) filters assessed by PhyloChip analysis,” Indoor Air, vol. 23, no. 1, pp. 50–61, 2013.
  42. F. Reith, J. Brugger, C. M. Zammit et al., “Influence of geogenic factors on microbial communities in metallogenic Australian soils,” The ISME Journal, vol. 6, pp. 2107–2118, 2012. View at Publisher · View at Google Scholar
  43. U. S. Sagaram, K. M. Deangelis, P. Trivedi, G. L. Andersen, S.-E. Lu, and N. Wang, “Bacterial diversity analysis of huanglongbing pathogen-infected citrus, using phyloChip arrays and 16S rRNA gene clone library sequencing,” Applied and Environmental Microbiology, vol. 75, no. 6, pp. 1566–1574, 2009. View at Publisher · View at Google Scholar · View at Scopus
  44. M. J. Cox, Y. J. Huang, K. E. Fujimura et al., “Lactobacillus casei abundance is associated with profound shifts in the infant gut microbiome,” PLoS One, vol. 5, no. 1, Article ID e8745, 2010. View at Publisher · View at Google Scholar · View at Scopus
  45. C. Rinke, P. Schwientek, A. Sczyrba et al., “Insights into the phylogeny and coding potential of microbial dark matter,” Nature, vol. 499, no. 7459, pp. 431–437, 2013.
  46. C. Palmer, E. M. Bik, M. B. Eisen et al., “Rapid quantitative profiling of complex microbial populations,” Nucleic Acids Research, vol. 34, no. 1, p. e5, 2006. View at Publisher · View at Google Scholar · View at Scopus
  47. J.-C. Cho and J. M. Tiedje, “Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays,” Applied and Environmental Microbiology, vol. 67, no. 8, pp. 3677–3682, 2001. View at Publisher · View at Google Scholar · View at Scopus
  48. E. A. Greene and G. Voordouw, “Analysis of environmental microbial communities by reverse sample genome probing,” Journal of Microbiological Methods, vol. 53, no. 2, pp. 211–219, 2003. View at Publisher · View at Google Scholar · View at Scopus
  49. J. D. Van Nostrand, Z. He, and J. Zhou, “Dynamics of microbes in the natural setting: development of the Geochip,” in Environmental Microbiology, K. Sen and N. J. Ashbolt, Eds., Caister Academic, Norfolk, UK, 2011.
  50. Z. He, Y. Deng, and J. Zhou, “Development of functional gene microarrays for microbial community analysis,” Current Opinion in Biotechnology, vol. 23, no. 1, pp. 49–55, 2012. View at Publisher · View at Google Scholar · View at Scopus
  51. J. Xie, Z. He, X. Liu et al., “GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage,” Applied and Environmental Microbiology, vol. 77, no. 3, pp. 991–999, 2011. View at Publisher · View at Google Scholar · View at Scopus
  52. Z. He, J. D. Van Nostrand, and J. Zhou, “Applications of functional gene microarrays for profiling microbial communities,” Current Opinion in Biotechnology, vol. 23, no. 3, pp. 460–466, 2012. View at Publisher · View at Google Scholar · View at Scopus
  53. M. J. Beazley, R. J. Martinez, S. Rajan et al., “Microbial community analysis of a coastal salt marsh affected by the Deepwater Horizon oil spill,” PLoS One, vol. 7, no. 7, Article ID e41305, 2012.
