Phylodynamics and movement of Phycodnaviruses among aquatic environments

Phycodnavirus comprises of six genera that infect a range of eukaryotic algae. Therefore, it has the ability to change the dynamics of phytoplankton community structure and succession in addition to nutrient cycles. Since phytoplankton fixes around half the planet’s carbon dioxide and some algae release DMSP when lysed by the virus, it is thought that Phycodnavirus could also affect atmosphere composition. However, little is known about the evolutionary history, phylogenetics and phylodynamics of this virus, which is what this study aimed to investigate.

The Amazon River was chosen for this study because it is an ancient freshwater environment and thus may function as a reservoir for viruses to transfer to other aquatic environments. Samples were collected in July 2007 from the Solimões, Negro and Cuieiras Rivers and taken to the lab where they were immediately processed. They were filtered, the remaining particulate matter concentrated and then ultracentrifuged. The pellets were resuspended and stored in the dark at 4°c until the DNA was extracted. This involved DNA amplification via PCR, cloning and sequencing, then phylogenetic and phylodynamic analysis. The BayesTraits software was used to estimate the movement of Phycodnavirus between aquatic environments.

In total, 64 and 39 polymerase sequences were found from the Solimões and Cuieiras Rivers respectively, however none were found from the Negro River. This was the first data of Phycodnavirus collected from a tropical river and therefore allowed the first comparisons of this virus between temperate and tropical climates. All of the 104 sequences from the Amazon were aligned to 550 polymerase sequences from other studies and further analysis conducted.

The population size of Phycodnaviruses were estimated by multiplying the effective population by generation time. This was represented on a Bayesian skyline plot, displaying the population dynamics over the past 1.5 million years. This demonstrated that the Phycodnavirus dynamics have fluctuated greatly over time. A large population decrease was observed between 500-300 thousand years before present (KYBP), then an increase in lineages after a bottleneck at 300KYBP, which finally plateaued at 100KYBP.

Since they had access to data from samples from a diverse range of places, phylogenetic associations could be used to investigate the movement of the Phycodnavirus between aquatic environments. This demonstrated significant genetic transfer between rivers and lakes, but not between freshwater and marine ecosystems. Since the virus may not be transferred between all water environments this provides evidence of restricted gene flow, which could affect their evolution and dispersal. Furthermore, they conducted a multi-state character change analysis using BayesTraits, which also proposed restrictions of the virus transmission as well as the colonisation of specific freshwater systems, which could explain why the Phycodnavirus was not found in the Negro River. Other studies have also shown a dramatic decrease in freshwater viral count when seawater was added, however the same was not observed when freshwater was added to seawater. This provides evidence that freshwater viruses may be unable to tolerate changes in salinity, perhaps giving reason for the lack of movement of Phycodnavirus to marine environments.

It must be noted that this study was based on the transmission of the virus between freshwater and marine environments from a limited number of samples. Moreover, the PCR required highly degenerate primers, which may have caused biased sampling, meaning not all Phycodnaviruses were detected. Nonetheless, this would not invalidate the findings concerning the phylodynamics and evidence of restricted transmission of the virus between aquatic environments. Overall, the study was important in demonstrating the long term fluctuations of the Phycodnavirus dynamics and the restriction of gene flow between freshwater and marine environments. Further studies would be valuable in determining whether the restriction in salinity tolerance is a limiting factor in Phycodnavirus survival and therefore a potential reason for the lack of transition between freshwater and marine ecosystems during its evolution.  

Manuela V Gimenes¹, Paolo M de A Zanotto¹, Curtis A Suttle², Hillândia B da Cunha³ and Dolores U Mehnert¹

The ISME Journal (2012) 6, 237–247; doi:10.1038/ismej.2011.93; published online 28 July 2011

http://www.nature.com/ismej/journal/v6/n2/full/ismej201193a.html