Abstract
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 Cyanobacteria, Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes, eukaryotic algae and amoebae. Whole genome comparisons revealed the majority of circular genome scaffolds (CGS) 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 utilize very unusual life strategies and genes to control their replication and maintain a long-term relationship with their hosts.
Highlights
Glaciers and ice sheets host a surprising microbial diversity (Stibal et al, 2006; Hodson et al, 2008; Edwards et al, 2013)
Sample Collection Samples were collected from the surface of two glaciers in Ny-Ålesund, Svalbard (78◦55′ N 11◦55′W), Midtre Lovénbreen (ML) and Austre Brøggerbreen (AB) in August 2009, and from the margin of the Greenland Ice Sheet, near Kangerlussuaq (67◦9′39.7′′N, 50◦0′52.7′′W) in June 2010
1 kg of cryoconite was pooled from a 10 m radius for each location and frozen at −20◦C for return to the laboratory
Summary
Glaciers and ice sheets host a surprising microbial diversity (Stibal et al, 2006; Hodson et al, 2008; Edwards et al, 2013). Diverse viruses are present and active in these ecosystems (Bellas and Anesio, 2013), with bacteria being subjected to some of the highest rates of virus infection in the literature, where up to 21% of bacterial cells display visual viral infection (Säwström et al, 2007; Bellas et al, 2013). The extreme nature and isolation of these environments, coupled with likely strong selection pressures by viruses (Anesio and Bellas, 2011), make cryoconite viruses an attractive choice to examine virus diversity and functional potential through metagenomics, addressing the hypothesis that novel viruses are present which encoded genomic functions relevant to their environment
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