Environmental microarray analyses of Antarctic soil microbial communities
International audience Antarctic ecosystems are fascinating in their limited trophic complexity, with decomposition and nutrient cycling functions being dominated by microbial activities. Not only are Antarctic habitats exposed to extreme environmental conditions, the Antarctic Peninsula is also exp...
Published in: | The ISME Journal |
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Main Authors: | , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2009
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Online Access: | https://hal.archives-ouvertes.fr/hal-01887980 https://doi.org/10.1038/ismej.2008.111 |
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ftccsdartic:oai:HAL:hal-01887980v1 |
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Open Polar |
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Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
op_collection_id |
ftccsdartic |
language |
English |
topic |
microbial community structure microbial diversity PhyloChip microarray GeoChip microarray Antarctic soil ecosystems [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] [SDE.BE]Environmental Sciences/Biodiversity and Ecology |
spellingShingle |
microbial community structure microbial diversity PhyloChip microarray GeoChip microarray Antarctic soil ecosystems [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] [SDE.BE]Environmental Sciences/Biodiversity and Ecology Yergeau, Etienne Schoondermark-Stolk, Sung Brodie, Eoin Dejean, Sébastien Desantis, Todd Gonçalves, Olivier Piceno, Yvette Andersen, Gary Kowalchuk, George Environmental microarray analyses of Antarctic soil microbial communities |
topic_facet |
microbial community structure microbial diversity PhyloChip microarray GeoChip microarray Antarctic soil ecosystems [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] [SDE.BE]Environmental Sciences/Biodiversity and Ecology |
description |
International audience Antarctic ecosystems are fascinating in their limited trophic complexity, with decomposition and nutrient cycling functions being dominated by microbial activities. Not only are Antarctic habitats exposed to extreme environmental conditions, the Antarctic Peninsula is also experiencing unequalled effects of global warming. Owing to their uniqueness and the potential impact of global warming on these pristine systems, there is considerable interest in determining the structure and function of microbial communities in the Antarctic. We therefore utilized a recently designed 16S rRNA gene microarray, the PhyloChip, which targets 8741 bacterial and archaeal taxa, to interrogate microbial communities inhabiting densely vegetated and bare fell-field soils along a latitudinal gradient ranging from 51 degrees S (Falkland Islands) to 72 degrees S (Coal Nunatak). Results indicated a clear decrease in diversity with increasing latitude, with the two southernmost sites harboring the most distinct Bacterial and Archaeal communities. The microarray approach proved more sensitive in detecting the breadth of microbial diversity than polymerase chain reaction-based bacterial 16S rRNA gene libraries of modest size ( approximately 190 clones per library). Furthermore, the relative signal intensities summed for phyla and families on the PhyloChip were significantly correlated with the relative occurrence of these taxa in clone libraries. PhyloChip data were also compared with functional gene microarray data obtained earlier, highlighting numerous significant relationships and providing evidence for a strong link between community composition and functional gene distribution in Antarctic soils. Integration of these PhyloChip data with other complementary methods provides an unprecedented understanding of the microbial diversity and community structure of terrestrial Antarctic habitats. |
author2 |
Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS) Lawrence Berkeley National Laboratory Berkeley (LBNL) Institut de Mathématiques de Toulouse UMR5219 (IMT) Institut National des Sciences Appliquées - Toulouse (INSA Toulouse) Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1) Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3) Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS) Bioprocédés Appliqués aux Microalgues (GEPEA-BAM) Laboratoire de génie des procédés - environnement - agroalimentaire (GEPEA) Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST) Université de Nantes (UN)-Université de Nantes (UN)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique) Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Polytechnique de l'Université de Nantes (EPUN) Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes) Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire) Université de Nantes (UN)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon) Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST) Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL) This study was supported by NWO grant 851.20.018 to Rien Aerts and GA Kowalchuk. Part of this work was performed under the auspices of the U.S. DOE's Office of Science, Biological and Environmental Research Program, and by the University of California, LBNL under contract no. DE-AC02-05CH11231. E Yergeau was partly supported by a FQRNT postgraduate scholarship. |
format |
Article in Journal/Newspaper |
author |
Yergeau, Etienne Schoondermark-Stolk, Sung Brodie, Eoin Dejean, Sébastien Desantis, Todd Gonçalves, Olivier Piceno, Yvette Andersen, Gary Kowalchuk, George |
author_facet |
Yergeau, Etienne Schoondermark-Stolk, Sung Brodie, Eoin Dejean, Sébastien Desantis, Todd Gonçalves, Olivier Piceno, Yvette Andersen, Gary Kowalchuk, George |
author_sort |
Yergeau, Etienne |
title |
Environmental microarray analyses of Antarctic soil microbial communities |
title_short |
Environmental microarray analyses of Antarctic soil microbial communities |
title_full |
Environmental microarray analyses of Antarctic soil microbial communities |
title_fullStr |
Environmental microarray analyses of Antarctic soil microbial communities |
