Table of Contents Author Guidelines Submit a Manuscript
Archaea
Volume 2016, Article ID 2690329, 12 pages
http://dx.doi.org/10.1155/2016/2690329
Research Article

Marine Subsurface Microbial Community Shifts Across a Hydrothermal Gradient in Okinawa Trough Sediments

Department of Geosciences, The Pennsylvania State University, 220 Deike Building, University Park, PA 16802, USA

Received 9 June 2016; Revised 12 October 2016; Accepted 23 October 2016

Academic Editor: André Antunes

Copyright © 2016 Leah D. Brandt and Christopher H. House. 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. K. Yanagawa, T. Nunoura, S. M. McAllister et al., “The first microbiological contamination assessment by deep-sea drilling and coring by the D/V chikyu at the iheya north hydrothermal field in the mid-okinawa trough (IODP Expedition 331),” Frontiers in Microbiology, vol. 4, article 327, 10 pages, 2013. View at Publisher · View at Google Scholar · View at Scopus
  2. K.-U. Hinrichs and F. Inagaki, “Downsizing the deep biosphere,” Science, vol. 338, no. 6104, pp. 204–205, 2012. View at Publisher · View at Google Scholar · View at Scopus
  3. C. R. Fisher, K. Takai, and N. le Bris, “Hydrothermal vent ecosystems,” Oceanography, vol. 20, no. 1, pp. 14–23, 2007. View at Google Scholar · View at Scopus
  4. R. J. Parkes, B. A. Cragg, and P. Wellsbury, “Recent studies on bacterial populations and processes in subseafloor sediments: a review,” Hydrogeology Journal, vol. 8, no. 1, pp. 11–28, 2000. View at Publisher · View at Google Scholar · View at Scopus
  5. B. N. Orcutt, J. B. Sylvan, N. J. Knab, and K. J. Edwards, “Microbial ecology of the dark ocean above, at, and below the seafloor,” Microbiology and Molecular Biology Reviews, vol. 75, no. 2, pp. 361–422, 2011. View at Publisher · View at Google Scholar · View at Scopus
  6. A. D. Miall, “Interarc and backarc basins on oceanic or transitional crust,” in Principles of Sedimentary Basin Analysis, pp. 504–507, Springer, Berlin, Germany, 2000. View at Google Scholar
  7. K. Takai, M. J. Mottl, S. H. Nielsen, and The Expedition 331 Scientists, “Deep hot biosphere,” in Proceedings of the Integrated Ocean Drilling Program, vol. 331, 2011.
  8. M.-C. Ciobanu, G. Burgaud, A. Dufresne et al., “Microorganisms persist at record depths in the subseafloor of the Canterbury Basin,” ISME Journal, vol. 8, no. 7, pp. 1370–1380, 2014. View at Publisher · View at Google Scholar · View at Scopus
  9. L. D. Brandt, J. Hser Wah Saw, T. Ettema, and C. H. House, “Marine subsurface microbial communities across a hydrothermal gradient in Okinawa Trough Sediments (B11I-0562),” in Proceedings of the American Geophysical Union Annual Fall Meeting, San Francisco, Calif, USA, December 2015.
  10. A. Herrera and C. S. Cockell, “Exploring microbial diversity in volcanic environments: a review of methods in DNA extraction,” Journal of Microbiological Methods, vol. 70, no. 1, pp. 1–12, 2007. View at Publisher · View at Google Scholar · View at Scopus
  11. M. E. Rhodes, A. Oren, and C. H. House, “Dynamics and persistence of dead sea microbial populations as shown by high-throughput sequencing of rRNA,” Applied and Environmental Microbiology, vol. 78, no. 7, pp. 2489–2492, 2012. View at Publisher · View at Google Scholar · View at Scopus
  12. P. D. Schloss, S. L. Westcott, T. Ryabin et al., “Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities,” Applied and Environmental Microbiology, vol. 75, no. 23, pp. 7537–7541, 2009. View at Publisher · View at Google Scholar · View at Scopus
