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...
Published in: | Frontiers in Microbiology |
---|---|
Main Authors: | , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Frontiers Media
2012
|
Subjects: | |
Online Access: | https://nrl.northumbria.ac.uk/id/eprint/11070/ https://doi.org/10.3389/fmicb.2012.00403 https://nrl.northumbria.ac.uk/id/eprint/11070/1/Pearce_D_Output_4_Metagenomic.pdf |
id |
ftunivnorthumb:oai:nrl.northumbria.ac.uk:11070 |
---|---|
record_format |
openpolar |
spelling |
ftunivnorthumb:oai:nrl.northumbria.ac.uk:11070 2023-05-15T13:15:19+02:00 Metagenomic Analysis of a Southern Maritime Antarctic Soil Pearce, David Newsham, Kevin Thorne, Michael Calvo-Bado, Leo Krsek, Martin Laskaris, Paris Hodson, Andy Wellington, Elizabeth 2012 application/pdf https://nrl.northumbria.ac.uk/id/eprint/11070/ https://doi.org/10.3389/fmicb.2012.00403 https://nrl.northumbria.ac.uk/id/eprint/11070/1/Pearce_D_Output_4_Metagenomic.pdf en eng Frontiers Media https://nrl.northumbria.ac.uk/id/eprint/11070/1/Pearce_D_Output_4_Metagenomic.pdf Pearce, David, Newsham, Kevin, Thorne, Michael, Calvo-Bado, Leo, Krsek, Martin, Laskaris, Paris, Hodson, Andy and Wellington, Elizabeth (2012) Metagenomic Analysis of a Southern Maritime Antarctic Soil. Frontiers in Microbiology, 3. ISSN 1664-302X cc_by CC-BY C700 Molecular Biology Biophysics and Biochemistry Article PeerReviewed 2012 ftunivnorthumb https://doi.org/10.3389/fmicb.2012.00403 2022-09-25T05:56:52Z 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 Northumbria University, Newcastle: Northumbria Research Link (NRL) 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 |
Northumbria University, Newcastle: Northumbria Research Link (NRL) |
op_collection_id |
ftunivnorthumb |
language |
English |
topic |
C700 Molecular Biology Biophysics and Biochemistry |
spellingShingle |
C700 Molecular Biology Biophysics and Biochemistry Pearce, David Newsham, Kevin Thorne, Michael Calvo-Bado, Leo Krsek, Martin Laskaris, Paris Hodson, Andy Wellington, Elizabeth Metagenomic Analysis of a Southern Maritime Antarctic Soil |
topic_facet |
C700 Molecular Biology Biophysics and Biochemistry |
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 Newsham, Kevin Thorne, Michael Calvo-Bado, Leo Krsek, Martin Laskaris, Paris Hodson, Andy Wellington, Elizabeth |
author_facet |
Pearce, David Newsham, Kevin Thorne, Michael Calvo-Bado, Leo Krsek, Martin Laskaris, Paris Hodson, Andy Wellington, Elizabeth |
author_sort |
Pearce, David |
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 |
publishDate |
2012 |
url |
https://nrl.northumbria.ac.uk/id/eprint/11070/ https://doi.org/10.3389/fmicb.2012.00403 https://nrl.northumbria.ac.uk/id/eprint/11070/1/Pearce_D_Output_4_Metagenomic.pdf |
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 |
https://nrl.northumbria.ac.uk/id/eprint/11070/1/Pearce_D_Output_4_Metagenomic.pdf Pearce, David, Newsham, Kevin, Thorne, Michael, Calvo-Bado, Leo, Krsek, Martin, Laskaris, Paris, Hodson, Andy and Wellington, Elizabeth (2012) Metagenomic Analysis of a Southern Maritime Antarctic Soil. Frontiers in Microbiology, 3. ISSN 1664-302X |
op_rights |
cc_by |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fmicb.2012.00403 |
container_title |
Frontiers in Microbiology |
container_volume |
3 |
_version_ |
1766268006004948992 |