Environmental microarray analyses of Antarctic soil microbial communities

• Published in: The ISME Journal
• Main Authors: Yergeau, Etienne, Schoondermark-Stolk, Sung, Brodie, Eoin, Dejean, Sébastien, Desantis, Todd, Gonçalves, Olivier, Piceno, Yvette, Andersen, Gary, Kowalchuk, George
• Other Authors: 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
• Language: English
• Published: HAL CCSD 2009
• Subjects: 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; Antarctic; Antarctic Peninsula; Coal nunatak; The Antarctic; Antarc*
• Online Access: https://hal.archives-ouvertes.fr/hal-01887980; https://doi.org/10.1038/ismej.2008.111

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.