Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea

DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses

Sequence classification facilitates a fundamental understanding of the structure of microbial communities. Binary metagenomic sequence classifiers are insufficient because environmental metagenomes are typically derived from multiple sequence sources. Here we introduce a deep-learning based sequence classifier, DeepMicroClass, that classifies metagenomic contigs into five sequence classes, i.e. viruses infecting prokaryotic or eukaryotic hosts, eukaryotic or prokaryotic chromosomes, and prokaryotic plasmids. DeepMicroClass achieved high performance for all sequence classes at various tested sequence lengths ranging from 500 bp to 100 kbps. By benchmarking on a synthetic dataset with variable sequence class composition, we showed that DeepMicroClass obtained better performance for eukaryotic, plasmid and viral contig classification than other state-of-the-art predictors. DeepMicroClass achieved comparable performance on viral sequence classification with geNomad and VirSorter2 when benchmarked on the CAMI II marine dataset. Using a coastal daily time-series metagenomic dataset as a case study, we showed that microbial eukaryotes and prokaryotic viruses are integral to microbial communities. By analyzing monthly metagenomes collected at HOT and BATS, we found relatively higher viral read proportions in the subsurface layer in late summer, consistent with the seasonal viral infection patterns prevalent in these areas. We expect DeepMicroClass will promote metagenomic studies of under-appreciated sequence types.

Long-read powered viral metagenomics in the oligotrophic Sargasso Sea

Dominant microorganisms of the Sargasso Sea are key drivers of the global carbon cycle. However, associated viruses that shape microbial community structure and function are not well characterised. Here, we combined short and long read sequencing to survey Sargasso Sea phage communities in virus- and cellular fractions at viral maximum (80 m) and mesopelagic (200 m) depths. We identified 2,301 Sargasso Sea phage populations from 186 genera. Over half of the phage populations identified here lacked representation in global ocean viral metagenomes, whilst 177 of the 186 identified genera lacked representation in genomic databases of phage isolates. Viral fraction and cell-associated viral communities were decoupled, indicating viral turnover occurred across periods longer than the sampling period of three days. Inclusion of long-read data was critical for capturing the breadth of viral diversity. Phage isolates that infect the dominant bacterial taxa Prochlorococcus and Pelagibacter, usually regarded as cosmopolitan and abundant, were poorly represented.

Role of Syndiniales parasites in depth-specific networks and carbon flux in the oligotrophic ocean

Microbial associations that result in phytoplankton mortality are important for carbon transport in the ocean. This includes parasitism, which in microbial food webs is dominated by the marine alveolate group, Syndiniales. Parasites are expected to contribute to carbon recycling via host lysis; however, knowledge on host dynamics and correlation to carbon export remain unclear and limit the inclusion of parasitism in biogeochemical models. We analyzed a 4-year 18S rRNA gene metabarcoding dataset (2016-19), performing network analysis for 12 discrete depths (1-1000 m) to determine Syndiniales-host associations in the seasonally oligotrophic Sargasso Sea. Analogous water column and sediment trap data were included to define environmental drivers of Syndiniales and their correlation with particulate carbon flux (150 m). Syndiniales accounted for 48-74% of network edges, most often associated with Dinophyceae and Arthropoda (mainly copepods) at the surface and Rhizaria (Polycystinea, Acantharea, and RAD-B) in the aphotic zone. Syndiniales were the only eukaryote group to be significantly (and negatively) correlated with particulate carbon flux, indicating their contribution to flux attenuation via remineralization. Examination of Syndiniales amplicons revealed a range of depth patterns, including specific ecological niches and vertical connection among a subset (19%) of the community, the latter implying sinking of parasites (infected hosts or spores) on particles. Our findings elevate the critical role of Syndiniales in marine microbial systems and reveal their potential use as biomarkers for carbon export.

Suboxic DOM is bioavailable to surface prokaryotes in a simulated overturn of an oxygen minimum zone, Devil's Hole, Bermuda

Oxygen minimum zones (OMZs) are expanding due to increased sea surface temperatures, subsequent increased oxygen demand through respiration, reduced oxygen solubility, and thermal stratification driven in part by anthropogenic climate change. Devil's Hole, Bermuda is a model ecosystem to study OMZ microbial biogeochemistry because the formation and subsequent overturn of the suboxic zone occur annually. During thermally driven stratification, suboxic conditions develop, with organic matter and nutrients accumulating at depth. In this study, the bioavailability of the accumulated dissolved organic carbon (DOC) and the microbial community response to reoxygenation of suboxic waters was assessed using a simulated overturn experiment. The surface inoculated prokaryotic community responded to the deep (formerly suboxic) 0.2 μm filtrate with cell densities increasing 2.5-fold over 6 days while removing 5 μmol L-1 of DOC. After 12 days, the surface community began to shift, and DOC quality became less diagenetically altered along with an increase in SAR202, a Chloroflexi that can degrade recalcitrant dissolved organic matter (DOM). Labile DOC production after 12 days coincided with an increase of Nitrosopumilales, a chemoautotrophic ammonia oxidizing archaea (AOA) that converts ammonia to nitrite based on the ammonia monooxygenase (amoA) gene copy number and nutrient data. In comparison, the inoculation of the deep anaerobic prokaryotic community into surface 0.2 μm filtrate demonstrated a die-off of 25.5% of the initial inoculum community followed by a 1.5-fold increase in cell densities over 6 days. Within 2 days, the prokaryotic community shifted from a Chlorobiales dominated assemblage to a surface-like heterotrophic community devoid of Chlorobiales. The DOM quality changed to less diagenetically altered material and coincided with an increase in the ribulose-1,5-bisphosphate carboxylase/oxygenase form I (cbbL) gene number followed by an influx of labile DOM. Upon reoxygenation, the deep DOM that accumulated under suboxic conditions is bioavailable to surface prokaryotes that utilize the accumulated DOC initially before switching to a community that can both produce labile DOM via chemoautotrophy and degrade the more recalcitrant DOM.

Increased cyanophage infection at the bottom of the euphotic zone, especially in the fall

Picocyanobacteria contribute greatly to offshore primary production with cells extending through the deep euphotic zone. Literature indicates high viral infection of cyanobacteria in ocean transition zones. We postulate that the bottom of the euphotic zone is a transition zone, where communities transition from phototrophic to aphotic processes. We use single-copy core genes to examine cyanophage to cyanobacteria ratios in cellular metagenomes in the subtropical North Atlantic and Pacific. Cyanophage to cyanobacteria terL/rpoB ratios generally increase to >10 in the deep euphotic zone. As light levels decrease in the fall, Prochlorococcus in the deep euphotic zone experience reduced light levels. We find clear differences between spring (Geotraces GA02) and fall (GA03) in the North Atlantic, with terL/rpoB ratios increasing to >40 in the fall. When examining 23 months of the North Pacific Hawaii Ocean Timeseries, the depth of elevated cyanophage to cyanobacteria ratios in cellular metagenomes negatively correlated with surface photosynthetic radiation (PAR), particularly with the change in PAR, which reflected the season. In fall, all picocyanobacteria ecotypes were found at depths enriched with viruses, while in summer, only low light ecotypes were affected. Thus, we find high cyanophage infection both in the deep euphotic zone and during seasonal transitions.

