Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records
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 po...
Published in: | Organic Geochemistry |
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Online Access: | https://hdl.handle.net/20.500.11937/15408 https://doi.org/10.1016/j.orggeochem.2011.08.005 |
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ftcurtin:oai:espace.curtin.edu.au:20.500.11937/15408 2023-06-11T04:06:54+02:00 Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records Boere, A. Sinninghe Damsté, J. Rijpstra, W. Volkman, J. Coolen, Marco 2011 restricted https://hdl.handle.net/20.500.11937/15408 https://doi.org/10.1016/j.orggeochem.2011.08.005 unknown http://hdl.handle.net/20.500.11937/15408 doi:10.1016/j.orggeochem.2011.08.005 Journal Article 2011 ftcurtin https://doi.org/20.500.11937/1540810.1016/j.orggeochem.2011.08.005 2023-05-30T19:27:57Z 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. Article in Journal/Newspaper Antarc* Antarctica Curtin University: espace Ellis Fjord ENVELOPE(78.132,78.132,-68.603,-68.603) Organic Geochemistry 42 10 1216 1225 |
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Open Polar |
collection |
Curtin University: espace |
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ftcurtin |
language |
unknown |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Boere, A. Sinninghe Damsté, J. Rijpstra, W. Volkman, J. Coolen, Marco |
spellingShingle |
Boere, A. Sinninghe Damsté, J. Rijpstra, W. Volkman, J. Coolen, Marco Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records |
author_facet |
Boere, A. Sinninghe Damsté, J. Rijpstra, W. Volkman, J. Coolen, Marco |
author_sort |
Boere, A. |
title |
Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records |
title_short |
Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records |
title_full |
Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records |
title_fullStr |
Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records |
title_full_unstemmed |
Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records |
title_sort |
source-specific variability in post-depositional dna preservation with potential implications for dna based paleoecological records |
publishDate |
2011 |
url |
https://hdl.handle.net/20.500.11937/15408 https://doi.org/10.1016/j.orggeochem.2011.08.005 |
long_lat |
ENVELOPE(78.132,78.132,-68.603,-68.603) |
geographic |
Ellis Fjord |
geographic_facet |
Ellis Fjord |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_relation |
http://hdl.handle.net/20.500.11937/15408 doi:10.1016/j.orggeochem.2011.08.005 |
op_doi |
https://doi.org/20.500.11937/1540810.1016/j.orggeochem.2011.08.005 |
container_title |
Organic Geochemistry |
container_volume |
42 |
container_issue |
10 |
container_start_page |
1216 |
op_container_end_page |
1225 |
_version_ |
1768379131991425024 |