  54. G. Yamey, “Scientists unveil first draft of human genome,” British Medical Journal, vol. 321, no. 7252, p. 7, 2000. View at Scopus
  55. J. Craig Venter, M. D. Adams, E. W. Myers et al., “The sequence of the human genome,” Science, vol. 291, no. 5507, pp. 1304–1351, 2001. View at Publisher · View at Google Scholar · View at Scopus
  56. E. S. Lander, L. M. Linton, B. Birren et al., “Initial sequencing and analysis of the human genome,” Nature, vol. 409, no. 6822, pp. 860–921, 2001. View at Publisher · View at Google Scholar · View at Scopus
  57. C. S. Pareek, R. Smoczynski, and A. Tretyn, “Sequencing technologies and genome sequencing,” Journal of Applied Genetics, vol. 52, no. 4, pp. 413–435, 2011. View at Publisher · View at Google Scholar · View at Scopus
  58. T. P. Niedringhaus, D. Milanova, M. B. Kerby, M. P. Snyder, and A. E. Barron, “Landscape of next-generation sequencing technologies,” Analytical Chemistry, vol. 83, no. 12, pp. 4327–4341, 2011. View at Publisher · View at Google Scholar · View at Scopus
  59. M. Ronaghi, S. Karamohamed, B. Pettersson, M. Uhlén, and P. Nyrén, “Real-time DNA sequencing using detection of pyrophosphate release,” Analytical Biochemistry, vol. 242, no. 1, pp. 84–89, 1996. View at Publisher · View at Google Scholar · View at Scopus
  60. M. Ronaghi, M. Uhlén, and P. Nyrén, “A sequencing method based on real-time pyrophosphate,” Science, vol. 281, no. 5375, pp. 363–365, 1998. View at Publisher · View at Google Scholar · View at Scopus
  61. M. Margulies, M. Egholm, W. E. Altman et al., “Genome sequencing in microfabricated high-density picolitre reactors,” Nature, vol. 437, no. 7057, pp. 376–380, 2005. View at Publisher · View at Google Scholar · View at Scopus
  62. E. R. Mardis, “A decade's perspective on DNA sequencing technology,” Nature, vol. 470, no. 7333, pp. 198–203, 2011. View at Publisher · View at Google Scholar · View at Scopus
  63. O. Morozova, M. Hirst, and M. A. Marra, “Applications of new sequencing technologies for transcriptome analysis,” Annual Review of Genomics and Human Genetics, vol. 10, pp. 135–151, 2009. View at Publisher · View at Google Scholar · View at Scopus
  64. H. L. Harris, L. J. Brennan, B. A. Keddie, and H. R. Braig, “Bacterial symbionts in insects: balancing life and death,” Symbiosis, vol. 51, no. 1, pp. 37–53, 2010. View at Publisher · View at Google Scholar · View at Scopus
  65. N. Whiteford, T. Skelly, C. Curtis et al., “Swift: primary data analysis for the Illumina Solexa sequencing platform,” Bioinformatics, vol. 25, no. 17, pp. 2194–2199, 2009. View at Publisher · View at Google Scholar · View at Scopus
  66. F. Tang, C. Barbacioru, Y. Wang et al., “mRNA-Seq whole-transcriptome analysis of a single cell,” Nature Methods, vol. 6, no. 5, pp. 377–382, 2009. View at Publisher · View at Google Scholar · View at Scopus
  67. N. Cloonan, A. R. R. Forrest, G. Kolle et al., “Stem cell transcriptome profiling via massive-scale mRNA sequencing,” Nature Methods, vol. 5, no. 7, pp. 613–619, 2008. View at Publisher · View at Google Scholar · View at Scopus
  68. J. M. Rothberg, W. Hinz, T. M. Rearick et al., “An integrated semiconductor device enabling non-optical genome sequencing,” Nature, vol. 475, no. 7356, pp. 348–352, 2011. View at Publisher · View at Google Scholar · View at Scopus
  69. M. A. Quail, M. Smith, P. Coupland et al., “A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers,” BMC Genomics, vol. 13, article 341, 2012.
  70. J. Eid, A. Fehr, J. Gray et al., “Real-time DNA sequencing from single polymerase molecules,” Science, vol. 323, no. 5910, pp. 133–138, 2009. View at Publisher · View at Google Scholar · View at Scopus
  71. N. J. Loman, R. V. Misra, T. J. Dallman et al., “Performance comparison of benchtop high-throughput sequencing platforms,” Nature Biotechnology, vol. 30, no. 5, pp. 434–439, 2012.
  72. N. R. Pace, D. A. Stahl, D. J. Lane, and G. J. Olsen, “The analysis of natural microbial populations by ribosomal RNA sequences,” ASM News, vol. 51, no. 4, pp. 4–12, 1985.
