Environmental microarray analyses of Antarctic soil microbial communities

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.

Microbiology of Eutrophic (Ornithogenic and Hydrocarbon-Contaminated) Soil

“…The phyla Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria, and Verrucomicrobia are frequently observed, and Proteobacteria makes up a substantial proportion of soil sequences in the region, with frequent representation of the Alpha, Beta, Delta, and Gamma Proteobacteria classes (Yergeau et al 2007b). Microarray analyses have indicated that Actinobacteria, Epsilonproteobacteria, and Verrucomicrobia decreased in relative abundance with increasing latitude, whereas Cyanobacteria representation increased (Yergeau et al 2009) findings that largely corroborated earlier clone-library analyses (Yergeau et al 2007b). Additionally, clone-library analyses have revealed a significant decrease in Acidobacteria representation with increasing latitude (Yergeau et al 2007b).…”

“…Additionally, clone-library analyses have revealed a significant decrease in Acidobacteria representation with increasing latitude (Yergeau et al 2007b). Bacteroidetes, Firmicutes, Cyanobacteria, and Alphaproteobacteria were found to be more abundant relative to other taxa in soils of Fossil Bluff (71°19 0 S) and Coal Nunatak (72°03 0 ) on Alexander Island than at sites on the Falkland Islands, Signy Island, and Anchorage Island (51°76 0 S-67°34 0 S) (Yergeau et al 2009). Several phyla were significantly influenced by soil physicochemical factors, as the proportion of Chloroflexi and Betaproteobacteria were negatively (Yergeau et al 2007b); West Antarctic soil sequences (180) are from a study in the Ellsworth Mountains (Yergeau et al 2007b); Victoria Land soil sequences, a total of 426 clone sequences and 25976 pyrosequencing reads, were included from the McMurdo Dry Valleys, from studies in the Miers Valley Tiao et al 2012), Beacon Valley, Wright Valley, Battleship Promontory , Luther Vale (Niederberger et al 2008), and Bull Pass and Vanda in the Wright Valley ); ornithogenic soil sequences (514) are from Cape Hallett and Cape Bird in the Ross Sea region (Aislabie et al 2009); East Antarctic soil sequences (1396) were included from the Larsmann Hills (Bajerski and Wagner 2013) and Schirmacher Oasis (Shivaji et al 2004); and the Transantarctic Mountain soil sequences (361) were from the Darwin Mountains (Aislabie et al 2013).…”

“…The trees were constructed using ARB (Ludwig et al 2004), with DNADIST and Neighbor joining analysis, and the percentage of sequences in each phyla is shown (in brackets). Abbreviations for labels are: Acido Acidobacteria; Actino Actinobacteria; Bact Bacteriodetes; Chloro Chloroflexi; Cyano Cyanobacteria; Deino/Ther Deinococcus/Thermus; Firmi Firmicutes; Gemma Gemmatimonadetes; Plancto Planctomycetes; Prot Proteobacteria; Verru Verrucomicrobia b correlated with pH, while the proportion of Firmicutes and Verrucomicrobia were positively correlated with pH (Yergeau et al 2009). Chloroflexi and Planctomycetes were positively associated with soil water, organic matter content, and soil nitrogen, and the proportion of Betaproteobacteria was positively correlated with soil nitrogen and nitrate (Yergeau et al 2009).…”

Abundance, composition, diversity and novelty of soil Proteobacteria

“…Although such larger proportion of Proteobacteria in pyrosequencing-based studies might be a true reflection of the communities analyzed, it might also indicate the existence of a cloning bias or that classification based on small 16S rRNA gene fragments could lead to different taxonomic assignments than classification based on near to full-length sequences, as suggested earlier (Elshahed et al, 2008). Nevertheless, Proteobacteria remains the most abundant soil phylum, regardless of the utilized approach, which aside from PCR-based clone libraries and pyrosequencing has included metagenomics (Liles et al, 2003;Tringe et al, 2005), fluorescent in situ hybridization (Zarda et al, 1997) and microarray analysis (Yergeau et al, 2009).…”

The Gut Microbiota: Ecology and Function

“…The Phylochip is a microarray that contains oligonucleotide probes designed based on all environmental sample sequences submitted to the RDP website. These sequences have passed a quality check and are deposited in the Greengenes database, http://greengenes.lbl.gov/cgi-bin/nph-index.cgi (Yergeau et al, 2009). The HITChip is another phylogenetic microarray that specifically contains probes for sequences isolated from the human intestinal tract ).…”