Seasonality of top-down control of bacterioplankton at two central Red Sea sites with different trophic status

The role of bottom-up (nutrient availability) and top-down (grazers and viruses mortality) controls on tropical bacterioplankton have been rarely investigated simultaneously from a seasonal perspective. We have assessed them through monthly samplings over 2 years in inshore and offshore waters of the central Red Sea differing in trophic status. Flow cytometric analysis allowed us to distinguish five groups of heterotrophic bacteria based on physiological properties (nucleic acid content, membrane integrity and active respiration), three groups of cyanobacteria (two populations of Synechococcus and Prochlorococcus), heterotrophic nanoflagellates (HNFs) and three groups of viruses based on nucleic acid content. The dynamics of bacterioplankton and their top-down controls varied with season and location, being more pronounced in inshore waters. HNFs abundances showed a strong preference for larger prey inshore (r = -0.62 to -0.59, p = 0.001-0.002). Positive relationships between viruses and heterotrophic bacterioplankton abundances were more marked inshore (r = 0.67, p < 0.001) than offshore (r = 0.44, p = 0.03). The negative correlation between HNFs and viruses abundances (r = -0.47, p = 0.02) in shallow waters indicates a persistent seasonal switch between protistan grazing and viral lysis that maintains the low bacterioplankton stocks in the central Red Sea area.

Novel pelagiphage isolate Polarivirus skadi is a polar specialist that dominates SAR11-associated bacteriophage communities at high latitudes

The SAR11 clade are the most abundant members of surface marine bacterioplankton and a critical component of global biogeochemical cycles. Similarly, pelagiphages that infect SAR11 are ubiquitous and highly abundant in the oceans. Pelagiphages are predicted to shape SAR11 community structures and increase carbon turnover throughout the oceans. Yet, ecological drivers of host and niche specificity of pelagiphage populations are poorly understood. Here we report the global distribution of a novel pelagiphage called "Polarivirus skadi", which is the sole representative of a novel genus. P. skadi was isolated from the Western English Channel using a cold-water ecotype of SAR11 as bait. P. skadi is closely related to the globally dominant pelagiphage HTVC010P. Along with other HTVC010P-type viruses, P. skadi belongs to a distinct viral family within the order Caudovirales, for which we propose the name Ubiqueviridae. Metagenomic read recruitment identified P. skadi as one of the most abundant pelagiphages on Earth. P. skadi is a polar specialist, replacing HTVC010P at high latitudes. Experimental evaluation of P. skadi host range against cold- and warm-water SAR11 ecotypes supported cold-water specialism. Relative abundance of P. skadi in marine metagenomes correlated negatively with temperature, and positively with nutrients, available oxygen, and chlorophyll concentrations. In contrast, relative abundance of HTVC010P correlated negatively with oxygen and positively with salinity, with no significant correlation to temperature. The majority of other pelagiphages were scarce in most marine provinces, with a few representatives constrained to discrete ecological niches. Our results suggest that pelagiphage populations persist within a global viral seed bank, with environmental parameters and host availability selecting for a few ecotypes that dominate ocean viromes.

Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics

Cyanophages exert important top-down controls on their cyanobacteria hosts; however, concurrent analysis of both phage and host populations is needed to better assess phage-host interaction models. We analyzed picocyanobacteria Prochlorococcus and Synechococcus and T4-like cyanophage communities in Pacific Ocean surface waters using five years of monthly viral and cellular fraction metagenomes. Cyanophage communities contained thousands of mostly low-abundance (<2% relative abundance) species with varying temporal dynamics, categorized as seasonally recurring or non-seasonal and occurring persistently, occasionally, or sporadically (detected in ≥85%, 15-85%, or <15% of samples, respectively). Viromes contained mostly seasonal and persistent phages (~40% each), while cellular fraction metagenomes had mostly sporadic species (~50%), reflecting that these sample sets capture different steps of the infection cycle-virions from prior infections or within currently infected cells, respectively. Two groups of seasonal phages correlated to Synechococcus or Prochlorococcus were abundant in spring/summer or fall/winter, respectively. Cyanophages likely have a strong influence on the host community structure, as their communities explained up to 32% of host community variation. These results support how both seasonally recurrent and apparent stochastic processes, likely determined by host availability and different host-range strategies among phages, are critical to phage-host interactions and dynamics, consistent with both the Kill-the-Winner and the Bank models.

Associations between picocyanobacterial ecotypes and cyanophage host genes across ocean basins and depth

Background

Cyanophages, viruses that infect cyanobacteria, are globally abundant in the ocean's euphotic zone and are a potentially important cause of mortality for marine picocyanobacteria. Viral host genes are thought to increase viral fitness by either increasing numbers of genes for synthesizing nucleotides for virus replication, or by mitigating direct stresses imposed by the environment. The encoding of host genes in viral genomes through horizontal gene transfer is a form of evolution that links viruses, hosts, and the environment. We previously examined depth profiles of the proportion of cyanophage containing various host genes in the Eastern Tropical North Pacific Oxygen Deficient Zone (ODZ) and at the subtropical North Atlantic (BATS). However, cyanophage host genes have not been previously examined in environmental depth profiles across the oceans.

Methodology

We examined geographical and depth distributions of picocyanobacterial ecotypes, cyanophage, and their viral-host genes across ocean basins including the North Atlantic, Mediterranean Sea, North Pacific, South Pacific, and Eastern Tropical North and South Pacific ODZs using phylogenetic metagenomic read placement. We determined the proportion of myo and podo-cyanophage containing a range of host genes by comparing to cyanophage single copy core gene terminase (terL). With this large dataset (22 stations), network analysis identified statistical links between 12 of the 14 cyanophage host genes examined here with their picocyanobacteria host ecotypes.

Results

Picyanobacterial ecotypes, and the composition and proportion of cyanophage host genes, shifted dramatically and predictably with depth. For most of the cyanophage host genes examined here, we found that the composition of host ecotypes predicted the proportion of viral host genes harbored by the cyanophage community. Terminase is too conserved to illuminate the myo-cyanophage community structure. Cyanophage cobS was present in almost all myo-cyanophage and did not vary in proportion with depth. We used the composition of cobS phylotypes to track changes in myo-cyanophage composition.

Conclusions

Picocyanobacteria ecotypes shift with changes in light, temperature, and oxygen and many common cyanophage host genes shift concomitantly. However, cyanophage phosphate transporter gene pstS appeared to instead vary with ocean basin and was most abundant in low phosphate regions. Abundances of cyanophage host genes related to nutrient acquisition may diverge from host ecotype constraints as the same host can live in varying nutrient concentrations. Myo-cyanophage community in the anoxic ODZ had reduced diversity. By comparison to the oxic ocean, we can see which cyanophage host genes are especially abundant (nirA, nirC, and purS) or not abundant (myo psbA) in ODZs, highlighting both the stability of conditions in the ODZ and the importance of nitrite as an N source to ODZ endemic LLV Prochlorococcus.

Energy-harnessing problem solving of primordial life: Modeling the emergence of catalytic host-nested parasite life cycles

All life forms on earth ultimately descended from a primordial population dubbed the last universal common ancestor or LUCA via Darwinian evolution. Extant living systems share two salient functional features, a metabolism extracting and transforming energy required for survival, and an evolvable, informational polymer-the genome-conferring heredity. Genome replication invariably generates essential and ubiquitous genetic parasites. Here we model the energetic, replicative conditions of LUCA-like organisms and their parasites, as well as adaptive problem solving of host-parasite pairs. We show using an adapted Lotka-Volterra frame-work that three host-parasite pairs-individually a unit of a host and a parasite that is itself parasitized, therefore a nested parasite pair-are sufficient for robust and stable homeostasis, forming a life cycle. This nested parasitism model includes competition and habitat restriction. Its catalytic life cycle efficiently captures, channels and transforms energy, enabling dynamic host survival and adaptation. We propose a Malthusian fitness model for a quasispecies evolving through a host-nested parasite life cycle with two core features, rapid replacement of degenerate parasites and increasing evolutionary stability of host-nested parasite units from one to three pairs.

