Large freshwater phages with the potential to augment aerobic methane oxidation

Eutrophication impacts the distribution and functional traits of viral communities in lakes

Viruses play a crucial role in aquatic ecosystems by regulating microbial composition and impacting biogeochemical cycling. While the response of viral diversity to the trophic status has been preliminarily explored in lake ecosystems, there is limited integrated exploration of the biogeography of viruses, host associations, and the auxiliary metabolic genes (AMGs), particularly for plateau lakes. Therefore, this research investigated the viral biogeography, virus-host association, and AMGs in the surface waters of 11 lakes varying in trophic levels (eutrophic and oligo-mesotrophic) in the Yunnan-Guizhou plateau region of China. A total of 73,105 viral operational taxonomic units were obtained from 11 samples, with 84.8 % remaining unannotated at the family level, indicating a predominance of novel viruses within these lakes. The most abundant viral family was Kyanoviridae (24.4 %), recognized as a common cyanophage. The vast majority of cyanobacteria and several eukaryotic algae were predicted as hosts for the viruses, with a lytic lifestyle predominating the life strategy of these cyanophages, implying the potential influence of the virus on algae. The viral community structure significantly correlated with both trophic status and the bacterial community. The structure equation model analysis revealed chlorophyll a was the primary factor affecting viral communities. Moreover, numerous AMGs linked to carbon metabolism, phosphorus metabolism, sulfur metabolism, and photosynthesis were found in these lakes, some of which showed virus preference for the trophic statuses, suggesting a vital role of the virus in driving biogeochemical cycling in the lake crossing different nutrient levels. In addition, a restricted presence of viruses was found to infect humans or harbor antibiotic resistance genes in the lakes, suggesting a subtle yet potential link to human health. Overall, these findings offer insights into the response of viral communities to eutrophication and their potential role in biogeochemical cycling and controlling algal propagation.

Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements

Methane emissions are mitigated by anaerobic methane-oxidizing archaea, including Methanoperedens. Some Methanoperedens host huge extrachromosomal genetic elements (ECEs) called Borgs that may modulate their activity, yet the broader diversity of Methanoperedens ECEs is understudied. Here we report small enigmatic linear ECEs, circular viruses and unclassified ECEs that are predicted to replicate within Methanoperedens. Linear ECEs have inverted terminal repeats, tandem repeats and coding patterns that are strongly reminiscent of Borgs, but they are only 52-145 kb in length. As they share proteins with Borgs and Methanoperedens, we refer to them as mini-Borgs. Mini-Borgs are genetically diverse and can be assigned to at least five family-level groups. We identify eight families of Methanoperedens viruses, some of which encode multi-haem cytochromes, and circular ECEs encoding transposon-associated TnpB genes with proximal population-heterogeneous CRISPR arrays. These ECEs exchange genetic information with each other and with Methanoperedens, probably impacting their archaeal host activity and evolution.

Unveiling the unknown viral world in groundwater

Viruses as the prevailing biological entities are poorly understood in underground realms. Here, we establish the first metagenomic Groundwater Virome Catalogue (GWVC) comprising 280,420 viral species ( ≥ 5 kb) detected from 607 monitored wells in seven geo-environmental zones throughout China. In expanding ~10-fold the global portfolio of known groundwater viruses, we uncover over 99% novel viruses and about 95% novel viral clusters. By linking viruses to hosts from 119 prokaryotic phyla, we double the number of microbial phyla known to be virus-infected in groundwater. As keystone ultrasmall symbionts in aquifers, CPR bacteria and DPANN archaea are susceptible to virulent viruses. Certain complete CPR viruses even likely infect non-CPR bacteria, while partial CPR/DPANN viruses harbor cell-surface modification genes that assist symbiont cell adhesion to free-living microbes. This study reveals the unknown viral world and auxiliary metabolism associated with methane, nitrogen, sulfur, and phosphorus cycling in groundwater, and highlights the importance of subsurface virosphere in viral ecology.

Viral and Bacterial Community Dynamics in Food Waste and Digestate from Full-Scale Biogas Plants

Anaerobic digestion (AD) is commonly used in food waste treatment. Prokaryotic microbial communities in AD of food waste have been comprehensively studied. The role of viruses, known to affect microbial dynamics and metabolism, remains largely unexplored. This study employed metagenomic analysis and recovered 967 high-quality viral bins within food waste and digestate derived from 8 full-scale biogas plants. The diversity of viral communities was higher in digestate. In silico predictions linked 20.8% of viruses to microbial host populations, highlighting possible virus predators of key functional microbes. Lineage-specific virus-host ratio varied, indicating that viral infection dynamics might differentially affect microbial responses to the varying process parameters. Evidence for virus-mediated gene transfer was identified, emphasizing the potential role of viruses in controlling the microbiome. AD altered the specific process parameters, potentially promoting a shift in viral lifestyle from lysogenic to lytic. Viruses encoding auxiliary metabolic genes (AMGs) were involved in microbial carbon and nutrient cycling, and most AMGs were transcriptionally expressed in digestate, meaning that viruses with active functional states were likely actively involved in AD. These findings provided a comprehensive profile of viral and bacterial communities and expanded knowledge of the interactions between viruses and hosts in food waste and digestate.

Thallium spill shifts the structural and functional characteristics of viral communities with different lifestyles in river sediments

Thallium (Tl), a highly toxic heavy metal, can affect microbial community, while little is known about its effect on viral community. The present study investigated the variation of viral communities, as well as their interactions with microbial hosts under Tl stress. Tl in sediments significantly altered the composition and diversity of the viral communities, but showed no significant links with the prokaryotic communities, which may reveal a potential discrepancy in the sensitivity of the viral and prokaryotic communities to heavy metal stress. Auxiliary metabolic genes (AMGs) involved in denitrification, methane oxidation and organic sulfur transformation were enriched at T1-contaminated sites, while the abundance of AMGs related to methanogenesis and sulfate reduction were higher at pristine sites. Specially, the enrichment of AMGs involved in assimilatory sulfate reduction in Tl-contaminated sites could possibly reduce Tl bioavailability by enhancing the microbially-driven sulfur cycling to generate sulfides that could be complexed with Tl. Moreover, there was a significantly positive correlation between virus-carrying metal resistant genes and the sedimentary Tl concentration, implying that Tl contamination might enhance the metal resistant potential of the viruses. Serving as the functional gene reservoir, the response of viral AMGs to Tl stress could represent a potential pathway for microorganisms to be adapted to the metal-polluted environments. Our study provided novel insights into the impact of Tl spill on viral communities, shedding light on functional characteristics and the links of virus-host interaction with Tl level.

Habitat- and lifestyle-dependent structural and functional characteristics of viruses in mangrove wetlands of different functional zonings

Mangrove wetlands, as one of the natural ecosystems with the most ecological services, have garnered widespread attention about their microbial driven biogeochemical cycling. Urbanization have led to different spatial patterns of environmental conditions and microbial communities in mangroves. However, viruses, as the pivotal drivers of biogeochemical cycling in mangroves, remain inadequately explored in terms of how their ecological potential and complex interactions with host respond to functional zonings. To address this knowledge gap, we conducted a comprehensive investigation on the structural and functional properties of temperate and lytic viruses in mangrove wetlands from different functional zonings by jointly using high-throughput sequencing, prokaryotic and viral metagenomics. Multiple environmental factors were found to significantly influence the taxonomic and functional composition, as well as lysogen-lysis decision-making of mangrove viruses. Furthermore, enriched auxiliary metabolic genes (AMGs) involved in methane, nitrogen and sulfur metabolism, and heavy metal resistance were unveiled in mangrove viruses, whose community composition was closely related to lifestyle and host. The virus-host pairs with different lifestyles were also discovered to react to environmental changes in different ways, which provided an empirical evidence for how virus and bacteria dynamics were specific to viral lifestyles in nature. This study expands our comprehension of the intricate interactions among virus, prokaryotic host and the environment in mangrove wetlands from multiple perspectives, including viral lifestyles, virus-host interactions, and habitat dependence. Importantly, it provides a new ecological perspective on how mangrove viruses are adapted to the stress posed by urbanization.

COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes

Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and joins contigs. Here we benchmarked COBRA using ocean and soil viral datasets. COBRA accurately joined the assembled sequences and achieved notably higher genome accuracy than binning tools. From 231 published freshwater metagenomes, we obtained 7,334 bacteriophage clusters, ~83% of which represent new phage species. Notably, ~70% of these were circular, compared with 34% before COBRA analyses. We expanded sampling of huge phages (≥200 kbp), the largest of which was curated to completion (717 kbp). Improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated the in situ activity of huge phages, whiB-encoding phages and cysC- and cysH-encoding phages. COBRA improves viral genome assembly contiguity and completeness, thus the accuracy and reliability of analyses of gene content, diversity and evolution.

Viral potential to modulate microbial methane metabolism varies by habitat

Methane is a potent greenhouse gas contributing to global warming. Microorganisms largely drive the biogeochemical cycling of methane, yet little is known about viral contributions to methane metabolism (MM). We analyzed 982 publicly available metagenomes from host-associated and environmental habitats containing microbial MM genes, expanding the known MM auxiliary metabolic genes (AMGs) from three to 24, including seven genes exclusive to MM pathways. These AMGs are recovered on 911 viral contigs predicted to infect 14 prokaryotic phyla including Halobacteriota, Methanobacteriota, and Thermoproteota. Of those 24, most were encoded by viruses from rumen (16/24), with substantially fewer by viruses from environmental habitats (0-7/24). To search for additional MM AMGs from an environmental habitat, we generate metagenomes from methane-rich sediments in Vrana Lake, Croatia. Therein, we find diverse viral communities, with most viruses predicted to infect methanogens and methanotrophs and some encoding 13 AMGs that can modulate host metabolisms. However, none of these AMGs directly participate in MM pathways. Together these findings suggest that the extent to which viruses use AMGs to modulate host metabolic processes (e.g., MM) varies depending on the ecological properties of the habitat in which they dwell and is not always predictable by habitat biogeochemical properties.

Viral communities in millipede guts: Insights into the diversity and potential role in modulating the microbiome

Millipedes are important detritivores harbouring a diverse microbiome. Previous research focused on bacterial and archaeal diversity, while the virome remained neglected. We elucidated the DNA and RNA viral diversity in the hindguts of two model millipede species with distinct microbiomes: the tropical Epibolus pulchripes (methanogenic, dominated by Bacillota) and the temperate Glomeris connexa (non-methanogenic, dominated by Pseudomonadota). Based on metagenomic and metatranscriptomic assembled viral genomes, the viral communities differed markedly and preferentially infected the most abundant prokaryotic taxa. The majority of DNA viruses were Caudoviricetes (dsDNA), Cirlivirales (ssDNA) and Microviridae (ssDNA), while RNA viruses consisted of Leviviricetes (ssRNA), Potyviridae (ssRNA) and Eukaryotic viruses. A high abundance of subtypes I-C, I-B and II-C CRISPR-Cas systems was found, primarily from Pseudomonadota, Bacteroidota and Bacillota. In addition, auxiliary metabolic genes that modulate chitin degradation, vitamins and amino acid biosynthesis and sulphur metabolism were also detected. Lastly, we found low virus-to-microbe-ratios and a prevalence of lysogenic viruses, supporting a Piggyback-the-Winner dynamic in both hosts.

Exploring virus-host-environment interactions in a chemotrophic-based underground estuary

BACKGROUND

Viruses play important roles in modulating microbial communities and influencing global biogeochemistry. There is now growing interest in characterising their ecological roles across diverse biomes. However, little is known about viral ecology in low-nutrient, chemotrophic-based environments. In such ecosystems, virus-driven manipulation of nutrient cycles might have profound impacts across trophic levels. In particular, anchialine environments, which are low-energy underground estuaries sustained by chemotrophic processes, represent ideal model systems to study novel virus-host-environment interactions.

RESULTS

Here, we employ metagenomic sequencing to investigate the viral community in Bundera Sinkhole, an anchialine ecosystem rich in endemic species supported by microbial chemosynthesis. We find that the viruses are highly novel, with less than 2% representing described viruses, and are hugely abundant, making up as much as 12% of microbial intracellular DNA. These highly abundant viruses largely infect important prokaryotic taxa that drive key metabolic processes in the sinkhole. Further, the abundance of viral auxiliary metabolic genes (AMGs) involved in nucleotide and protein synthesis was strongly correlated with declines in environmental phosphate and sulphate concentrations. These AMGs encoded key enzymes needed to produce sulphur-containing amino acids, and phosphorus metabolic enzymes involved in purine and pyrimidine nucleotide synthesis. We hypothesise that this correlation is either due to selection of these AMGs under low phosphate and sulphate concentrations, highlighting the dynamic interactions between viruses, their hosts, and the environment; or, that these AMGs are driving increased viral nucleotide and protein synthesis via manipulation of host phosphorus and sulphur metabolism, consequently driving nutrient depletion in the surrounding water.

CONCLUSION

This study represents the first metagenomic investigation of viruses in anchialine ecosystems, and provides new hypotheses and insights into virus-host-environment interactions in such 'dark', low-energy environments. This is particularly important since anchialine ecosystems are characterised by diverse endemic species, both in their microbial and faunal assemblages, which are primarily supported by microbial chemosynthesis. Thus, virus-host-environment interactions could have profound effects cascading through all trophic levels.

Effects of small heat shock proteins from thermotolerant bacteria on the stress resistance of Escherichia coli to temperature, pH, and hyperosmolarity

Small heat shock proteins (HSPs), such as HSP20, represent cellular thermal resistance mechanisms, to avoid protein aggregation at elevated temperatures. Recombinantly expressed HSP20s serve as a molecular tool for improving the tolerance of living cells to various physical and chemical stressors. Here, we aimed to heterologously express 18 HSP20s from 12 thermotolerant bacteria in Escherichia coli and evaluate their effects on various physical and chemical cellular stresses. Seventeen HSP20s were successfully expressed as soluble proteins. Recombinant E. coli cells were subjected to heat, cold, acidic, alkaline, and hyperosmolar stress to evaluate the effects of HSP20 proteins on stress resistance. Notably, the overexpression of 15 HSP20s enhanced the stress resistance of E. coli compared to that of the control strain. In particular, HSPs from Tepidimonas sediminis and Oceanithermus profundus improved the stress tolerance of E. coli under all tested conditions. In addition, E. coli harboring HSP20 from T. sediminis retained cell viability even after heat treatment at 52 °C for 5 days. To our knowledge, this is the first report of E. coli tolerance to prolonged (> 100 h) high-temperature stress. These findings indicate the potential of thermotolerant HSPs as molecular tools for improving stress tolerance in E. coli.

