Ice shelves provide similar habitats for microbial colonization and growth in the North and South polar regions, with liquid water conditions that persist for only a few weeks to months each year. Aqueous temperatures may occasionally rise above 5°C but are more typically around 0°C. During freeze-up, salts are excluded from the ice and the resultant brines may have temperatures that fall well below zero (13
). Calculations based on production-to-biomass ratios have shown that the ice shelf mats are perennial, with the standing stock representing many years of microbial biomass accumulation (29
). The whole-mat metagenomes are therefore likely to reflect genetic responses to the ensemble of environmental conditions, including persistent cold, freeze-up, and variable salinities.
Consistent with the similar extreme conditions imposed by the ice shelf environments, the protein-coding genes indicated largely similar taxonomic compositions in the Arctic and Antarctica. Most of the matched sequences could be attributed to Proteobacteria
, which likely profit from the organic carbon-rich environment within the mats, and Cyanobacteria
, which provide the phototrophic energy source and structural biomass of the mats (55
) while likely benefiting from the decomposition and nutrient recycling activities of the Proteobacteria
) (). Archaea
were a minor but detectable component of all three metagenomes, as were eukaryotes, including metazoans.
Cyanobacterial mats are generally found anywhere that larger metazoan grazers are absent or marginalized because of extremes in temperature, salinity, and UV (10
). The vast range of temperatures where cyanobacterial mats are found, from continental polar regions to geothermal hot springs, suggests a diversity of strategies for coping with extremes in temperature (1
). Previous work has shown a relative absence in the High Arctic of cyanobacterial ribotypes from warmer latitudes and that many High Arctic 16S rRNA gene cyanobacterial sequences are >99% similar to sequences from Antarctica, including taxa previously assumed to be endemic to Antarctica (18
). This apparent bipolar distribution might also imply similarities in the mechanisms of stress tolerance throughout the cold biosphere.
Despite the similarities, there were some conspicuous differences between the polar regions, both in the relative abundances of bacteria and in the proportions of the major classes of bacteria within the mats. The Antarctic mats had a higher representation of Cyanobacteria
, and this was also reflected in the functional analysis, with a higher percentage of genes coding for photosynthetic functions found in MCM samples than in MIS-WHI samples. The greater proteobacterial and actinobacterial representation in the Arctic may reflect increased inputs of bacteria and terrigenous materials from the adjacent ice-free land. In addition to terrestrial inocula, the Arctic ice shelves are also exposed to diasporas from marine sources (12
). This was reflected in the higher representation of bacteria, such as marine Alphaproteobacteria
, in the Arctic mats than in the Antarctic. In addition, the shallower, more ephemeral ponds of the Arctic may be more prone to invasions by new groups (49
) than the deeper, longer-persisting ponds in Antarctica.
The microbial mats showed broadly similar functional gene repertoires for acclimation to environmental stress. Among the detected genes were sequences coding for EPS production, cold shock proteins, and membrane modification. There were, however, some differences between the mats. The Arctic mats had higher representation of copper homeostasis genes, possibly indicating their greater exposure to long-range pollutants, including metals (for examples, see reference 31
). Conversely, the Antarctic mat had a greater representation of the alternative sigma factor (sigma B) gene, which appears to be a general stress regulon that induces more than 100 genes in response to a great variety of stresses, including heat, acid, salt, and starvation (58
). The greater frequency of this gene in Antarctica might reflect greater osmotic stresses at freeze-up in the more saline waters of the Antarctic ponds, which are more persistent and subject to salt accumulation over time.
