Metagenomic Analysis of a Southern Maritime Antarctic Soil
Our current understanding of Antarctic soils is derived from direct culture on selective media, biodiversity studies based on clone library construction and analysis, quantitative PCR amplification of specific gene sequences and the application of generic microarrays for microbial community analysis...
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ftpubmed:oai:pubmedcentral.nih.gov:3514609 2023-05-15T13:15:19+02:00 Metagenomic Analysis of a Southern Maritime Antarctic Soil Pearce, David A. Newsham, Kevin K. Thorne, Michael A. S. Calvo-Bado, Leo Krsek, Martin Laskaris, Paris Hodson, Andy Wellington, Elizabeth M. 2012-12-05 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514609 http://www.ncbi.nlm.nih.gov/pubmed/23227023 https://doi.org/10.3389/fmicb.2012.00403 en eng Frontiers Media S.A. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514609 http://www.ncbi.nlm.nih.gov/pubmed/23227023 http://dx.doi.org/10.3389/fmicb.2012.00403 Copyright © 2012 Pearce, Newsham, Thorne, Calvo-Bado, Krsek, Laskaris, Hodson and Wellington. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc. CC-BY Microbiology Text 2012 ftpubmed https://doi.org/10.3389/fmicb.2012.00403 2013-09-04T16:48:54Z Our current understanding of Antarctic soils is derived from direct culture on selective media, biodiversity studies based on clone library construction and analysis, quantitative PCR amplification of specific gene sequences and the application of generic microarrays for microbial community analysis. Here, we investigated the biodiversity and functional potential of a soil community at Mars Oasis on Alexander Island in the southern Maritime Antarctic, by applying 454 pyrosequencing technology to a metagenomic library constructed from soil genomic DNA. The results suggest that the commonly cited range of phylotypes used in clone library construction and analysis of 78–730 OTUs (de-replicated to 30–140) provides low coverage of the major groups present (∼5%). The vast majority of functional genes (>77%) were for structure, carbohydrate metabolism, and DNA/RNA processing and modification. This study suggests that prokaryotic diversity in Antarctic terrestrial environments appears to be limited at the generic level, with Proteobacteria, Actinobacteria being common. Cyanobacteria were surprisingly under-represented at 3.4% of sequences, although ∼1% of the genes identified were involved in CO2 fixation. At the sequence level there appeared to be much greater heterogeneity, and this might be due to high divergence within the relatively restricted lineages which have successfully colonized Antarctic terrestrial environments. Text Alexander Island Antarc* Antarctic PubMed Central (PMC) Alexander Island ENVELOPE(-69.895,-69.895,-71.287,-71.287) Antarctic Mars Oasis ENVELOPE(-68.250,-68.250,-71.879,-71.879) Frontiers in Microbiology 3 |
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English |
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Microbiology |
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Microbiology Pearce, David A. Newsham, Kevin K. Thorne, Michael A. S. Calvo-Bado, Leo Krsek, Martin Laskaris, Paris Hodson, Andy Wellington, Elizabeth M. Metagenomic Analysis of a Southern Maritime Antarctic Soil |
topic_facet |
Microbiology |
description |
Our current understanding of Antarctic soils is derived from direct culture on selective media, biodiversity studies based on clone library construction and analysis, quantitative PCR amplification of specific gene sequences and the application of generic microarrays for microbial community analysis. Here, we investigated the biodiversity and functional potential of a soil community at Mars Oasis on Alexander Island in the southern Maritime Antarctic, by applying 454 pyrosequencing technology to a metagenomic library constructed from soil genomic DNA. The results suggest that the commonly cited range of phylotypes used in clone library construction and analysis of 78–730 OTUs (de-replicated to 30–140) provides low coverage of the major groups present (∼5%). The vast majority of functional genes (>77%) were for structure, carbohydrate metabolism, and DNA/RNA processing and modification. This study suggests that prokaryotic diversity in Antarctic terrestrial environments appears to be limited at the generic level, with Proteobacteria, Actinobacteria being common. Cyanobacteria were surprisingly under-represented at 3.4% of sequences, although ∼1% of the genes identified were involved in CO2 fixation. At the sequence level there appeared to be much greater heterogeneity, and this might be due to high divergence within the relatively restricted lineages which have successfully colonized Antarctic terrestrial environments. |
format |
Text |
author |
Pearce, David A. Newsham, Kevin K. Thorne, Michael A. S. Calvo-Bado, Leo Krsek, Martin Laskaris, Paris Hodson, Andy Wellington, Elizabeth M. |
author_facet |
Pearce, David A. Newsham, Kevin K. Thorne, Michael A. S. Calvo-Bado, Leo Krsek, Martin Laskaris, Paris Hodson, Andy Wellington, Elizabeth M. |
author_sort |
Pearce, David A. |
title |
Metagenomic Analysis of a Southern Maritime Antarctic Soil |
title_short |
Metagenomic Analysis of a Southern Maritime Antarctic Soil |
title_full |
Metagenomic Analysis of a Southern Maritime Antarctic Soil |
title_fullStr |
Metagenomic Analysis of a Southern Maritime Antarctic Soil |
title_full_unstemmed |
Metagenomic Analysis of a Southern Maritime Antarctic Soil |
title_sort |
metagenomic analysis of a southern maritime antarctic soil |
publisher |
Frontiers Media S.A. |
publishDate |
2012 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514609 http://www.ncbi.nlm.nih.gov/pubmed/23227023 https://doi.org/10.3389/fmicb.2012.00403 |
long_lat |
ENVELOPE(-69.895,-69.895,-71.287,-71.287) ENVELOPE(-68.250,-68.250,-71.879,-71.879) |
geographic |
Alexander Island Antarctic Mars Oasis |
geographic_facet |
Alexander Island Antarctic Mars Oasis |
genre |
Alexander Island Antarc* Antarctic |
genre_facet |
Alexander Island Antarc* Antarctic |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514609 http://www.ncbi.nlm.nih.gov/pubmed/23227023 http://dx.doi.org/10.3389/fmicb.2012.00403 |
op_rights |
Copyright © 2012 Pearce, Newsham, Thorne, Calvo-Bado, Krsek, Laskaris, Hodson and Wellington. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fmicb.2012.00403 |
container_title |
Frontiers in Microbiology |
container_volume |
3 |
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1766268015901409280 |