High niche specificity and host genetic diversity of groundwater viruses

Viruses are key members of microbial communities that exert control over host abundance and metabolism, thereby influencing ecosystem processes and biogeochemical cycles. Aquifers are known to host taxonomically diverse microbial life, yet little is known about viruses infecting groundwater microbial communities. Here, we analysed 16 metagenomes from a broad range of groundwater physicochemistries. We recovered 1571 viral genomes that clustered into 468 high-quality viral operational taxonomic units. At least 15% were observed to be transcriptionally active, although lysis was likely constrained by the resource-limited groundwater environment. Most were unclassified (95%), and the remaining 5% were Caudoviricetes. Comparisons with viruses inhabiting other aquifers revealed no shared species, indicating substantial unexplored viral diversity. In silico predictions linked 22.4% of the viruses to microbial host populations, including to ultra-small prokaryotes, such as Patescibacteria and Nanoarchaeota. Many predicted hosts were associated with the biogeochemical cycling of carbon, nitrogen, and sulfur. Metabolic predictions revealed the presence of 205 putative auxiliary metabolic genes, involved in diverse processes associated with the utilization of the host's intracellular resources for biosynthesis and transformation reactions, including those involved in nucleotide sugar, glycan, cofactor, and vitamin metabolism. Viruses, prokaryotes overall, and predicted prokaryotic hosts exhibited narrow spatial distributions, and relative abundance correlations with the same groundwater parameters (e.g. dissolved oxygen, nitrate, and iron), consistent with host control over viral distributions. Results provide insights into underexplored groundwater viruses, and indicate the large extent to which viruses may manipulate microbial communities and biogeochemistry in the terrestrial subsurface.

Bacteria and bacteriophage consortia are associated with protective intestinal metabolites in patients receiving stem cell transplantation

The microbiome is a predictor of clinical outcome in patients receiving allogeneic hematopoietic stem cell transplantation (allo-SCT). Microbiota-derived metabolites can modulate these outcomes. How bacteria, fungi and viruses contribute to the production of intestinal metabolites is still unclear. We combined amplicon sequencing, viral metagenomics and targeted metabolomics from stool samples of patients receiving allo-SCT (n = 78) and uncovered a microbiome signature of Lachnospiraceae and Oscillospiraceae and their associated bacteriophages, correlating with the production of immunomodulatory metabolites (IMMs). Moreover, we established the IMM risk index (IMM-RI), which was associated with improved survival and reduced relapse. A high abundance of short-chain fatty acid-biosynthesis pathways, specifically butyric acid via butyryl-coenzyme A (CoA):acetate CoA-transferase (BCoAT, which catalyzes EC 2.8.3.8) was detected in IMM-RI low-risk patients, and virome genome assembly identified two bacteriophages encoding BCoAT as an auxiliary metabolic gene. In conclusion, our study identifies a microbiome signature associated with protective IMMs and provides a rationale for considering metabolite-producing consortia and metabolite formulations as microbiome-based therapies.

Narrow host range phages infect essential bacteria for water purification reactions in groundwater-fed rapid sand filters

Biofiltration is used worldwide to provide safe potable water due to its low energy demand and excellent treatment performance. For instance, in Denmark, over 95% of drinking water is supplied through groundwater-fed rapid sand filters (RSF). Bacteriophages, viruses that infect bacteria, have been shown to shape the taxonomic and functional composition of microbial communities across a range of natural and engineering systems. However, phages in the biofiltration systems are rarely studied, despite the central role microbes play in water purification. To probe this, metagenomic data from surface water, groundwater and mixed source water biofiltration units (n = 26 from China, Europe and USA) for drinking water production were analysed to characterize prokaryotic viruses and to identify their potential microbial hosts. The source water type and geographical location are found to exert influence on the composition of the phageome in biofilters. Although the viral abundance (71,676 ± 17,841 RPKM) in biofilters is only 14.4% and 17.0% lower than those of the nutrient-rich wastewater treatment plants and fresh surface waters, the richness (1,441 ± 1,046) and diversity (Inverse Simpson: 91 ± 61) in biofiltration units are significantly less by a factor of 2-5 and 3-4, respectively. In depth analysis of data from 24 groundwater-fed RSFs in Denmark revealed a core phageome shared by most RSFs, which was consistently linked to dominant microbial hosts involved in key biological reactions for water purification. Finally, the high number of specific links detected between phages and bacterial species and the large proportion of lytic phages (77%) led to the conjecture that phages regulate bacterial populations through predation, preventing the proliferation of dominant species and contributing to the established functional redundancy among the dominant microbial groups. In conclusion, bacteriophages are likely to play a significant role in water treatment within biofilters, particularly through interactions with key bacterial species.

Metagenomic analysis unveils the underexplored roles of prokaryotic viruses in a full-scale landfill leachate treatment plant

Enormous viral populations have been identified in activated sludge systems, but their ecological and biochemical roles in landfill leachate treatment plants remain poorly understood. To address this knowledge gap, we conducted an in-depth analysis using 36 metagenomic datasets that we collected and sequenced during a half-year time-series sampling campaign at six sites in a full-scale landfill leachate treatment plant (LLTP), elucidating viral distribution, virus‒host dynamics, virus-encoded auxiliary metabolic genes (AMGs), and viral contributions to the spread of virulence and antibiotic resistance genes. Our findings demonstrated that viral and prokaryotic communities differed widely among different treatment units, with stability over time. LLTP viruses were linked to various prokaryotic hosts, spanning 35 bacterial phyla and one archaeal phylum, which included the core microbes involved in biological treatments, as well as some of the less well-characterized microbial dark matter phyla. By encoding 2364 auxiliary metabolic genes (AMGs), viruses harbored the potential to regulate microbial nucleotide metabolism, facilitate the biodegradation of complex organic matter, and enhance flocculation and settling in biological treatment plants. The abundance distribution of AMGs varied considerably across treatment units and showed a lifestyle-dependent pattern with temperate virus-associated AMGs exhibiting a higher average abundance in downstream biological treatment units and effluent water. Meanwhile, temperate viruses tended to carry a higher load of virulence factor genes (VFGs), antibiotic resistance genes (ARGs), and biotic and metal resistance genes (BMRGs), and engaged in more frequent gene exchanges with prokaryotes than lytic viruses, thus acting as a pivotal contributor to the dissemination of pathogenicity and resistance genes in downstream LLTP units. This study provided a comprehensive profile of viral and prokaryotic communities in the LLTP and unveiled the varying roles of different-lifestyle viruses in biochemical processes and water quality safety.

Presence and role of viruses in anaerobic digestion of food waste under environmental variability

BACKGROUND

The interaction among microorganisms in the anaerobic digestion of food waste (ADFW) reactors lead to the degradation of organics and the recycling of energy. Viruses are an important component of the microorganisms involved in ADFW, but are rarely investigated. Furthermore, little is known about how viruses affect methanogenesis.

RESULTS

Thousands of viral sequences were recovered from five full-scale ADFW reactors. Gene-sharing networks indicated that the ADFW samples contained substantial numbers of unexplored anaerobic-specific viruses. Moreover, the viral communities in five full-scale reactors exhibited both commonalities and heterogeneities. The lab-scale dynamic analysis of typical ADFW scenarios suggested that the viruses had similar kinetic characteristics to their prokaryotic hosts. By associating with putative hosts, a majority of the bacteria and archaea phyla were found to be infected by viruses. Viruses may influence prokaryotic ecological niches, and thus methanogenesis, by infecting key functional microorganisms, such as sulfate-reducing bacteria (SRB), syntrophic acetate-oxidizing bacteria (SAOB), and methanogens. Metabolic predictions for the viruses suggested that they may collaborate with hosts at key steps of sulfur and long-chain fatty acid (LCFA) metabolism and could be involved in typical methanogenesis pathways to participate in methane production.

CONCLUSIONS

Our results expanded the diversity of viruses in ADFW systems and suggested two ways that viral manipulated ADFW biochemical processes. Video Abstract.

