Prasinoviruses of the marine green alga Ostreococcus tauri are mainly species specific

The dimensionality of infection networks among viruses infecting microbial eukaryotes and bacteria

Diverse viruses and their hosts are interconnected through complex networks of infection, which are thought to influence ecological and evolutionary processes, but the principles underlying infection network structure are not well understood. Here we focus on network dimensionality and how it varies across 37 networks of viruses infecting eukaryotic phytoplankton and bacteria. We find that dimensionality is often strikingly low, with most networks being one- or two-dimensional, although dimensionality increases with network richness, suggesting that the true dimensionality of natural systems is higher. Low-dimensional networks generally exhibit a mixture of host partitioning among viruses and nestededness of host ranges. Networks of bacteria-infecting and eukaryote-infecting viruses possess comparable distributions of dimensionality and prevalence of nestedness, indicating that fundamentals of network structure are similar among domains of life and different viral lineages. The relative simplicity of many infection networks suggests that coevolutionary dynamics are often driven by a modest number of underlying mechanisms.

Kratosvirus quantuckense: the history and novelty of an algal bloom disrupting virus and a model for giant virus research

Since the discovery of the first "giant virus," particular attention has been paid toward isolating and culturing these large DNA viruses through Acanthamoeba spp. bait systems. While this method has allowed for the discovery of plenty novel viruses in the Nucleocytoviricota, environmental -omics-based analyses have shown that there is a wealth of diversity among this phylum, particularly in marine datasets. The prevalence of these viruses in metatranscriptomes points toward their ecological importance in nutrient turnover in our oceans and as such, in depth study into non-amoebal Nucleocytoviricota should be considered a focal point in viral ecology. In this review, we report on Kratosvirus quantuckense (née Aureococcus anophagefferens Virus), an algae-infecting virus of the Imitervirales. Current systems for study in the Nucleocytoviricota differ significantly from this virus and its relatives, and a litany of trade-offs within physiology, coding potential, and ecology compared to these other viruses reveal the importance of K. quantuckense. Herein, we review the research that has been performed on this virus as well as its potential as a model system for algal-virus interactions.

Seasonality and Strain Specificity Drive Rapid Co-evolution in an Ostreococcus-Virus System from the Western Baltic Sea

Marine viruses are a major driver of phytoplankton mortality and thereby influence biogeochemical cycling of carbon and other nutrients. Phytoplankton-targeting viruses are important components of ecosystem dynamics, but broad-scale experimental investigations of host-virus interactions remain scarce. Here, we investigated in detail a picophytoplankton (size 1 µm) host's responses to infections by species-specific viruses from distinct geographical regions and different sampling seasons. Specifically, we used Ostreococcus tauri and O. mediterraneus and their viruses (size ca. 100 nm). Ostreococcus sp. is globally distributed and, like other picoplankton species, play an important role in coastal ecosystems at certain times of the year. Further, Ostreococcus sp. is a model organism, and the Ostreococcus-virus system is well-known in marine biology. However, only few studies have researched its evolutionary biology and the implications thereof for ecosystem dynamics. The Ostreococcus strains used here stem from different regions of the Southwestern Baltic Sea that vary in salinity and temperature and were obtained during several cruises spanning different sampling seasons. Using an experimental cross-infection set-up, we explicitly confirm species and strain specificity in Ostreococcus sp. from the Baltic Sea. Moreover, we found that the timing of virus-host co-existence was a driver of infection patterns as well. In combination, these findings prove that host-virus co-evolution can be rapid in natural systems.

Genomic adaptation of giant viruses in polar oceans

Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phyla Nucleocytoviricota and Mirusviricota are groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate the biogeography and functional repertoire of these viruses at a global scale. We first confirm the existence of an ecological barrier that clearly separates polar and nonpolar viral communities, and then demonstrate that temperature drives dramatic changes in the virus-host network at the polar-nonpolar boundary. Ancestral niche reconstruction suggests that adaptation of these viruses to polar conditions has occurred repeatedly over the course of evolution, with polar-adapted viruses in the modern ocean being scattered across their phylogeny. Numerous viral genes are specifically associated with polar adaptation, although most of their homologues are not identified as polar-adaptive genes in eukaryotes. These results suggest that giant viruses adapt to cold environments by changing their functional repertoire, and this viral evolutionary strategy is distinct from the polar adaptation strategy of their hosts.

