Do viral genes correlate with environmental variables?

The Arctic is incredibly important for carbon sequestration and is helping to mitigate anthropogenic carbon dioxide. Phytoplankton are responsible for fixing large amounts of carbon during bloom events, and viruses are often the reason these blooms desist. Two viruses known to be responsible for collapsing blooms are the T4 virus and the Phycodnaviridae, which infect cyanobacteria and eukaryotic phytoplankton, respectively.  Both viruses are phylogenetically diverse due to variations in particular genes allowing them to infect a substantial host range. The extensive seasonal changes occurring in this region have resulted in a diverse and abundant community of host organisms, which are governed by these environmental conditions, but little was known about how the environment affects the viruses genetic make-up.

Payet and Suttle (2006) showed that on the Canadian Arctic Shelf, viral abundance was positively correlated with season (warmer waters) and with location (closer to a river plume), where chlorophyll a concentration were high. Viral abundance was also positively correlated with bacterial abundance. They suggested that two types of viruses were present: The T4 virus and the Phycodnaviridae. However the methods used (epifluourescence and flow cytometry) allowed them to show abundance but not to identify the viruses.

Payet and Suttle (2014) therefore went back to the Canadian Arctic Shelf, this time using molecular fingerprinting. They wanted to see how specific genes (known to allow the viruses their phylogenetic diversity) changed with variations in chemical and physical conditions, attributed to season and spatio-scale.

By using denaturing gradient gel electrophoresis (DGGE) of PCR products, the authors were specifically looking at the g23 gene in T4 viruses, and the polB in the Phycodnaviridae.

Water samples were collected during all 4 seasons, as well as at seven locations stretching from the Mackenzie River plume, across the Mackenzie Shelf (mid-shelf), to the Amundsen Gulf, during summer. At each collection, three depths were sampled: chlorophyll maximum (<10m), temperature inversion layer (10-30m) and the pycnocline (30-60m).

By filtering the water through a number of filters of different sizes they collected the bacteria and eukaryotic phytoplankton from samples, along with the viruses, for molecular analysis and comparison.

Environmental variables were also recorded for each sample (temperature, salinity, depth, bacterial abundance, chlorophyll a content and viral abundance).

The polB gene, from the Phycodnarviridae, showed significant differences at all seasons, and between the Mackenzie River plume and the Amundsen Gulf. The depths were not significant for season or location. But there was some weak correlation with the environmental variables: salinity, chlorophyll a and bacterial abundance. Bacterial abundance was best correlated.

The g23 gene, encoding a capsid protein from the T4-virus, was significantly different during season and at all three locations (Mackenzie river plume, Mid-shelf, Amundsen Gulf). No significant difference was apparent for depth, and no correlation was observed for the environmental variables.

The composition of the16S and 18S rRNA sequences were compared to viral sequences and environmental variables. The results showed the polB was correlated to the eukaryotic 18S sequences and the environmental variables. The g23 wasn’t correlated to 16S or 18S sequences, no the environment.

I would have expected that there would have been some correlation between the g23 gene and bacterial abundance and 16S rRNA as the T4 virus infects bacteria. The authors suggest that the g23 gene may have captured a much broader spectrum of viruses, which therefore didn’t show any trends. Or perhaps the T4 viruses don’t fluctuate in composition the same as the polB, as its host (bacteria) aren’t fluctuating as much as the eukaryotic phytoplankton. It’s also interesting that the polB was correlated with bacterial abundance. Possibly because nutrients will be leaching from phytoplankton cells and bacteria might be utilising it.

References: 

Payet, J. P., & Suttle, C. A. (2014). Viral infection of bacteria and phytoplankton in the Arctic Ocean as viewed through the lens of fingerprint analysis. Aquatic Microbial Ecology, 72, 47-61.

Payet, J. P., & Suttle, C. A. (2008). Physical and biological correlates of virus dynamics in the southern Beaufort Sea and Amundsen Gulf. Journal of Marine Systems, 74(3), 933-945.