Phylogenetic analysis of Ostreococcus virus sequences from the Patagonian Coast

Prasinovirus distribution in the Northwest Mediterranean Sea is affected by the environment and particularly by phosphate availability

Numerous seawater lagoons punctuate the southern coastline of France. Exchanges of seawater between these lagoons and the open sea are limited by narrow channels connecting them. Lagoon salinities vary according to evaporation and to the volume of freshwater arriving from influent streams, whose nutrients also promote the growth of algae. We compared Prasinovirus communities, whose replication is supported by microscopic green algae, in four lagoons and at a coastal sampling site. Using high-throughput sequencing of DNA from a giant virus-specific marker gene, we show that the environmental conditions significantly affect the types of detectable viruses across samples. In spatial comparisons between 5 different sampling sites, higher levels of phosphates, nitrates, nitrites, ammonium and silicates tend to increase viral community richness independently of geographical distances between the sampling sites. Finally, comparisons of Prasinovirus communities at 2 sampling sites over a period of 10 months highlighted seasonal effects and the preponderant nature of phosphate concentrations in constraining viral distribution.

An optimized DNA extraction protocol for benthic Didymosphenia geminata

Didymosphenia geminata mats display few cells in relation to extracellular material and contain polysaccharides and heavy metals that interfere with molecular studies. We describe an optimized DNA extraction protocol that help to overcome these difficulties. Our protocol outperformed five previously described DNA extraction techniques.

Unveiling of the diversity of Prasinoviruses (Phycodnaviridae) in marine samples by using high-throughput sequencing analyses of PCR-amplified DNA polymerase and major capsid protein genes

Viruses strongly influence the ecology and evolution of their eukaryotic hosts in the marine environment, but little is known about their diversity and distribution. Prasinoviruses infect an abundant and widespread class of phytoplankton, the Mamiellophyceae, and thereby exert a specific and important role in microbial ecosystems. However, molecular tools to specifically identify this viral genus in environmental samples are still lacking. We developed two primer sets, designed for use with polymerase chain reactions and 454 pyrosequencing technologies, to target two conserved genes, encoding the DNA polymerase (PolB gene) and the major capsid protein (MCP gene). While only one copy of the PolB gene is present in Prasinovirus genomes, there are at least seven paralogs for MCP, the copy we named number 6 being shared with other eukaryotic alga-infecting viruses. Primer sets for PolB and MCP6 were thus designed and tested on 6 samples from the Tara Oceans project. The results suggest that the MCP6 amplicons show greater richness but that PolB gave a wider coverage of Prasinovirus diversity. As a consequence, we recommend use of the PolB primer set, which will certainly reveal exciting new insights about the diversity and distribution of prasinoviruses at the community scale.

Genetic data generated from virus-host complexes obtained by membrane co-immobilization are equivalent to data obtained from tangential filtrate virus concentrates and virus cultures

The sieving and immobilization of virus-host complexes using impact filtration (aka membrane co-immobilization or MCI) is a novel approach to the study of plankton viruses. One of the most interesting characteristics of the method is the possibility of generating data on potential viral hosts without the need of culturing hosts cells. MCI has demonstrated to be useful for studying viruses of picoalgae, but studies comparing data generated by MCI to data obtained by other techniques are lacking. In this work, Ostreococcus virus (OV) and Ostreococcus sp. sequences generated from virus-host complexes obtained by MCI were compared to sequences obtained from tangential filtration (TF) concentrates and virus cultures (VC). Statistical parsimony, phylogenetic analyses, pairwise distance comparisons, and analysis of molecular variance showed that the viral and host sequences obtained by the three methods were highly related to each other, indicating that MCI, TF, and VC produce equivalent results. Minor differences were observed among viral sequences obtained from VC and TF concentrates as well as among host sequences generated from VC and MCI. As discussed in the body of the paper, the divergence observed for cultured cells could be due to selective pressures exerted by culture conditions, whereas the correlate observed for the corresponding viral sequences could obey to a hitchhiking effect.