Diversity and Evolution of Mamiellophyceae: Early-Diverging Phytoplanktonic Green Algae Containing Many Cosmopolitan Species

The genomic revolution has bridged a gap in our knowledge about the diversity, biology and evolution of unicellular photosynthetic eukaryotes, which bear very few discriminating morphological features among species from the same genus. The high-quality genome resources available in the class Mamiellophyceae (Chlorophyta) have been paramount to estimate species diversity and screen available metagenomic data to assess the biogeography and ecological niches of different species on a global scale. Here we review the current knowledge about the diversity, ecology and evolution of the Mamiellophyceae and the large double-stranded DNA prasinoviruses infecting them, brought by the combination of genomic and metagenomic analyses, including 26 metabarcoding environmental studies, as well as the pan-oceanic GOS and the Tara Oceans expeditions.

Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts

The marine picoeukaryote Bathycoccus prasinos has been considered a cosmopolitan alga, although recent studies indicate two ecotypes exist, Clade BI (B. prasinos) and Clade BII. Viruses that infect Bathycoccus Clade BI are known (BpVs), but not that infect BII. We isolated three dsDNA prasinoviruses from the Sargasso Sea against Clade BII isolate RCC716. The BII-Vs do not infect BI, and two (BII-V2 and BII-V3) have larger genomes (~210 kb) than BI-Viruses and BII-V1. BII-Vs share ~90% of their proteins, and between 65% to 83% of their proteins with sequenced BpVs. Phylogenomic reconstructions and PolB analyses establish close-relatedness of BII-V2 and BII-V3, yet BII-V2 has 10-fold higher infectivity and induces greater mortality on host isolate RCC716. BII-V1 is more distant, has a shorter latent period, and infects both available BII isolates, RCC716 and RCC715, while BII-V2 and BII-V3 do not exhibit productive infection of the latter in our experiments. Global metagenome analyses show Clade BI and BII algal relative abundances correlate positively with their respective viruses. The distributions delineate BI/BpVs as occupying lower temperature mesotrophic and coastal systems, whereas BII/BII-Vs occupy warmer temperature, higher salinity ecosystems. Accordingly, with molecular diagnostic support, we name Clade BII Bathycoccus calidus sp. nov. and propose that molecular diversity within this new species likely connects to the differentiated host-virus dynamics observed in our time course experiments. Overall, the tightly linked biogeography of Bathycoccus host and virus clades observed herein supports species-level host specificity, with strain-level variations in infection parameters.

Adaptive evolution of viruses infecting marine microalgae (haptophytes), from acute infections to stable coexistence

Collectively known as phytoplankton, photosynthetic microbes form the base of the marine food web, and account for up to half of the primary production on Earth. Haptophytes are key components of this phytoplankton community, playing important roles both as primary producers and as mixotrophs that graze on bacteria and protists. Viruses influence the ecology and diversity of phytoplankton in the ocean, with the majority of microalgae-virus interactions described as 'boom and bust' dynamics, which are characteristic of acute virus-host systems. Most haptophytes are, however, part of highly diverse communities and occur at low densities, decreasing their chance of being infected by viruses with high host specificity. Viruses infecting these microalgae have been isolated in the laboratory, and there are several characteristics that distinguish them from acute viruses infecting bloom-forming haptophytes. Herein we synthesise what is known of viruses infecting haptophyte hosts in the ocean, discuss the adaptive evolution of haptophyte-infecting viruses -from those that cause acute infections to those that stably coexist with their host - and identify traits of importance for successful survival in the ocean.

Growth strategies of a model picoplankter depend on social milieu and pCO2

Phytoplankton exist in genetically diverse populations, but are often studied as single lineages (single strains), so that interpreting single-lineage studies relies critically on understanding how microbial growth differs with social milieu, defined as the presence or absence of conspecifics. The properties of lineages grown alone often fail to predict the growth of these same lineages in the presence of conspecifics, and this discrepancy points towards an opportunity to improve our understanding of the factors that affect lineage growth rates. We demonstrate that different lineages of a marine picoplankter modulate their maximum lineage growth rate in response to the presence of non-self conspecifics, even when resource competition is effectively absent. This explains why growth rates of lineages in isolation do not reliably predict their growth rates in mixed culture, or the lineage composition of assemblages under conditions of rapid growth. The diversity of growth strategies observed here are consistent with lineage-specific energy allocation that depends on social milieu. Since lineage growth is only one of many traits determining fitness in natural assemblages, we hypothesize that intraspecific variation in growth strategies should be common, with more strategies possible in ameliorated environments that support higher maximum growth rates, such as high CO2 for many marine picoplankton.

