Quantification of virus genes provides evidence for seed-bank populations of phycodnaviruses in Lake Ontario, Canada

Metatranscriptomic analysis reveals dissimilarity in viral community activity between an ice-free and ice-covered winter in Lake Erie

Winter is a relatively under-studied season in freshwater ecology. The paucity of wintertime surveys has led to a lack of knowledge regarding microbial community activity during the winter in Lake Erie, a North American Great Lake. Viruses shape microbial communities and regulate biogeochemical cycles by acting as top-down controls, yet very few efforts have been made to examine active virus populations during the winter in Lake Erie. Furthermore, climate change-driven declines in seasonal ice cover have been shown to influence microbial community structure, but no studies have compared viral community activity between different ice cover conditions. We surveyed surface water metatranscriptomes for viral hallmark genes as a proxy for active virus populations and compared activity metrics between ice-covered and ice-free conditions from two sampled winters. Transcriptionally active viral communities were detected in both winters, spanning diverse phylogenetic clades of putative bacteriophage (Caudoviricetes), giant viruses (Nucleocytoviricota, or NCLDV), and RNA viruses (Orthornavirae). However, viral community activity metrics revealed pronounced differences between the ice-covered and ice-free winters. Viral community composition was distinct between winters and viral hallmark gene richness was reduced in the ice-covered relative to the ice-free conditions. In addition, the observed differences in viral communities correlated with microbial community activity metrics. Overall, these findings contribute to our understanding of the viral populations that are active during the winter in Lake Erie and suggest that viral community activity may be associated with ice cover extent.IMPORTANCEAs seasonal ice cover is projected to become increasingly rare on large temperate lakes, there is a need to understand how microbial communities might respond to changing ice conditions. Although it is widely recognized that viruses impact microbial community structure and function, there is little known regarding wintertime viral activity or the relationship between viral activity and ice cover extent. Our metatranscriptomic analyses indicated that viruses were transcriptionally active in the winter surface waters of Lake Erie. These findings also expanded the known diversity of viral lineages in the Great Lakes. Notably, viral community activity metrics were significantly different between the two sampled winters. The pronounced differences we observed in active viral communities between the ice-covered and ice-free samples merit further research regarding how viral communities will function in future, potentially ice-free, freshwater systems.

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.

Metatranscriptome Library Preparation Influences Analyses of Viral Community Activity During a Brown Tide Bloom

There is growing interest in the use of metatranscriptomics to study virus community dynamics. We used RNA samples collected from harmful brown tides caused by the eukaryotic alga Aureococcus anophagefferens within New York (United States) estuaries and in the process observed how preprocessing of libraries by either selection for polyadenylation or reduction in ribosomal RNA (rRNA) influenced virus community analyses. As expected, more reads mapped to the A. anophagefferens genome in polyadenylation-selected libraries compared to the rRNA-reduced libraries, with reads mapped in each sample correlating to one another regardless of preprocessing of libraries. Yet, this trend was not seen for reads mapping to the Aureococcus anophagefferens Virus (AaV), where significantly more reads (approximately two orders of magnitude) were mapped to the AaV genome in the rRNA-reduced libraries. In the rRNA-reduced libraries, there was a strong and significant correlation between reads mappings to AaV and A. anophagefferens. Overall, polyadenylation-selected libraries produced fewer viral contigs, fewer reads mapped to viral contigs, and different proportions across viral realms and families, compared to their rRNA-reduced pairs. This study provides evidence that libraries generated by rRNA reduction and not selected for polyadenylation are more appropriate for quantitative characterization of viral communities in aquatic ecosystems by metatranscriptomics.

