Metagenomic Insights into Anaerobic Metabolism along an Arctic Peat Soil Profile
A metagenomic analysis was performed on a soil profile from a wet tundra site in northern Alaska. The goal was to link existing biogeochemical knowledge of the system with the organisms and genes responsible for the relevant metabolic pathways. We specifically investigated how the importance of iron...
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ftpubmed:oai:pubmedcentral.nih.gov:3669403 2023-05-15T15:09:26+02:00 Metagenomic Insights into Anaerobic Metabolism along an Arctic Peat Soil Profile Lipson, David A. Haggerty, John Matthew Srinivas, Archana Raab, Theodore K. Sathe, Shashank Dinsdale, Elizabeth A. 2013-05-31 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669403 http://www.ncbi.nlm.nih.gov/pubmed/23741360 https://doi.org/10.1371/journal.pone.0064659 en eng Public Library of Science http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669403 http://www.ncbi.nlm.nih.gov/pubmed/23741360 http://dx.doi.org/10.1371/journal.pone.0064659 This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. CC-BY Research Article Text 2013 ftpubmed https://doi.org/10.1371/journal.pone.0064659 2013-09-05T00:30:17Z A metagenomic analysis was performed on a soil profile from a wet tundra site in northern Alaska. The goal was to link existing biogeochemical knowledge of the system with the organisms and genes responsible for the relevant metabolic pathways. We specifically investigated how the importance of iron (Fe) oxides and humic substances (HS) as terminal electron acceptors in this ecosystem is expressed genetically, and how respiratory and fermentative processes varied with soil depth into the active layer and into the upper permafrost. Overall, the metagenomes reflected a microbial community enriched in a diverse range of anaerobic pathways, with a preponderance of known Fe reducing species at all depths in the profile. The abundance of sequences associated with anaerobic metabolic processes generally increased with depth, while aerobic cytochrome c oxidases decreased. Methanogenesis genes and methanogen genomes followed the pattern of CH4 fluxes : they increased steeply with depth into the active layer, but declined somewhat over the transition zone between the lower active layer and the upper permafrost. The latter was relatively enriched in fermentative and anaerobic respiratory pathways. A survey of decaheme cytochromes (MtrA, MtrC and their homologs) revealed that this is a promising approach to identifying potential reducers of Fe(III) or HS, and indicated a possible role for Acidobacteria as Fe reducers in these soils. Methanogens appear to coexist in the same layers, though in lower abundance, with Fe reducing bacteria and other potential competitors, including acetogens. These observations provide a rich set of hypotheses for further targeted study. Text Arctic permafrost Tundra Alaska PubMed Central (PMC) Arctic PLoS ONE 8 5 e64659 |
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Research Article |
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Research Article Lipson, David A. Haggerty, John Matthew Srinivas, Archana Raab, Theodore K. Sathe, Shashank Dinsdale, Elizabeth A. Metagenomic Insights into Anaerobic Metabolism along an Arctic Peat Soil Profile |
topic_facet |
Research Article |
description |
A metagenomic analysis was performed on a soil profile from a wet tundra site in northern Alaska. The goal was to link existing biogeochemical knowledge of the system with the organisms and genes responsible for the relevant metabolic pathways. We specifically investigated how the importance of iron (Fe) oxides and humic substances (HS) as terminal electron acceptors in this ecosystem is expressed genetically, and how respiratory and fermentative processes varied with soil depth into the active layer and into the upper permafrost. Overall, the metagenomes reflected a microbial community enriched in a diverse range of anaerobic pathways, with a preponderance of known Fe reducing species at all depths in the profile. The abundance of sequences associated with anaerobic metabolic processes generally increased with depth, while aerobic cytochrome c oxidases decreased. Methanogenesis genes and methanogen genomes followed the pattern of CH4 fluxes : they increased steeply with depth into the active layer, but declined somewhat over the transition zone between the lower active layer and the upper permafrost. The latter was relatively enriched in fermentative and anaerobic respiratory pathways. A survey of decaheme cytochromes (MtrA, MtrC and their homologs) revealed that this is a promising approach to identifying potential reducers of Fe(III) or HS, and indicated a possible role for Acidobacteria as Fe reducers in these soils. Methanogens appear to coexist in the same layers, though in lower abundance, with Fe reducing bacteria and other potential competitors, including acetogens. These observations provide a rich set of hypotheses for further targeted study. |
format |
Text |
author |
Lipson, David A. Haggerty, John Matthew Srinivas, Archana Raab, Theodore K. Sathe, Shashank Dinsdale, Elizabeth A. |
author_facet |
Lipson, David A. Haggerty, John Matthew Srinivas, Archana Raab, Theodore K. Sathe, Shashank Dinsdale, Elizabeth A. |
author_sort |
Lipson, David A. |
title |
Metagenomic Insights into Anaerobic Metabolism along an Arctic Peat Soil Profile |
title_short |
Metagenomic Insights into Anaerobic Metabolism along an Arctic Peat Soil Profile |
title_full |
Metagenomic Insights into Anaerobic Metabolism along an Arctic Peat Soil Profile |
title_fullStr |
Metagenomic Insights into Anaerobic Metabolism along an Arctic Peat Soil Profile |
title_full_unstemmed |
Metagenomic Insights into Anaerobic Metabolism along an Arctic Peat Soil Profile |
title_sort |
metagenomic insights into anaerobic metabolism along an arctic peat soil profile |
publisher |
Public Library of Science |
publishDate |
2013 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669403 http://www.ncbi.nlm.nih.gov/pubmed/23741360 https://doi.org/10.1371/journal.pone.0064659 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic permafrost Tundra Alaska |
genre_facet |
Arctic permafrost Tundra Alaska |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669403 http://www.ncbi.nlm.nih.gov/pubmed/23741360 http://dx.doi.org/10.1371/journal.pone.0064659 |
op_rights |
This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0064659 |
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PLoS ONE |
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8 |
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5 |
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e64659 |
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