Quantitative Assessment of Nucleocytoplasmic Large DNA Virus and Host Interactions Predicted by Co-occurrence Analyses

Nucleocytoplasmic large DNA viruses (NCLDVs) are highly diverse and abundant in marine environments. However, the knowledge of their hosts is limited because only a few NCLDVs have been isolated so far. Taking advantage of the recent large-scale marine metagenomics census, in silico host prediction approaches are expected to fill the gap and further expand our knowledge of virus-host relationships for unknown NCLDVs. In this study, we built co-occurrence networks of NCLDVs and eukaryotic taxa to predict virus-host interactions using Tara Oceans sequencing data. Using the positive likelihood ratio to assess the performance of host prediction for NCLDVs, we benchmarked several co-occurrence approaches and demonstrated an increase in the odds ratio of predicting true positive relationships 4-fold compared to random host predictions. To further refine host predictions from high-dimensional co-occurrence networks, we developed a phylogeny-informed filtering method, Taxon Interaction Mapper, and showed it further improved the prediction performance by 12-fold. Finally, we inferred virophage-NCLDV networks to corroborate that co-occurrence approaches are effective for predicting interacting partners of NCLDVs in marine environments.IMPORTANCE NCLDVs can infect a wide range of eukaryotes, although their life cycle is less dependent on hosts compared to other viruses. However, our understanding of NCLDV-host systems is highly limited because few of these viruses have been isolated so far. Co-occurrence information has been assumed to be useful to predict virus-host interactions. In this study, we quantitatively show the effectiveness of co-occurrence inference for NCLDV host prediction. We also improve the prediction performance with a phylogeny-guided method, which leads to a concise list of candidate host lineages for three NCLDV families. Our results underpin the usage of co-occurrence approaches for the metagenomic exploration of the ecology of this diverse group of viruses.

A thermal trade-off between viral production and degradation drives virus-phytoplankton population dynamics

Marine viruses interact with microbial hosts in dynamic environments shaped by variation in abiotic factors, including temperature. However, the impacts of temperature on viral infection of phytoplankton are not well understood. Here we coupled mathematical modelling with experiments to explore the effect of temperature on virus-phytoplankton interactions. Our model shows the negative consequences of high temperatures on infection and suggests a temperature-dependent threshold between viral production and degradation. Modelling long-term dynamics in environments with different average temperatures revealed the potential for long-term host-virus coexistence, epidemic free or habitat loss states. We generalised our model to variation in global sea surface temperatures corresponding to present and future seas and show that climate change may differentially influence virus-host dynamics depending on the virus-host pair. Temperature-dependent changes in the infectivity of virus particles may lead to shifts in virus-host habitats in warmer oceans, analogous to projected changes in the habitats of macro-, microorganisms and pathogens.

Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in Ostreococcus tauri

Ostreococcus tauri is a simple unicellular green alga representing an ecologically important group of phytoplankton in oceans worldwide. Modern molecular techniques must be developed in order to understand the mechanisms that permit adaptation of microalgae to their environment. We present for the first time in O. tauri a detailed characterization of individual genomic integration events of foreign DNA of plasmid origin after PEG-mediated transformation. Vector integration occurred randomly at a single locus in the genome and mainly as a single copy. Thus, we confirmed the utility of this technique for insertional mutagenesis. While the mechanism of double-stranded DNA repair in the O. tauri model remains to be elucidated, we clearly demonstrate by genome resequencing that the integration of the vector leads to frequent structural variations (deletions/insertions and duplications) and some chromosomal rearrangements in the genome at the insertion loci. Furthermore, we often observed variations in the vector sequence itself. From these observations, we speculate that a nonhomologous end-joining-like mechanism is employed during random insertion events, as described in plants and other freshwater algal models. PEG-mediated transformation is therefore a promising molecular biology tool, not only for functional genomic studies, but also for biotechnological research in this ecologically important marine alga.