Widespread yet persistent low abundance of TIM5-like cyanophages in the oceans

Ocean ecosystems are inhabited by a diverse set of viruses that impact microbial mortality and evolution. However, the distribution and abundances of specific viral lineages, particularly those from the large bank of rare viruses, remains largely unknown. Here, we assessed the diversity and abundance of the TIM5-like cyanophages. The sequencing of three new TIM5-like cyanophage genomes and environmental amplicons of a signature gene from the Red Sea revealed highly conserved gene content and sequence similarity. We adapted the polony method, a solid-phase polymerase chain reaction assay, to quantify TIM5-like cyanophages during three 2000 km expeditions in the Pacific Ocean and four annual cycles in the Red Sea. TIM5-like cyanophages were widespread, detected at all latitudes and seasons surveyed throughout the photic zone. Yet they were generally rare, ranging between <100 and 4000 viruses·ml^-1 . Occasional peaks in abundance of 10- to 100-fold were observed, reaching 71,000 viruses·ml^-1 . These peaks were ephemeral and seasonally variable in the Red Sea. Infection levels, quantified during one such peak, were very low. These characteristics of low diversity and abundance, as well as variable outbreaks, distinguishes the TIM5-like lineage from other major cyanophage lineages and illuminates that rare virus lineages can be persistent and widespread in the oceans.

Novel lineages of single-stranded DNA phages that coevolved with the symbiotic bacteria Rhizobium

This study describes novel single-stranded DNA phages isolated from common bean agriculture soils by infection of the nitrogen-fixing symbiotic bacteria Rhizobium etli and R. phaseoli. A total of 29 phages analyzed have 4.3–6 kb genomes in size and GC 59–60%. They belong to different clades unrelated to other Microviridae subfamilies. Three-dimensional models of the major capsid protein (MCP) showed a conserved β-barrel structural “jelly-roll” fold. A variable-length loop in the MCPs distinguished three Rhizobium microvirus groups. Microviridae subfamilies were consistent with viral clusters determined by the protein-sharing network. All viral clusters, except for Bullavirinae, included mostly microviruses identified in metagenomes from distinct ecosystems. Two Rhizobium microvirus clusters, chaparroviruses, and chicoviruses, were included within large viral unknown clusters with microvirus genomes identified in diverse metagenomes. A third Rhizobium microvirus cluster belonged to the subfamily Amoyvirinae. Phylogenetic analysis of the MCP confirms the divergence of the Rhizobium microviruses into separate clades. The phylogeny of the bacterial hosts matches the microvirus MCP phylogeny, suggesting a coevolutionary history between the phages and their bacterial host. This study provided essential biological information on cultivated microvirus for understanding the evolution and ecological diversification of the Microviridae family in diverse microbial ecosystems.

Adaptation of the polony technique to quantify Gokushovirinae, a diverse group of single-stranded DNA phage

Advances in metagenomics have revealed the ubiquity of single-stranded DNA (ssDNA) phage belonging to the subfamily Gokushovirinae in the oceans; however, the abundance and ecological roles of this group are unknown. Here, we quantify gokushoviruses through adaptation of the polony method, in which viral template DNA is immobilized in a gel, amplified by PCR, and subsequently detected by hybridization. Primers and probes for this assay were designed based on PCR amplicon diversity of gokushovirus major capsid protein gene sequences from a depth profile in the Gulf of Aqaba, Red Sea sampled in September 2015. At ≥95% identity, these 87 gokushovirus sequences formed 14 discrete clusters with the largest clades showing distinct depth distributions. The application of the polony method enabled the first quantification of gokushoviruses in any environment. The gokushoviruses were most abundant in the upper 40 m of the stratified water column, with a subsurface peak in abundance of 1.26 × 10⁵ viruses ml^-1 . These findings suggest that discrete gokushovirus genotypes infect bacterial hosts that differentially partition in the water column. Since the designed primers and probe are conserved across marine ecosystems, this polony method can be applied broadly for the quantification of gokushoviruses throughout the global oceans.

Interactions between bacterial and phage communities in natural environments

We commonly acknowledge that bacterial viruses (phages) shape the composition and evolution of bacterial communities in nature and therefore have important roles in ecosystem functioning. This view stems from studies in the 1990s to the first decade of the twenty-first century that revealed high viral abundance, high viral diversity and virus-induced microbial death in aquatic ecosystems as well as an association between collapses in bacterial density and peaks in phage abundance. The recent surge in metagenomic analyses has provided deeper insight into the abundance, genomic diversity and spatio-temporal dynamics of phages in a wide variety of ecosystems, ranging from deep oceans to soil and the mammalian digestive tract. However, the causes and consequences of variations in phage community compositions remain poorly understood. In this Review, we explore current knowledge of the composition and evolution of phage communities, as well as their roles in controlling the population and evolutionary dynamics of bacterial communities. We discuss the need for greater ecological realism in laboratory studies to capture the complexity of microbial communities that thrive in natural environments.

The Seasonal Flux and Fate of Dissolved Organic Carbon Through Bacterioplankton in the Western North Atlantic

The oceans teem with heterotrophic bacterioplankton that play an appreciable role in the uptake of dissolved organic carbon (DOC) derived from phytoplankton net primary production (NPP). As such, bacterioplankton carbon demand (BCD), or gross heterotrophic production, represents a major carbon pathway that influences the seasonal accumulation of DOC in the surface ocean and, subsequently, the potential vertical or horizontal export of seasonally accumulated DOC. Here, we examine the contributions of bacterioplankton and DOM to ecological and biogeochemical carbon flow pathways, including those of the microbial loop and the biological carbon pump, in the Western North Atlantic Ocean (∼39-54°N along ∼40°W) over a composite annual phytoplankton bloom cycle. Combining field observations with data collected from corresponding DOC remineralization experiments, we estimate the efficiency at which bacterioplankton utilize DOC, demonstrate seasonality in the fraction of NPP that supports BCD, and provide evidence for shifts in the bioavailability and persistence of the seasonally accumulated DOC. Our results indicate that while the portion of DOC flux through bacterioplankton relative to NPP increased as seasons transitioned from high to low productivity, there was a fraction of the DOM production that accumulated and persisted. This persistent DOM is potentially an important pool of organic carbon available for export to the deep ocean via convective mixing, thus representing an important export term of the biological carbon pump.

Efficient dilution-to-extinction isolation of novel virus-host model systems for fastidious heterotrophic bacteria

Microbes and their associated viruses are key drivers of biogeochemical processes in marine and soil biomes. While viruses of phototrophic cyanobacteria are well-represented in model systems, challenges of isolating marine microbial heterotrophs and their viruses have hampered experimental approaches to quantify the importance of viruses in nutrient recycling. A resurgence in cultivation efforts has improved the availability of fastidious bacteria for hypothesis testing, but this has not been matched by similar efforts to cultivate their associated bacteriophages. Here, we describe a high-throughput method for isolating important virus-host systems for fastidious heterotrophic bacteria that couples advances in culturing of hosts with sequential enrichment and isolation of associated phages. Applied to six monthly samples from the Western English Channel, we first isolated one new member of the globally dominant bacterial SAR11 clade and three new members of the methylotrophic bacterial clade OM43. We used these as bait to isolate 117 new phages, including the first known siphophage-infecting SAR11, and the first isolated phage for OM43. Genomic analyses of 13 novel viruses revealed representatives of three new viral genera, and infection assays showed that the viruses infecting SAR11 have ecotype-specific host ranges. Similar to the abundant human-associated phage ɸCrAss001, infection dynamics within the majority of isolates suggested either prevalent lysogeny or chronic infection, despite a lack of associated genes, or host phenotypic bistability with lysis putatively maintained within a susceptible subpopulation. Broader representation of important virus-host systems in culture collections and genomic databases will improve both our understanding of virus-host interactions, and accuracy of computational approaches to evaluate ecological patterns from metagenomic data.

