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Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records

Citation

Boere, AC and Damste, JSS and Rijpstra, WIC and Volkman, JK and Coolen, MJL, Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records, Organic Geochemistry, 42, (10) pp. 1216-1225. ISSN 0146-6380 (2011) [Refereed Article]


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DOI: doi:10.1016/j.orggeochem.2011.08.005

Abstract

Recent studies have shown that genotyping preserved plankton DNA in marine and lacustrine sediment records using ancient DNA methods is a promising approach for refining paleoenvironmental information. However, the extent to which the preservation of fossil plankton DNA differs between species is poorly understood. Using a continuous 2700 year sediment record from Watts Basin in Ellis Fjord (Antarctica), we compared the level of preservation of fossil DNA derived from important plankton members with varying cellular architecture. The amount of preserved small subunit ribosomal DNA (SSU rDNA; ca. 500 base pair fragments) of dinoflagellates (as extracellular DNA rather than as preserved cysts) that could be amplified by way of PCR declined up to five orders of magnitude with increasing sediment depth and age. In contrast, the amount of similar-sized, PCR-amplifiable, diatom SSU rDNA (predominantly from a cyst-forming Chaetoceros sp.) declined only up to tenfold over 2700 years of deposition. No obvious decline in copy numbers with increasing sediment age was observed for similar-sized SSU rDNA of past chemocline-associated photosynthetic green sulfur bacteria (GSB), which do not have a protective resting stage. In good agreement with the quantitative data, the extent of post-depositional natural degradation to fragments too small to serve as a template for the quantitative PCR assays was greatest for dinoflagellates and lowest for GSB. An increase in the ratio between GSB-derived DNA and intact carotenoids with sediment depth implies that short GSB DNA fragments were better preserved than intact carotenoids and provide a more accurate view into paleoproductivity and the sediment flux of GSB in Watts Basin. We discuss the possible causes behind the variation in the level of DNA preservation among the plankton groups investigated, as well as consequences for the use of using fossil DNA records in paleoecology studies.

Item Details

Item Type:Refereed Article
Keywords:quantitative PCR, ribosomal DNA, sediment age sediment depth, sediment flux, small subunits
Research Division:Biological Sciences
Research Group:Genetics
Research Field:Quantitative Genetics (incl. Disease and Trait Mapping Genetics)
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Chemical Sciences
Author:Volkman, JK (Dr John Volkman)
ID Code:120245
Year Published:2011
Web of Science® Times Cited:20
Deposited By:Chemistry
Deposited On:2017-08-17
Last Modified:2017-08-17
Downloads:0

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