Host-virus interactions and defense mechanisms for giant viruses

Giant viruses, with virions larger than 200 nm and genomes larger than 340 kilobase pairs, modified the now outdated perception of the virosphere. With virions now reported reaching up to 1.5 μm in size and genomes of up to 2.5 Mb encoding components shared with cellular life forms, giant viruses exhibit a complexity similar to microbes, such as bacteria and archaea. Here, we review interactions of giant viruses with their hosts and defense strategies of giant viruses against their hosts and coinfecting microorganisms or virophages. We also searched by comparative genomics for homologies with proteins described or suspected to be involved in defense mechanisms. Our search reveals that natural immunity and apoptosis seem to be crucial components of the host defense against giant virus infection. Conversely, giant viruses possess methods of hijacking host functions to counteract cellular antiviral responses. In addition, giant viruses may encode other unique and complex pathways to manipulate the host machinery and eliminate other competing microorganisms. Notably, giant viruses have evolved defense mechanisms against their virophages and they might trigger defense systems against other viruses through sequence integration. We anticipate that comparative genomics may help identifying genes involved in defense strategies of both giant viruses and their hosts.

Visualization of Viral Infection Dynamics in a Unicellular Eukaryote and Quantification of Viral Production Using Virus Fluorescence in situ Hybridization

One of the major challenges in viral ecology is to assess the impact of viruses in controlling the abundance of specific hosts in the environment. To this end, techniques that enable the detection and quantification of virus-host interactions at the single-cell level are essential. With this goal in mind, we implemented virus fluorescence in situ hybridization (VirusFISH) using as a model the marine picoeukaryote Ostreococcus tauri and its virus Ostreococcus tauri virus 5 (OtV5). VirusFISH allowed the visualization and quantification of the proportion of infected cells during an infection cycle in experimental conditions. We were also able to quantify the abundance of free viruses released during cell lysis, discriminating OtV5 from other mid-level fluorescence phages in our non-axenic infected culture that were not easily distinguishable with flow cytometry. Our results showed that although the major lysis of the culture occurred between 24 and 48 h after OtV5 inoculation, some new viruses were already produced between 8 and 24 h. With this work, we demonstrate that VirusFISH is a promising technique to study specific virus-host interactions in non-axenic cultures and establish a framework for its application in complex natural communities.

Rapidity of Genomic Adaptations to Prasinovirus Infection in a Marine Microalga

Prasinoviruses are large dsDNA viruses commonly found in aquatic systems worldwide, where they can infect and lyse unicellular prasinophyte algae such as Ostreococcus. Host susceptibility is virus strain-specific, but resistance of susceptible Ostreococcus tauri strains to a virulent virus arises frequently. In clonal resistant lines that re-grow, viruses are usually present for many generations, and genes clustered on chromosome 19 show physical rearrangements and differential expression. Here, we investigated changes occurring during the first two weeks after inoculation of the prasinovirus OtV5. By serial dilutions of cultures at the time of inoculation, we estimated the frequency of resistant cells arising in virus-challenged O. tauri cultures to be 10^-3⁻10^-4 of the inoculated population. Re-growing resistant cells were detectable by flow cytometry 3 days post-inoculation (dpi), visible re-greening of cultures occurred by 6 dpi, and karyotypic changes were visually detectable at 8 dpi. Resistant cell lines showed a modified spectrum of host-virus specificities and much lower levels of OtV5 adsorption.

The genome of a prasinoviruses-related freshwater virus reveals unusual diversity of phycodnaviruses

Background

Phycodnaviruses are widespread algae-infecting large dsDNA viruses and presently contain six genera: Chlorovirus, Prasinovirus, Prymnesiovirus, Phaeovirus, Coccolithovirus and Raphidovirus. The members in Prasinovirus are identified as marine viruses due to their marine algal hosts, while prasinovirus freshwater relatives remain rarely reported.