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.

Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types

Viral metagenomes (viromes) are a valuable untargeted tool for studying viral diversity and the central roles viruses play in host disease, ecology, and evolution. Establishing effective methods to concentrate and purify viral genomes prior to sequencing is essential for high quality viromes. Using virus spike-and-recovery experiments, we stepwise compared two common approaches for virus concentration, ultrafiltration and iron chloride flocculation, across diverse matrices: wastewater influent, wastewater secondary effluent, river water, and seawater. Viral DNA was purified by removing cellular DNA via chloroform cell lysis, filtration, and enzymatic degradation of extra-viral DNA. We found that viral genomes were concentrated 1-2 orders of magnitude more with ultrafiltration than iron chloride flocculation for all matrices and resulted in higher quality DNA suitable for amplification-free and long-read sequencing. Given its widespread use and utility as an inexpensive field method for virome sampling, we nonetheless sought to optimize iron flocculation. We found viruses were best concentrated in seawater with five-fold higher iron concentrations than the standard used, inhibition of DNase activity reduced purification effectiveness, and five-fold more iron was needed to flocculate viruses from freshwater than seawater—critical knowledge for those seeking to apply this broadly used method to freshwater virome samples. Overall, our results demonstrated that ultrafiltration and purification performed better than iron chloride flocculation and purification in the tested matrices. Given that the method performance depended on the solids content and salinity of the samples, we suggest spike-and-recovery experiments be applied when concentrating and purifying sample types that diverge from those tested here.

Filling the Gaps in the Cyanobacterial Tree of Life-Metagenome Analysis of Stigonema ocellatum DSM 106950, Chlorogloea purpurea SAG 13.99 and Gomphosphaeria aponina DSM 107014

Cyanobacteria represent one of the most important and diverse lineages of prokaryotes with an unparalleled morphological diversity ranging from unicellular cocci and characteristic colony-formers to multicellular filamentous strains with different cell types. Sequencing of more than 1200 available reference genomes was mainly driven by their ecological relevance (Prochlorococcus, Synechococcus), toxicity (Microcystis) and the availability of axenic strains. In the current study three slowly growing non-axenic cyanobacteria with a distant phylogenetic positioning were selected for metagenome sequencing in order to (i) investigate their genomes and to (ii) uncover the diversity of associated heterotrophs. High-throughput Illumina sequencing, metagenomic assembly and binning allowed us to establish nearly complete high-quality draft genomes of all three cyanobacteria and to determine their phylogenetic position. The cyanosphere of the limnic isolates comprises up to 40 heterotrophic bacteria that likely coexisted for several decades, and it is dominated by Alphaproteobacteria and Bacteriodetes. The diagnostic marker protein RpoB ensured in combination with our novel taxonomic assessment via BLASTN-dependent text-mining a reliable classification of the metagenome assembled genomes (MAGs). The detection of one new family and more than a dozen genera of uncultivated heterotrophic bacteria illustrates that non-axenic cyanobacteria are treasure troves of hidden microbial diversity.

Frequency of mispackaging of Prochlorococcus DNA by cyanophage

Prochlorococcus cells are the numerically dominant phototrophs in the open ocean. Cyanophages that infect them are a notable fraction of the total viral population in the euphotic zone, and, as vehicles of horizontal gene transfer, appear to drive their evolution. Here we examine the propensity of three cyanophages-a podovirus, a siphovirus, and a myovirus-to mispackage host DNA in their capsids while infecting Prochlorococcus, the first step in phage-mediated horizontal gene transfer. We find the mispackaging frequencies are distinctly different among the three phages. Myoviruses mispackage host DNA at low and seemingly fixed frequencies, while podo- and siphoviruses vary in their mispackaging frequencies by orders of magnitude depending on growth light intensity. We link this difference to the concentration of intracellular reactive oxygen species and protein synthesis rates, both parameters increasing in response to higher light intensity. Based on our findings, we propose a model of mispackaging frequency determined by the imbalance between the production of capsids and the number of phage genome copies during infection: when protein synthesis rate increase to levels that the phage cannot regulate, they lead to an accumulation of empty capsids, in turn triggering more frequent host DNA mispackaging errors.

Weekly variations of viruses and heterotrophic nanoflagellates and their potential impact on bacterioplankton in shallow waters of the central Red Sea

Bacterioplankton play a pivotal role in marine ecosystems. However, their temporal dynamics and underlying control mechanisms are poorly understood in tropical regions such as the Red Sea. Here, we assessed the impact of bottom-up (resource availability) and top-down (viruses and heterotrophic nanoflagellates) controls on bacterioplankton abundances by weekly sampling a coastal central Red Sea site in 2017. We monitored microbial abundances by flow cytometry together with a set of environmental variables including temperature, salinity, dissolved organic and inorganic nutrients and chlorophyll a. We distinguished five groups of heterotrophic bacteria depending on their physiological properties relative nucleic acid content, membrane integrity and cell-specific respiratory activity, two groups of Synechococcus cyanobacteria and three groups of viruses. Viruses controlled heterotrophic bacteria for most of the year, as supported by a negative correlation between their respective abundances and a positive one between bacterial mortality rates and mean viral abundances. On the contrary, heterotrophic nanoflagellates abundance covaried with that of heterotrophic bacteria. Heterotrophic nanoflagellates showed preference for larger bacteria from both the high and low nucleic acid content groups. Our results demonstrate that top-down control is fundamental in keeping heterotrophic bacterioplankton abundances low (< 5 × 10 ⁵ cells mL⁻¹) in Red Sea coastal waters.

Seasonal impact of grazing, viral mortality, resource availability and light on the group-specific growth rates of coastal Mediterranean bacterioplankton

Estimation of prokaryotic growth rates is critical to understand the ecological role and contribution of different microbes to marine biogeochemical cycles. However, there is a general lack of knowledge on what factors control the growth rates of different prokaryotic groups and how these vary between sites and along seasons at a given site. We carried out several manipulation experiments during the four astronomical seasons in the coastal NW Mediterranean in order to evaluate the impact of grazing, viral mortality, resource competition and light on the growth and loss rates of prokaryotes. Gross and net growth rates of different bacterioplankton groups targeted by group-specific CARD-FISH probes and infrared microscopy (for aerobic anoxygenic phototrophs, AAP), were calculated from changes in cell abundances. Maximal group-specific growth rates were achieved when both predation pressure and nutrient limitation were experimentally minimized, while only a minimal effect of viral pressure on growth rates was observed; nevertheless, the response to predation removal was more remarkable in winter, when the bacterial community was not subjected to nutrient limitation. Although all groups showed increases in their growth rates when resource competition as well as grazers and viral pressure were reduced, Alteromonadaceae consistently presented the highest rates in all seasons. The response to light availability was generally weaker than that to the other factors, but it was variable between seasons. In summer and spring, the growth rates of AAP were stimulated by light whereas the growth of the SAR11 clade (likely containing proteorhodopsin) was enhanced by light in all seasons. Overall, our results set thresholds on bacterioplankton group-specific growth and mortality rates and contribute to estimate the seasonally changing contribution of various bacterioplankton groups to the function of microbial communities. Our results also indicate that the least abundant groups display the highest growth rates, contributing to the recycling of organic matter to a much greater extent than what their abundances alone would predict.

