Original Article

Subject Category: Integrated genomics and post-genomics approaches in microbial ecology

The ISME Journal (2009) 3, 340–351; doi:10.1038/ismej.2008.111; published online 20 November 2008

Environmental microarray analyses of Antarctic soil microbial communities

Etienne Yergeau1,6, Sung A Schoondermark-Stolk1,7, Eoin L Brodie2, Sébastien Déjean3, Todd Z DeSantis2, Olivier Gonçalves4, Yvette M Piceno2, Gary L Andersen2 and George A Kowalchuk1,5

  1. 1Netherlands Institute of Ecology (NIOO-KNAW), Centre for Terrestrial Ecology, Heteren, The Netherlands
  2. 2Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
  3. 3Institut de mathématiques, Université Paul Sabatier, Toulouse, France
  4. 4Laboratoire ‘Microorganismes: Génome et Environnement’, UMR CNRS 6023, Université Blaise Pascal, Clermond-Ferrand II, France
  5. 5Institute of Ecological Science, Free University of Amsterdam, Amsterdam, The Netherlands

Correspondence: GA Kowalchuk, Netherlands Institute of Ecology (NIOO-KNAW), Centre for Terrestrial Ecology, PO BOX 40, Heteren 6666 ZG, The Netherlands. E-mail: g.kowalchuk@nioo.knaw.nl

6Present address: Biotechnology Research Institute, National Research Council of Canada, Montréal, Canada.

7Present address: Diakonessenhuis, Medical Microbiology and Immunology, Unit Molecular Diagnostics, Utrecht, The Netherlands.

Received 4 August 2008; Revised 8 October 2008; Accepted 9 October 2008; Published online 20 November 2008.

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Abstract

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°S (Falkland Islands) to 72°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 (~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.

Keywords:

Antarctic soil ecosystems, GeoChip microarray, microbial community structure, microbial diversity, PhyloChip microarray