Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions

Microbial communities in glacial ecosystems are diverse, active, and subjected to strong viral pressures and infection rates. In this study we analyse putative virus genomes assembled from three dsDNA viromes from cryoconite hole ecosystems of Svalbard and the Greenland Ice Sheet to assess the potential hosts and functional role viruses play in these habitats. We assembled 208 million reads from the virus-size fraction and developed a procedure to select genuine virus scaffolds from cellular contamination. Our curated virus library contained 546 scaffolds up to 230 Kb in length, 54 of which were circular virus consensus genomes. Analysis of virus marker genes revealed a wide range of viruses had been assembled, including bacteriophages, cyanophages, nucleocytoplasmic large DNA viruses and a virophage, with putative hosts identified as Actinobacteria, Alphaproteobacteria, Cyanobacteria, Firmicutes, Gammaproteobacteria, eukaryotic algae and amoebae. Whole genome comparisons revealed the majority of circular genome scaffolds formed 12 novel groups, two of which contained multiple phage members with plasmid-like properties, including a group of phage-plasmids possessing plasmid-like partition genes and toxin-antitoxin addiction modules to ensure their replication and a satellite phage-plasmid group. Surprisingly we also assembled a phage that not only encoded plasmid partition genes, but a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas adaptive bacterial immune system. One of the spacers was an exact match for another phage in our virome, indicating that in a novel use of the system, the lysogen was potentially capable of conferring immunity on its bacterial host against other phage. Together these results suggest that highly novel and diverse groups of viruses are present in glacial environments, some of which utilise very unusual life strategies and genes to control their replication and maintain a long-term relationship with their hosts

Microbial nitrogen cycling on the Greenland Ice Sheet

Nitrogen inputs and microbial nitrogen cycling were investigated along a 79 km transect into the Greenland Ice Sheet (GrIS) during the main ablation season in summer 2010. The depletion of dissolved nitrate and production of ammonium (relative to icemelt) in cryoconite holes on Leverett Glacier, within 7.5 km of the ice sheet margin, suggested microbial uptake and ammonification respectively. Positive in situ acetylene assays indicated nitrogen fixation both in a debris-rich 100 m marginal zone and up to 5.7 km upslope on Leverett Glacier (with rates up to 16.3 μmoles C<sub>2</sub>H<sub>4</sub> m<sup>−2</sup> day<sup>−1</sup>). No positive acetylene assays were detected > 5.7 km into the ablation zone of the ice sheet. Potential nitrogen fixation only occurred when concentrations of dissolved and sediment-bound inorganic nitrogen were undetectable. Estimates of nitrogen fluxes onto the transect suggest that nitrogen fixation is likely of minor importance to the overall nitrogen budget of Leverett Glacier and of negligible importance to the nitrogen budget on the main ice sheet itself. Nitrogen fixation is however potentially important as a source of nitrogen to microbial communities in the debris-rich marginal zone close to the terminus of the glacier, where nitrogen fixation may aid the colonization of subglacial and moraine-derived debris

Supporting information for "Flexible genes establish widespread bacteriophage pan-genomes in cryoconite hole ecosystems"

Bacteriophage genomes rapidly evolve via mutation and horizontal gene transfer to counter evolving bacterial host defenses; such arms race dynamics should lead to divergence between phages from similar, geographically isolated ecosystems. However, near-identical phage genomes can reoccur over large geographical distances and several years apart, conversely suggesting many are stably maintained. Here, we show that phages with near-identical core genomes in distant, discrete aquatic ecosystems maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants. By repeatedly reconstructing the core and flexible regions of phage genomes from different metagenomes, we show a pool of homologous gene variants co-exist for each module in each location, however, the dominant variant shuffles independently in each module. These results suggest that in a natural community, recombination is the largest contributor to phage diversity, allowing a variety of host recognition receptors and genes to counter bacterial defenses to co-exist for each phage