  73. G. Muyzer, “DGGE/TGGE a method for identifying genes from natural ecosystems,” Current Opinion in Microbiology, vol. 2, no. 3, pp. 317–322, 1999. View at Publisher · View at Google Scholar · View at Scopus
  74. G. Laguerre, M.-R. Allard, F. Revoy, and N. Amarger, “Rapid identification of rhizobia by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes,” Applied and Environmental Microbiology, vol. 60, no. 1, pp. 56–63, 1994. View at Scopus
  75. J. Dunbar, L. O. Ticknor, and C. R. Kuske, “Assessment of microbial diversity in four Southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis,” Applied and Environmental Microbiology, vol. 66, no. 7, pp. 2943–2950, 2000. View at Publisher · View at Google Scholar · View at Scopus
  76. D.-H. Lee, Y.-G. Zo, and S.-J. Kim, “Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism,” Applied and Environmental Microbiology, vol. 62, no. 9, pp. 3112–3120, 1996. View at Scopus
  77. D. Medini, D. Serruto, J. Parkhill et al., “Microbiology in the post-genomic era,” Nature Reviews Microbiology, vol. 6, no. 6, pp. 419–430, 2008. View at Publisher · View at Google Scholar · View at Scopus
  78. A. Fabrice and R. Didier, “Exploring microbial diversity using 16S rRNA high-throughput methods,” Journal of Computer Science and Systems Biology, pp. 074–092, 2009. View at Publisher · View at Google Scholar
  79. P. D. Schloss, D. Gevers, and S. L. Westcott, “Reducing the effects of PCR amplification and sequencing Artifacts on 16s rRNA-based studies,” PLoS One, vol. 6, no. 12, Article ID e27310, 2011. View at Publisher · View at Google Scholar · View at Scopus
  80. B. J. Baker and J. F. Banfield, “Microbial communities in acid mine drainage,” FEMS Microbiology Ecology, vol. 44, no. 2, pp. 139–152, 2003. View at Publisher · View at Google Scholar · View at Scopus
  81. C. W. Nossa, W. E. Oberdorf, L. Yang et al., “Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome,” World Journal of Gastroenterology, vol. 16, no. 33, pp. 4135–4144, 2010. View at Publisher · View at Google Scholar · View at Scopus
  82. N. Youssef, C. S. Sheik, L. R. Krumholz, F. Z. Najar, B. A. Roe, and M. S. Elshahed, “Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys,” Applied and Environmental Microbiology, vol. 75, no. 16, pp. 5227–5236, 2009. View at Publisher · View at Google Scholar · View at Scopus
  83. Y. Wang and P.-Y. Qian, “Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies,” PLoS One, vol. 4, no. 10, Article ID e7401, 2009. View at Publisher · View at Google Scholar · View at Scopus
  84. B. J. Paster, S. K. Boches, J. L. Galvin et al., “Bacterial diversity in human subgingival plaque,” Journal of Bacteriology, vol. 183, no. 12, pp. 3770–3783, 2001. View at Publisher · View at Google Scholar · View at Scopus
  85. J. E. Clarridge III, “Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases,” Clinical Microbiology Reviews, vol. 17, no. 4, pp. 840–862, 2004. View at Publisher · View at Google Scholar · View at Scopus
  86. B. Wang, J. Wang, W. Zhang, and D. R. Meldrum, “Application of synthetic biology in cyanobacteria and algae,” Frontiers in Microbiology, vol. 3, article 344, 2012.
  87. S. Chakravorty, D. Helb, M. Burday, N. Connell, and D. Alland, “A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria,” Journal of Microbiological Methods, vol. 69, no. 2, pp. 330–339, 2007. View at Publisher · View at Google Scholar · View at Scopus
  88. P. S. Kumar, M. R. Brooker, S. E. Dowd, and T. Camerlengo, “Target region selection is a critical determinant of community fingerprints generated by 16S Pyrosequencing,” PLoS One, vol. 6, no. 6, Article ID e20956, 2011. View at Publisher · View at Google Scholar · View at Scopus
  89. S. Vasileiadis, E. Puglisi, M. Arena, F. Cappa, P. S. Cocconcelli, and M. Trevisan, “Soil bacterial diversity screening using single 16S rRNA gene V regions coupled with multi-million read generating sequencing technologies,” PLoS One, vol. 7, no. 8, Article ID e42671, 2012.