Results

Here we present the complete genomic sequence of a novel phycodnavirus, Dishui Lake Phycodnavirus 1 (DSLPV1), which was assembled from Dishui Lake metagenomic datasets. DSLPV1 harbors a linear genome of 181,035 bp in length (G + C content: 52.7%), with 227 predicted genes and 2 tRNA encoding regions. Both comparative genomic and phylogenetic analyses indicate that the freshwater algal virus DSLPV1 is closely related to the members in Prasinovirus, a group of marine algae infecting viruses. In addition, a complete eukaryotic histone H3 variant was identified in the genome of DSLPV1, which is firstly detected in phycodnaviruses and contributes to understand the interaction between algal virus and its eukaryotic hosts.

Conclusion

It is in a freshwater ecosystem that a novel Prasinovirus-related viral complete genomic sequence is discovered, which sheds new light on the evolution and diversity of the algae infecting Phycodnaviridae.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4432-4) contains supplementary material, which is available to authorized users.

Population genomics of picophytoplankton unveils novel chromosome hypervariability

Tiny photosynthetic microorganisms that form the picoplankton (between 0.3 and 3 μm in diameter) are at the base of the food web in many marine ecosystems, and their adaptability to environmental change hinges on standing genetic variation. Although the genomic and phenotypic diversity of the bacterial component of the oceans has been intensively studied, little is known about the genomic and phenotypic diversity within each of the diverse eukaryotic species present. We report the level of genomic diversity in a natural population of Ostreococcus tauri (Chlorophyta, Mamiellophyceae), the smallest photosynthetic eukaryote. Contrary to the expectations of clonal evolution or cryptic species, the spectrum of genomic polymorphism observed suggests a large panmictic population (an effective population size of 1.2 × 10⁷) with pervasive evidence of sexual reproduction. De novo assemblies of low-coverage chromosomes reveal two large candidate mating-type loci with suppressed recombination, whose origin may pre-date the speciation events in the class Mamiellophyceae. This high genetic diversity is associated with large phenotypic differences between strains. Strikingly, resistance of isolates to large double-stranded DNA viruses, which abound in their natural environment, is positively correlated with the size of a single hypervariable chromosome, which contains 44 to 156 kb of strain-specific sequences. Our findings highlight the role of viruses in shaping genome diversity in marine picoeukaryotes.

Marine Prasinoviruses and Their Tiny Plankton Hosts: A Review

Viruses play a crucial role in the marine environment, promoting nutrient recycling and biogeochemical cycling and driving evolutionary processes. Tiny marine phytoplankton called prasinophytes are ubiquitous and significant contributors to global primary production and biomass. A number of viruses (known as prasinoviruses) that infect these important primary producers have been isolated and characterised over the past decade. Here we review the current body of knowledge about prasinoviruses and their interactions with their algal hosts. Several genes, including those encoding for glycosyltransferases, methyltransferases and amino acid synthesis enzymes, which have never been identified in viruses of eukaryotes previously, have been detected in prasinovirus genomes. The host organisms are also intriguing; most recently, an immunity chromosome used by a prasinophyte in response to viral infection was discovered. In light of such recent, novel discoveries, we discuss why the cellular simplicity of prasinophytes makes for appealing model host organism-virus systems to facilitate focused and detailed investigations into the dynamics of marine viruses and their intimate associations with host species. We encourage the adoption of the prasinophyte Ostreococcus and its associated viruses as a model host-virus system for examination of cellular and molecular processes in the marine environment.

Virus Resistance Is Not Costly in a Marine Alga Evolving under Multiple Environmental Stressors

Viruses are important evolutionary drivers of host ecology and evolution. The marine picoplankton Ostreococcus tauri has three known resistance types that arise in response to infection with the Phycodnavirus OtV5: susceptible cells (S) that lyse following viral entry and replication; resistant cells (R) that are refractory to viral entry; and resistant producers (RP) that do not all lyse but maintain some viruses within the population. To test for evolutionary costs of maintaining antiviral resistance, we examined whether O. tauri populations composed of each resistance type differed in their evolutionary responses to several environmental drivers (lower light, lower salt, lower phosphate and a changing environment) in the absence of viruses for approximately 200 generations. We did not detect a cost of resistance as measured by life-history traits (population growth rate, cell size and cell chlorophyll content) and competitive ability. Specifically, all R and RP populations remained resistant to OtV5 lysis for the entire 200-generation experiment, whereas lysis occurred in all S populations, suggesting that resistance is not costly to maintain even when direct selection for resistance was removed, or that there could be a genetic constraint preventing return to a susceptible resistance type. Following evolution, all S population densities dropped when inoculated with OtV5, but not to zero, indicating that lysis was incomplete, and that some cells may have gained a resistance mutation over the evolution experiment. These findings suggest that maintaining resistance in the absence of viruses was not costly.