ViWrap: A modular pipeline to identify, bin, classify, and predict viral-host relationships for viruses from metagenomes

Viruses are increasingly being recognized as important components of human and environmental microbiomes. However, viruses in microbiomes remain difficult to study because of the difficulty in culturing them and the lack of sufficient model systems. As a result, computational methods for identifying and analyzing uncultivated viral genomes from metagenomes have attracted significant attention. Such bioinformatics approaches facilitate the screening of viruses from enormous sequencing datasets originating from various environments. Though many tools and databases have been developed for advancing the study of viruses from metagenomes, there is a lack of integrated tools enabling a comprehensive workflow and analyses platform encompassing all the diverse segments of virus studies. Here, we developed ViWrap, a modular pipeline written in Python. ViWrap combines the power of multiple tools into a single platform to enable various steps of virus analysis, including identification, annotation, genome binning, species- and genus-level clustering, assignment of taxonomy, prediction of hosts, characterization of genome quality, comprehensive summaries, and intuitive visualization of results. Overall, ViWrap enables a standardized and reproducible pipeline for both extensive and stringent characterization of viruses from metagenomes, viromes, and microbial genomes. Our approach has flexibility in using various options for diverse applications and scenarios, and its modular structure can be easily amended with additional functions as necessary. ViWrap is designed to be easily and widely used to study viruses in human and environmental systems. ViWrap is publicly available via GitHub (https://github.com/AnantharamanLab/ViWrap). A detailed description of the software, its usage, and interpretation of results can be found on the website.

Viral community structure and functional potential vary with lifestyle and altitude in soils of Mt. Everest

More and more focus has been placed on the processes by which viruses interact with bacteria to influence the biogeochemical cycles. The intricacy of soil matrix and the incompleteness of databases, however, constrains the investigation on the mechanisms of soil viruses exerting ecological functions. The modification of ICTV classification system in 2021 was also a huge shock to the results of the existing studies on virome. We used viral metagenomes combined with soil properties to investigate the viral community composition and auxiliary metabolic genes (AMGs) profiles of various lifestyles in soils of Mount Everest at different altitudes. Viral lifestyles and soil nutrient levels were found to significantly influence the diversity and composition of viral communities. Temperate virus lifestyle dominated in high-altitude soils with lower level of nutrients because of its stronger survival adaptability, and the structural and functional diversity of viral communities was positively correlated with the contents of nutrients (total carbon and total nitrogen). The primary types of AMGs carried by temperate and virulent viruses differed, while a variety of genes involved in carbon metabolism highlighted the potential importance of viruses in the soil carbon cycle of Mount Everest. Moreover, the abundance of AMGs encoding carbohydrate-active enzymes had a significant and positive correlation with soil C/N ratio. Overall, these findings provide a context for further exploration on the regulatory mechanisms of viruses in carbon cycle via interactions with microorganisms.

Virus impacted community adaptation in oligotrophic groundwater environment revealed by Hi-C coupled metagenomic and viromic study

Viruses play a crucial role in microbial mortality, diversity and biogeochemical cycles. Groundwater is the largest global freshwater and one of the most oligotrophic aquatic systems on Earth, but how microbial and viral communities are shaped in this special habitat is largely unexplored. In this study, we collected groundwater samples from 23 to 60 m aquifers at Yinchuan Plain, China. In total, 1920 non-reductant viral contigs were retrieved from metagenomes and viromes constructed by Illumina and Nanopore hybrid sequencing. Only 3% of them could be clustered with known viruses, most of which were Caudoviricetes. Coupling 1.2 Tb Hi-C sequencing with CRISPR matching and homology search, we connected 469 viruses with their hosts while some viral clusters presented a broad-host-range trait. Meanwhile, a large proportion of biosynthesis related auxiliary metabolism genes were identified. Those characteristics might benefit viruses for a better survival in this special oligotrophic environment. Additionally, the groundwater virome showed genomic features distinct from those of the open ocean and wastewater treatment facilities in GC distribution and unannotated gene compositions. This paper expands the current knowledge of the global viromic records and serves as a foundation for a more thorough understanding of viruses in groundwater.

Abiotic and biotic constituents of oil sands process-affected waters

The oil sands in Northern Alberta are the largest oil sands in the world, providing an important economic resource for the Canadian energy industry. The extraction of petroleum in the oil sands begins with the addition of hot water to the bituminous sediment, generating oil sands process-affected water (OSPW), which is acutely toxic to organisms. Trillions of litres of OSPW are stored on oil sands mining leased sites in man-made reservoirs called tailings ponds. As the volume of OSPW increases, concerns arise regarding the reclamation and eventual release of this water back into the environment. OSPW is composed of a complex and heterogeneous mix of components that vary based on factors such as company extraction techniques, age of the water, location, and bitumen ore quality. Therefore, the effective remediation of OSPW requires the consideration of abiotic and biotic constituents within it to understand short and long term effects of treatments used. This review summarizes selected chemicals and organisms in these waters and their interactions to provide a holistic perspective on the physiochemical and microbial dynamics underpinning OSPW .

Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting

While decomposition of organic matter by bacteria plays a major role in nutrient cycling in terrestrial ecosystems, the significance of viruses remains poorly understood. Here we combined metagenomics and metatranscriptomics with temporal sampling to study the significance of mesophilic and thermophilic bacteria and their viruses on nutrient cycling during industrial-scale hyperthermophilic composting (HTC). Our results show that virus-bacteria density dynamics and activity are tightly coupled, where viruses specific to mesophilic and thermophilic bacteria track their host densities, triggering microbial community succession via top-down control during HTC. Moreover, viruses specific to mesophilic bacteria encoded and expressed several auxiliary metabolic genes (AMGs) linked to carbon cycling, impacting nutrient turnover alongside bacteria. Nutrient turnover correlated positively with virus-host ratio, indicative of a positive relationship between ecosystem functioning, viral abundances, and viral activity. These effects were predominantly driven by DNA viruses as most detected RNA viruses were associated with eukaryotes and not associated with nutrient cycling during the thermophilic phase of composting. Our findings suggest that DNA viruses could drive nutrient cycling during HTC by recycling bacterial biomass through cell lysis and by expressing key AMGs. Viruses could hence potentially be used as indicators of microbial ecosystem functioning to optimize productivity of biotechnological and agricultural systems.

Potential Auxiliary Metabolic Capabilities and Activities Reveal Biochemical Impacts of Viruses in Municipal Wastewater Treatment Plants

Viruses influence biogeochemical cycles in oceans, freshwater, soil, and human gut through infection and by modulating virocell metabolism through virus-encoded auxiliary metabolic genes (vAMGs). However, the geographical distribution, potential metabolic function, and engineering significance of vAMGs in wastewater treatment plants (WWTPs) remain to be explored. Here, 752 single-contig viral genomes with high confidence, 510 of which belonged to Caudovirales, were recovered from the activated sludge metagenomes of 32 geographically distributed WWTPs. A total of 101 vAMGs involved in various metabolic pathways were identified, the most common of which were the queuosine biosynthesis genes folE, queD, and queE and the sulfur metabolism gene cysH. Phylogenetic analysis and virus-host relationship prediction revealed the probable evolutionary histories of vAMGs involved in carbon (acpP and prsA), nitrogen (amoC), sulfur (cysH), and phosphate (phoH) metabolism, which potentially mediate microbial carbon and nutrient cycling. Notably, 11 of the 38 (28.3%) vAMGs identified in the metagenomes with corresponding metatranscriptomes were transcriptionally expressed, implying an active functional state. This meta-analysis provides the first broad catalog of vAMGs in municipal WWTPs and how they may assist in the basic physiological reactions of their microbial hosts or nutrient cycling in the WWTPs, and therefore, may have important effects on the engineering of wastewater treatment processes.