  90. L. F. W. Roesch, R. R. Fulthorpe, A. Riva et al., “Pyrosequencing enumerates and contrasts soil microbial diversity,” ISME Journal, vol. 1, no. 4, pp. 283–290, 2007. View at Publisher · View at Google Scholar · View at Scopus
  91. V. Acosta-Martínez, S. Dowd, Y. Sun, and V. Allen, “Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use,” Soil Biology and Biochemistry, vol. 40, no. 11, pp. 2762–2770, 2008. View at Publisher · View at Google Scholar · View at Scopus
  92. S. Vasileiadis, E. Puglisi, M. Arena et al., “Soil microbial diversity patterns of a lowland spring environment,” FEMS Microbiology Ecology, 2013. View at Publisher · View at Google Scholar
  93. J. Rousk, E. Bååth, P. C. Brookes et al., “Soil bacterial and fungal communities across a pH gradient in an arable soil,” ISME Journal, vol. 4, no. 10, pp. 1340–1352, 2010. View at Publisher · View at Google Scholar · View at Scopus
  94. H. Nacke, A. Thürmer, A. Wollherr et al., “Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils,” PLoS One, vol. 6, no. 2, Article ID e17000, 2011. View at Publisher · View at Google Scholar · View at Scopus
  95. M. Buée, M. Reich, C. Murat et al., “454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity,” New Phytologist, vol. 184, no. 2, pp. 449–456, 2009. View at Publisher · View at Google Scholar · View at Scopus
  96. A. Jumpponen, K. L. Jones, and J. Blair, “Vertical distribution of fungal communities in tallgrass prairie soil,” Mycologia, vol. 102, no. 5, pp. 1027–1041, 2010. View at Publisher · View at Google Scholar · View at Scopus
  97. T. Stoeck, D. Bass, M. Nebel et al., “Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water,” Molecular Ecology, vol. 19, no. 1, pp. 21–31, 2010. View at Publisher · View at Google Scholar · View at Scopus
  98. R. Logares, S. Audic, S. Santini, M. C. Pernice, C. de Vargas, and R. Massana, “Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing,” ISME Journal, vol. 6, no. 10, pp. 1823–1833, 2012. View at Publisher · View at Google Scholar · View at Scopus
  99. J. A. Gilbert, J. A. Steele, J. G. Caporaso et al., “Defining seasonal marine microbial community dynamics,” ISME Journal, vol. 6, no. 2, pp. 298–308, 2012. View at Publisher · View at Google Scholar · View at Scopus
  100. S. Monchy, G. Sanciu, M. Jobard et al., “Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing,” Environmental Microbiology, vol. 13, no. 6, pp. 1433–1453, 2011. View at Publisher · View at Google Scholar · View at Scopus
  101. R. Logares, E. S. Lindström, S. Langenheder et al., “Biogeography of bacterial communities exposed to progressive long-term environmental change,” The ISME Journal, vol. 7, no. 5, pp. 937–948, 2013.
  102. N. Taib, J. F. Mangot, I. Domaizon, G. Bronner, and D. Debroas, “Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: new insights into the freshwater protist diversity,” PLoS One, vol. 8, article e58950, no. 3, 2013.
  103. C. E. Robertson, L. K. Baumgartner, J. K. Harris et al., “Culture-independent analysis of aerosol microbiology in a metropolitan subway system,” Applied and Environmental Microbiology, vol. 79, no. 11, pp. 3485–3493, 2013.
  104. C. Pedrós-Alió, “Marine microbial diversity: can it be determined?” Trends in Microbiology, vol. 14, no. 6, pp. 257–263, 2006. View at Publisher · View at Google Scholar · View at Scopus
  105. E. Pelletier, A. Kreimeyer, S. Bocs et al., “‘Candidatus Cloacamonas acidaminovorans’: genome sequence reconstruction provides a first glimpse of a new bacterial division,” Journal of Bacteriology, vol. 190, no. 7, pp. 2572–2579, 2008. View at Publisher · View at Google Scholar · View at Scopus
  106. K. F. Ettwig, M. K. Butler, D. Le Paslier et al., “Nitrite-driven anaerobic methane oxidation by oxygenic bacteria,” Nature, vol. 464, no. 7288, pp. 543–548, 2010. View at Publisher · View at Google Scholar · View at Scopus
  107. J. G. Elkins, M. Podar, D. E. Graham et al., “A korarchaeal genome reveals insights into the evolution of the Archaea,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 23, pp. 8102–8107, 2008. View at Publisher · View at Google Scholar · View at Scopus
  108. H. Tamaki, Y. Tanaka, H. Matsuzawa et al., “Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10,” International Journal of Systematic and Evolutionary Microbiology, vol. 61, no. 6, pp. 1442–1447, 2011. View at Publisher · View at Google Scholar · View at Scopus
  109. K. C. Wrighton, B. C. Thomas, I. Sharon et al., “Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla,” Science, vol. 337, no. 6102, pp. 1661–1665, 2012.