A Viral Immunity Chromosome in the Marine Picoeukaryote, Ostreococcus tauri

Micro-algae of the genus Ostreococcus and related species of the order Mamiellales are globally distributed in the photic zone of world's oceans where they contribute to fixation of atmospheric carbon and production of oxygen, besides providing a primary source of nutrition in the food web. Their tiny size, simple cells, ease of culture, compact genomes and susceptibility to the most abundant large DNA viruses in the sea render them attractive as models for integrative marine biology. In culture, spontaneous resistance to viruses occurs frequently. Here, we show that virus-producing resistant cell lines arise in many independent cell lines during lytic infections, but over two years, more and more of these lines stop producing viruses. We observed sweeping over-expression of all genes in more than half of chromosome 19 in resistant lines, and karyotypic analyses showed physical rearrangements of this chromosome. Chromosome 19 has an unusual genetic structure whose equivalent is found in all of the sequenced genomes in this ecologically important group of green algae.

We propose that chromosome 19 of O. tauri is specialized in defence against viral attack, a constant threat for all planktonic life, and that the most likely cause of resistance is the over-expression of numerous predicted glycosyltransferase genes. O. tauri thus provides an amenable model for molecular analysis of genome evolution under environmental stress and for investigating glycan-mediated host-virus interactions, such as those seen in herpes, influenza, HIV, PBCV and mimivirus.

Mode of resistance to viral lysis affects host growth across multiple environments in the marine picoeukaryote Ostreococcus tauri

Viruses play important roles in population dynamics and as drivers of evolution in single-celled marine phytoplankton. Viral infection of Ostreococcus tauri often causes cell lysis, but two spontaneously arising resistance mechanisms occur: resistant cells that cannot become infected and resistant producer cells that are infected but not lysed, and which may slowly release viruses. As of yet, little is known about how consistent the effects of viruses on their hosts are across different environments. To measure the effect of host resistance on host growth, and to determine whether this effect is environmentally dependent, we compared the growth and survival of susceptible, resistant and resistant producer O. tauri cells under five environmental conditions with and without exposure to O. tauri virus. While the effects of exposure to virus on growth rates did not show a consistent pattern in populations of resistant cells, there were several cases where exposure to virus affected growth in resistant hosts, sometimes positively. In the absence of virus, there was no detectable cost of resistance in any environment, as measured by growth rate. In fact, the opposite was the case, with populations of resistant producer cells having the highest growth rates across four of the five environments.

Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes

High-throughput sequencing of Prasinovirus DNA polymerase and host green algal (Mamiellophyceae) ribosomal RNA genes was used to analyse the diversity and distribution of these taxa over a ∼10 000 km latitudinal section of the Indian Ocean. New viral and host groups were identified among the different trophic conditions observed, and highlighted that although unknown prasinoviruses are diverse, the cosmopolitan algal genera Bathycoccus, Micromonas and Ostreococcus represent a large proportion of the host diversity. While Prasinovirus communities were correlated to both the geography and the environment, host communities were not, perhaps because the genetic marker used lacked sufficient resolution. Nevertheless, analysis of single environmental variables showed that eutrophic conditions strongly influence the distributions of both hosts and viruses. Moreover, these communities were not correlated, in their composition or specific richness. These observations could result from antagonistic dynamics, such as that illustrated in a prey-predator model, and/or because hosts might be under a complex set of selective pressures. Both of these reasons must be considered to interpret environmental surveys of viruses and hosts, because covariation does not always imply interaction.