ViWrap: A modular pipeline to identify, bin, classify, and predict viral-host relationships for viruses from metagenomes

Viruses are increasingly being recognized as important components of human and environmental microbiomes. However, viruses in microbiomes remain difficult to study because of difficulty in culturing them and the lack of sufficient model systems. As a result, computational methods for identifying and analyzing uncultivated viral genomes from metagenomes have attracted significant attention. Such bioinformatics approaches facilitate screening of viruses from enormous sequencing datasets originating from various environments. Though many tools and databases have been developed for advancing the study of viruses from metagenomes, there is a lack of integrated tools enabling a comprehensive workflow and analyses platform encompassing all the diverse segments of virus studies. Here, we developed ViWrap, a modular pipeline written in Python. ViWrap combines the power of multiple tools into a single platform to enable various steps of virus analysis including identification, annotation, genome binning, species- and genus-level clustering, assignment of taxonomy, prediction of hosts, characterization of genome quality, comprehensive summaries, and intuitive visualization of results. Overall, ViWrap enables a standardized and reproducible pipeline for both extensive and stringent characterization of viruses from metagenomes, viromes, and microbial genomes. Our approach has flexibility in using various options for diverse applications and scenarios, and its modular structure can be easily amended with additional functions as necessary. ViWrap is designed to be easily and widely used to study viruses in human and environmental systems. ViWrap is publicly available via GitHub (https://github.com/AnantharamanLab/ViWrap). A detailed description of the software, its usage, and interpretation of results can be found on the website.

Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin

BACKGROUND

Permanently stratified lakes contain diverse microbial communities that vary with depth and so serve as useful models for studying the relationships between microbial community structure and geochemistry. Recent work has shown that these lakes can also harbor numerous bacteria and archaea from novel lineages, including those from the Candidate Phyla Radiation (CPR). However, the extent to which geochemical stratification differentially impacts carbon metabolism and overall genetic potential in CPR bacteria compared to other organisms is not well defined.

RESULTS

Here, we determine the distribution of microbial lineages along an oxygen gradient in Lac Pavin, a deep, stratified lake in central France, and examine the influence of this gradient on their metabolism. Genome-based analyses revealed an enrichment of distinct C1 and CO2 fixation pathways in the oxic lake interface and anoxic zone/sediments, suggesting that oxygen likely plays a role in structuring metabolic strategies in non-CPR bacteria and archaea. Notably, we find that the oxidation of methane and its byproducts is largely spatially separated from methane production, which is mediated by diverse communities of sediment methanogens that vary on the centimeter scale. In contrast, we detected evidence for RuBisCO throughout the water column and sediments, including form II/III and form III-related enzymes encoded by CPR bacteria in the water column and DPANN archaea in the sediments. On the whole, though, CPR bacteria and phages did not show strong signals of gene content differentiation by depth, despite the fact that distinct species groups populate different lake and sediment compartments.

CONCLUSIONS

Overall, our analyses suggest that environmental gradients in Lac Pavin select for capacities of CPR bacteria and phages to a lesser extent than for other bacteria and archaea. This may be due to the fact that selection in the former groups is indirect and depends primarily on host characteristics. Video Abstract.

Biogeochemical sulfur cycling of virus auxiliary metabolic genes involved in Napahai plateau wetland

Virus plays important roles in regulating microbial community structure, horizontal gene transfer, and promoting biological evolution, also augmenting host metabolism during infection via the expression of auxiliary metabolic genes (AMGs), and thus affect biogeochemical cycling in the oceans. As the "kidney of the earth," wetlands have rich biodiversity and abundant resources. Based on metagenomic data, 10 AMGs associated with sulfur cycling, i.e., tusA, moaD, dsrE, soxA, soxB, soxC, soxD, soxX, soxY, and soxZ, were analyzed in Napahai plateau wetland. The phylogenetic trees of AMGs involved in sulfur metabolism from different habitats and host origins were constructed. Combined with principal coordinate analysis, it revealed that most AMGs associated with sulfur metabolism clustered separately, indicating the abundance and uniqueness in this region. The sulfur metabolism pathways involved by AMGs were mainly SOX systems, among which sulfur oxidation was associated with moaD and dsrE genes, while sulfur transport was related to tusA genes. It provides an insight into the biogeochemical sulfur cycling in plateau wetlands and lays the foundation for further study on the co-evolution of virus and host.

Three Phages from a Boreal Lake during Ice Cover Infecting Xylophilus, Caulobacter, and Polaromonas Species

Although the important role of microbes in freshwater is well understood, studies on phage-host systems in such environments during ice cover are completely lacking. Here, we describe the isolation and characterization of three new bacteriophages infecting Xylophilus sp., Caudobacter sp., and Polaromonas sp. from freshwater samples taken under the ice cover of Lake Konnevesi, Finland. Lumi, Kuura, and Tiera bacteriophages have tailed icosahedral virions and double-stranded DNA. Lumi is a siphophage with a genome of 80,496 bp, and Kuura and Tiera are podophages, and their genomes are 43,205 and 45,327 bp in length, resembling viruses in the class Caudoviricetes. Their host ranges were very limited among the winter-isolated bacterial strains from Konnevesi, each infecting only their own hosts. They can infect efficiently at 4 °C, showing that they are adapted to living in lake water under ice cover. Analysis of the viral genome sequences showed that a significant number of the gene products of each virus are unique, indicating that there is unexplored viral diversity in freshwaters. To our knowledge, Lumi and Tiera are the first phages isolated on the Xylophilus sp. and Polaromonas sp. strains, allowing their exploitation in further studies of freshwater bacterial-phage interactions.

Ecological and functional roles of bacteriophages in contrasting environments: marine, terrestrial and human gut

While they are the most abundant biological entities on the planet, the role of bacteriophages (phages) in the microbiome remains enigmatic and understudied. With a rise in the number of metagenomics studies and the publication of highly efficient phage mining programmes, we now have extensive data on the genomic and taxonomic diversity of (mainly) DNA bacteriophages in a wide range of environments. In addition, the higher throughput and quality of sequencing is allowing for strain-level reconstructions of phage genomes from metagenomes. These factors will ultimately help us to understand the role these phages play as part of specific microbial communities, enabling the tracking of individual virus genomes through space and time. Using lessons learned from the latest metagenomic studies, we focus on two explicit aspects of the role bacteriophages play within the microbiome, their ecological role in structuring bacterial populations, and their contribution to microbiome functioning by encoding auxiliary metabolism genes.

Metagenome-Assembled Genomes from Amazonian Soil Microbial Consortia

Here, we report 17 metagenome-assembled genomes (MAGs) recovered from microbial consortia of forest and pasture soils in the Brazilian Eastern Amazon. The bacterial MAGs have the potential to act in important ecological processes, including carbohydrate degradation and sulfur and nitrogen cycling.

Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts

BACKGROUND

Viral-encoded auxiliary metabolic genes (AMGs) are important toolkits for modulating their hosts' metabolisms and the microbial-driven biogeochemical cycles. Although the functions of AMGs have been extensively reported in numerous environments, we still know little about the drivers that shape the viral community-wide AMG compositions in natural ecosystems. Exploring the drivers of viral community-wide AMG compositions is critical for a deeper understanding of the complex interplays among viruses, hosts, and the environments.

