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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Online Access: | http://wrap.warwick.ac.uk/56284/ http://wrap.warwick.ac.uk/56284/1/WRAP_Wellington_fmicb-03-00403.pdf https://doi.org/10.3389/fmicb.2012.00403 |
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ftuwarwick:oai:wrap.warwick.ac.uk:56284 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 A. Krsek, Martin Laskaris, Paris Hodson, Andrew J. Wellington, E. M. H. 2012 text http://wrap.warwick.ac.uk/56284/ http://wrap.warwick.ac.uk/56284/1/WRAP_Wellington_fmicb-03-00403.pdf https://doi.org/10.3389/fmicb.2012.00403 unknown Frontiers Research Foundation http://wrap.warwick.ac.uk/56284/1/WRAP_Wellington_fmicb-03-00403.pdf Pearce, David A., Newsham, Kevin K., Thorne, Michael A. S., Calvo-Bado, Leo A., Krsek, Martin, Laskaris, Paris, Hodson, Andrew J. and Wellington, E. M. H. (2012) Metagenomic analysis of a southern maritime Antarctic soil. Frontiers in Microbiology, Volume 3 . Article number 403. doi:10.3389/fmicb.2012.00403 <http://dx.doi.org/10.3389/fmicb.2012.00403 > QH301 Biology QK Botany QR Microbiology Journal Article NonPeerReviewed 2012 ftuwarwick https://doi.org/10.3389/fmicb.2012.00403 2022-03-16T20:48:12Z 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. Article in Journal/Newspaper Alexander Island Antarc* Antarctic The University of Warwick: WRAP - Warwick Research Archive Portal 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 |
institution |
Open Polar |
collection |
The University of Warwick: WRAP - Warwick Research Archive Portal |
op_collection_id |
ftuwarwick |
language |
unknown |
topic |
QH301 Biology QK Botany QR Microbiology |
spellingShingle |
QH301 Biology QK Botany QR Microbiology Pearce, David A. Newsham, Kevin K. Thorne, Michael A. S. Calvo-Bado, Leo A. Krsek, Martin Laskaris, Paris Hodson, Andrew J. Wellington, E. M. H. Metagenomic analysis of a southern maritime Antarctic soil |
topic_facet |
QH301 Biology QK Botany QR 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 |
Article in Journal/Newspaper |
author |
Pearce, David A. Newsham, Kevin K. Thorne, Michael A. S. Calvo-Bado, Leo A. Krsek, Martin Laskaris, Paris Hodson, Andrew J. Wellington, E. M. H. |
author_facet |
Pearce, David A. Newsham, Kevin K. Thorne, Michael A. S. Calvo-Bado, Leo A. Krsek, Martin Laskaris, Paris Hodson, Andrew J. Wellington, E. M. H. |
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 Research Foundation |
publishDate |
2012 |
url |
http://wrap.warwick.ac.uk/56284/ http://wrap.warwick.ac.uk/56284/1/WRAP_Wellington_fmicb-03-00403.pdf 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://wrap.warwick.ac.uk/56284/1/WRAP_Wellington_fmicb-03-00403.pdf Pearce, David A., Newsham, Kevin K., Thorne, Michael A. S., Calvo-Bado, Leo A., Krsek, Martin, Laskaris, Paris, Hodson, Andrew J. and Wellington, E. M. H. (2012) Metagenomic analysis of a southern maritime Antarctic soil. Frontiers in Microbiology, Volume 3 . Article number 403. doi:10.3389/fmicb.2012.00403 <http://dx.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_ |
1766268049012293632 |