Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica

Abstract

Green sulfur bacteria (GSB) (Chlorobiaceae) are primary producers that are important in global carbon and sulfur cycling in natural environments. An almost complete genome sequence for a single, dominant GSB species ('C-Ace') was assembled from shotgun sequence data of an environmental sample taken from the O(2)-H(2)S interface of the water column of Ace Lake, Antarctica. Approximately 34 Mb of DNA sequence data were assembled into nine scaffolds totaling 1.79 Mb, representing approximately 19-fold coverage for the C-Ace composite genome. A high level ( approximately 31%) of metaproteomic coverage was achieved using matched biomass. The metaproteogenomic approach provided unique insight into the protein complement required for dominating the microbial community under cold, nutrient-limited, oxygen-limited and extremely varied annual light conditions. C-Ace shows physiological traits that promote its ability to compete very effectively with other GSB and gain dominance (for example, specific bacteriochlorophylls, mechanisms of cold adaptation) as well as a syntrophic relationship with sulfate-reducing bacteria that provides a mechanism for the exchange of sulfur compounds. As a result we are able to propose an explanation of the active biological processes promoted by cold-adapted GSB and the adaptive strategies they use to thrive under the severe physiochemical conditions prevailing in polar environments.

An integrative study of a meromictic lake ecosystem in Antarctica

“…A previous study reported that Nif proteins were not detected in the metaproteome and that the GSB were likely to be assimilating ammonia (Ng et al, 2010). Although it is likely that at the time of sampling the levels of ammonia present at the oxycline were sufficient to inhibit the expression of nitrogen fixation genes, when ammonia levels drop diazotrophy would need to occur.…”

“…The size fractionation not only reflected cell size differences (Supplementary Figure S4), but also trophic distinction , with the cells captured on the 0.8 and 3.0 mm fractions being overall less oligotrophic than the 0.1 mm fraction (Supplementary Figure S5). At 12.7 m depth, the light levels and the sharp transition in oxygen content and salinity (Supplementary Figure S1) favor the dominance of a very high-density (2.2 Â 10 8 cells ml À1 ) of a single type of GSB of the genus Chlorobium, referred to as C-Ace (Ng et al, 2010). Viral signatures were essentially absent from this zone.…”

“…A total of 8 926 759 ORFs were identified, of which B28% were assigned matches to a COG category, and B26% to a KEGG pathway (Supplementary Figure S1D). Metaproteomics was performed on matched samples from 0.1 mm filters (Ng et al, 2010), generating 490 612 mass spectra and a total of 1824 protein identifications. The phylogenetic diversity in the lake was determined by two approaches: analyzing a total of 5054 16S and 218 18S rRNA gene sequences retrieved from the metagenomic data set, and by read-based taxonomic binning of a total of 8 103 379 reads with matches to RefSeq.…”

“…A 2 m hole positioned above the deepest point (25 m depth) of the lake was drilled through the ice cover of Ace Lake to reach the lake surface. A volume of 1-10 l was collected by sequential size fractionation through a 20 mm prefilter directly onto filters 3.0, 0.8 and 0.1 mm poresized, 293 mm polyethersulfone membrane filters (Rusch et al, 2007), along the depth profile as described previously (Ng et al, 2010). Samples were taken in the order, 23, 18, 14, 12.7, 5 and finally, 11.5 m. After samples from each depth were collected, the sample racks were sequentially washed with 2 Â 25 l 0.1 N NaOH, 2 Â 25 l 0.053% NaOCl, and 2 Â 25 l fresh water.…”

“…Proteins were extracted from membrane filters from all 0.1 mm fractions from the six depths (5, 11.5, 12.7, 14, 18 and 23 m), and one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis and in gel trypsin digestion, liquid chromatography and mass spectrometry (MS), and MS/MS data analysis and validation of protein identifications performed as previously described (Ng et al, 2010), with minor modifications. The spectra generated were searched against the protein sequence database corresponding to that depth constructed from the 0.1 mm mosaic assemblies.…”