  13. F. Meyer, D. Paarmann, M. D'Souza et al., “The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes,” BMC Bioinformatics, vol. 9, article 386, 2008. View at Publisher · View at Google Scholar
  14. C. Quast, E. Pruesse, P. Yilmaz et al., “The SILVA ribosomal RNA gene database project: improved data processing and web-based tools,” Nucleic Acids Research, vol. 41, no. 1, pp. D590–D596, 2013. View at Publisher · View at Google Scholar · View at Scopus
  15. E. Pruesse, J. Peplies, and F. O. Glöckner, “SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes,” Bioinformatics, vol. 28, no. 14, Article ID bts252, pp. 1823–1829, 2012. View at Publisher · View at Google Scholar · View at Scopus
  16. W. Li and A. Godzik, “Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences,” Bioinformatics, vol. 22, no. 13, pp. 1658–1659, 2006. View at Publisher · View at Google Scholar · View at Scopus
  17. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990. View at Publisher · View at Google Scholar · View at Scopus
  18. C. Camacho, G. Coulouris, V. Avagyan et al., “BLAST+: architecture and applications,” BMC Bioinformatics, vol. 10, article 421, 2009. View at Publisher · View at Google Scholar · View at Scopus
  19. S. M. Huse, D. B. M. Welch, A. Voorhis et al., “VAMPS: a website for visualization and analysis of microbial population structures,” BMC Bioinformatics, vol. 15, article 41, 2014. View at Publisher · View at Google Scholar · View at Scopus
  20. T. Sowers, S. Bernard, O. Aballain, J. Chappellaz, J.-M. Barnola, and T. Marik, “Records of the δ13C of atmospheric CH4 over the last 2 centuries as recorded in Antarctic snow and ice,” Global Biogeochemical Cycles, vol. 19, no. 2, Article ID GB2002, pp. 1–12, 2005. View at Publisher · View at Google Scholar · View at Scopus
  21. J. Schmitt, B. Seth, M. Bock et al., “On the interference of 86Kr2+ during carbon isotope analysis of atmospheric methane using continuous flow combustion—isotope ratio mass spectrometry,” Atmospheric Measurement Techniques, vol. 6, pp. 1409–1460, 2013. View at Publisher · View at Google Scholar
  22. V. P. Edgcomb, D. Beaudoin, R. Gast, J. F. Biddle, and A. Teske, “Marine subsurface eukaryotes: the fungal majority,” Environmental Microbiology, vol. 13, no. 1, pp. 172–183, 2011. View at Publisher · View at Google Scholar · View at Scopus
  23. W. D. Orsi, V. P. Edgcomb, G. D. Christman, and J. F. Biddle, “Gene expression in the deep biosphere,” Nature, vol. 499, no. 7457, pp. 205–208, 2013. View at Publisher · View at Google Scholar · View at Scopus
  24. M. S. Rappé and S. J. Giovannoni, “The uncultured microbial majority,” Annual Review of Microbiology, vol. 57, pp. 369–394, 2003. View at Publisher · View at Google Scholar · View at Scopus
  25. A. Schippers, L. N. Neretin, J. Kallmeyer et al., “Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria,” Nature, vol. 433, no. 7028, pp. 861–864, 2005. View at Publisher · View at Google Scholar · View at Scopus
  26. J. F. Biddle, J. S. Lipp, M. A. Lever et al., “Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 10, pp. 3846–3851, 2006. View at Publisher · View at Google Scholar · View at Scopus
  27. A. Teske and K. B. Sørensen, “Uncultured archaea in deep marine subsurface sediments: have we caught them all?” ISME Journal, vol. 2, no. 1, pp. 3–18, 2008. View at Publisher · View at Google Scholar · View at Scopus
  28. J. Meng, J. Xu, D. Qin, Y. He, X. Xiao, and F. Wang, “Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses,” ISME Journal, vol. 8, no. 3, pp. 650–659, 2014. View at Publisher · View at Google Scholar · View at Scopus
