Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome - PubMed (original) (raw)

Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome

Carola Simon et al. Appl Environ Microbiol. 2009 Dec.

Abstract

The largest part of the Earth's microbial biomass is stored in cold environments, which represent almost untapped reservoirs of novel species, processes, and genes. In this study, the first metagenomic survey of the metabolic potential and phylogenetic diversity of a microbial assemblage present in glacial ice is presented. DNA was isolated from glacial ice of the Northern Schneeferner, Germany. Pyrosequencing of this DNA yielded 1,076,539 reads (239.7 Mbp). The phylogenetic composition of the prokaryotic community was assessed by evaluation of a pyrosequencing-derived data set and sequencing of 16S rRNA genes. The Proteobacteria (mainly Betaproteobacteria), Bacteroidetes, and Actinobacteria were the predominant phylogenetic groups. In addition, isolation of psychrophilic microorganisms was performed, and 13 different bacterial isolates were recovered. Analysis of the 16S rRNA gene sequences of the isolates revealed that all were affiliated to the predominant groups. As expected for microorganisms residing in a low-nutrient environment, a high metabolic versatility with respect to degradation of organic substrates was detected by analysis of the pyrosequencing-derived data set. The presence of autotrophic microorganisms was indicated by identification of genes typical for different ways of carbon fixation. In accordance with the results of the phylogenetic studies, in which mainly aerobic and facultative aerobic bacteria were detected, genes typical for central metabolism of aerobes were found. Nevertheless, the capability of growth under anaerobic conditions was indicated by genes involved in dissimilatory nitrate/nitrite reduction. Numerous characteristics for metabolic adaptations associated with a psychrophilic lifestyle, such as formation of cryoprotectants and maintenance of membrane fluidity by the incorporation of unsaturated fatty acids, were detected. Thus, analysis of the glacial metagenome provided insights into the microbial life in frozen habitats on Earth, thereby possibly shedding light onto microbial life in analogous extraterrestrial environments.

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Figures

FIG. 1.

FIG. 1.

Distribution of phylogenetic groups in glacier ice. Three different approaches were applied: analysis of amplified 16S rRNA gene sequences (A), comparison of pyrosequencing-derived sequences with the RDP II database (B) (cutoffs: match length >200 nucleotides; RDP Classifier [53] confidence estimate >60%), and taxonomic assignment of the pyrosequencing-derived sequences using CARMA (C) (25). Shown are the percentages of the phylogenetically classified sequences. Phylogenetic groups accounting for <1% of the sequences are summarized in the artificial group “Other.”

FIG. 2.

FIG. 2.

Rarefaction curves indicating the observed number of OTUs within the 16S rRNA gene libraries derived from glacial ice. The curves were calculated with DOTUR (39). OTUs are shown at the 1, 3, and 20% genetic distance level. Error bars represent the 95% confidence interval.

FIG. 3.

FIG. 3.

Distribution of phylogenetic groups in glacier ice determined by using the CARMA algorithm. A total of 14% of the pyrosequencing-derived data set (150,478 sequences) were phylogenetically classified at the superkingdom level. Shown are the percentages of all classified sequences. The group “Unknown” represents sequences, which match Pfam database entries that cannot be assigned to a taxonomic group.

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