Role of Phylogenetic Structure in the Dynamics of Coastal Viral Assemblages

Marine microbes, including viruses, are an essential part of the marine ecosystem, forming the base of the food web and driving biogeochemical cycles. Within this system, the composition of viral assemblages changes markedly with time, and some of these changes are repeatable through time; however, the extent to which these dynamics are reflected within versus among evolutionarily related groups of viruses is largely unexplored. To examine these dynamics, changes in the composition of two groups of ecologically important viruses and communities of their potential hosts were sampled every 2 weeks for 13 months at a coastal site in British Columbia, Canada. We sequenced two marker genes for viruses-the gene encoding the major capsid protein of T4-like phages and their relatives (gp23) and the RNA-dependent RNA polymerase (RdRp) gene of marnavirus-like RNA viruses-as well as marker genes for their bacterial and eukaryotic host communities, the genes encoding 16S rRNA and 18S rRNA. There were strong lagged correlations between viral diversity and community similarity of putative hosts, implying that the viruses influenced the composition of the host communities. The results showed that for both viral assemblages, the dominant clusters of phylogenetically related viruses shifted over time, and this was correlated with environmental changes. Viral clusters contained many ephemeral taxa and few persistent taxa, but within a viral assemblage, the ephemeral and persistent taxa were closely related, implying ecological dynamics within these clusters. Furthermore, these dynamics occurred in both the RNA and DNA viral assemblages surveyed, implying that this structure is common in natural viral assemblages.IMPORTANCE Viruses are major agents of microbial mortality in marine systems, yet little is known about changes in the composition of viral assemblages in relation to those of the microbial communities that they infect. Here, we sampled coastal seawater every 2 weeks for 1 year and used high-throughput sequencing of marker genes to follow changes in the composition of two groups of ecologically important viruses, as well as the communities of bacteria and protists that serve as their respective hosts. Different subsets of genetically related viruses dominated at different times. These results demonstrate that although the genetic composition of viral assemblages is highly dynamic temporally, for the most part the shuffling of genotypes occurs within a few clusters of phylogenetically related viruses. Thus, it appears that even in temperate coastal waters with large seasonal changes, the highly dynamic shuffling of viral genotypes occurs largely within a few subsets of related individuals.

T4-like myovirus community shaped by dispersal and deterministic processes in the South China Sea

As the most abundant and genetically diverse biological entities, viruses significantly influence ecological, biogeographical and evolutionary processes in the ocean. However, the biogeography of marine viruses and the drivers shaping viral community are unclear. Here, the biogeographic patterns of T4-like viruses and the relative impacts of deterministic (environmental selection) and dispersal (spatial distance) processes were investigated in the northern South China Sea. The dominant viral operational taxonomic units were affiliated with previously defined Marine, Estuary, Lake and Paddy Groups. A clear viral biogeographic pattern was observed along the environmental gradient from the estuary to open sea. Marine Groups I and IV had a wide geographical distribution, whereas Marine Groups II, III and V were abundant in lower-salinity continental or eutrophic environments. A significant distance-decay pattern was noted for the T4-like viral community, especially for those infecting cyanobacteria. Both deterministic and dispersal processes influenced viral community assembly, although environmental selection (e.g. temperature, salinity, bacterial abundance and community, etc.) had a greater impact than spatial distance. Network analysis confirmed the strong association between viral and bacterial community composition, and suggested a diverse ecological relationship (e.g. lysis, co-infection or mutualistic) between and within viruses and their potential bacterial hosts.

Specific quantification of Scenedesmus obliquus and Chlorella vulgaris in mixed-species algal biofilms

Two TaqMan® qPCR assays were developed to specifically quantify the absolute abundance of Scenedesmus obliquus and Chlorella vulgaris in mixed-species algal biofilms by targeting the psbA gene. Standard curves were developed with amplification efficiencies of 92.4% and 96.6% for S. obliquus and C. vulgaris, respectively, and an R² value of 0.99 for both. Calibration curves for estimating absolute cell abundances resulted in slopes of 0.98 and 1.11 for C. vulgaris and S. obliquus, respectively, and an R² value of 0.95 for both. The assays were applied to cultivated mixed-species biofilms and approximately 10⁷ cells of each algal species were quantified when 10⁷ cells were added into biofilms. The developed qPCR assays were concluded to be specific and accurate for the quantification of S. obliquus and C. vulgaris in mixed-species biofilms. This will contribute to the control and optimization of algal cultivation systems for the production of algal biofuels and bioproducts.

Viruses of Eukaryotic Algae: Diversity, Methods for Detection, and Future Directions

The scope for ecological studies of eukaryotic algal viruses has greatly improved with the development of molecular and bioinformatic approaches that do not require algal cultures. Here, we review the history and perceived future opportunities for research on eukaryotic algal viruses. We begin with a summary of the 65 eukaryotic algal viruses that are presently in culture collections, with emphasis on shared evolutionary traits (e.g., conserved core genes) of each known viral type. We then describe how core genes have been used to enable molecular detection of viruses in the environment, ranging from PCR-based amplification to community scale "-omics" approaches. Special attention is given to recent studies that have employed network-analyses of -omics data to predict virus-host relationships, from which a general bioinformatics pipeline is described for this type of approach. Finally, we conclude with acknowledgement of how the field of aquatic virology is adapting to these advances, and highlight the need to properly characterize new virus-host systems that may be isolated using preliminary molecular surveys. Researchers can approach this work using lessons learned from the Chlorella virus system, which is not only the best characterized algal-virus system, but is also responsible for much of the foundation in the field of aquatic virology.