Seasonal and diel patterns of abundance and activity of viruses in the Red Sea

Virus-microbe interactions have been studied in great molecular details for many years in cultured model systems, yielding a plethora of knowledge on how viruses use and manipulate host machinery. Since the advent of molecular techniques and high-throughput sequencing, methods such as cooccurrence, nucleotide composition, and other statistical frameworks have been widely used to infer virus-microbe interactions, overcoming the limitations of culturing methods. However, their accuracy and relevance is still debatable as cooccurrence does not necessarily mean interaction. Here we introduce an ecological perspective of marine viral communities and potential interaction with their hosts, using analyses that make no prior assumptions on specific virus-host pairs. By size fractionating water samples into free viruses and microbes (i.e., also viruses inside or attached to their hosts) and looking at how viral group abundance changes over time along both fractions, we show that the viral community is undergoing a change in rank abundance across seasons, suggesting a seasonal succession of viruses in the Red Sea. We use abundance patterns in the different size fractions to classify viral clusters, indicating potential diverse interactions with their hosts and potential differences in life history traits between major viral groups. Finally, we show hourly resolved variations of intracellular abundance of similar viral groups, which might indicate differences in their infection cycles or metabolic capacities.

Bacteriophages presence in nature and their role in the natural selection of bacterial populations

Phages are the obligate parasite of bacteria and have complex interactions with their hosts. Phages can live in, modify, and shape bacterial communities by bringing about changes in their abundance, diversity, physiology, and virulence. In addition, phages mediate lateral gene transfer, modify host metabolism and reallocate bacterially-derived biochemical compounds through cell lysis, thus playing an important role in ecosystem. Phages coexist and coevolve with bacteria and have developed several antidefense mechanisms in response to bacterial defense strategies against them. Phages owe their existence to their bacterial hosts, therefore they bring about alterations in their host genomes by transferring resistance genes and genes encoding toxins in order to improve the fitness of the hosts. Application of phages in biotechnology, environment, agriculture and medicines demands a deep insight into the myriad of phage-bacteria interactions. However, to understand their complex interactions, we need to know how unique phages are to their bacterial hosts and how they exert a selective pressure on the microbial communities in nature. Consequently, the present review focuses on phage biology with respect to natural selection of bacterial populations.

Cyanophage host-derived genes reflect contrasting selective pressures with depth in the oxic and anoxic water column of the Eastern Tropical North Pacific

Cyanophages encode host-derived genes that may increase their fitness. We examined the relative abundance of 18 host-derived cyanophages genes in metagenomes and viromes along depth profiles from the Eastern Tropical North Pacific Oxygen Deficient Zone (ETNP ODZ) where Prochlorococcus dominates a secondary chlorophyll maximum within the ODZ. Cyanophages at the oxic primary chlorophyll maximum encoded genes related to light and phosphate stress (psbA, psbD and pstS in T4-like and psbA in T7-like), but the proportion of cyanophage with these genes decreased with depth. The proportion of cyanophage with purine biosynthesis genes increased with depth in T4-like, but not T7-like cyanophages. No additional host-derived genes were found in deep T7-like cyanophages, suggesting that T4-like and T7-like cyanophages have different host-derived gene acquisition strategies, possibly linked to their different genome packaging mechanisms. In contrast to the ETNP, in the oxic North Atlantic T4-like cyanophages encoded psbA and pstS throughout the euphotic zone. Differences in pstS between the ETNP and the North Atlantic stations were consistent with differences in phosphate concentrations in those regimes. We suggest that the low proportion of cyanophage with psbA within the ODZ reflects the stably stratified low-light conditions occupied by their hosts, a Prochlorococcus ecotype endemic to ODZs.

Quantification of Lysogeny Caused by Phage Coinfections in Microbial Communities from Biophysical Principles

The association of temperate phages and bacterial hosts during lysogeny manipulates microbial dynamics from the oceans to the human gut. Lysogeny is well studied in laboratory models, but its environmental drivers remain unclear. Here, we quantified the probability of lysogenization caused by phage coinfections, a well-known trigger of lysogeny, in marine and gut microbial environments. Coinfections were quantified by developing a biophysical model that incorporated the traits of viral and bacterial communities. Lysogenization via coinfection was more frequent in highly productive environments like the gut, due to higher microbial densities and higher phage adsorption rates. At low cell densities, lysogenization occurred in bacteria with long duplication times. These results bridge the molecular understanding of lysogeny with the ecology of complex microbial communities.

Temperate phages can associate with their bacterial host to form a lysogen, often modifying the phenotype of the host. Lysogens are dominant in the microbially dense environment of the mammalian gut. This observation contrasts with the long-standing hypothesis of lysogeny being favored at low microbial densities, such as in oligotrophic marine environments. Here, we hypothesized that phage coinfections—a well-understood molecular mechanism of lysogenization—increase at high microbial abundances. To test this hypothesis, we developed a biophysical model of coinfection for marine and gut microbiomes. The model stochastically sampled ranges of phage and bacterial concentrations, adsorption rates, lysogenic commitment times, and community diversity from each environment. In 90% of the sampled marine communities, less than 10% of the bacteria were predicted to be lysogenized via coinfection. In contrast, 25% of the sampled gut communities displayed more than 25% of lysogenization. The probability of lysogenization in the gut was a consequence of the higher densities and higher adsorption rates. These results suggest that, on average, coinfections can form two trillion lysogens in the human gut every day. In marine microbiomes, which were characterized by lower densities and phage adsorption rates, lysogeny via coinfection was still possible for communities with long lysogenic commitment times. Our study indicates that different physical factors causing coinfections can reconcile the traditional view of lysogeny at poor host growth (long commitment times) and the recent Piggyback-the-Winner framework proposing that lysogeny is favored in rich environments (high densities and adsorption rates).

IMPORTANCE The association of temperate phages and bacterial hosts during lysogeny manipulates microbial dynamics from the oceans to the human gut. Lysogeny is well studied in laboratory models, but its environmental drivers remain unclear. Here, we quantified the probability of lysogenization caused by phage coinfections, a well-known trigger of lysogeny, in marine and gut microbial environments. Coinfections were quantified by developing a biophysical model that incorporated the traits of viral and bacterial communities. Lysogenization via coinfection was more frequent in highly productive environments like the gut, due to higher microbial densities and higher phage adsorption rates. At low cell densities, lysogenization occurred in bacteria with long duplication times. These results bridge the molecular understanding of lysogeny with the ecology of complex microbial communities.

Adaptations of Interferon Regulatory Factor 3 with Transition from Terrestrial to Aquatic Life

Interferon regulatory factor 3 (IRF3) and IRF7 are closely related IRF members and the major factors for the induction of interferons, a key component in vertebrate innate immunity. However, there is limited knowledge regarding the evolution and adaptation of those IRFs to the environments. Two unique motifs in IRF3 and 7 were identified. One motif, GASSL, is highly conserved throughout the evolution of IRF3 and 7 and located in the signal response domain. Another motif, DPHK, is in the DNA-binding domain. The ancestral protein of IRF3 and 7 seemed to possess the DPHK motif. In the ray-finned fish lineage, while the DPHK is maintained in IRF7, the motif in IRF3 is changed to NPHK with a D → N amino acid substitution. The D → N substitution are also found in amphibian IRF3 but not in amphibian IRF7. Terrestrial animals such as reptiles and mammals predominantly use DPHK sequences in both IRF3 and 7. However, the D → N substitution in IRF3 DPHK is again found in cetaceans such as whales and dolphins as well as in marsupials. These observations suggest that the D → N substitutions in the IRF3 DPHK motif is likely to be associated with vertebrate's adaptations to aquatic environments and other environmental changes.

