Article: Bellas, C.M., Anesia, A.M., Barker, G. 2015. Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions. Frontiers in Microbiology. doi:10.3389/fmicb.2015.00656
Glaciers are oftentimes depicted as barren, frozen wastelands. They are typically located in cold and remote areas and are not generally associated with high biological activity, or even presence. But a closer look at glaciers will reveal an abundance of life that form complex ecosystems – particularly in cryoconite holes (Fig. 1). Cryoconite is a dark dust-like material that deposits on glaciers, consisting of anything from dirt, dust, or aerosols from nearby areas. This dark material absorbs more incoming solar radiation than the surrounding areas, causing the local area to melt faster, which results in small water filled pools (cryoconite holes). Recently, scientists have found that these cryoconite holes hold a wealth of biodiversity in algae, microbial eukaryotes (like the indomitable tardigrade, or water bear), to small insects. Due to the localized nature of cryoconite holes, many scientists consider each individual cryoconite hole as its own separate ecosystem!
Drs. Christopher Bellas, Alexandre Anesio, and Gary Barker at the University of Bristol, UK, are particularly interested in the wealth of viruses that can be found in these cryoconite holes. In a previous OceanBites post, we’ve outlined the potentially large role viruses play in controlling marine algae and bacteria populations and many scientists have found that it may be much of the same in cryoconite holes – some of the highest rates of bacterial infection by viruses are from cryoconite holes. Unfortunately, our current state of knowledge regarding viruses is extremely limited, not to mention how our knowledge of marine viruses (or even viruses that don’t infect humans) is even more paltry in comparison. Drs. Bellas, Anesio, and Barker set out to understand a little bit more about the viral community in these cryoconite holes by using genomic analyses to pinpoint virus/bacteria interactions to shine light on the biological activities of these highly complex micro-ecosystems.
How they did it
Drs. Bellas, Anesio, and Barker collected water from cryoconite holes from two different locations: one sample each from two glaciers in Svalbard, Norway, and another from the margin of the Greenland Ice Sheet. Sample water was kept frozen during transport to the laboratory, where they then extracted DNA from the water. The samples were then sequenced at the Bristol Genomics Facility.
The sequencing runs produced over 208 million small chunks of DNA sequences! The researchers then used a series of newly developed computer programs to filter out DNA sequences that were more likely to belong to viruses as opposed to bacteria or microbial eukaryotes. These programs then pieced together the small chunks of virus DNA into larger fragments until they had a nearly complete picture of all the virus DNA (or virome, for virus genome) found in the cryoconite hole. They tried comparing their virome to known virus genome sequences to try and identify (at least generally) what types of viruses were present. They repeated this process for the non-viral DNA as well and used that information to determine what types of hosts some of these viruses target by looking for chunks of sequences that match between virus and potential host.
What they found
Dr. Bellas, Anesio, and Barker were only able to identify between 80-90% of the viruses in the samples. Even then, they were only able to assign them down to the family level (no genus of species identification). This isn’t entirely surprising considering how little scientists know about viral diversity. Additionally, not many people study viruses (outside a human health context) so not many people are contributing sequences to these viral databases that the researchers used. Nevertheless, they were able to identify viruses from the Myoviridae, Podoviridae, and Siphoviridae families in all three samples (Fig. 2).
Despite not being able to identify many of the viruses in the samples, the scientists were able to find many virus/host matches. They identified cyanobacteria, alphaproteobacteria, gammaproteobacteria, actinobacteria, firmicutes, eukaryotic algae, and amoebas as potential hosts of many of these viruses (Fig 3). Many of the virus genes that were identified point to a lifestyle that does not completely kill their hosts – instead, they either integrate their genome into their hosts, which allows them to wait for favorable conditions (like when their hosts are able to divide and create many new hosts for the viruses), or create stable plasmids out of their genome, essentially creating a dormant stage that, again, would allow them to wait for favorable conditions (large host availability).
What was really surprising though, was that they found many viruses that likely target other viruses! These virophages (or satellite viruses) may not have all the genes required to infect a host, so instead, they piggy-back on a virus that can infect a host, and then once inside the host, will kill the other virus to prevent any competition. To combat this, host cells can use a second line of defense called a CRISPR/Cas system. If the host integrates their parasites’ DNA sequence in a CRISPR/Cas set-up, they will be able to attack and destroy any infectious agent that has a matching sequence to their CRISPR/Cas system (learn more about CRISPR/Cas here). The scientists identified a virus that had CRISPR/Cas system that perfectly matched another virus, indicating the presence of virus-on-virus activity and evolved defenses to protect against that.
Why is this important?
Glaciers are no longer just slow geologic forces trudge down mountains and make icebergs. Studies like these show that glaciers can host a huge biological diversity in microbial life. These diverse communities, despite the cold, are very dynamic and active, where viruses and hosts alike employ many different adaptations to persist in harsh environments, as well as to try and out live and compete each other.
Glaciers worldwide are declining in their size as climate change forces them to move into the ocean faster as temperatures rise and increase melting. While the climate implications are abundantly clear, studies like this one also highlight the potential loss of dynamic but very poorly understood biological communities. We as scientists are only beginning to understand the complex life that occurs on glaciers, and it’s very possible that they might all disappear before we get a chance to learn about and from them.
A recent convert to oceanography, I’m studying under Dr. Anne McElroy at Stony Brook University’s School of Marine and Atmospheric Sciences. My research uses biochemical and genomic methods to investigate how coastal organisms respond to environmental stress.