Phage puppet masters of the marine microbial realm

Viruses numerically dominate our oceans; however, we have only just begun to document the diversity, host range and infection dynamics of marine viruses, as well as the subsequent effects of infection on both host cell metabolism and oceanic biogeochemistry. Bacteriophages (that is, phages: viruses that infect bacteria) are highly abundant and are known to play critical roles in bacterial mortality, biogeochemical cycling and horizontal gene transfer. This Review Article summarizes current knowledge of marine viral ecology and highlights the importance of phage particles to the dissolved organic matter pool, as well as the complex interactions between phages and their bacterial hosts. We emphasize the newly recognized roles of phages as puppet masters of their bacterial hosts, where phages are capable of altering the metabolism of infected bacteria through the expression of auxiliary metabolic genes and the redirection of host gene expression patterns. Finally, we propose the 'royal family model' as a hypothesis to describe successional patterns of bacteria and phages over time in marine systems, where despite high richness and significant seasonal differences, only a small number of phages appear to continually dominate a given marine ecosystem. Although further testing is required, this model provides a framework for assessing the specificity and ecological consequences of phage-host dynamics.

Seasonal patterns in Arctic prasinophytes and inferred ecology of Bathycoccus unveiled in an Arctic winter metagenome

Prasinophytes occur in all oceans but rarely dominate phytoplankton populations. In contrast, a single ecotype of the prasinophyte Micromonas is frequently the most abundant photosynthetic taxon reported in the Arctic from summer through autumn. However, seasonal dynamics of prasinophytes outside of this period are little known. To address this, we analyzed high-throughput V4 18S rRNA amplicon data collected from November to July in the Amundsen Gulf Region, Beaufort Sea, Arctic. Surprisingly during polar sunset in November and December, we found a high proportion of reads from both DNA and RNA belonging to another prasinophyte, Bathycoccus. We then analyzed a metagenome from a December sample and the resulting Bathycoccus metagenome assembled genome (MAG) covered ~90% of the Bathycoccus Ban7 reference genome. In contrast, only ~20% of a reference Micromonas genome was found in the metagenome. Our phylogenetic analysis of marker genes placed the Arctic Bathycoccus in the B1 coastal clade. In addition, substitution rates of 129 coding DNA sequences were ~1.6% divergent between the Arctic MAG and coastal Chilean upwelling MAGs and 17.3% between it and a South East Atlantic open ocean MAG in the B2 Clade. The metagenomic analysis also revealed a winter viral community highly skewed toward viruses targeting Micromonas, with a much lower diversity of viruses targeting Bathycoccus. Overall a combination of Micromonas being relatively less able to maintain activity under dark winter conditions and viral suppression of Micromonas may have contributed to the success of Bathycoccus in the Amundsen Gulf during winter.

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.

Influence of Iron-Doped Apatite Nanoparticles on Viral Infection Examined in Bacterial Versus Algal Systems

