Metagenomic analysis of a 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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ftnerc:oai:nora.nerc.ac.uk:21223 2023-05-15T13:15:19+02:00 Metagenomic analysis of a 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 http://nora.nerc.ac.uk/id/eprint/21223/ https://doi.org/10.3389/fmicb.2012.00403 unknown Frontiers Media Pearce, David A. orcid:0000-0001-5292-4596 Newsham, Kevin K. orcid:0000-0002-9108-0936 Thorne, Michael A.S. orcid:0000-0001-7759-612X Calvo-Bado, Leo; Krsek, Martin; Laskaris, Paris; Hodson, Andy; Wellington, Elizabeth M. 2012 Metagenomic analysis of a a southern maritime Antarctic soil. Frontiers in Microbiology, 3, 403. 13, pp. https://doi.org/10.3389/fmicb.2012.00403 <https://doi.org/10.3389/fmicb.2012.00403> Publication - Article PeerReviewed 2012 ftnerc https://doi.org/10.3389/fmicb.2012.00403 2023-02-04T19:33:21Z 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 78–730OTUs (de-replicated to 30–140) provides low coverage of the major groups present (s5%). 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. Cyanobacteriawere surprisingly under-represented at 3.4% of sequences, although s1% 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. Article in Journal/Newspaper Alexander Island Antarc* Antarctic Natural Environment Research Council: NERC Open Research Archive 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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Natural Environment Research Council: NERC Open Research Archive |
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ftnerc |
language |
unknown |
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 78–730OTUs (de-replicated to 30–140) provides low coverage of the major groups present (s5%). 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. Cyanobacteriawere surprisingly under-represented at 3.4% of sequences, although s1% 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 |
Article in Journal/Newspaper |
author |
Pearce, David A. Newsham, Kevin K. Thorne, Michael A.S. Calvo-Bado, Leo Krsek, Martin Laskaris, Paris Hodson, Andy Wellington, Elizabeth M. |
spellingShingle |
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 a southern maritime Antarctic soil |
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 a southern maritime Antarctic soil |
title_short |
Metagenomic analysis of a a southern maritime Antarctic soil |
title_full |
Metagenomic analysis of a a southern maritime Antarctic soil |
title_fullStr |
Metagenomic analysis of a a southern maritime Antarctic soil |
title_full_unstemmed |
Metagenomic analysis of a a southern maritime Antarctic soil |
title_sort |
metagenomic analysis of a a southern maritime antarctic soil |
publisher |
Frontiers Media |
publishDate |
2012 |
url |
http://nora.nerc.ac.uk/id/eprint/21223/ 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 |
Pearce, David A. orcid:0000-0001-5292-4596 Newsham, Kevin K. orcid:0000-0002-9108-0936 Thorne, Michael A.S. orcid:0000-0001-7759-612X Calvo-Bado, Leo; Krsek, Martin; Laskaris, Paris; Hodson, Andy; Wellington, Elizabeth M. 2012 Metagenomic analysis of a a southern maritime Antarctic soil. Frontiers in Microbiology, 3, 403. 13, pp. https://doi.org/10.3389/fmicb.2012.00403 <https://doi.org/10.3389/fmicb.2012.00403> |
op_doi |
https://doi.org/10.3389/fmicb.2012.00403 |
container_title |
Frontiers in Microbiology |
container_volume |
3 |
_version_ |
1766268013953155072 |