Isolation and characterization of a moderately halophilic Marinobacter phage-host system from the Arabian Sea

Marinobacter is an ecologically important genus of Gammaproteobacteria found in diverse marine habitats, many species of which are capable of degrading hydrocarbons. In this study, we isolated a Marinobacter phage-host system from the surface waters of the Arabian Sea using enrichment culture methods, studied their growth characteristics and investigated the effect of salinity and nitrate concentrations on phage-host interactions. The bacterial isolate had maximum identity to Marinobacter salsuginis based on 16S rRNA similarities and was termed as Marinobacter sp., strain D1S9. It could tolerate up to 14% of NaCl with maximum growth at 11% NaCl. The host grew optimally between 35 and 40 °C and at pH 8. It had a generation time of 3.7 h with a mean growth rate of 0.27 h^-1. The phage infected the host forming clear, round plaques of 1-2 mm diameter. It had a narrow host range restricted to the strain Marinobacter D1S9. The latent period and burst size of the phage were estimated to be 30 min and 106 phages per infected cell, respectively. The phage had an adsorption rate of 3.4 × 10^-8 ml min^-1 and retained 40.4% of its adsorption efficiency at 16% NaCl with a maximum at 4% NaCl (76.1%). Inorganic nitrate was found to have a direct role in controlling host growth and phage burst size.

A Phage Protein Aids Bacterial Symbionts in Eukaryote Immune Evasion

Phages are increasingly recognized as important members of host-associated microbiomes, with a vast genomic diversity. The new frontier is to understand how phages may affect higher order processes, such as in the context of host-microbe interactions. Here, we use marine sponges as a model to investigate the interplay between phages, bacterial symbionts, and eukaryotic hosts. Using viral metagenomics, we find that sponges, although massively filtering seawater, harbor species-specific and even individually unique viral signatures that are taxonomically distinct from other environments. We further discover a symbiont phage-encoded ankyrin-domain-containing protein, which is widely spread in phages of many host-associated contexts including human. We confirm in macrophage infection assays that the ankyrin protein (ANKp) modulates the eukaryotic host immune response against bacteria. We predict that the role of ANKp in nature is to facilitate coexistence in the tripartite interplay between phages, symbionts, and sponges and possibly many other host-microbe associations.

Daily variation in the prokaryotic community during a spring bloom in shelf waters of the East China Sea

To understand prokaryotic responses during a spring bloom in offshore shelf waters, prokaryotic parameters were measured daily at a station located in the middle of the East China Sea over a six-week period from March 25 to May 19. The site experienced a phytoplankton bloom in late April, triggering changes in prokaryotic abundance and production after a lag of approximately one week. Before the bloom, changes in prokaryotic composition were small. Both during the bloom and in the post-bloom period, successive changes among bacterial groups were apparent. A SAR11 group became more dominant during the bloom period, and diverse groups belonging to the Flavobacteriia occurred dominantly during both the bloom and post-bloom periods. However, bacterial community changes at the species level during the bloom and post-bloom periods occurred rapidly in a time scale of a few days. Especially, NS5, NS4 and Formosa bacteria belonging to Flavobacteriia and bacteria belonging to Halieaceae and Arenicellaceae families of Gammaproteobacteria showed a successive pattern with large short-term variation during the period. The changes in prokaryotic composition were found to be related to phytoplankton biomass and composition, as well as seawater temperature and variations in nutrients.

Genetic Diversity and Cooccurrence Patterns of Marine Cyanopodoviruses and Picocyanobacteria

Picocyanobacteria Prochlorococcus and Synechococcus are abundant in the global oceans and subject to active viral infection. In this study, the genetic diversity of picocyanobacteria and the genetic diversity of cyanopodoviruses were synchronously investigated along water columns in the equatorial Indian Ocean and over a seasonal time course in the coastal Sanya Bay, South China Sea. Using the 16S-23S rRNA internal transcribed spacer (ITS)-based clone library and quantitative PCR (qPCR) analyses, the picocyanobacterial community composition and abundance were determined. Sanya Bay was dominated by clade II Synechococcus during all the seasons, and a typical population shift from high-light-adapted Prochlorococcus to low-light-adapted Prochlorococcus was found along the vertical profiles. Strikingly, the DNA polymerase gene sequences of cyanopodoviruses revealed a much greater genetic diversity than we expected. Nearly one-third of the phylogenetic groups were newly described here. No apparent seasonal pattern was observed for the Sanya Bay picocyanobacterial or cyanopodoviral communities. Different dominant cyanopodovirus lineages were identified for the coastal area, upper euphotic zone, and middle-to-lower euphotic zone of the open ocean. Diversity indices of both picocyanobacteria and cyanopodoviruses were highest in the middle euphotic zone and both were lower in the upper euphotic zone, reflecting a host-virus interaction. Cyanopodoviral communities differed significantly between the upper euphotic zone and the middle-to-lower euphotic zone, showing a vertical pattern similar to that of picocyanobacteria. However, in the surface waters of the open ocean, cyanopodoviruses exhibited no apparent biogeographic pattern, differing from picocyanobacteria. This study demonstrates correlated distribution patterns of picocyanobacteria and cyanopodoviruses, as well as the complex biogeography of cyanopodoviruses.IMPORTANCE Picocyanobacteria are highly diverse and abundant in the ocean and display remarkable global biogeography and a vertical distribution pattern. However, how the diversity and distribution of picocyanobacteria affect those of the viruses that infect them remains largely unknown. Here we synchronously analyzed the community structures of cyanopodoviruses and picocyanobacteria at spatial and temporal scales. Both spatial and temporal variations of cyanopodoviral communities can be linked to those of picocyanobacteria. The coastal area, upper euphotic zone, and middle-to-lower euphotic zone of the open ocean have distinct cyanopodoviral communities, showing horizontal and vertical variation patterns closely related to those of picocyanobacteria. These findings emphasize the driving force of host community in shaping the biogeographic structure of viruses. Our work provides important information for future assessments of the ecological roles of viruses and hosts for each other.

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.

Viruses in Marine Ecosystems: From Open Waters to Coral Reefs

Viruses infect all kingdoms of marine life from bacteria to whales. Viruses in the world's oceans play important roles in the mortality of phytoplankton, and as drivers of evolution and biogeochemical cycling. They shape host population abundance and distribution and can lead to the termination of algal blooms. As discoveries about this huge reservoir of genetic and biological diversity grow, our understanding of the major influences viruses exert in the global marine environment continues to expand. This chapter discusses the key discoveries that have been made to date about marine viruses and the current direction of this field of research.