The Centers for Disease Control and Prevention have estimated that each year, two million people in the United States become infected with antibiotic-resistant bacteria, of which, approximately 23000 die as a direct result of these infections. Phage therapy, or the treatment of bacterial infection by specific, antagonistic viruses, provides one alternative to traditional antibiotics. Bacteriophages, or phages, are bacteria-specific viruses that possess biological traits that allow for not only the removal of bacterial infection, but also the evasion of bacterial resistance, which renders antibiotics ineffective. Previous research has shown the addition of iron-doped apatite nanoparticles (IDANPs) to bacteria prior to phage exposure results in increased bacterial plaques in vitro. Coupled with the biocompatible nature of apatite, these results provide promise for future use of IDANPs as adjuvants to phage therapy along with anti-bacterial applications yet to be explored. Although IDANP enhancement of phage infection has been replicated many times in gram-positive and gram-negative prokaryotic hosts as well as with the utilization of both RNA and DNA viruses, the specific mechanisms involved remain elusive. To further understand increased phage infections in a prokaryotic system, and to evaluate the safety of IDANPs as a treatment used in a eukaryotic system, we have replicated plaque assay experiments in an algal system using Chlorella variabilis NC64A and its virus, Paramecium bursaria chlorella virus 1 (PBCV-1). Statistical modeling was used to evaluate alteration in numbers of plaques observed after viral introduction in IDANP-exposed versus non-IDANP-exposed bacterial and algal cell cultures. While IDANPs synthesized between 25°C-45°C and doped with 30% iron have been shown to influence dramatic increases in phage-induced bacterial death, experiments replicated in an algal system indicated viral infections do not increase when C. variabilis cells are pre-exposed to IDANPs. It is essential to potential use of IDANPs as an antibacterial adjuvant that IDANPs do not increase viral infection of eukaryotic host cells during treatment.

Three-year survey of abundance, prevalence and genetic diversity of chlorovirus populations in a small urban lake

Inland water environments cover about 2.5 percent of our planet and harbor huge numbers of known and still unknown microorganisms. In this report, we examined water samples for the abundance, prevalence, and genetic diversity of a group of infectious viruses (chloroviruses) that infect symbiotic chlorella-like green algae. Samples were collected on a weekly basis for a period of 24 to 36 months from a recreational freshwater lake in Lincoln, Nebraska, and assayed for infectious viruses by plaque assay. The numbers of infectious virus particles were both host- and site-dependent. The consistent fluctuations in numbers of viruses suggest their impact as key factors in shaping microbial community structures in the water surface. Even in low-viral-abundance months, infectious chlorovirus populations were maintained, suggesting either that the viruses are very stable or that there is ongoing viral production in natural hosts.

Seasonal determinations of algal virus decay rates reveal overwintering in a temperate freshwater pond

To address questions about algal virus persistence (i.e., continued existence) in the environment, rates of decay of infectivity for two viruses that infect Chlorella-like algae, ATCV-1 and CVM-1, and a virus that infects the prymnesiophyte Chrysochromulina parva, CpV-BQ1, were estimated from in situ incubations in a temperate, seasonally frozen pond. A series of experiments were conducted to estimate rates of decay of infectivity in all four seasons with incubations lasting 21 days in spring, summer and autumn, and 126 days in winter. Decay rates observed across this study were relatively low compared with previous estimates obtained for other algal viruses, and ranged from 0.012 to 11% h(-1). Overall, the virus CpV-BQ1 decayed most rapidly whereas ATCV-1 decayed most slowly, but for all viruses the highest decay rates were observed during the summer and the lowest were observed during the winter. Furthermore, the winter incubations revealed the ability of each virus to overwinter under ice as ATCV-1, CVM-1 and CpV-BQ1 retained up to 48%, 19% and 9% of their infectivity after 126 days, respectively. The observed resilience of algal viruses in a seasonally frozen freshwater pond provides a mechanism that can support the maintenance of viral seed banks in nature. However, the high rates of decay observed in the summer demonstrate that virus survival and therefore environmental persistence can be subject to seasonal bottlenecks.

Spatial and temporal dynamics of virus occurrence in two freshwater lakes captured through metagenomic analysis

Viruses are the most abundant microorganisms in the aquatic environment, yet the identification of viruses and assessing their diversity still remains a challenge. Here, we present a robust, routinely usable approach to identify viruses from two freshwater lakes of the lower Great Lakes region, Lake Ontario, and Lake Erie. We collected water samples from six different beaches of these two lakes during the summer period of 2012 and 2013, and separated into three distinct fractions, namely a bacterial fraction, a virus like particle (VLP) fraction, and a fraction of eDNA (environmental DNA). DNA extracted from all three fractions was sequenced and bioinformatic analyses of sequences revealed the presence of viruses from major viral families. The analyzed viral sequences were dominated by bacteriophage sequences, but also contained many plant and animal viruses. Within the context of this study, geographic location does not appear to have a major impact on viral abundance and diversity, since virome composition of both lakes were similar. Comparative analyses between eDNA and viral fractions showed that eDNA can be used in combination with VLP fractions to identify viruses from the environment.