Many studies have shown the important role of EPS in buffering and cryoprotection for diverse microorganisms against ice crystal damage and high salinity (25
produce large amounts of EPS (24
) and were the primary source of EPS genes in the mats from both Antarctica and the Arctic. EPS allow bacterial aggregate formation, which in turn provides opportunities for close biogeochemical interactions (34
). In the cryophilic gammaproteobacterium Psychromonas ingrahamii
, production of EPS may sequester water from the ambient saltwater, lowering the freezing point (44
). Junge et al. (19
) demonstrated a significant correlation between concentrations of local bacteria and EPS in Arctic winter sea ice. In harsh environments, such as the polar regions, it is likely that EPS contributes to the physical stability of microbial communities (40
). Sulfate-reducing bacteria in the Deltaproteobacteria
may also produce large amounts of EPS (5
). Nichols et al. (34
) showed that Proteobacteria
) and Bacteroidetes
, which were common phyla in all three polar metagenomes, are able to synthesize EPS in response to low temperatures, implying that this is a cold-adaptation process.
In all three polar samples, genes coding for xylose, mannose, rhamnose, and fucose synthesis were among the most abundant monosaccharide synthesis genes. These sugars are typically found in bacterial EPS (21
), but the exact monosaccharide composition of EPS varies largely among bacterial strains (35
). EPS produced by marine bacteria generally contains 20 to 50% of the total polysaccharide as uronic acid (22
). Sequences assigned to uronic acid synthesis were rare in all three microbial mat samples. This is consistent with the presence of taxa, such as Pseudoalteromonas
, that are known to produce EPS rich in neutral sugars (especially mannose and fucose) but with little uronic acid (35
All of the polar metagenomes contained genes encoding cold shock proteins, which are a common feature of prokaryotes growing in low temperatures (47
). RNA chaperones (cold shock proteins CspA, CspB, CspE, CspI, and CspG) are essential for proper protein folding, especially at low temperatures, guiding nascent polypeptides into functional three-dimensional configurations (44
). All three polar metagenomes contained cold shock protein sequences. Matches assigned to the genes of more-constitutive proteins associated with cold adaptation, such as DNA transcription regulators (DnaA), recombination factors (RecA), topoisomerases (GyrA), trehalose synthesis proteins (OstA and OstB), and chaperones DnaK and DnaJ, were all numerous in the three polar microbial communities. These genes are known to be induced in bacteria upon exposure to cold temperatures (20
), and DnaA and GyrA are involved in the maintenance of functional DNA topology at cold temperatures (45
It has long been known that exposure of microorganisms to lower temperatures results in substantial alteration of their membrane compositions, with changes in the ratio of saturated to unsaturated fatty acids (for examples, see reference 27
). Saturation of the membrane fatty acids decreases at low temperatures in the psychrophilic gammaproteobacterium Psychrobacter arcticus
), a widespread cold-adapted species that can survive for long periods under harsh conditions, including deep permafrost (3
sequences with close similarity to those of P. arcticus
were identified in the MIS, WHI, and MCM metagenomes. In cold environments, maintenance of cell membrane integrity requires an increased proportion of unsaturated and branched fatty acids (15
). In cyanobacteria, this membrane composition adjustment occurred via desaturases (39
), and the genes coding for these enzymes were prevalent in the three polar mat metagenomes. In P. arcticus
, the effects of low temperatures on enzyme activity are compensated for by structural modifications that increase the flexibility of at least 50% of its proteome, thereby reducing energetic requirements (3
In summary, this metagenomic analysis of polar microbial mat consortia has revealed the presence of many cold stress genes that to date have mostly been known only from laboratory studies on isolated microorganisms. Consistent with our hypothesis, the analyses showed diverse mechanisms of potential responses to cold and other stresses, and this reflects the taxonomic diversity within the mats. In both polar regions, Proteobacteria and Cyanobacteria dominated the sequences, including the cold stress genes. However, there were distinct differences in terms of taxonomy and preferred biological functions between the Antarctic and Arctic mats. For example, the greater representation of Cyanobacteria in MCM was reflected by a significantly higher percentage of genes coding for photosynthetic functions. Factors such as habitat stability and the connectivity to marine and terrestrial sources of microbiota may account for the differences between the Arctic and Antarctic ice shelf mats noted here; however, additional data from a broader range of sites and habitats are required to evaluate whether these reflect fundamental, consistent differences between the two poles of the cold biosphere.