New cell extraction procedure applied to deep subsurface sediments
A new method is presented for the separation of cells from a marine sediment matrix. Different methods and reagents were tested for detaching microbial cells from sediment particles; the highest yields were achieved in a solution of EDTA, Tween 80, sodium‐pyrophosphate, and methanol plus gentle ultr...
Published in: | Limnology and Oceanography: Methods |
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2008
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Online Access: | https://gfzpublic.gfz-potsdam.de/pubman/item/item_238232 |
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ftgfzpotsdam:oai:gfzpublic.gfz-potsdam.de:item_238232 2023-05-15T15:07:00+02:00 New cell extraction procedure applied to deep subsurface sediments Kallmeyer, J. Smith, D. Spivack, A. D’Hondt, S. 4.3 Organic Geochemistry, 4.0 Chemistry and Material Cycles, Departments, GFZ Publication Database, Deutsches GeoForschungsZentrum 2008 https://gfzpublic.gfz-potsdam.de/pubman/item/item_238232 unknown info:eu-repo/semantics/altIdentifier/doi/10.4319/lom.2008.6.236 https://gfzpublic.gfz-potsdam.de/pubman/item/item_238232 Limnology and Oceanography - Methods 550 - Earth sciences info:eu-repo/semantics/article 2008 ftgfzpotsdam https://doi.org/10.4319/lom.2008.6.236 2022-09-14T05:57:16Z A new method is presented for the separation of cells from a marine sediment matrix. Different methods and reagents were tested for detaching microbial cells from sediment particles; the highest yields were achieved in a solution of EDTA, Tween 80, sodium‐pyrophosphate, and methanol plus gentle ultrasonic treatment, followed by density centrifugation through a cushion of Nycodenz. If present, carbonates were dissolved before extraction. Comparison with untreated sediments and pure cultures verified that this technique minimizes cell lysis. The new procedure was tested on seafloor sediment from several locations and water depths (<1 to >4000 m) and subseafloor sediment from the Arctic Ocean (IODP Expedition 302). Cell extraction efficiency was relatively high (65% to 100%) and consistent for each sediment type, with significantly (P < 0.01) lower variability of counts of separated cells compared with conventional counts on slurried sediments. Concentrating cells before enumeration allows for a much lower minimum detection limit and lower uncertainty than the conventional approach of simply slurrying sediment. Resolving relatively small differences in the distribution of microorganisms will allow for comparisons to other parameters (porewater chemistry, lithology, etc). Additionally, this method has potential for the use of molecular techniques that were previously difficult owing to coelution of interfering compounds from the sediment matrix. Article in Journal/Newspaper Arctic Arctic Ocean GFZpublic (German Research Centre for Geosciences, Helmholtz-Zentrum Potsdam) Arctic Arctic Ocean Limnology and Oceanography: Methods 6 6 236 245 |
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Open Polar |
collection |
GFZpublic (German Research Centre for Geosciences, Helmholtz-Zentrum Potsdam) |
op_collection_id |
ftgfzpotsdam |
language |
unknown |
topic |
550 - Earth sciences |
spellingShingle |
550 - Earth sciences Kallmeyer, J. Smith, D. Spivack, A. D’Hondt, S. New cell extraction procedure applied to deep subsurface sediments |
topic_facet |
550 - Earth sciences |
description |
A new method is presented for the separation of cells from a marine sediment matrix. Different methods and reagents were tested for detaching microbial cells from sediment particles; the highest yields were achieved in a solution of EDTA, Tween 80, sodium‐pyrophosphate, and methanol plus gentle ultrasonic treatment, followed by density centrifugation through a cushion of Nycodenz. If present, carbonates were dissolved before extraction. Comparison with untreated sediments and pure cultures verified that this technique minimizes cell lysis. The new procedure was tested on seafloor sediment from several locations and water depths (<1 to >4000 m) and subseafloor sediment from the Arctic Ocean (IODP Expedition 302). Cell extraction efficiency was relatively high (65% to 100%) and consistent for each sediment type, with significantly (P < 0.01) lower variability of counts of separated cells compared with conventional counts on slurried sediments. Concentrating cells before enumeration allows for a much lower minimum detection limit and lower uncertainty than the conventional approach of simply slurrying sediment. Resolving relatively small differences in the distribution of microorganisms will allow for comparisons to other parameters (porewater chemistry, lithology, etc). Additionally, this method has potential for the use of molecular techniques that were previously difficult owing to coelution of interfering compounds from the sediment matrix. |
author2 |
4.3 Organic Geochemistry, 4.0 Chemistry and Material Cycles, Departments, GFZ Publication Database, Deutsches GeoForschungsZentrum |
format |
Article in Journal/Newspaper |
author |
Kallmeyer, J. Smith, D. Spivack, A. D’Hondt, S. |
author_facet |
Kallmeyer, J. Smith, D. Spivack, A. D’Hondt, S. |
author_sort |
Kallmeyer, J. |
title |
New cell extraction procedure applied to deep subsurface sediments |
title_short |
New cell extraction procedure applied to deep subsurface sediments |
title_full |
New cell extraction procedure applied to deep subsurface sediments |
title_fullStr |
New cell extraction procedure applied to deep subsurface sediments |
title_full_unstemmed |
New cell extraction procedure applied to deep subsurface sediments |
title_sort |
new cell extraction procedure applied to deep subsurface sediments |
publishDate |
2008 |
url |
https://gfzpublic.gfz-potsdam.de/pubman/item/item_238232 |
geographic |
Arctic Arctic Ocean |
geographic_facet |
Arctic Arctic Ocean |
genre |
Arctic Arctic Ocean |
genre_facet |
Arctic Arctic Ocean |
op_source |
Limnology and Oceanography - Methods |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.4319/lom.2008.6.236 https://gfzpublic.gfz-potsdam.de/pubman/item/item_238232 |
op_doi |
https://doi.org/10.4319/lom.2008.6.236 |
container_title |
Limnology and Oceanography: Methods |
container_volume |
6 |
container_issue |
6 |
container_start_page |
236 |
op_container_end_page |
245 |
_version_ |
1766338586718765056 |