Development of DNA mismatch repair gene, MutS, as a diagnostic marker for detection and phylogenetic analysis of algal Megaviruses

Megaviruses are generically defined as giant viruses with genomes up to 1.26Mb that infect eukaryotic unicellular protists; they are clearly delineated in DNA polymerase B phylogenetic trees; in addition, common features often include an associated virophage observed during infection; the presence of an amino acyl tRNA synthetase gene; and a nucleic acid mismatch repair protein, MutS gene. The archetypal representative of this evolving putative family is Mimivirus, an opportunistic pathogen of Acanthamoeba spp. originally thought to be a bacterium until its genome sequence was published in 2004. Subsequent analysis of marine metagenomic data revealed Megaviruses are likely ubiquitous on the surface ocean. Analysis of genome sequences of giant viruses isolated from naturally occurring marine protists such as microalgae and a microflagellate grazer, started the expansion of the Megaviridae. Here, we explored the possibility of developing Megavirus specific markers for mutS that could be used in virus molecular ecology studies. MutS is split into 15 different clades representing a wide range of cellular life, and two that contain Megaviruses, clade MutS7 and clade MutS8. We developed specific PCR primers that recognized Megavirus clade MutS8, a clade that we propose discriminates most of the algal Megaviruses. Analysis of seawater off the coast of Maine, US, revealed novel groups of algal Megaviruses that were present in all samples tested. The Megavirus clade MutS8 marker should be considered as a tool to reveal new diversity and distribution of this enigmatic group of viruses.

Variations in abundance, genome size, morphology, and functional role of the virioplankton in Lakes Annecy and Bourget over a 1-year period

We sampled the surface waters (2-50 m) of two deep peri-alpine lakes over a 1-year period in order to examine (1) the abundance, vertical distribution, genome size, and morphology structures of the virioplankton; (2) the virus-mediated bacterial mortality; and (3) the specific genome size range of double-stranded DNA (dsDNA) phytoplankton viruses. Virus-like particle (VLP) concentrations varied between 4.16 × 10(7) (January) and 2.08 × 10(8) part mL(-1) (May) in Lake Bourget and between 2.7 × 10(7) (June) and 8.39 × 10(7) part mL(-1) (November) in Lake Annecy. Our flow cytometry analysis revealed at least three viral groups (referred to as virus-like particles 1, 2, and 3) that exhibited distinctive dynamics suggestive of different host types. Phage-induced bacterial mortality varied between 6.1% (June) and 33.2% (October) in Lake Bourget and between 7.4% (June) and 52.6% (November) in Lake Annecy, suggesting that viral lysis may be a key cause of mortality of the bacterioplankton. Virioplankton genome size ranged from 27 to 486 kb in Lake Bourget, while it reached 620 kb in Lake Annecy for which larger genome sizes were recorded. Our analysis of pulsed field gel electrophoresis bands using different PCR primers targeting both cyanophages and algal viruses showed that (1) dsDNA viruses infecting phytoplankton may range from 65 to 486 kb, and (2) both cyanophage and algal "diversity" were higher in Lake Annecy. Lakes Annecy and Bourget also differed regarding the proportions of both viral families (with the dominance of myoviruses vs. podoviruses) and infected bacterial morphotypes (short rods vs. elongated rods), in each of these lakes, respectively. Overall, our results reveal that (1) viruses displayed distinct temporal and vertical distribution, dynamics, community structure in terms of genome size and morphology, and viral activity in the two lakes; (2) the Myoviridae seemed to be the main cause of bacterial mortality in both lakes and this group seemed to be related to VLP2; and (3) phytoplankton viruses may have a broader range of genome size than previously thought. This study adds to growing evidence that viruses are diverse and play a significant role in freshwater microbial dynamics and more globally lake functioning. It highlights the importance of further considering this biological compartment for a better understanding of plankton ecology in peri-alpine lakes.

Prevalence of viral photosynthetic and capsid protein genes from cyanophages in two large and deep perialpine lakes

Cyanophages are important components of aquatic ecosystems, but their genetic diversity has been little investigated in freshwaters. A yearlong survey was conducted in surface waters of the two largest natural perialpine lakes in France (Lake Annecy and Lake Bourget) to investigate part of this cyanophage diversity through the analysis of both structural (e.g., g20) and functional (e.g., psbA) genes. We found that these cyanophage signature genes were prevalent throughout the year but that the community compositions of g20 cyanomyoviruses were significantly different between the two lakes. In contrast, psbA-containing cyanophages seemed to be more similar between the two ecosystems. We also found that a large proportion of g20 sequences grouped with cyanomyophage isolates. psbA sequences, belonging to phages of Synechococcus spp., were characterized by distinct triplet motifs (with a novel viral triplet motif, EFE). Thus, our results show that cyanophages (i) are a diverse viral community in alpine lakes and (ii) are clearly distinct from some other freshwater and marine environments, suggesting the influence of unique biogeographic factors.

