Metagenomic Exploration of Koumiss from Kazakhstan

Here, we report a metagenomic analysis of koumiss from Kazakhstan. In this study, shotgun metagenomic sequencing of the RNA and DNA viral community was performed.

RNA viral communities are structured by host plant phylogeny in oak and conifer leaves

Wild plants can suffer devastating diseases, experience asymptomatic, persistent infections, and serve as reservoirs for viruses of agricultural crops, yet we have a limited understanding of the natural plant virosphere. To access representatives of locally and globally distinct wild plants and investigate their viral diversity, we extracted and sequenced dsRNA from leaves from 16 healthy oak and conifer trees in the UC Davis Arboretum (Davis, California). From de novo assemblies, we recovered 389 RNA-dependent RNA polymerase (RdRp) gene sequences from 384 putative viral species, and a further 580 putative viral contigs were identified with virus prediction software followed by manual confirmation of virus annotation. Based on similarity to known viruses, most recovered viruses were predicted to infect plants or fungi, with the highest diversity and abundance observed in the Totiviridae and Mitoviridae families. Phyllosphere viral community composition differed significantly by host plant phylogeny, suggesting the potential for host-specific viromes. The phyllosphere viral community of one oak tree differed substantially from other oak viral communities and contained a greater proportion of putative mycoviral sequences, potentially due to the tree's more advanced senescence at the time of sampling. These results suggest that oaks and conifers harbor a vast diversity of viruses with as-yet unknown roles in plant health and phyllosphere microbial ecology.

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

Background Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. Results Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. Conclusions Results suggest strong viral “species” boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics.

Coral Reef Viruses in Kane'ohe Bay, Hawai'i: Abundance, Diversity & Environmental Drivers

<p>Viruses are a ubiquitous component of coral reef ecosystems, with several viral types, from at least seven prokaryotic and 20 eukaryotic virus families currently characterised from the surface mucopolysaccharide layer (SML), coral tissue and the water column. However, little is known about the ecology and function of these viruses. For example, what are the environmental drivers of viral abundance and diversity on coral reefs? In this study, the abundance and distribution of virus-like particles (VLPs) associated with the SML and reef water of the coral Montipora capitata were determined using epifluorescence microscopy, while transmission electron microscopy was employed to determine the morphological diversity of VLPs. Sampling was conducted across the Coconut Island Marine Reserve (CIMR) reef system, Kane’ohe Bay, O’ahu, Hawai’i. Viral abundance was correlated with select environmental drivers and prokaryote abundance, while non-metric multidimensional scaling was used to determine the key environmental drivers of the viral community assemblage. The water column contained high concentrations of VLPs (5.98 × 107 ml-1) and prokaryotes (3.11 × 106 ml-1), consistent with the considerable anthropogenic impacts at this location. In comparison, the SML contained lower concentrations of VLPs (2.61 × 107 ml-1) and prokaryotes (2.08 × 106 ml-1); of note, the densities of viruses and prokaryotes in the SML were strongly coupled while those in the reef water were not. VLP density in the water column varied spatially across the reef, with the most sheltered site and the only one not situated on the reef crest having a greater VLP density than the other sites. Temporal variations in the density of microbes (i.e. viruses and prokaryotes) in the reef water were pronounced, while in the SML microbial densities remained constant. However, no specific environmental drivers of this variability could be identified. In contrast, temperature and water quality were correlated with shifts in the morphological diversity of VLPs across the reef. Small (< 50 nm) polyhedral/spherical VLPs were dominant, and were positively correlated to chlorophyll-a concentration when in the SML. In this same habitat, Fuselloviridae-like VLPs, filamentous VLPs and bead-shaped VLPs were positively correlated to temperature. In the reef water a different pattern was apparent: large (> 100 nm) Podoviridae-like VLPs and elongate Myoviridae-like VLPs, as well as lemon-shaped VLPs of both size classes showed positive associations with turbidity, while large filamentous VLPs, Geminiviridae-like VLPs and rod-shaped VLPs were positively associated with temperature. These results demonstrate that the viral community of Coconut Island’s reef is highly diverse, and subject to spatial and temporal change, especially in the water column. However, while the environmental drivers of viral diversity were partly elucidated, we are still a long way from understanding the drivers of viral abundance. More detailed study, both spatially and temporally, of the CIMR environment is required, as is comprehensive molecular analysis of the viral community of Kane’ohe Bay. Only then can we begin to understand the importance of viruses to the health and function of this, and other reef sites.</p>

Coral Reef Viruses in Kane'ohe Bay, Hawai'i: Abundance, Diversity & Environmental Drivers