RESULTS

Here, we investigated the impact of viral lifestyles (i.e., lytic and lysogenic), habitats (i.e., water, particle, and sediment), and prokaryotic hosts on viral AMG profiles by utilizing metagenomic and metatranscriptomic techniques. We found that viral lifestyles were the most important drivers, followed by habitats and host identities. Specifically, irrespective of what habitats viruses came from, lytic viruses exhibited greater AMG diversity and tended to encode AMGs for chaperone biosynthesis, signaling proteins, and lipid metabolism, which could boost progeny reproduction, whereas temperate viruses were apt to encode AMGs for host survivability. Moreover, the lytic and temperate viral communities tended to mediate the microbial-driven biogeochemical cycles, especially nitrogen metabolism, in different manners via AMGs. When focusing on each lifestyle, we further found clear dissimilarity in AMG compositions between water and sediment, as well the divergent AMGs encoded by viruses infecting different host orders.

CONCLUSIONS

Overall, our study provides a first systematic characterization of the drivers of viral community-wide AMG compositions and further expands our knowledge of the distinct interactions of lytic and temperate viruses with their prokaryotic hosts from an AMG perspective, which is critical for understanding virus-host-environment interactions in natural conditions. Video Abstract.

Borgs are giant genetic elements with potential to expand metabolic capacity

Anaerobic methane oxidation exerts a key control on greenhouse gas emissions1, yet factors that modulate the activity of microorganisms performing this function remain poorly understood. Here we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins through studying groundwater, sediments and wetland soil where methane production and oxidation occur. Four curated, complete genomes are linear, up to approximately 1 Mb in length and share genome organization, including replichore structure, long inverted terminal repeats and genome-wide unique perfect tandem direct repeats that are intergenic or generate amino acid repeats. We infer that these are highly divergent archaeal extrachromosomal elements with a distinct evolutionary origin. Gene sequence similarity, phylogeny and local divergence of sequence composition indicate that many of their genes were assimilated from methane-oxidizing Methanoperedens archaea. We refer to these elements as 'Borgs'. We identified at least 19 different Borg types coexisting with Methanoperedens spp. in four distinct ecosystems. Borgs provide methane-oxidizing Methanoperedens archaea access to genes encoding proteins involved in redox reactions and energy conservation (for example, clusters of multihaem cytochromes and methyl coenzyme M reductase). These data suggest that Borgs might have previously unrecognized roles in the metabolism of this group of archaea, which are known to modulate greenhouse gas emissions, but further studies are now needed to establish their functional relevance.

Viral Complexity

Although traditionally viewed as streamlined and simple, discoveries over the last century have revealed that viruses can exhibit surprisingly complex physical structures, genomic organization, ecological interactions, and evolutionary histories. Viruses can have physical dimensions and genome lengths that exceed many cellular lineages, and their infection strategies can involve a remarkable level of physiological remodeling of their host cells. Virus-virus communication and widespread forms of hyperparasitism have been shown to be common in the virosphere, demonstrating that dynamic ecological interactions often shape their success. And the evolutionary histories of viruses are often fraught with complexities, with chimeric genomes including genes derived from numerous distinct sources or evolved de novo. Here we will discuss many aspects of this viral complexity, with particular emphasis on large DNA viruses, and provide an outlook for future research.

Viral diversity and biogeochemical potential revealed in different prawn-culture sediments by virus-enriched metagenome analysis

As the most numerous biological entities on Earth, viruses affect the microbial dynamics, metabolism and biogeochemical cycles in the aquatic ecosystems. Viral diversity and functions in ocean have been relatively well studied, but our understanding of viruses in mariculture systems is limited. To fill this knowledge gap, we studied viral diversity and potential biogeochemical impacts of sediments from four different prawn-mariculture ecosystems (mono-culture of prawn and poly-culture of prawn with jellyfish, sea cucumber, and clam) using a metagenomic approach with prior virus-like particles (VLPs) separation. We found that the order Caudovirales was the predominant viral category and accounted for the most volume (78.39% of classified viruses). Sediment viruses were verified to have a high diversity by using the construct phylogenetic tree of terL gene, with three potential novel clades being identified. Meanwhile, compared with viruses inhabiting other ecosystems based on gene-sharing network, our results revealed that mariculture sediments harbored considerable unexplored viral diversity and that maricultural species were potentially important drivers of the viral community structure. Notably, viral auxiliary metabolic genes were identified and suggested that viruses influence carbon and sulfur cycling, as well as cofactors/vitamins and amino acid metabolism, which indirectly participate in biogeochemical cycling. Overall, our findings revealed the genomic diversity and ecological function of viral communities in prawn mariculture sediments, and suggested the role of viruses in microbial ecology and biogeochemistry.

Computational Tools for the Analysis of Uncultivated Phage Genomes

Over a century of bacteriophage research has uncovered a plethora of fundamental aspects of their biology, ecology, and evolution. Furthermore, the introduction of community-level studies through metagenomics has revealed unprecedented insights on the impact that phages have on a range of ecological and physiological processes. It was not until the introduction of viral metagenomics that we began to grasp the astonishing breadth of genetic diversity encompassed by phage genomes. Novel phage genomes have been reported from a diverse range of biomes at an increasing rate, which has prompted the development of computational tools that support the multilevel characterization of these novel phages based solely on their genome sequences. The impact of these technologies has been so large that, together with MAGs (Metagenomic Assembled Genomes), we now have UViGs (Uncultivated Viral Genomes), which are now officially recognized by the International Committee for the Taxonomy of Viruses (ICTV), and new taxonomic groups can now be created based exclusively on genomic sequence information. Even though the available tools have immensely contributed to our knowledge of phage diversity and ecology, the ongoing surge in software programs makes it challenging to keep up with them and the purpose each one is designed for. Therefore, in this review, we describe a comprehensive set of currently available computational tools designed for the characterization of phage genome sequences, focusing on five specific analyses: (i) assembly and identification of phage and prophage sequences, (ii) phage genome annotation, (iii) phage taxonomic classification, (iv) phage-host interaction analysis, and (v) phage microdiversity.

A mixed blessing of viruses in wastewater treatment plants

Activated sludge of wastewater treatment plants harbors a very high diversity of both microorganisms and viruses, wherein the latter control microbial dynamics and metabolisms by infection and lysis of cells. However, it remains poorly understood how viruses impact the biochemical processes of activated sludge, for example in terms of treatment efficiency and pollutant removal. Using metagenomic and metatranscriptomic deep sequencing, the present study recovered thousands of viral sequences from activated sludge samples of three conventional wastewater treatment plants. Gene-sharing network indicated that most of viruses could not be assigned to known viral genera, implying activated sludge as an underexplored reservoir for new viruses and viral diversity. In silico predictions of virus-host linkages demonstrated that infected microbial hosts, mostly belonging to bacteria, were transcriptionally active and able to hydrolyze polymers including starches, celluloses, and proteins. Some viruses encode auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and sulfur cycling, and antibiotic resistance genes (ARGs) for resistance to multiple drugs. The virus-encoded AMGs may enhance the biodegradation of contaminants like starches and celluloses, suggesting a positive role for viruses in strengthening the performance of activated sludge. However, ARGs would be disseminated to different microorganisms using viruses as gene shuttles, demonstrating the possibility for viruses to facilitate the spread of antibiotic resistance in the environment. Collectively, this study highlights the mixed blessing of viruses in wastewater treatment plants, and deciphers how they manipulate the biochemical processes in the activated sludge, with implications for both environmental protection and ecosystem security.