Strong seasonality and interannual recurrence in marine myovirus communities

The temporal community dynamics and persistence of different viral types in the marine environment are still mostly obscure. Polymorphism of the major capsid protein gene, g23, was used to investigate the community composition dynamics of T4-like myoviruses in a North Atlantic fjord for a period of 2 years. A total of 160 unique operational taxonomic units (OTUs) were identified by terminal restriction fragment length polymorphism (TRFLP) of the gene g23. Three major community profiles were identified (winter-spring, summer, and autumn), which resulted in a clear seasonal succession pattern. These seasonal transitions were recurrent over the 2 years and significantly correlated with progression of seawater temperature, Synechococcus abundance, and turbidity. The appearance of the autumn viral communities was concomitant with the occurrence of prominent Synechococcus blooms. As a whole, we found a highly dynamic T4-like viral community with strong seasonality and recurrence patterns. These communities were unexpectedly dominated by a group of persistently abundant viruses.

Ocean viruses: rigorously evaluating the metagenomic sample-to-sequence pipeline

As new environments are studied, viruses consistently emerge as important and prominent players in natural and man-made ecosystems. However, much of what we know is built both upon the foundation of the culturable minority and using methods that are often insufficiently ground-truthed. Here, we review the modern culture-independent viral metagenomic sample-to-sequence pipeline and how next-generation sequencing techniques are drastically altering our ability to systematically and rigorously evaluate them. Together, a series of studies quantitatively evaluate existing and new methods that allow-even for ultra-low DNA samples-the generation of replicable, near-quantitative datasets that maximize inter-comparability and biological inference.

Contrasting community versus population-based estimates of grazing and virus-induced mortality of phytoplankton

In this study, grazing and virus-induced mortality of phytoplankton was investigated in a freshwater pond at the University of Toronto Mississauga, Canada, during September 2009. The modified dilution assay, which partitions phytoplankton mortality into virus and grazing-induced fractions, was used along with newly designed, taxon-specific quantitative polymerase chain reaction (qPCR) assays that target psbA gene fragments to estimate growth and mortality rates for both the entire phytoplankton community and four distinct phytoplankton populations. Community mortality was estimated via fluorometric determination of chlorophyll a (Chl a) concentrations, whereas the relative mortality of individual phytoplankton populations was estimated via qPCR. The sources and amounts of mortality for individual phytoplankton populations differed from those of the whole community, as well as from each other. Grazing was found to be the only significant source of mortality for the community (0.32 day(-1)), and the Prymnesiales (1.65 day(-1)) and Chroococcales (2.79 day(-1)) populations studied. On the other hand, the Chlamydomonadales population examined experienced both significant grazing (1.01 day(-1)) and viral lysis (0.96 day(-1)), while the Chlorellales population only experienced significant mortality as a result of viral lysis (1.38 day(-1)). Our results demonstrate that the combination of qPCR and the modified dilution method can be used to estimate both viral lysis and grazing pressure on several individual phytoplankton populations within a community simultaneously. Further, previously noted limitations of the modified dilution method associated with the dilution of specific phytoplankton populations at low abundances can be overcome with the qPCR-based approach. Most importantly, this study demonstrates that when used alone, whole community-based methods of assessing mortality can overlook valuable information about carbon flow in aquatic microbial food webs.

