Biology subjects

Anantharaman, K.

Publications and source records attributed to Anantharaman, K..

At least 19 recordsLinked to original sources

bioRxiv2026

CheckAMG: Accurate Identification of Auxiliary Viral Genes with Genome-Language Models

Viruses shape microbial metabolism through auxiliary viral genes (AVGs) that reprogram host metabolism, physiology, and gene regulation during infection. Identifying AVGs is complicated by ambiguous viral versus cellular assignment, inconsistent curation, and reliance on sequence homology that misses divergent functions. Here we present CheckAMG, which pairs annotation-based AVG prediction, curated with a per-gene viral scoring system and ontological mapping of metabolic function, with a finetuned genome-language model for annotation-independent discovery. Benchmarked against DRAM-V and VIBRANT across three ecosystems, CheckAMG produced more strongly supported auxiliary metabolic gene (AMG) calls, and uniquely among AMG tools reports auxiliary physiological (APGs) and regulatory (AReGs) genes. Applied to 1,005,980 fragmented or complete soil and human-gut viral genomes, CheckAMG identified 541,199 AVGs tracking biome-specific protein clusters and functions, including 109,107 proteins with no detectable sequence similarity to any reference database. CheckAMG thus provides a reproducible, scalable framework for identifying the genes through which viruses reprogram host biology.

bioinformatics↗

bioRxiv2026

Widespread phages exhibit depth-structured infection coupled with ammonia oxidation

Ammonia oxidation is a rate-limiting step in the nitrogen cycle, yet viral contributions to this process remain largely unresolved. Here, we identify three genomically distinct groups of amoC-encoding phages (155-338 kilobases in length; termed as amoC-phages) from multiple freshwater lakes in Europe and North America, including the Laurentian Great Lakes. These phages are highly divergent in phylogeny, genome architecture, and gene content, and are predicted to infect two distinct Nitrosomonadaceae ammonia-oxidizing bacterial lineages. The placement of phage-encoded amoC genes across these divergent viral clades indicates independent acquisition of amoC. Time-series and depth-resolved metagenomes and metatranscriptomes reveal persistent and depth-structured distributions of amoC-phages and their predicted hosts, with seasonal mixing periodically reshaping their co-occurrence patterns. Furthermore, virome data from Lake Mendota show that some of the amoC-phages occur as free viral particles, supporting active viral lysis and particle redistribution along the water column. Metatranscriptomes of the Laurentian Great Lakes reveal coordinated expression of phage structural genes (e.g., major capsid protein) together with phage-encoded amoC, indicating active infection in situ. Together, these results support a framework in which amoC-phage infection is depth-structured, seasonally dynamic, and coupled to ammonia-oxidizing bacterial host activity, highlighting viruses as previously overlooked components of freshwater nitrogen cycling.

microbiology↗

bioRxiv2026

Revisiting phage-host inference from metagenome-assembled genomes reveals the need for scaffold-level validation

Accurate phage-host prediction underpins ecological interpretation and experimental validation of uncultivated phages, yet most current approaches rely heavily on metagenome-assembled genomes (MAGs). This reliance implicitly assumes that MAG-level quality metrics, such as completeness and contamination, ensure scaffold-level correctness. Here, we demonstrate that this assumption is frequently violated. Tetranucleotide frequency (TNF) analyses reveal that CRISPR-associated regions often diverge compositionally from their host genomes, increasing the risk of misbinning, while experimentally validated phage-host genome pairs show consistent TNF separation between phages and their hosts, challenging compositional binning assumptions. Through controlled simulations, we further show that the incorporation of substantial amounts of TNF-matched, non-host phage sequences into high-quality MAGs does not substantially alter standard completeness and contamination estimates, rendering such errors largely undetectable. Together, these results expose a systematic and underappreciated source of bias in MAG-based phage-host inference and highlight the need for explicit scaffold-level validation beyond conventional genome-quality metrics. We further propose a practical scaffold-level validation framework that integrates structural linkage and taxonomic consistency to improve the reliability of phage-host inference from MAGs.