<p>Viruses are a ubiquitous component of coral reef ecosystems, with several viral types, from at least seven prokaryotic and 20 eukaryotic virus families currently characterised from the surface mucopolysaccharide layer (SML), coral tissue and the water column. However, little is known about the ecology and function of these viruses. For example, what are the environmental drivers of viral abundance and diversity on coral reefs? In this study, the abundance and distribution of virus-like particles (VLPs) associated with the SML and reef water of the coral Montipora capitata were determined using epifluorescence microscopy, while transmission electron microscopy was employed to determine the morphological diversity of VLPs. Sampling was conducted across the Coconut Island Marine Reserve (CIMR) reef system, Kane’ohe Bay, O’ahu, Hawai’i. Viral abundance was correlated with select environmental drivers and prokaryote abundance, while non-metric multidimensional scaling was used to determine the key environmental drivers of the viral community assemblage. The water column contained high concentrations of VLPs (5.98 × 107 ml-1) and prokaryotes (3.11 × 106 ml-1), consistent with the considerable anthropogenic impacts at this location. In comparison, the SML contained lower concentrations of VLPs (2.61 × 107 ml-1) and prokaryotes (2.08 × 106 ml-1); of note, the densities of viruses and prokaryotes in the SML were strongly coupled while those in the reef water were not. VLP density in the water column varied spatially across the reef, with the most sheltered site and the only one not situated on the reef crest having a greater VLP density than the other sites. Temporal variations in the density of microbes (i.e. viruses and prokaryotes) in the reef water were pronounced, while in the SML microbial densities remained constant. However, no specific environmental drivers of this variability could be identified. In contrast, temperature and water quality were correlated with shifts in the morphological diversity of VLPs across the reef. Small (< 50 nm) polyhedral/spherical VLPs were dominant, and were positively correlated to chlorophyll-a concentration when in the SML. In this same habitat, Fuselloviridae-like VLPs, filamentous VLPs and bead-shaped VLPs were positively correlated to temperature. In the reef water a different pattern was apparent: large (> 100 nm) Podoviridae-like VLPs and elongate Myoviridae-like VLPs, as well as lemon-shaped VLPs of both size classes showed positive associations with turbidity, while large filamentous VLPs, Geminiviridae-like VLPs and rod-shaped VLPs were positively associated with temperature. These results demonstrate that the viral community of Coconut Island’s reef is highly diverse, and subject to spatial and temporal change, especially in the water column. However, while the environmental drivers of viral diversity were partly elucidated, we are still a long way from understanding the drivers of viral abundance. More detailed study, both spatially and temporally, of the CIMR environment is required, as is comprehensive molecular analysis of the viral community of Kane’ohe Bay. Only then can we begin to understand the importance of viruses to the health and function of this, and other reef sites.</p>

Coral Reef Viruses in Kane'ohe Bay, Hawai'i: Abundance, Diversity & Environmental Drivers

<p>Viruses are a ubiquitous component of coral reef ecosystems, with several viral types, from at least seven prokaryotic and 20 eukaryotic virus families currently characterised from the surface mucopolysaccharide layer (SML), coral tissue and the water column. However, little is known about the ecology and function of these viruses. For example, what are the environmental drivers of viral abundance and diversity on coral reefs? In this study, the abundance and distribution of virus-like particles (VLPs) associated with the SML and reef water of the coral Montipora capitata were determined using epifluorescence microscopy, while transmission electron microscopy was employed to determine the morphological diversity of VLPs. Sampling was conducted across the Coconut Island Marine Reserve (CIMR) reef system, Kane’ohe Bay, O’ahu, Hawai’i. Viral abundance was correlated with select environmental drivers and prokaryote abundance, while non-metric multidimensional scaling was used to determine the key environmental drivers of the viral community assemblage. The water column contained high concentrations of VLPs (5.98 × 107 ml-1) and prokaryotes (3.11 × 106 ml-1), consistent with the considerable anthropogenic impacts at this location. In comparison, the SML contained lower concentrations of VLPs (2.61 × 107 ml-1) and prokaryotes (2.08 × 106 ml-1); of note, the densities of viruses and prokaryotes in the SML were strongly coupled while those in the reef water were not. VLP density in the water column varied spatially across the reef, with the most sheltered site and the only one not situated on the reef crest having a greater VLP density than the other sites. Temporal variations in the density of microbes (i.e. viruses and prokaryotes) in the reef water were pronounced, while in the SML microbial densities remained constant. However, no specific environmental drivers of this variability could be identified. In contrast, temperature and water quality were correlated with shifts in the morphological diversity of VLPs across the reef. Small (< 50 nm) polyhedral/spherical VLPs were dominant, and were positively correlated to chlorophyll-a concentration when in the SML. In this same habitat, Fuselloviridae-like VLPs, filamentous VLPs and bead-shaped VLPs were positively correlated to temperature. In the reef water a different pattern was apparent: large (> 100 nm) Podoviridae-like VLPs and elongate Myoviridae-like VLPs, as well as lemon-shaped VLPs of both size classes showed positive associations with turbidity, while large filamentous VLPs, Geminiviridae-like VLPs and rod-shaped VLPs were positively associated with temperature. These results demonstrate that the viral community of Coconut Island’s reef is highly diverse, and subject to spatial and temporal change, especially in the water column. However, while the environmental drivers of viral diversity were partly elucidated, we are still a long way from understanding the drivers of viral abundance. More detailed study, both spatially and temporally, of the CIMR environment is required, as is comprehensive molecular analysis of the viral community of Kane’ohe Bay. Only then can we begin to understand the importance of viruses to the health and function of this, and other reef sites.</p>