Unravelling the ecological complexity of soil viromes: Challenges and opportunities

Viruses are extremely abundant and ubiquitous in soil, and significantly contribute to various terrestrial ecosystem processes such as biogeochemical nutrient cycling, microbiome regulation and community assembly, and host evolutionary dynamics. Despite their numerous dominance and functional importance, understanding soil viral ecology is a formidable challenge, because of the technological challenges to characterize the abundance, diversity and community compositions of viruses, and their interactions with other organisms in the complex soil environment. Viruses may engage in a myriad of biological interactions within soil food webs across a broad range of spatiotemporal scales and are exposed to various biotic and abiotic disturbances. Current studies on the soil viromes, however, often describe the complexity of their tremendous diversity, but lack of exploring their potential ecological roles. In this article, we summarized the major methods to decipher the ecology of soil viruses, discussed biotic and abiotic factors and global change factors that shape the diversity and composition of soil viromes, and the ecological roles of soil viruses. We also proposed a new framework to understand the ecological complexity of viruses from micro to macro ecosystem scales and to predict and unravel their activities in terrestrial ecosystems.

Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing

The microbial biogas network is complex and intertwined, and therefore relatively stable in its overall functionality. However, if key functional groups of microorganisms are affected by biotic or abiotic factors, the entire efficacy may be impaired. Bacteriophages are hypothesized to alter the steering process of the microbial network. In this study, an enriched fraction of virus-like particles was extracted from a mesophilic biogas reactor and sequenced on the Illumina MiSeq and Nanopore GridION sequencing platforms. Metagenome data analysis resulted in identifying 375 metagenome-assembled viral genomes (MAVGs). Two-thirds of the classified sequences were only assigned to the superkingdom Viruses and the remaining third to the family Siphoviridae, followed by Myoviridae, Podoviridae, Tectiviridae, and Inoviridae. The metavirome showed a close relationship to the phage genomes that infect members of the classes Clostridia and Bacilli. Using publicly available biogas metagenomic data, a fragment recruitment approach showed the widespread distribution of the MAVGs studied in other biogas microbiomes. In particular, phage sequences from mesophilic microbiomes were highly similar to the phage sequences of this study. Accordingly, the virus particle enrichment approach and metavirome sequencing provided additional genome sequence information for novel virome members, thus expanding the current knowledge of viral genetic diversity in biogas reactors.

Microbial Ecology of Oxygen Minimum Zones Amidst Ocean Deoxygenation

Oxygen minimum zones (OMZs) have substantial effects on the global ecology and biogeochemical processes of marine microbes. However, the diversity and activity of OMZ microbes and their trophic interactions are only starting to be documented, especially in regard to the potential roles of viruses and protists. OMZs have expanded over the past 60 years and are predicted to expand due to anthropogenic climate change, furthering the need to understand these regions. This review summarizes the current knowledge of OMZ formation, the biotic and abiotic factors involved in OMZ expansion, and the microbial ecology of OMZs, emphasizing the importance of bacteria, archaea, viruses, and protists. We describe the recognized roles of OMZ microbes in carbon, nitrogen, and sulfur cycling, the potential of viruses in altering host metabolisms involved in these cycles, and the control of microbial populations by grazers and viruses. Further, we highlight the microbial community composition and roles of these organisms in oxic and anoxic depths within the water column and how these differences potentially inform how microbial communities will respond to deoxygenation. Additionally, the current literature on the alteration of microbial communities by other key climate change parameters such as temperature and pH are considered regarding how OMZ microbes might respond to these pressures. Finally, we discuss what knowledge gaps are present in understanding OMZ microbial communities and propose directions that will begin to close these gaps.

Biogeochemistry Goes Viral: towards a Multifaceted Approach To Study Viruses and Biogeochemical Cycling

Viruses are ubiquitous on Earth and are keystone components of environments, ecosystems, and human health. Yet, viruses remain poorly studied because most cannot be isolated in a laboratory. In the field of biogeochemistry, which aims to understand the interactions between biology, geology, and chemistry, there is progress to be made in understanding the different roles played by viruses in nutrient cycling, food webs, and elemental transformations. In this commentary, we outline current microbial ecology frameworks for understanding biogeochemical cycling in aquatic ecosystems. Next, we review some existing experimental and computational techniques that are enabling us to study the role of viruses in biogeochemical cycling, using examples from aquatic environments. Finally, we provide a conceptual model that balances limitations of computational tools when combined with biogeochemistry and ecological data. We envision meeting the grand challenge of understanding how viruses impact biogeochemical cycling by using a multifaceted approach to viral ecology.

A new family of "megaphages" abundant in the marine environment

Megaphages, bacteriophages harbouring extremely large genomes, have recently been found to be ubiquitous, being described from a variety of microbiomes ranging from the animal gut to soil and freshwater systems. However, no complete marine megaphage has been identified to date. Here, using both short and long read sequencing, we assembled >900 high-quality draft viral genomes from water in the English Channel. One of these genomes included a novel megaphage, Mar_Mega_1 at >650 Kb, making it one of the largest phage genomes assembled to date. Utilising phylogenetic and network approaches, we found this phage represents a new family of megaphages. Genomic analysis showed Mar_Mega_1 shares relatively few homologues with its closest relatives, but, as with other megaphages Mar_Mega_1 contained a variety of auxiliary metabolic genes responsible for carbon metabolism and nucleotide biosynthesis, including a NADP-dependent isocitrate dehydrogenase [Idh] and nicotinamide-nucleotide amidohydrolase [PncC], which have not previously been identified in megaphages. Mar_Mega_1 was abundant in a marine virome sample and related phages are widely prevalent in the oceans.

Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes

Boreal lakes and ponds produce two-thirds of the total natural methane emissions above the latitude of 50° North. These lake emissions are regulated by methanotrophs which can oxidize up to 99% of the methane produced in the sediments and the water column. Despite their importance, the diversity and distribution of the methanotrophs in lakes are still poorly understood. Here, we used shotgun metagenomic data to explore the diversity and distribution of methanotrophs in 40 oxygen-stratified water bodies in boreal and subarctic areas in Europe and North America. In our data, gammaproteobacterial methanotrophs (order Methylococcales) generally dominated the methanotrophic communities throughout the water columns. A recently discovered lineage of Methylococcales, Candidatus Methylumidiphilus, was present in all the studied water bodies and dominated the methanotrophic community in lakes with a high relative abundance of methanotrophs. Alphaproteobacterial methanotrophs were the second most abundant group of methanotrophs. In the top layer of the lakes, characterized by low CH4 concentration, their abundance could surpass that of the gammaproteobacterial methanotrophs. These results support the theory that the alphaproteobacterial methanotrophs have a high affinity for CH4 and can be considered stress-tolerant strategists. In contrast, the gammaproteobacterial methanotrophs are competitive strategists. In addition, relative abundances of anaerobic methanotrophs, Candidatus Methanoperedenaceae and Candidatus Methylomirabilis, were strongly correlated, suggesting possible co-metabolism. Our data also suggest that these anaerobic methanotrophs could be active even in the oxic layers. In non-metric multidimensional scaling, alpha- and gammaproteobacterial methanotrophs formed separate clusters based on their abundances in the samples, except for the gammaproteobacterial Candidatus Methylumidiphilus, which was separated from these two clusters. This may reflect similarities in the niche and environmental requirements of the different genera within alpha- and gammaproteobacterial methanotrophs. Our study confirms the importance of O2 and CH4 in shaping the methanotrophic communities and suggests that one variable cannot explain the diversity and distribution of the methanotrophs across lakes. Instead, we suggest that the diversity and distribution of freshwater methanotrophs are regulated by lake-specific factors.