microbiology↗

bioRxiv2026

A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination

Closely related prophages are frequently found in phylogenetically distant bacteria in the human gut, despite limited evidence of productive phage infections across broad host ranges. Thus, it remains unclear how the wide distribution of prophages could emerge. Here, we identify a potential mechanism of prophage dissemination. We describe two deeply diverged groups of conjugative megaplasmids (>300 kilobases) in the human gut microbiome, which we term Hodors. Hodors encode conserved replication, partitioning, and type IV secretion systems, together with a complex surface-associated gene module. A subset of Hodors harbor complete, intact prophage genomes, and closely related prophages are detected across phylogenetically distant Bacillota lineages, including both Bacilli and Clostridia. Further analysis indicates that Hodor-associated prophages can exist as extracellular particles and demonstrate their transcriptional activity. Our findings support a model in which conjugative megaplasmids act as composite mobile platforms that disseminate prophage genomes across bacterial lineages, providing a mechanistic explanation for the widespread occurrence of closely related prophages in phylogenetically distant gut bacteria and effectively decoupling lysogenic host range from infective host range.

microbiology↗

bioRxiv2025

Mapping Structural Constraints and Adaptive Potential in a Capsule-Degrading Phage Tailspike Protein

Bacteriophage tailspike proteins (TSPs) degrade bacterial capsules to enable infection, yet the molecular determinants of their function and host range remain unclear. We applied deep mutational scanning (DMS) to the endosialidase TSP of Escherichia coli K1 phage K1F, generating 22,365 single-amino-acid variants using an enhanced ORACLE phage engineering platform. Functional scores revealed the TSP is structurally fragile yet harbors pockets of adaptive flexibility. Mutations within the {beta}-propeller active site uncovered residues accommodating longer sialic acid chains than captured by structural studies, while the {beta}-helix stalk emerged as an adaptive "tuning knob" modulating processivity and specificity. Comparative selections across K1 strains identified discrimination hotspots in {beta}-barrel loops and distal residues outside canonical binding sites, implicating capsule modifications and O-antigen presence as key modulators of host range. By resolving how specific mutations modulate function and host range, this study offers a roadmap for designing phages that overcome capsule-based defenses in pathogenic bacteria.

biochemistry↗

bioRxiv2025

Phage interactions may contribute to the population structure and dynamics of hydrothermal vent microbial symbionts

Deep-sea hydrothermal vent ecosystems are sustained by chemoautotrophic bacteria that symbiotically provide organic matter to their animal hosts through the oxidation of chemical reductants in vent fluids. Hydrothermal vents also support unique viral communities that often exhibit high host-specificity and frequently integrate into host genomes as prophages; however, little is known about the role of viruses in influencing the chemosynthetic symbionts of vent foundation fauna. Here, we present a comprehensive examination of contemporary lysogenic and lytic bacteriophage infections, auxiliary metabolic genes, and CRISPR spacers associated with the intracellular bacterial endosymbionts of snails and mussels at hydrothermal vents in the Lau Basin (Tonga). Our investigation of contemporary phage infection among bacterial symbiont species and across distant vent locations indicated that each symbiont species interacts with different phage species across a large geographic range. However, our analysis of historical phage interactions via assessment of CRISPR spacer content suggested that phages may contribute to strain-level variation within a symbiont species. Surprisingly, prophages were absent from almost all symbiont genomes, suggesting that phage interactions with intracellular symbionts may differ from free-living microbes at vents. Altogether, these findings suggest that species-specific phages play a key role in regulating chemosynthetic symbionts via lytic infections, potentially shaping strain-level diversity and altering the composition and dynamics of symbiont populations.

microbiology↗

bioRxiv2024

Unraveling Keystone Taxa: Interactions Within Microbial Networks and Environmental Dynamics in Lake Mendota

