Tapping into the virome of glaciers and ice sheets

Lead Research Organisation: University of Bristol
Department Name: Geographical Sciences


It is only during the last 10 years that microbial investigations of glacial habitats have revealed that glaciers should be considered as part of the Earth's biosphere, since they harbour active microbial communities that mediate important nutrient transformations such as C fixation, iron cycling and production of methane that are important at local and potentially global scales. Different components of glaciers provide different habitats (and challenges) for microbial communities. For instance, plenty of meltwater becomes available at the surface of glaciers during the summer and several habitats are created for microbial colonisation. On average, a staggering 10 billion virus particles are found in every litre of seawater. More recently, our own data have shown that viruses are both abundant and dynamic at the surface of glaciers too. In fact, we have recently argued that low temperature habitats are hot spots of microbial evolution driven by viruses. Viruses at the surface of glaciers cause significant mortality to bacterial communities and consequently, they have an important effect on the cycling of nutrients of these habitats. Further, viruses affect bacterial communities in two ways: they control their total number and they also influence which types are present in the community. Many viruses are believed infect only one specific host (i.e., they are host specific). When that host is abundant, the viruses that infect it will also become abundant, leading eventually to a crash in the host population. Viruses can carry genetic material from one host cell to another and some of them can even persist in their hosts and change their properties without actually killing them. In this way they play a very important role in the evolution and genetic diversity of their hosts.

Surprisingly, nothing is known regarding the genetic diversity of viruses in glacial habitats. The composition and the metabolic potential within the glacial viral community can be explored by isolating and characterising their genetic material recovered directly from the environment using a metagenomic approach. Each sample of glacial habitat analysed represents a snapshot of the complex mixture of different viral types. In this project, we shall obtain a picture of the virus communities at the surface of 3 small valley glaciers in Svalbard and along a 50Km transect of the Greenland Ice Sheet. Although virus diversity is probably very high at a local scale, we want to test whether many of the same viruses are present in both Arctic environments and how they compare with viruses from other environments (both cold and warmer localities, freshwater and marine, other extreme habitats). Knowledge of viral diversity in low temperature habitats, particularly in relatively isolated systems, are necessary to demonstrate that microbial diversity in those systems is unexpectedly high and that virus genomes might contain important microbial metabolic genes, including those responsible for life adaptation to cold conditions.

Geographically, glaciers and Ice Sheets cover ca 15 million km2, or ca 10% of Earth's land surface area. This coverage was considerably higher during periods of glacial maxima. Thus, glaciers and ice sheets represent a substantial fraction of unexplored genetic material on the planet. Considering that worldwide glaciers and ice sheets are retreating, particularly in the Alpine and Arctic regions, the understanding of the genetic diversity of the glacial and ice sheet biome and its unique features is urgent.

Planned Impact

Data sets will be made available to the relevant NERC Data Centre and also be publically available on the standard genetic databases such as NCBI and SRA at EMBL and for use on metagenomic databases and workflow software such as CAMERA and SEED to allow our viral metagenomes from these unique environments to make an important contribution to the growing global pool of viral metagenomic data.

The database has an obvious impact for researchers interested in biodiversity of extreme cold habitats as well as viral ecology in general. Nevertheless, we foresee that the database can easily be relevant for any researcher interested in microbial diversity (genetic and metabolic) as the database can also be compared to other types of ecosystems. Furthermore, we foresee that our database could be exploited by the industry. For instance, a number of genes associated with cold adaptation (e.g. genes associated with the biosynthesis of unsaturated fatty acids, genes involved in the synthesis of cryo- and osmoprotectants) may be abundant in our glacial samples. Although there are potentially many genes associated with cold adaptation that are still to be discovered, the public databases will be long lasting and could still be explored many years after the completion of the project. Cold-adapted organisms and their products have potential biotechnological applications and we believe that the database delivered by the project is not a purely academic output.


10 25 50
Description It is only during the last 10 years that microbial investigations of glacial habitats have revealed that glaciers should be considered as part of the Earth's biosphere, since they harbour active microbial communities that mediate important nutrient transformations such as carbon fixation, iron cycling and production of methane that are important at local and potentially global scales. Microbial communities in glacial ecosystems are diverse, active, and subjected to strong viral pressures and infection rates. In this project we analysed 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.
Exploitation Route Discovery science about the understanding of virus distribution and their diversity in cold environments.
Sectors Agriculture, Food and Drink,Environment,Healthcare

URL http://journal.frontiersin.org/article/10.3389/fmicb.2015.00656/abstract