Paramecium bursaria chlorella virus 1 proteome reveals novel architectural and regulatory features of a giant virus

The 331-kbp chlorovirus Paramecium bursaria chlorella virus 1 (PBCV-1) genome was resequenced and annotated to correct errors in the original 15-year-old sequence; 40 codons was considered the minimum protein size of an open reading frame. PBCV-1 has 416 predicted protein-encoding sequences and 11 tRNAs. A proteome analysis was also conducted on highly purified PBCV-1 virions using two mass spectrometry-based protocols. The mass spectrometry-derived data were compared to PBCV-1 and its host Chlorella variabilis NC64A predicted proteomes. Combined, these analyses revealed 148 unique virus-encoded proteins associated with the virion (about 35% of the coding capacity of the virus) and 1 host protein. Some of these proteins appear to be structural/architectural, whereas others have enzymatic, chromatin modification, and signal transduction functions. Most (106) of the proteins have no known function or homologs in the existing gene databases except as orthologs with proteins of other chloroviruses, phycodnaviruses, and nuclear-cytoplasmic large DNA viruses. The genes encoding these proteins are dispersed throughout the virus genome, and most are transcribed late or early-late in the infection cycle, which is consistent with virion morphogenesis.

Seasonality and monthly dynamics of marine myovirus communities

Marine myoviruses (i.e. bacteriophages with a contractile tail sheath) are numerically abundant and genetically diverse. We developed a terminal restriction fragment length polymorphism assay (TRFLP) for g23, the conserved gene encoding the major capsid protein, to investigate T4-like myovirus communities at USC's Microbial Observatory at the San Pedro Ocean Time-series (SPOT), where we previously reported bacterial seasonality. Between 71 and 154 operational taxonomic units (OTUs) were observed monthly over 3 years. Roughly 25% of OTUs were detected in 31 or more months. T4-like myoviral community structure varied seasonally with some OTUs peaking repeatedly in spring-summer and others in fall-winter, while moderately abundant OTUs persisted year-round. Recurring community structure was demonstrated using discriminant function analysis (DFA, selecting taxa that best predict months) and average Bray-Curtis similarity. DFA showed communities from adjacent months or 12 months apart were positively auto-correlated, while communities 3-7 months apart were negatively auto-correlated. Bray-Curtis similarity was highest between adjacent months - with a local maximum at 12-month and local minima at 6- and 18- to 20-month lags. The T4-like virus community at SPOT exhibited seasonality, yet the somewhat unexpected persistence of moderately abundant OTUs and predictability of the community add new twists to existing conceptual models of marine viruses.

The ecology of viruses that infect eukaryotic algae

Because viruses of eukaryotic algae are incredibly diverse, sweeping generalizations about their ecology are rare. These obligate parasites infect a range of algae and their diversity can be illustrated by considering that isolates range from small particles with ssRNA genomes to much larger particles with 560 kb dsDNA genomes. Molecular research has also provided clues about the extent of their diversity especially considering that genetic signatures of algal viruses in the environment rarely match cultivated viruses. One general concept in algal virus ecology that has emerged is that algal viruses are very host specific and most infect only certain strains of their hosts; with the exception of viruses of brown algae, evidence for interspecies infectivity is lacking. Although some host-virus systems behave with boom-bust oscillations, complex patterns of intraspecies infectivity can lead to host-virus coexistence obfuscating the role of viruses in host population dynamics. Within the framework of population dynamics, host density dependence is an important phenomenon that influences virus abundances in nature. Variable burst sizes of different viruses also influence their abundances and permit speculations about different life strategies, but as exceptions are common in algal virus ecology, life strategy generalizations may not be broadly applicable. Gaps in knowledge of virus seasonality and persistence are beginning to close and investigations of environmental reservoirs and virus resilience may answer questions about virus inter-annual recurrences. Studies of algal mortality have shown that viruses are often important agents of mortality reinforcing notions about their ecological relevance, while observations of the surprising ways viruses interact with their hosts highlight the immaturity of our understanding. Considering that just two decades ago algal viruses were hardly acknowledged, recent progress affords the optimistic perspective that future studies will provide keys to unlocking our understanding of algal virus ecology specifically, and aquatic ecosystems generally.

Virophages to viromes: a report from the frontier of viral oceanography

The investigation of marine viruses has advanced our understanding of ecology, evolution, microbiology, oceanography and virology. Significant findings discussed in this review include the discovery of giant viruses that have genome sizes and metabolic capabilities that distort the line between virus and cell, viruses that participate in photosynthesis and apoptosis, the detection of communities of viruses of all genomic compositions and the preeminence of viruses in the evolution of marine microbes. Although we have made great progress, we have yet to synthesize the rich archive of viral genomic data with oceanographic processes. The development of cutting edge methods such as single virus genomics now provide a toolset to better integrate viruses into the ecology of the ocean.