Microbial communities in freshwater ecosystems drive critical biogeochemical cycles, nutrient transformations, and energy flows essential for ecosystem stability. Yet, in the face of accelerating environmental changes, the responses of these microbial networks to spatial and temporal shifts remain underexplored, particularly with rising anoxia. We investigated the microbial ecosystems of Lake Mendota, Wisconsin, USA, through comprehensive metagenomic and metatranscriptomic analyses to elucidate their adaptations to environmental fluctuations across temporal and spatial dimensions. Employing tools like Sparse Inverse Covariance Estimation for Ecological Association Inference (SPIEC-EASI) and Conditional Auto-Regressive Least Absolute Shrinkage and Selection Operator (CARlasso), we identified key microbial taxa and their interactions with environmental parameters such as depth, temperature, pH, and dissolved oxygen. Our findings reveal that biological interactions more than environmental variables shape microbial community assembly and function. Specifically, keystone taxa from the phylum Bacteroidota emerged as pivotal in nutrient cycling and organic matter decomposition, processes crucial for sustaining water quality. Notably, these keystone taxa demonstrate dynamic adaptability, suggesting that microbial networks can rapidly adjust to changes in composition, a trait essential for resilience in the face of warming temperatures and altered precipitation patterns. This study provides critical insights into the resilience and adaptability of freshwater microbiomes, highlighting the role of microbial interactions in maintaining ecosystem health. By understanding how these microbial networks respond to environmental pressures, we can better predict shifts in microbial dynamics and anticipate the broader ecological impacts of climate change on freshwater systems. ImportanceThis research underscores the critical role of keystone taxa in freshwater ecosystems, highlighting how these organisms maintain water quality and contribute to the stability of aquatic environments. Understanding the ecological roles of these taxa is essential for developing strategies to manage ecosystems and conserve freshwater resources, particularly in the face of ongoing environmental challenges like climate change. The insights provided by this study not only enhance our comprehension of microbial interactions but also support effective ecosystem management and conservation efforts.

microbiology↗

bioRxiv2024

V- and VL-Scores Uncover Viral Signatures and Origins of Protein Families

Viruses are key drivers of microbial diversity, nutrient cycling, and co-evolution in ecosystems, yet their study is hindered due to challenges in culturing. Traditional gene-centric methods, which focus on a few hallmark genes like for capsids, miss much of the viral genome, leaving key viral proteins and functions undiscovered. Here, we introduce two powerful annotation-free metrics, V-score and VL-score, designed to quantify the "virus-likeness" of protein families and genomes and create an open-access searchable database, V-Score-Search. By applying V- and VL-scores to public databases (KEGG, Pfam, and eggNOG), we link 38-77% of protein families with viruses, a 9-16x increase over current estimates. These metrics outperform existing approaches, enabling precise detection of viral genomes, prophages, and host-derived auxiliary viral genes (AVGs) from fragmented sequences, and significantly improving genome binning. Remarkably, we identify up to 17x more AVGs, dominated by non-metabolic proteins of unknown function. This innovation unlocks new insights into virus signatures and host interactions, with wide-ranging implications from genomics to biotechnology.

bioinformatics↗

bioRxiv2024

Pangenome analysis of Clostridium scindens: a collection of diverse bile acid and steroid metabolizing commensal gut bacterial strains