'TIME': A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data

Realization of the importance of microbiome studies, coupled with the decreasing sequencing cost, has led to the exponential growth of microbiome data. A number of these microbiome studies have focused on understanding changes in the microbial community over time. Such longitudinal microbiome studies have the potential to offer unique insights pertaining to the microbial social networks as well as their responses to perturbations. In this communication, we introduce a web based framework called 'TIME' (Temporal Insights into Microbial Ecology'), developed specifically to obtain meaningful insights from microbiome time series data. The TIME web-server is designed to accept a wide range of popular formats as input with options to preprocess and filter the data. Multiple samples, defined by a series of longitudinal time points along with their metadata information, can be compared in order to interactively visualize the temporal variations. In addition to standard microbiome data analytics, the web server implements popular time series analysis methods like Dynamic time warping, Granger causality and Dickey Fuller test to generate interactive layouts for facilitating easy biological inferences. Apart from this, a new metric for comparing metagenomic time series data has been introduced to effectively visualize the similarities/differences in the trends of the resident microbial groups. Augmenting the visualizations with the stationarity information pertaining to the microbial groups is utilized to predict the microbial competition as well as community structure. Additionally, the 'causality graph analysis' module incorporated in TIME allows predicting taxa that might have a higher influence on community structure in different conditions. TIME also allows users to easily identify potential taxonomic markers from a longitudinal microbiome analysis. We illustrate the utility of the web-server features on a few published time series microbiome data and demonstrate the ease with which it can be used to perform complex analysis.

100 Days of marine Synechococcus-Ruegeria pomeroyi interaction: A detailed analysis of the exoproteome

Marine phototroph and heterotroph interactions are vital in maintaining the nutrient balance in the oceans as essential nutrients need to be rapidly cycled before sinking to aphotic layers. The aim of this study was to highlight the molecular mechanisms that drive these interactions. For this, we generated a detailed exoproteomic time‐course analysis of a 100‐day co‐culture between the model marine picocyanobacterium Synechococcus sp. WH7803 and the Roseobacter strain Ruegeria pomeroyi DSS‐3, both in nutrient‐enriched and natural oligotrophic seawater. The proteomic data showed a transition between the initial growth phase and stable‐state phase that, in the case of the heterotroph, was caused by a switch in motility attributed to organic matter availability. The phototroph adapted to seawater oligotrophy by reducing its selective leakiness, increasing the acquisition of essential nutrients and secreting conserved proteins of unknown function. We also report a surprisingly high abundance of extracellular superoxide dismutase produced by Synechococcus and a dynamic secretion of potential hydrolytic enzyme candidates used by the heterotroph to cleave organic groups and hydrolase polymeric organic matter produced by the cyanobacterium. The time course dataset we present here will become a reference for understanding the molecular processes underpinning marine phototroph‐heterotroph interactions.

Double stranded RNA is processed differently in two oyster species

Ostreid herpes virus causes serious disease in the Pacific oyster (Crassostrea gigas), but not in the Sydney Rock Oyster (Saccostrea glomerata). To investigate differences in disease progression, we injected oysters with double stranded RNA (dsRNA). dsRNA is known to mimic viral infection, and can evoke immune responses when Toll-like receptors detect the dsRNA, leading to the production of type 1 interferon and inflammation cytokines. The uptake and processing of dsRNA was tracked in gill and mantle tissue of Crassostrea gigas and Saccostrea glomerata after injection of fluorochrome labelled poly (I:C) dsRNA. The two species showed significant differences in tissue uptake and clearance, and differences in immune responses confirmed by real time PCR. These results showed that S. glomerata was more efficient in processing dsRNA than C. gigas, and that the gill tissue is an important site of dsRNA processing and response.

Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD)

Environmental surveys on soil viruses are still rare and mostly anecdotal, i. e., they mostly report on viruses at one location or for only a few sampling dates. Detailed time-series analysis with multiple samples can reveal the spatio-temporal dynamics of viral communities and provide important input as to how viruses interact with their potential hosts and the environment. Such surveys, however, require fast, easy-to-apply and reliable methods. In the present study we surveyed monthly across 13 months the abundance of virus-like particles (VLP) and the structure of the viral communities in soils along a land use transect (i.e., forest, pasture, and cropland). We evaluated 32 procedures to extract VLP from soil using different buffers and mechanical methods. The most efficient extraction was achieved with 1× saline magnesium buffer in combination with 20 min vortexing. For community structure analysis we developed an optimized fingerprinting approach (fluorescent RAPD-PCR; fRAPD) by combining RAPD-PCR with fluorescently labeled primers in order to size the obtained fragments on a capillary sequencing machine. With the concomitantly collected data of soil specific factors and weather data, we were able to find correlations of viral abundance and community structure with environmental variables and sampling site. More specifically, we found that soil specific factors such as pH and total nitrogen content played a significant role in shaping both soil viral abundance and community structure. The fRAPD analysis revealed high temporal changes and clustered the viral communities according to sampling sites. In particular we observed that temperature and rainfall shaped soil viral communities in non-forest sites. In summary our findings suggest that sampling site was a key factor for shaping the abundance and community structure of soil viruses, and when site vegetation was reduced, temperature and rainfall were also important factors.

Contrasting seasonal drivers of virus abundance and production in the North Pacific Ocean

The North Pacific Ocean (between approximately 0°N and 50°N) contains the largest continuous ecosystem on Earth. This region plays a vital role in the cycling of globally important nutrients as well as carbon. Although the microbial communities in this region have been assessed, the dynamics of viruses (abundances and production rates) remains understudied. To address this gap, scientific cruises during the winter and summer seasons (2013) covered the North Pacific basin to determine factors that may drive virus abundances and production rates. Along with information on virus particle abundance and production, we collected a spectrum of oceanographic metrics as well as information on microbial diversity. The data suggest that both biotic and abiotic factors affect the distribution of virus particles. Factors influencing virus dynamics did not vary greatly between seasons, although the abundance of viruses was almost an order of magnitude greater in the summer. When considered in the context of microbial community structure, our observations suggest that members of the bacterial phyla Proteobacteria, Planctomycetes, and Bacteroidetes were correlated to both virus abundances and virus production rates: these phyla have been shown to be enriched in particle associated communities. The findings suggest that environmental factors influence virus community functions (e.g., virion particle degradation) and that particle-associated communities may be important drivers of virus activity.

Unveiling the role and life strategies of viruses from the surface to the dark ocean

Viruses are a key component of marine ecosystems, but the assessment of their global role in regulating microbial communities and the flux of carbon is precluded by a paucity of data, particularly in the deep ocean. We assessed patterns in viral abundance and production and the role of viral lysis as a driver of prokaryote mortality, from surface to bathypelagic layers, across the tropical and subtropical oceans. Viral abundance showed significant differences between oceans in the epipelagic and mesopelagic, but not in the bathypelagic, and decreased with depth, with an average power-law scaling exponent of -1.03 km^-1 from an average of 7.76 × 10⁶ viruses ml^-1 in the epipelagic to 0.62 × 10⁶ viruses ml^-1 in the bathypelagic layer with an average integrated (0 to 4000 m) viral stock of about 0.004 to 0.044 g C m^-2, half of which is found below 775 m. Lysogenic viral production was higher than lytic viral production in surface waters, whereas the opposite was found in the bathypelagic, where prokaryotic mortality due to viruses was estimated to be 60 times higher than grazing. Free viruses had turnover times of 0.1 days in the bathypelagic, revealing that viruses in the bathypelagic are highly dynamic. On the basis of the rates of lysed prokaryotic cells, we estimated that viruses release 145 Gt C year^-1 in the global tropical and subtropical oceans. The active viral processes reported here demonstrate the importance of viruses in the production of dissolved organic carbon in the dark ocean, a major pathway in carbon cycling.