Coral Reef Viruses in Kane'ohe Bay, Hawai'i: Abundance, Diversity & Environmental Drivers

<p>Viruses are a ubiquitous component of coral reef ecosystems, with several viral types, from at least seven prokaryotic and 20 eukaryotic virus families currently characterised from the surface mucopolysaccharide layer (SML), coral tissue and the water column. However, little is known about the ecology and function of these viruses. For example, what are the environmental drivers of viral abundance and diversity on coral reefs? In this study, the abundance and distribution of virus-like particles (VLPs) associated with the SML and reef water of the coral Montipora capitata were determined using epifluorescence microscopy, while transmission electron microscopy was employed to determine the morphological diversity of VLPs. Sampling was conducted across the Coconut Island Marine Reserve (CIMR) reef system, Kane’ohe Bay, O’ahu, Hawai’i. Viral abundance was correlated with select environmental drivers and prokaryote abundance, while non-metric multidimensional scaling was used to determine the key environmental drivers of the viral community assemblage. The water column contained high concentrations of VLPs (5.98 × 107 ml-1) and prokaryotes (3.11 × 106 ml-1), consistent with the considerable anthropogenic impacts at this location. In comparison, the SML contained lower concentrations of VLPs (2.61 × 107 ml-1) and prokaryotes (2.08 × 106 ml-1); of note, the densities of viruses and prokaryotes in the SML were strongly coupled while those in the reef water were not. VLP density in the water column varied spatially across the reef, with the most sheltered site and the only one not situated on the reef crest having a greater VLP density than the other sites. Temporal variations in the density of microbes (i.e. viruses and prokaryotes) in the reef water were pronounced, while in the SML microbial densities remained constant. However, no specific environmental drivers of this variability could be identified. In contrast, temperature and water quality were correlated with shifts in the morphological diversity of VLPs across the reef. Small (< 50 nm) polyhedral/spherical VLPs were dominant, and were positively correlated to chlorophyll-a concentration when in the SML. In this same habitat, Fuselloviridae-like VLPs, filamentous VLPs and bead-shaped VLPs were positively correlated to temperature. In the reef water a different pattern was apparent: large (> 100 nm) Podoviridae-like VLPs and elongate Myoviridae-like VLPs, as well as lemon-shaped VLPs of both size classes showed positive associations with turbidity, while large filamentous VLPs, Geminiviridae-like VLPs and rod-shaped VLPs were positively associated with temperature. These results demonstrate that the viral community of Coconut Island’s reef is highly diverse, and subject to spatial and temporal change, especially in the water column. However, while the environmental drivers of viral diversity were partly elucidated, we are still a long way from understanding the drivers of viral abundance. More detailed study, both spatially and temporally, of the CIMR environment is required, as is comprehensive molecular analysis of the viral community of Kane’ohe Bay. Only then can we begin to understand the importance of viruses to the health and function of this, and other reef sites.</p>

Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state

Microbial communities in oxygen minimum zones (OMZs) are known to have significant impacts on global biogeochemical cycles, but viral influence on microbial processes in these regions are much less studied. Here we provide baseline ecological patterns using microscopy and viral metagenomics from the Eastern Tropical North Pacific (ETNP) OMZ region that enhance our understanding of viruses in these climate-critical systems. While extracellular viral abundance decreased below the oxycline, viral diversity and lytic infection frequency remained high within the OMZ, demonstrating that viral influences on microbial communities were still substantial without the detectable presence of oxygen. Viral community composition was strongly related to oxygen concentration, with viral populations in low-oxygen portions of the water column being distinct from their surface layer counterparts. However, this divergence was not accompanied by the expected differences in viral-encoded auxiliary metabolic genes (AMGs) relating to nitrogen and sulfur metabolisms that are known to be performed by microbial communities in these low-oxygen and anoxic regions. Instead, several abundant AMGs were identified in the oxycline and OMZ that may modulate host responses to low-oxygen stress. We hypothesize that this is due to selection for viral-encoded genes that influence host survivability rather than modulating host metabolic reactions within the ETNP OMZ. Together, this study shows that viruses are not only diverse throughout the water column in the ETNP, including the OMZ, but their infection of microorganisms has the potential to alter host physiological state within these biogeochemically important regions of the ocean.