  110. T. Kalisky and S. R. Quake, “Single-cell genomics,” Nature Methods, vol. 8, no. 4, pp. 311–314, 2011. View at Publisher · View at Google Scholar · View at Scopus
  111. B. K. Swan, M. Martinez-Garcia, C. M. Preston et al., “Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean,” Science, vol. 333, no. 6047, pp. 1296–1300, 2011. View at Publisher · View at Google Scholar · View at Scopus
  112. T. Woyke, G. Xie, A. Copeland et al., “Assembling the marine metagenome, one cell at a time,” PLoS One, vol. 4, no. 4, Article ID e5299, 2009. View at Publisher · View at Google Scholar · View at Scopus
  113. T. Woyke, D. Tighe, K. Mavromatis et al., “One bacterial cell, one complete genome,” PLoS One, vol. 5, no. 4, Article ID e10314, 2010. View at Publisher · View at Google Scholar · View at Scopus
  114. A. Raghunathan, H. R. Ferguson Jr., C. J. Bornarth, W. Song, M. Driscoll, and R. S. Lasken, “Genomic DNA amplification from a single bacterium,” Applied and Environmental Microbiology, vol. 71, no. 6, pp. 3342–3347, 2005. View at Publisher · View at Google Scholar · View at Scopus
  115. K. Leung, H. Zahn, T. Leaver et al., “A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities,” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 20, pp. 7665–7670, 2012.
  116. M. Podar, C. B. Abulencia, M. Walcher et al., “Targeted access to the genomes of low-abundance organisms in complex microbial communities,” Applied and Environmental Microbiology, vol. 73, no. 10, pp. 3205–3214, 2007. View at Publisher · View at Google Scholar · View at Scopus
  117. N. H. Youssef, P. C. Blainey, S. R. Quake, and M. S. Elshahed, “Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone spring, Oklahoma),” Applied and Environmental Microbiology, vol. 77, no. 21, pp. 7804–7814, 2011. View at Publisher · View at Google Scholar · View at Scopus
  118. A. Siegl, J. Kamke, T. Hochmuth et al., “Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges,” ISME Journal, vol. 5, no. 1, pp. 61–70, 2011. View at Publisher · View at Google Scholar · View at Scopus
  119. H. S. Yoon, D. C. Price, R. Stepanauskas et al., “Single-cell genomics reveals organismal interactions in uncultivated marine protists,” Science, vol. 332, no. 6030, pp. 714–717, 2011. View at Publisher · View at Google Scholar · View at Scopus
  120. R. Ghai, L. Pašić, A. B. Fernández et al., “New abundant microbial groups in aquatic hypersaline environments,” Scientific Reports, vol. 1, 135, 2011.
  121. H. Chitsaz, J. L. Yee-Greenbaum, G. Tesler et al., “Efficient de novo assembly of single-cell bacterial genomes from short-read data sets,” Nature Biotechnology, vol. 29, no. 10, pp. 915–922, 2011. View at Publisher · View at Google Scholar · View at Scopus
  122. P. C. Blainey, A. C. Mosier, A. Potanina, C. A. Francis, and S. R. Quake, “Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis,” PLoS One, vol. 6, no. 2, Article ID e16626, 2011. View at Publisher · View at Google Scholar · View at Scopus
  123. O. U. Mason, T. C. Hazen, S. Borglin et al., “Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill,” The ISME Journal, vol. 6, no. 9, pp. 1715–1727, 2012.