Methane-derived carbon flows into host-virus networks at different trophic levels in soil

The concentration of atmospheric methane (CH₄) continues to increase with microbial communities controlling soil-atmosphere fluxes. While there is substantial knowledge of the diversity and function of prokaryotes regulating CH₄ production and consumption, their active interactions with viruses in soil have not been identified. Metagenomic sequencing of soil microbial communities enables identification of linkages between viruses and hosts. However, this does not determine if these represent current or historical interactions nor whether a virus or host are active. In this study, we identified active interactions between individual host and virus populations in situ by following the transfer of assimilated carbon. Using DNA stable-isotope probing combined with metagenomic analyses, we characterized CH₄-fueled microbial networks in acidic and neutral pH soils, specifically primary and secondary utilizers, together with the recent transfer of CH₄-derived carbon to viruses. A total of 63% of viral contigs from replicated soil incubations contained homologs of genes present in known methylotrophic bacteria. Genomic sequences of ¹³C-enriched viruses were represented in over one-third of spacers in CRISPR arrays of multiple closely related Methylocystis populations and revealed differences in their history of viral interaction. Viruses infecting nonmethanotrophic methylotrophs and heterotrophic predatory bacteria were also identified through the analysis of shared homologous genes, demonstrating that carbon is transferred to a diverse range of viruses associated with CH₄-fueled microbial food networks.

Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans to assess viral diversity, virus-host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.

Virus-associated organosulfur metabolism in human and environmental systems

Viruses influence the fate of nutrients and human health by killing microorganisms and altering metabolic processes. Organosulfur metabolism and biologically derived hydrogen sulfide play dynamic roles in manifestation of diseases, infrastructure degradation, and essential biological processes. Although microbial organosulfur metabolism is well studied, the role of viruses in organosulfur metabolism is unknown. Here, we report the discovery of 39 gene families involved in organosulfur metabolism encoded by 3,749 viruses from diverse ecosystems, including human microbiomes. The viruses infect organisms from all three domains of life. Six gene families encode for enzymes that degrade organosulfur compounds into sulfide, whereas others manipulate organosulfur compounds and may influence sulfide production. We show that viral metabolic genes encode key enzymatic domains, are translated into protein, and are maintained after recombination, and sulfide provides a fitness advantage to viruses. Our results reveal viruses as drivers of organosulfur metabolism with important implications for human and environmental health.

Geochemical Stability of Oil Sands Tailings in Mine Closure Landforms

Oil sands surface mining in Alberta has generated over a billion cubic metres of waste, known as tailings, consisting of sands, silts, clays, and process-affected water that contains toxic organic compounds and chemical constituents. All of these tailings will eventually be reclaimed and integrated into one of two types of mine closure landforms: end pit lakes (EPLs) or terrestrial landforms with a wetland feature. In EPLs, tailings deposits are capped with several metres of water while in terrestrial landforms, tailings are capped with solid materials, such as sand or overburden. Because tailings landforms are relatively new, past research has heavily focused on the geotechnical and biogeochemical characteristics of tailings in temporary storage ponds, referred to as tailings ponds. As such, the geochemical stability of tailings landforms remains largely unknown. This review discusses five mechanisms of geochemical change expected in tailings landforms: consolidation, chemical mass loading via pore water fluxes, biogeochemical cycling, polymer degradation, and surface water and groundwater interactions. Key considerations and knowledge gaps with regard to the long-term geochemical stability of tailings landforms are identified, including salt fluxes and subsequent water quality, bioremediation and biogenic greenhouse gas emissions, and the biogeochemical implications of various tailings treatment methods meant to improve geotechnical properties of tailings, such as flocculant (polyacrylamide) and coagulant (gypsum) addition.

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs for oxidation of sulfur and thiosulfate (dsrA, dsrC/tusE, soxC, soxD and soxYZ). Evidence for retention of AMGs during niche-differentiation of diverse phage populations provided evidence that auxiliary metabolism imparts measurable fitness benefits to phages with ramifications for ecosystem biogeochemistry. Gene abundance and expression profiles of AMGs suggested significant contributions by phages to sulfur and thiosulfate oxidation in freshwater lakes and oceans, and a sensitive response to changing sulfur concentrations in hydrothermal environments. Overall, our study provides fundamental insights on the distribution, diversity, and ecology of phage auxiliary metabolism associated with sulfur and reinforces the necessity of incorporating viral contributions into biogeochemical configurations.

Proteomic and Transcriptomic Analysis of Microviridae φX174 Infection Reveals Broad Upregulation of Host Escherichia coli Membrane Damage and Heat Shock Responses

A major part of the healthy human gut microbiome is the Microviridae bacteriophage, exemplified by the model φX174 phage, and their E. coli hosts. Although much has been learned from studying φX174 over the last half-century, until this work, the E. coli host response to infection has never been investigated in detail.

Measuring host-bacteriophage dynamics is an important approach to understanding bacterial survival functions and responses to infection. The model Microviridae bacteriophage φX174 is endemic to the human gut and has been studied for over 70 years, but the host response to infection has never been investigated in detail. To address this gap in our understanding of this important interaction within our microbiome, we have measured host Escherichia coli C proteomic and transcriptomic response to φX174 infection. We used mass spectrometry and RNA sequencing (RNA-seq) to identify and quantify all 11 φX174 proteins and over 1,700 E. coli proteins, enabling us to comprehensively map host pathways involved in φX174 infection. Most notably, we see significant host responses centered on membrane damage and remodeling, cellular chaperone and translocon activity, and lipoprotein processing, which we speculate is due to the peptidoglycan-disruptive effects of the φX174 lysis protein E on MraY activity. We also observe the massive upregulation of small heat shock proteins IbpA/B, along with other heat shock pathway chaperones, and speculate on how the specific characteristics of holdase protein activity may be beneficial for viral infections. Together, this study enables us to begin to understand the proteomic and transcriptomic host responses of E. coli to Microviridae infections and contributes insights to the activities of this important model host-phage interaction.

IMPORTANCE A major part of the healthy human gut microbiome is the Microviridae bacteriophage, exemplified by the model φX174 phage, and their E. coli hosts. Although much has been learned from studying φX174 over the last half-century, until this work, the E. coli host response to infection has never been investigated in detail. We reveal the proteomic and transcriptomic pathways differentially regulated during the φX174 infection cycle and uncover the details of a coordinated cellular response to membrane damage that results in increased lipoprotein processing and membrane trafficking, likely due to the phage antibiotic-like lysis protein. We also reveal that small heat shock proteins IbpA/B are massively upregulated during infection and that these holdase chaperones are highly conserved across the domains of life, indicating that reliance on them is likely widespread across viruses.

Metaviromics coupled with phage-host identification to open the viral 'black box'

Viruses are found in almost all biomes on Earth, with bacteriophages (phages) accounting for the majority of viral particles in most ecosystems. Phages have been isolated from natural environments using the plaque assay and liquid medium-based dilution culturing. However, phage cultivation is restricted by the current limitations in the number of culturable bacterial strains. Unlike prokaryotes, which possess universally conserved 16S rRNA genes, phages lack universal marker genes for viral taxonomy, thus restricting cultureindependent analyses of viral diversity. To circumvent these limitations, shotgun viral metagenome sequencing (i.e., metaviromics) has been developed to enable the extensive sequencing of a variety of viral particles present in the environment and is now widely used. Using metaviromics, numerous studies on viral communities have been conducted in oceans, lakes, rivers, and soils, resulting in many novel phage sequences. Furthermore, auxiliary metabolic genes such as ammonic monooxygenase C and β-lactamase have been discovered in viral contigs assembled from viral metagenomes. Current attempts to identify putative bacterial hosts of viral metagenome sequences based on sequence homology have been limited due to viral sequence variations. Therefore, culture-independent approaches have been developed to predict bacterial hosts using single-cell genomics and fluorescentlabeling. This review focuses on recent viral metagenome studies conducted in natural environments, especially in aquatic ecosystems, and their contributions to phage ecology. Here, we concluded that although metaviromics is a key tool for the study of viral ecology, this approach must be supplemented with phage-host identification, which in turn requires the cultivation of phage-bacteria systems.