title_full_unstemmed |
Environmental microarray analyses of Antarctic soil microbial communities |
title_sort |
environmental microarray analyses of antarctic soil microbial communities |
publisher |
HAL CCSD |
publishDate |
2009 |
url |
https://hal.archives-ouvertes.fr/hal-01887980 https://doi.org/10.1038/ismej.2008.111 |
long_lat |
ENVELOPE(-68.534,-68.534,-72.071,-72.071) |
geographic |
Antarctic Antarctic Peninsula Coal nunatak The Antarctic |
geographic_facet |
Antarctic Antarctic Peninsula Coal nunatak The Antarctic |
genre |
Antarc* Antarctic Antarctic Peninsula |
genre_facet |
Antarc* Antarctic Antarctic Peninsula |
op_source |
ISSN: 1751-7362 EISSN: 1751-7370 ISME Journal https://hal.archives-ouvertes.fr/hal-01887980 ISME Journal, Nature Publishing Group, 2009, 3 (3), pp.340 - 351. ⟨10.1038/ismej.2008.111⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/pmid/19020556 info:eu-repo/semantics/altIdentifier/doi/10.1038/ismej.2008.111 hal-01887980 https://hal.archives-ouvertes.fr/hal-01887980 PUBMED: 19020556 doi:10.1038/ismej.2008.111 |
op_doi |
https://doi.org/10.1038/ismej.2008.111 |
container_title |
The ISME Journal |
container_volume |
3 |
container_issue |
3 |
container_start_page |
340 |
op_container_end_page |
351 |
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ftccsdartic:oai:HAL:hal-01887980v1 2023-05-15T13:30:56+02:00 Environmental microarray analyses of Antarctic soil microbial communities Yergeau, Etienne Schoondermark-Stolk, Sung Brodie, Eoin Dejean, Sébastien Desantis, Todd Gonçalves, Olivier Piceno, Yvette Andersen, Gary Kowalchuk, George Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS) Lawrence Berkeley National Laboratory Berkeley (LBNL) Institut de Mathématiques de Toulouse UMR5219 (IMT) Institut National des Sciences Appliquées - Toulouse (INSA Toulouse) Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1) Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3) Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS) Bioprocédés Appliqués aux Microalgues (GEPEA-BAM) Laboratoire de génie des procédés - environnement - agroalimentaire (GEPEA) Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST) Université de Nantes (UN)-Université de Nantes (UN)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique) Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Polytechnique de l'Université de Nantes (EPUN) Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes) Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire) Université de Nantes (UN)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon) Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST) Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL) This study was supported by NWO grant 851.20.018 to Rien Aerts and GA Kowalchuk. Part of this work was performed under the auspices of the U.S. DOE's Office of Science, Biological and Environmental Research Program, and by the University of California, LBNL under contract no. DE-AC02-05CH11231. E Yergeau was partly supported by a FQRNT postgraduate scholarship. 2009-03 https://hal.archives-ouvertes.fr/hal-01887980 https://doi.org/10.1038/ismej.2008.111 en eng HAL CCSD Nature Publishing Group info:eu-repo/semantics/altIdentifier/pmid/19020556 info:eu-repo/semantics/altIdentifier/doi/10.1038/ismej.2008.111 hal-01887980 https://hal.archives-ouvertes.fr/hal-01887980 PUBMED: 19020556 doi:10.1038/ismej.2008.111 ISSN: 1751-7362 EISSN: 1751-7370 ISME Journal https://hal.archives-ouvertes.fr/hal-01887980 ISME Journal, Nature Publishing Group, 2009, 3 (3), pp.340 - 351. ⟨10.1038/ismej.2008.111⟩ microbial community structure microbial diversity PhyloChip microarray GeoChip microarray Antarctic soil ecosystems [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] [SDE.BE]Environmental Sciences/Biodiversity and Ecology info:eu-repo/semantics/article Journal articles 2009 ftccsdartic https://doi.org/10.1038/ismej.2008.111 2021-12-25T23:59:05Z International audience Antarctic ecosystems are fascinating in their limited trophic complexity, with decomposition and nutrient cycling functions being dominated by microbial activities. Not only are Antarctic habitats exposed to extreme environmental conditions, the Antarctic Peninsula is also experiencing unequalled effects of global warming. Owing to their uniqueness and the potential impact of global warming on these pristine systems, there is considerable interest in determining the structure and function of microbial communities in the Antarctic. We therefore utilized a recently designed 16S rRNA gene microarray, the PhyloChip, which targets 8741 bacterial and archaeal taxa, to interrogate microbial communities inhabiting densely vegetated and bare fell-field soils along a latitudinal gradient ranging from 51 degrees S (Falkland Islands) to 72 degrees S (Coal Nunatak). Results indicated a clear decrease in diversity with increasing latitude, with the two southernmost sites harboring the most distinct Bacterial and Archaeal communities. The microarray approach proved more sensitive in detecting the breadth of microbial diversity than polymerase chain reaction-based bacterial 16S rRNA gene libraries of modest size ( approximately 190 clones per library). Furthermore, the relative signal intensities summed for phyla and families on the PhyloChip were significantly correlated with the relative occurrence of these taxa in clone libraries. PhyloChip data were also compared with functional gene microarray data obtained earlier, highlighting numerous significant relationships and providing evidence for a strong link between community composition and functional gene distribution in Antarctic soils. Integration of these PhyloChip data with other complementary methods provides an unprecedented understanding of the microbial diversity and community structure of terrestrial Antarctic habitats. Article in Journal/Newspaper Antarc* Antarctic Antarctic Peninsula Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) Antarctic Antarctic Peninsula Coal nunatak ENVELOPE(-68.534,-68.534,-72.071,-72.071) The Antarctic The ISME Journal 3 3 340 351 |