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  • Data report: the DNA event horizon in the Guaymas Basin subsurface biosphere: technical advances and redefined limits in bulk extractions of nucleic acids from deep marine sediments, IODP Expedition 385
Title: Data report: the DNA event horizon in the Guaymas Basin subsurface biosphere: technical advances and redefined limits in bulk extractions of nucleic acids from deep marine sediments, IODP Expedition 385
We compiled DNA and RNA isolation protocols for sediment bulk extraction and their yields from Guaymas Basin subsurface sediments recovered during International Ocean Discovery Program Expedition 385 and evaluated their sensitivity for metagenomic and amplicon analyses of subsurface microbial communities. Guaymas Basin sediments present a challenge for DNA and RNA recovery due to high concentrations of hydrocarbons, steep thermal gradients, and rapidly declining cell numbers downhole. Metagenomic library construction and sequencing was possible from as little as 0.2 to 0.5 ng DNA/cm3 sediment; polymerase chain reaction (PCR) amplification of 16S rRNA genes required in most cases approximately 1–2 ng DNA/cm3 sediment. At in situ temperatures of 50° to 60°C, decreasing DNA recovery leads to increasingly uncertain hit or miss outcomes and failures for metagenomic and amplicon analyses. DNA concentration profiles show that, even before these hot temperatures are reached, relatively moderate temperatures (near 40°C) have a major effect on microbial abundance and DNA yield. Comparison with cell count profiles shows that hydrothermal influence reduces downhole cell densities by multiple orders of magnitude compared to nonhydrothermal sediments. This effect is also visible at relatively moderate temperatures. RNA recovery is highly sensitive to downhole increasing temperatures and decreasing cell numbers, and was most efficient for microbial communities in cool, relatively shallow subsurface sediments.  more » « less
Award ID(s):
1326927 2412279
PAR ID:
10572653
Author(s) / Creator(s):
; ; ; ; ; ; ; ;
Publisher / Repository:
International Ocean Discovery Program
Date Published:
Journal Name:
Proceedings of the International Ocean Discovery Program Expedition reports
Volume:
385
Issue:
204
ISSN:
2377-3189
ISBN:
978-1-954252-77-6
Subject(s) / Keyword(s):
International Ocean Discovery Program IODP JOIDES Resolution Expedition 385 Guaymas Basin Tectonics and Biosphere Site U1545 Site U1546 Site U1547 Site U1548 Site U1549 Site U1550 Site U1551 Site U1552
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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