  124. M. Hess, A. Sczyrba, R. Egan et al., “Metagenomic discovery of biomass-degrading genes and genomes from cow rumen,” Science, vol. 331, no. 6016, pp. 463–467, 2011. View at Publisher · View at Google Scholar · View at Scopus
  125. P. Lorenz and J. Eck, “Metagenomics and industrial applications,” Nature Reviews Microbiology, vol. 3, no. 6, pp. 510–516, 2005. View at Publisher · View at Google Scholar · View at Scopus
  126. P. D. Schloss and J. Handelsman, “Biotechnological prospects from metagenomics,” Current Opinion in Biotechnology, vol. 14, no. 3, pp. 303–310, 2003. View at Publisher · View at Google Scholar · View at Scopus
  127. A. Siegl and U. Hentschel, “PKS and NRPS gene clusters from microbial symbiont cells of marine sponges by whole genome amplification,” Environmental Microbiology Reports, vol. 2, no. 4, pp. 507–513, 2010. View at Publisher · View at Google Scholar · View at Scopus
  128. M. Hess, A. Sczyrba, R. Egan et al., “Metagenomic discovery of biomass-degrading genes and genomes from cow rumen,” Science, vol. 331, no. 6016, pp. 463–467, 2011. View at Publisher · View at Google Scholar · View at Scopus
  129. M. Martinez-Garcia, D. M. Brazel, B. K. Swan et al., “Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of verrucomicrobia,” PLoS One, vol. 7, no. 4, Article ID e35314, 2012. View at Publisher · View at Google Scholar · View at Scopus
  130. M. A. Moran, “Metatranscriptomics: eavesdropping on complex microbial communities,” Microbe, vol. 4, no. 7, pp. 329–335, 2009. View at Scopus
  131. J. Zhou, L. Wu, Y. Deng et al., “Reproducibility and quantitation of amplicon sequencing-based detection,” ISME Journal, vol. 5, no. 8, pp. 1303–1313, 2011. View at Publisher · View at Google Scholar · View at Scopus
  132. J. Zhou, S. Kang, C. W. Schadt, and C. T. Garten Jr., “Spatial scaling of functional gene diversity across various microbial taxa,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 22, pp. 7768–7773, 2008. View at Publisher · View at Google Scholar · View at Scopus
  133. S. Turner, K. M. Pryer, V. P. W. Miao, and J. D. Palmer, “Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis,” Journal of Eukaryotic Microbiology, vol. 46, no. 4, pp. 327–338, 1999. View at Scopus
  134. D. J. Lane, “16S/23S rRNA sequencing,” in Nucleic Acid Techniques in Bacterial Systematics, E. Stackebrandt and M. Goodfellow, Eds., pp. 115–175, John Wiley & Son, New York, NY, USA, 1991.
  135. M. T. Suzuki and S. J. Giovannoni, “Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR,” Applied and Environmental Microbiology, vol. 62, no. 2, pp. 625–630, 1996. View at Scopus
  136. J. C. Makemson, N. R. Fulayfil, W. Landry et al., “Shewanella woodyi sp. nov., an Exclusively respiratory luminous bacterium isolated from the Alboran sea,” International Journal of Systematic Bacteriology, vol. 47, no. 4, pp. 1034–1039, 1997. View at Scopus
  137. N. Boon, W. De Windt, W. Verstraete, and E. M. Top, “Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants,” FEMS Microbiology Ecology, vol. 39, no. 2, pp. 101–112, 2002. View at Publisher · View at Google Scholar · View at Scopus
  138. H. Heuer, K. Hartung, G. Wieland, I. Kramer, and K. Smalla, “Polynucleotide probes that target a hypervariable region of 16S rRNA genes to identify bacterial isolates corresponding to bands of community fingerprints,” Applied and Environmental Microbiology, vol. 65, no. 3, pp. 1045–1049, 1999. View at Scopus
  139. J. Jonasson, M. Olofsson, and H.-J. Monstein, “Classification, identification and subtyping of bacteria based on pyrosequencing and signature matching of 16S rDNA fragments,” APMIS, vol. 110, no. 3, pp. 263–272, 2002. View at Publisher · View at Google Scholar · View at Scopus