Drivers of interannual variability in virioplankton abundance at the coastal western Antarctic peninsula and the potential effects of climate change

An 8-year time-series in the Western Antarctic Peninsula (WAP) with an approximately weekly sampling frequency was used to elucidate changes in virioplankton abundance and their drivers in this climatically sensitive region. Virioplankton abundances at the coastal WAP show a pronounced seasonal cycle with interannual variability in the timing and magnitude of the summer maxima. Bacterioplankton abundance is the most influential driving factor of the virioplankton, and exhibit closely coupled dynamics. Sea ice cover and duration predetermine levels of phytoplankton stock and thus, influence virioplankton by dictating the substrates available to the bacterioplankton. However, variations in the composition of the phytoplankton community and particularly the prominence of Diatoms inferred from silicate drawdown, drive interannual differences in the magnitude of the virioplankton bloom; likely again mediated through changes in the bacterioplankton. Their findings suggest that future warming within the WAP will cause changes in sea ice that will influence viruses and their microbial hosts through changes in the timing, magnitude and composition of the phytoplankton bloom. Thus, the flow of matter and energy through the viral shunt may be decreased with consequences for the Antarctic food web and element cycling.

Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans

Marine viruses are key drivers of host diversity, population dynamics and biogeochemical cycling and contribute to the daily flux of billions of tons of organic matter. Despite recent advancements in metagenomics, much of their biodiversity remains uncharacterized. Here we report a data set of 27,346 marine virome contigs that includes 44 complete genomes. These outnumber all currently known phage genomes in marine habitats and include members of previously uncharacterized lineages. We designed a new method for host prediction based on co-occurrence associations that reveals these viruses infect dominant members of the marine microbiome such as Prochlorococcus and Pelagibacter. A negative association between host abundance and the virus-to-host ratio supports the recently proposed Piggyback-the-Winner model of reduced phage lysis at higher host densities. An analysis of the abundance patterns of viruses throughout the oceans revealed how marine viral communities adapt to various seasonal, temperature and photic regimes according to targeted hosts and the diversity of auxiliary metabolic genes.

Nutrient recycling facilitates long-term stability of marine microbial phototroph-heterotroph interactions

Biological interactions underpin the functioning of marine ecosystems, be it via competition, predation, mutualism, or symbiosis processes. Microbial phototroph-heterotroph interactions propel the engine that results in the biogeochemical cycling of individual elements and are critical for understanding and modelling global ocean processes. Unfortunately, studies thus far have focused on exponentially-growing cultures in nutrient-rich media, meaning knowledge of such interactions under in situ conditions is rudimentary at best. Here, we performed long-term phototroph-heterotroph co-culture experiments under nutrient-amended and natural seawater conditions which showed that it is not the concentration of nutrients but rather their circulation that maintains a stable interaction and a dynamic system. Using the Synechococcus-Roseobacter interaction as a model phototroph-heterotroph case study we show that whilst Synechococcus is highly specialised for carrying out photosynthesis and carbon-fixation it relies on the heterotroph to re-mineralise the inevitably leaked organic matter making nutrients circulate in a mutualistic system. In this sense we challenge the general belief that marine phototrophs and heterotrophs compete for the same scarce nutrients and niche space, but instead suggest these organisms more likely benefit from each other because of their different levels of specialization and complementarity within long-term stable-state systems.

Genetic hurdles limit the arms race between Prochlorococcus and the T7-like podoviruses infecting them

Phages and hosts coexist in nature with a high degree of population diversity. This is often explained through coevolutionary models, such as the arms race or density-dependent fluctuating selection, which differ in assumptions regarding the emergence of phage mutants that overcome host resistance. Previously, resistance in the abundant marine cyanobacterium, Prochlorococcus, was found to occur frequently. However, little is known about the ability of phages to overcome this resistance. Here we report that, in some cases, T7-like cyanophage mutants emerge to infect resistant Prochlorococcus strains. These resistance-breaking phages retained the ability to infect the wild-type host. However, fitness of the mutant phages differed on the two hosts. Furthermore, in one case, resistance-breaking was accompanied by costs of decreased fitness on the wild-type host and decreased adsorption specificity, relative to the wild-type phage. In two other cases, fitness on the wild-type host increased. Whole-genome sequencing revealed mutations in probable tail-related genes. These were highly diverse in isolates and natural populations of T7-like cyanophages, suggesting that antagonistic coevolution enhances phage genome diversity. Intriguingly, most interactions did not yield resistance-breaking phages. Thus, resistance mutations raise genetic barriers to continuous arms race cycles and are indicative of an inherent asymmetry in coevolutionary capacity, with hosts having the advantage. Nevertheless, phages coexist with hosts, which we propose relies on combined, parallel action of a limited arms race, fluctuating selection and passive host-switching within diverse communities. Together, these processes generate a constantly changing network of interactions, enabling stable coexistence between hosts and phages in nature.

The effect of extrinsic mortality on genome size evolution in prokaryotes

Mortality has a significant role in prokaryotic ecology and evolution, yet the impact of variations in extrinsic mortality on prokaryotic genome evolution has received little attention. We used both mathematical and agent-based models to reveal how variations in extrinsic mortality affect prokaryotic genome evolution. Our results suggest that the genome size of bacteria increases with increased mortality. A high extrinsic mortality increases the pool of free resources and shortens life expectancy, which selects for faster reproduction, a phenotype we called 'scramblers'. This phenotype is realised by the expansion of gene families involved in nutrient acquisition and metabolism. In contrast, a low mortality rate increases an individual's life expectancy, which results in natural selection favouring tolerance to starvation when conditions are unfavourable. This leads to the evolution of small, streamlined genomes ('stayers'). Our models predict that large genomes, gene family expansion and horizontal gene transfer should be observed in prokaryotes occupying ecosystems exposed to high abiotic stress, as well as those under strong predator- and/or pathogen-mediated selection. A comparison of genome size of cyanobacteria in relatively stable marine versus more turbulent freshwater environments corroborates our predictions, although other factors between these environments could also be responsible.

Membrane vesicles in sea water: heterogeneous DNA content and implications for viral abundance estimates

Diverse microbes release membrane-bound extracellular vesicles from their outer surfaces into the surrounding environment. Vesicles are found in numerous habitats including the oceans, where they likely have a variety of functional roles in microbial ecosystems. Extracellular vesicles are known to contain a range of biomolecules including DNA, but the frequency with which DNA is packaged in vesicles is unknown. Here, we examine the quantity and distribution of DNA associated with vesicles released from five different bacteria. The average quantity of double-stranded DNA and size distribution of DNA fragments released within vesicles varies among different taxa. Although some vesicles contain sufficient DNA to be visible following staining with the SYBR fluorescent DNA dyes typically used to enumerate viruses, this represents only a small proportion (<0.01-1%) of vesicles. Thus DNA is packaged heterogeneously within vesicle populations, and it appears that vesicles are likely to be a minor component of SYBR-visible particles in natural sea water compared with viruses. Consistent with this hypothesis, chloroform treatment of coastal and offshore seawater samples reveals that vesicles increase epifluorescence-based particle (viral) counts by less than an order of magnitude and their impact is variable in space and time.

Gut Virome and Inflammatory Bowel Disease

Gut virome has been shown to yield some beneficial effects on humans, being deeply involved in physiology, inflammation, immunity, and disease. Together with transkingdom interactions, it can interplay with genetic variation in the host to establish specific phenotypes. These interactions can lead to phenotypes not observed with either the virus or the host variation alone. Unfavorable alteration of gut virome composition has been implicated in chronic, and perhaps also systemic, immune disorders, such as in the pathogenesis of inflammatory bowel disease. This review focuses on what is currently known regarding the role of commensal gut virome in chronic gut inflammation, and speculate on the important translational implications in regard to gut virome modulation in inflammatory bowel disease with the end goal of promoting gut health.