The application of 454 FLX pyrosequencing to characterize active bacterial populations from the marine subsurface biosphere

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Author(s): Shepard, A.; Riedinger, N.; Dowd, S.; Reese, B. K.; Ferdelman, T. G.; Mills, H. J.
Author Affiliation(s): Primary:
Texas A & M University, College Station, TX, United States
Max-Planck Institute for Marine Microbiology, Germany
Medical Biofilm Research Institute, United States
Volume Title: AGU 2010 fall meeting
Source: Eos (Washington, DC), 91(Suppl.); American Geophysical Union 2010 fall meeting, San Francisco, CA, Dec. 13-17, 2010. Publisher: American Geophysical Union, Washington, DC, United States. ISSN: 0096-3941
Note: In English
Summary: Prokaryotes in the marine subsurface may represent up to 1/3 of Earth's total biomass yet the diversity, activity, metabolic processes, and impacts on global biogeochemical cycles of these organisms are relatively unknown. Therefore, prokaryotic community structure and metabolic diversity was determined from Nankai Trough sediment cores collected during Integrated Ocean Drilling Program (IODP) Leg 316. The application of 454-based high-throughput pyrosequencing of RNA transcripts provides the sequence data set resolution required to correlate geochemical profiles to the active microbial populations. The combination of methods promotes a more complete understanding of subsurface microbial ecology. Geochemical analysis of multiple sediment cores to depths greater than 200 meters below the seafloor (mbsf) was completed at sea as a part of standard IODP shipboard operations, or at the Max Planck Institute for Marine Microbiology in Bremen, Germany. Subsequent metagenomic analysis on the same sediment cores at similar depths determined the metabolically active fraction of the microbial community. RNA transcript copy numbers were quantified using a real time PCR machine and the bacterial population was characterized by pyrosequencing the SSU rRNA cDNA amplicons. Highest SSU rRNA copy numbers were observed in the shallower sediments, as predicted from higher concentrations of microbial cells and total organic carbon. A general reduction in total community structure diversity was also observed with depth. A shift in sulfate reducing populations from Deltaproteobacteria to Firmicutes-related lineages was detected from above to below the sulfate/methane transition zone. Interestingly, our results also suggested that some genres in the marine subsurface are metabolically active outside of geochemically predicted redox zones. For example, lineages capable of iron and sulfur oxidation and reduction were detected tens of meters below the sulfate/methane transition zone, suggesting that a tight microscale redox recycling of sulfur and iron may exist but is not detectable based solely on geochemical profiles. Thus, it is possible that microbial metabolic pathways previously thought to be restricted to specific geochemical zones may continue to impact geochemical cycling at unanticipated depths. The 454-based pyrosequencing analysis used in this study allowed multiple samples of understudied subsurface microbial communities to be simultaneously characterized, providing meaningful comparisons between community structure and geochemical profiles.
Year of Publication: 2010
Research Program: IODP Integrated Ocean Drilling Program
Key Words: 07 Marine Geology and Oceanography; Bacteria; Communities; Expedition 316; Integrated Ocean Drilling Program; Marine environment; NanTroSEIZE; North Pacific; Northwest Pacific; Pacific Ocean; Prokaryotes; Sediments; West Pacific
Coordinates: N330100 N331400 E1364800 E1364300
Record ID: 2019038139
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