Interplay between the genetic clades of Micromonas and their viruses in the Western English Channel

The genus Micromonas comprises distinct genetic clades that commonly dominate eukaryotic phytoplankton community from polar to tropical waters. This phytoplankter is also recurrently infected by abundant and genetically diverse prasinoviruses. Here we report on the interplay between prasinoviruses and Micromonas with regard to the genetic diversity of this host. For 1 year, we monitored the abundance of three clades of Micromonas and their viruses in the Western English Channel, both in the environment using clade-specific probes and flow cytometry, and in the laboratory using clonal strains of Micromonas clades to assay for their viruses by plaque-forming units. We showed that the seasonal fluctuations of Micromonas clades were closely mirrored by the abundance of their corresponding viruses, indicating that the members of Micromonas genus are susceptible to viral infection, regardless of their genetic affiliation. The characterization of 45 viral isolates revealed that Micromonas clades are attacked by specific virus populations, which exhibit distinctive clade specificity, life strategies and genetic diversity. However, some viruses can also cross-infect different host clades, suggesting a mechanism of horizontal gene transfer within the Micromonas genus. This study provides novel insights into the impact of viral infection for the ecology and evolution of the prominent phytoplankter Micromonas.

Biogeography of Viruses in the Sea

Viral ecology is a rapidly progressing area of research, as molecular methods have improved significantly for targeted research on specific populations and whole communities. To interpret and synthesize global viral diversity and distribution, it is feasible to assess whether macroecology concepts can apply to marine viruses. We review how viral and host life history and physical properties can influence viral distribution in light of biogeography and metacommunity ecology paradigms. We highlight analytical approaches that can be applied to emerging global data sets and meta-analyses to identify individual taxa with global influence and drivers of emergent properties that influence microbial community structure by drawing on examples across the spectrum of viral taxa, from RNA to ssDNA and dsDNA viruses.

Tsv-N1: A Novel DNA Algal Virus that Infects Tetraselmis striata

Numbering in excess of 10 million per milliliter of water, it is now undisputed that aquatic viruses are one of the major factors shaping the ecology and evolution of Earth’s microbial world. Nonetheless, environmental viral diversity and roles remain poorly understood. Here we report the first thorough characterization of a virus (designated TsV) that infects the coastal marine microalga Tetraselmis striata. Unlike previously known microalgae-infecting viruses, TsV is a small (60 nm) DNA virus, with a 31 kb genome. From a range of eight different strains belonging to the Chlamydomonadaceae family, TsV was only able to infect T. striata. Gene expression dynamics revealed an up-regulation of viral transcripts already 1 h post-infection (p.i.). First clear signs of infection were observed 24 h p.i., with the appearance of viral factories inside the nucleus. TsV assembly was exclusively nuclear. TsV-N1 genome revealed very different from previously known algae viruses (Phycodnaviridae). Putative function and/or homology could be resolved for only 9 of the 33 ORFs encoded. Among those was a surprising DNA polymerase type Delta (only found in Eukaryotes), and two genes with closest homology to genes from human parasites of the urogenital tract. These results support the idea that the diversity of microalgae viruses goes far beyond the Phycodnaviridae family and leave the door open for future studies on implications of microalgae viruses for human health.

Genomic comparison of closely related Giant Viruses supports an accordion-like model of evolution

Genome gigantism occurs so far in Phycodnaviridae and Mimiviridae (order Megavirales). Origin and evolution of these Giant Viruses (GVs) remain open questions. Interestingly, availability of a collection of closely related GV genomes enabling genomic comparisons offer the opportunity to better understand the different evolutionary forces acting on these genomes. Whole genome alignment for five groups of viruses belonging to the Mimiviridae and Phycodnaviridae families show that there is no trend of genome expansion or general tendency of genome contraction. Instead, GV genomes accumulated genomic mutations over the time with gene gains compensating the different losses. In addition, each lineage displays specific patterns of genome evolution. Mimiviridae (megaviruses and mimiviruses) and Chlorella Phycodnaviruses evolved mainly by duplications and losses of genes belonging to large paralogous families (including movements of diverse mobiles genetic elements), whereas Micromonas and Ostreococcus Phycodnaviruses derive most of their genetic novelties thought lateral gene transfers. Taken together, these data support an accordion-like model of evolution in which GV genomes have undergone successive steps of gene gain and gene loss, accrediting the hypothesis that genome gigantism appears early, before the diversification of the different GV lineages.

