Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales
John B. Kirkpatrick, Emily A. Walsh and Steven D’Hondt
- Author Affiliations
Graduate School of Oceanography, University of Rhode Island, 215 South Ferry Road, Narragansett, Rhode Island 02882, USA
Source/Fonte: Illuminating Fossils
Abstract
DNA in marine sediment contains both fossil sequences and sequences from organisms that live in the sediment. The demarcation between these two pools and their respective rates of turnover are generally unknown. We address these issues by comparing the total extractable DNA pool to the fraction of sequenced chloroplast DNA (cpDNA) in sediment from two sites in the Bering Sea. We assume that cpDNA is a tracer of non-reproducing fossil DNA. Given >150,000 sequence reads per sample, cpDNA is easily detectable in the shallowest samples but decays with depth, suggesting that sequencing-based richness assessments of communities in deep subseafloor sediment are relatively unaffected by fossil DNA. The initial decrease in cpDNA reads suggests that most cpDNA decays within 100–200 k.y. of deposition. However, cpDNA from a few phylotypes, including some that match fossil diatoms, are present throughout the cored sediment, ranging in age to 1.4 Ma. The relative fraction of sequences composed by cpDNA decreases non-linearly with increasing sediment age, suggesting that detectable cpDNA becomes more recalcitrant with age. This can be explained by biological activity decreasing with sediment age and/or by preferential long-term survival of only the most thoroughly protected DNA. The association of cpDNA reads with published records of siliceous microfossils, including diatom spores, at the same sites suggests that microfossils may help to preserve DNA. This DNA may be useful for studies of paleoenvironmental conditions and biological evolution on time scales that approach or exceed 1 m.y.
Acknowledgments
We thank the IODP; the staff, crew, and science party of Expedition 323; and Heather Schrum, Nils Risgaard-Petersen, Dennis Graham, Victoria Fulfer, Paul Johnson, and Janet Atoyan. We thank the National Science Foundation (NSF)–funded Center for Dark Energy Biosphere Investigations (C-DEBI: NSF grant OCE-0939564). We used the Rhode Island Marine Science Research Facility and the Genomics and Sequencing Center, supported in part by NSF under EPSCoR Grants Nos. 0554548 and EPS-1004057. This is C-DEBI contribution #329. We thank the editor and reviewers for their contributions to this manuscript.
Footnotes
↵1GSA Data Repository item 2016199, details of methods protocols, taxa-specific depth and site profiles, comparative trees, and a table of sample data, is available online at www.geosociety.org/pubs/ft2016.htm, or on request from editing@geosociety.org.
Received 25 March 2016. Revision received 31 May 2016. Accepted 3 June 2016.
© The Authors
Gold Open Access: This paper is published under the terms of the CC-BY license.
FREE PAPER GRATIS: Geologyy
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DESTAQUE DESTE BLOGGER:
"We do not know the mechanism behind the apparent relative slowdown of DNA degradation with age. Whether this decreased turnover is due to decreased lability of residual DNA, an overall decrease in enzyme activity, a decrease in spontaneous decay rates, or some combination of these and other factors remains presently unknown."
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DESTAQUE DESTE BLOGGER:
"We do not know the mechanism behind the apparent relative slowdown of DNA degradation with age. Whether this decreased turnover is due to decreased lability of residual DNA, an overall decrease in enzyme activity, a decrease in spontaneous decay rates, or some combination of these and other factors remains presently unknown."
