Characterization of microbial population shifts during sample storage

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doi: 10.3389/fmicb.2012.00049
Author(s): Mills, Heath J.; Reese, Brandi Kiel; St. Peter, Cruz
Author Affiliation(s): Primary:
Texas A&M University, Department of Oceanography, College Station, TX, United States
University of Southern California, United States
Volume Title: Frontiers in Microbiology
Source: Frontiers in Microbiology, Vol.3(Article 49), p.1-16. Publisher: Frontiers Research Foundation, Lausanne, Switzerland. ISSN: 1664-302X
Note: In English. Includes appendices. 30 refs.; illus., incl. 2 tables
Summary: The objective of this study was to determine shifts in the microbial community structure and potential function based on standard Integrated Ocean Drilling Program (IODP) storage procedures for sediment cores. Standard long-term storage protocols maintain sediment temperature at 4°C for mineralogy, geochemical, and/or geotechnical analysis whereas standard microbiological sampling immediately preserves sediments at -80°C. Storage at 4°C does not take into account populations may remain active over geologic time scales at temperatures similar to storage conditions. Identification of active populations within the stored core would suggest geochemical and geophysical conditions within the core change over time. To test this potential, the metabolically active fraction of the total microbial community was characterized from IODP Expedition 325 Great Barrier Reef sediment cores prior to and following a 3-month storage period. Total RNA was extracted from complementary 2, 20, and 40 m below sea floor sediment samples, reverse transcribed to complementary DNA and then sequenced using 454 FLX sequencing technology, yielding over 14,800 sequences from the six samples. Interestingly, 97.3% of the sequences detected were associated with lineages that changed in detection frequency during the storage period including key biogeochemically relevant lineages associated with nitrogen, iron, and sulfur cycling. These lineages have the potential to permanently alter the physical and chemical characteristics of the sediment promoting misleading conclusions about the in situ biogeochemical environment. In addition, the detection of new lineages after storage increases the potential for a wider range of viable lineages within the subsurface that may be underestimated during standard community characterizations.
Year of Publication: 2012
Research Program: IODP Integrated Ocean Drilling Program
Key Words: 22 Environmental Geology; Communities; Coral Sea; Cores; Ecology; Effects; Expedition 325; Genetics; Geochemistry; Great Barrier Reef; Great Barrier Reef Environmental Changes; Hydrochemistry; IODP Site M0058; Integrated Ocean Drilling Program; Marine sediments; Microorganisms; Nucleic acids; Pacific Ocean; Phylogeny; Pore water; RNA; Sediments; South Pacific; Southwest Pacific; Storage; Variations; West Pacific
Coordinates: S170550 S170550 E1463521 E1463521
Record ID: 2013048187
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