Diversity of Viruses Infecting the Green Microalga Ostreococcus lucimarinus

The functional diversity of eukaryotic viruses infecting a single host strain from seawater samples originating from distant marine locations is unknown. To estimate this diversity, we used lysis plaque assays to detect viruses that infect the widespread species Ostreococcus lucimarinus, which is found in coastal and mesotrophic systems, and O. tauri, which was isolated from coastal and lagoon sites from the northwest Mediterranean Sea. Detection of viral lytic activities against O. tauri was not observed using seawater from most sites, except those close to the area where the host strain was isolated. In contrast, the more cosmopolitan O. lucimarinus species recovered viruses from locations in the Atlantic and Pacific Oceans and the Mediterranean Sea. Six new O. lucimarinus viruses (OlVs) then were characterized and their genomes sequenced. Two subgroups of OlVs were distinguished based on their genetic distances and on the inversion of a central 32-kb-long DNA fragment, but overall their genomes displayed a high level of synteny. The two groups did not correspond to proximity of isolation sites, and the phylogenetic distance between these subgroups was higher than the distances observed among viruses infecting O. tauri. Our study demonstrates that viruses originating from very distant sites are able to infect the same algal host strain and can be more diverse than those infecting different species of the same genus. Finally, distinctive features and evolutionary distances between these different viral subgroups does not appear to be linked to biogeography of the viral isolates.

IMPORTANCE

Marine eukaryotic phytoplankton virus diversity has yet to be addressed, and more specifically, it is unclear whether diversity is connected to geographical distance and whether differential infection and lysis patterns exist among such viruses that infect the same host strain. Here, we assessed the genetic distance of geographically segregated viruses that infect the ubiquitous green microalga Ostreococcus. This study provides the first glimpse into the diversity of predicted gene functions in Ostreococcus viruses originating from distant sites and provides new insights into potential host distributions and restrictions in the world oceans.

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.

Environmental bacteriophages: viruses of microbes in aquatic ecosystems

Since the discovery 2–3 decades ago that viruses of microbes are abundant in marine ecosystems, viral ecology has grown increasingly to reach the status of a full scientific discipline in environmental sciences. A dedicated ISVM society, the International Society for Viruses of Microorganisms, (http://www.isvm.org/) was recently launched. Increasing studies in viral ecology are sources of novel knowledge related to the biodiversity of living things, the functioning of ecosystems, and the evolution of the cellular world. This is because viruses are perhaps the most diverse, abundant, and ubiquitous biological entities in the biosphere, although local environmental conditions enrich for certain viral types through selective pressure. They exhibit various lifestyles that intimately depend on the deep-cellular mechanisms, and are ultimately replicated by members of all three domains of cellular life (Bacteria, Eukarya, Archaea), as well as by giant viruses of some eukaryotic cells. This establishes viral parasites as microbial killers but also as cell partners or metabolic manipulators in microbial ecology. The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e., phages) in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology.

Cophylogenetic interactions between marine viruses and eukaryotic picophytoplankton

Background

Numerous studies have investigated cospeciation (or cophylogeny) in various host-symbiont systems, and different patterns were inferred, from strict cospeciation where symbiont phylogeny mirrors host phylogeny, to complete absence of correspondence between trees. The degree of cospeciation is generally linked to the level of host specificity in the symbiont species and the opportunity they have to switch hosts. In this study, we investigated cophylogeny for the first time in a microalgae-virus association in the open sea, where symbionts are believed to be highly host-specific but have wide opportunities to switch hosts. We studied prasinovirus-Mamiellales associations using 51 different viral strains infecting 22 host strains, selected from the characterisation and experimental testing of the specificities of 313 virus strains on 26 host strains.

Results

All virus strains were restricted to their host genus, and most were species-specific, but some of them were able to infect different host species within a genus. Phylogenetic trees were reconstructed for viruses and their hosts, and their congruence was assessed based on these trees and the specificity data using different cophylogenetic methods, a topology-based approach, Jane, and a global congruence method, ParaFit. We found significant congruence between virus and host trees, but with a putatively complex evolutionary history.

Conclusions

Mechanisms other than true cospeciation, such as host-switching, might explain a part of the data. It has been observed in a previous study on the same taxa that the genomic divergence between host pairs is larger than between their viruses. It implies that if cospeciation predominates in this algae-virus system, this would support the hypothesis that prasinoviruses evolve more slowly than their microalgal hosts, whereas host switching would imply that these viruses speciated more recently than the divergence of their host genera.

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.