  29. T. B. Meador, M. Bowles, C. S. Lazar, C. Zhu, A. Teske, and K.-U. Hinrichs, “The archaeal lipidome in estuarine sediment dominated by members of the Miscellaneous Crenarchaeotal Group,” Environmental Microbiology, vol. 17, no. 7, pp. 2441–2458, 2015. View at Publisher · View at Google Scholar · View at Scopus
  30. C. S. Lazar, B. J. Baker, K. Seitz et al., “Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments,” Environmental Microbiology, vol. 18, no. 4, pp. 1200–1211, 2016. View at Publisher · View at Google Scholar · View at Scopus
  31. K. Kubo, K. G. Lloyd, J. F Biddle, R. Amann, A. Teske, and K. Knittel, “Archaea of the miscellaneous crenarchaeotal group are abundant, diverse and widespread in marine sediments,” ISME Journal, vol. 6, no. 10, pp. 1949–1965, 2012. View at Publisher · View at Google Scholar · View at Scopus
  32. K. G. Lloyd, L. Schreiber, D. G. Petersen et al., “Predominant archaea in marine sediments degrade detrital proteins,” Nature, vol. 496, no. 7444, pp. 215–218, 2013. View at Publisher · View at Google Scholar · View at Scopus
  33. P. N. Evans, D. H. Parks, G. L. Chadwick et al., “Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics,” Science, vol. 350, no. 6259, pp. 434–438, 2015. View at Publisher · View at Google Scholar · View at Scopus
  34. K. Takai and K. Horikoshi, “Genetic diversity of archaea in deep-sea hydrothermal vent environments,” Genetics, vol. 152, no. 4, pp. 1285–1297, 1999. View at Google Scholar · View at Scopus
  35. A. Boetius, K. Ravenschlag, C. J. Schubert et al., “A marine microbial consortium apparently mediating anaerobic oxidation of methane,” Nature, vol. 407, pp. 623–626, 2000. View at Publisher · View at Google Scholar
  36. K. Knittel, T. Lösekann, A. Boetius, R. Kort, and R. Amann, “Diversity and distribution of methanotrophic archaea at cold seeps,” Applied and Environmental Microbiology, vol. 71, no. 1, pp. 467–479, 2005. View at Publisher · View at Google Scholar · View at Scopus
  37. L. D. Kulm, E. Suess, J. C. Moore et al., “Oregon subduction zone: venting, fauna, and carbonates,” Science, vol. 231, no. 4738, pp. 561–566, 1986. View at Publisher · View at Google Scholar · View at Scopus
  38. A. Teske, K.-U. Hinrichs, V. Edgcomb et al., “Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities,” Applied and Environmental Microbiology, vol. 68, no. 4, pp. 1994–2007, 2002. View at Publisher · View at Google Scholar · View at Scopus
  39. J. F. Biddle, Z. Cardman, H. Mendlovitz et al., “Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments,” ISME Journal, vol. 6, no. 5, pp. 1018–1031, 2012. View at Publisher · View at Google Scholar · View at Scopus
  40. K. Knittel and A. Boetius, “Anaerobic oxidation of methane: progress with an unknown process,” Annual Review of Microbiology, vol. 63, pp. 311–334, 2009. View at Publisher · View at Google Scholar · View at Scopus
  41. M. J. Whiticar and E. Faber, “Methane oxidation in sediment and water column environments-Isotope evidence,” Organic Geochemistry, vol. 10, no. 4–6, pp. 759–768, 1986. View at Publisher · View at Google Scholar · View at Scopus
  42. F. J. Sansone, M. E. Holmes, and B. N. Popp, “Methane stable isotopic ratios and concentrations as indicators of methane dynamics in estuaries,” Global Biogeochemical Cycles, vol. 13, no. 2, pp. 463–474, 1999. View at Publisher · View at Google Scholar · View at Scopus
  43. K. Yanagawa, A. Ijiri, A. Breuker et al., “Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor,” The ISME Journal, 2016. View at Publisher · View at Google Scholar