Clostridium scindens is a commensal gut bacterium capable of forming the secondary bile acids deoxycholic acid and lithocholic acid from the primary bile acids cholic acid and chenodeoxycholic acid, respectively, as well as converting glucocorticoids to androgens. Historically, only two strains, C. scindens ATCC 35704 and C. scindens VPI 12708, have been characterized in vitro and in vivo to any significant extent. The formation of secondary bile acids is important in maintaining normal gastrointestinal function, in regulating the structure of the gut microbiome, in the etiology of such diseases such as cancers of the GI tract, and in the prevention of Clostridium difficile infection. We therefore wanted to determine the pangenome of 34 cultured strains of C. scindens and a set of 200 metagenome-assembled genomes (MAGs) to understand the variability among strains. The results indicate that the 34 strains of C. scindens have an open pangenome with 12,720 orthologous gene groups, and a core genome with 1,630 gene families, in addition to 7,051 and 4,039 gene families in the accessory and unique (i.e., strain-exclusive) genomes, respectively. The core genome contains 39% of the proteins with predicted metabolic function, and, in the unique genome, the function of storage and processing of information prevails, with 34% of the proteins being in that category. The pangenome profile including the MAGs also proved to be open. The presence of bile acid inducible (bai) and steroid-17,20-desmolase (des) genes was identified among groups of strains. The analysis reveals that C. scindens strains are distributed into two clades, indicating the possible onset of C. scindens separation into two species, confirmed by gene content, phylogenomic, and average nucleotide identity (ANI) analyses. This study provides insight into the structure and function of the C. scindens pangenome, offering a genetic foundation of significance for many aspects of research on the intestinal microbiota and bile acid metabolism.

microbiology↗

bioRxiv2024

Protein Set Transformer: A protein-based genome language model to power high diversity viromics

Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperformed other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrated protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.

bioinformatics↗

bioRxiv2024

Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages

BackgroundViruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored. Phages are classified as virulent or temperate based on their life cycles. Temperate phages adopt the lysogenic mode of infection, where the genome integrates into the host cell genome forming a prophage. Prophages enable viral genome replication without host cell lysis, and often contribute novel and beneficial traits to the host genome. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles. ResultsHere we develop and describe Prophage-DB, a database of prophages, their proteins, and associated metadata that will serve as a resource for viral genomics and microbial ecology. To create the database, we identified and characterized prophages from genomes in three of the largest publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster and taxonomically classify them, and detect their respective auxiliary metabolic genes. In total, we identify and characterize over 350,000 prophages and 35,000 auxiliary metabolic genes. Our prophage database is highly representative based on statistical results and contains prophages from a diverse set of archaeal and bacterial hosts which show a wide environmental distribution. ConclusionProphages are particularly overlooked in viral ecology and merit increased attention due to their vital implications for microbiomes and their hosts. Here, we created Prophage-DB to advance our comprehension of prophages in microbiomes through a comprehensive characterization of prophages in publicly available genomes. We propose that Prophage-DB will serve as a valuable resource for advancing phage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution.

bioinformatics↗

bioRxiv2024

Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems

Viruses are ubiquitous in deep-sea hydrothermal environments, where they exert a major influence on microbial communities and biogeochemistry. Yet, viral ecology and evolution remain understudied in these environments. Here, we identified 49,962 viruses from 52 globally distributed hydrothermal vent samples (10 plumes, 40 deposits, and 2 diffuse flow), and reconstructed 5,708 viral metagenome-assembled genomes (vMAGs), the majority of which were bacteriophages. Hydrothermal viruses were largely endemic. However, some viruses were shared between geographically separated vents, predominantly between the Lau Basin and Brothers Volcano in the Pacific Ocean. Geographically distant viruses often shared proteins related to core functions such as structural proteins, and rarely, proteins of auxiliary functions. Common microbial hosts of viruses included members of Campylobacterota, Alpha-, and Gammaproteobacteria in deposits, and Gammaproteobacteria in plumes. Campylobacterota- and Gammaproteobacteria-infecting viruses reflected variations in hydrothermal chemistry and functional redundancy in their predicted microbial hosts, suggesting that hydrothermal geology is a driver of viral ecology and coevolution of viruses and hosts. Our study indicates that viral ecology and evolution in globally distributed hydrothermal vents is shaped by endemism, and thus may have increased susceptibility to the negative impacts of deep-sea mining and anthropogenic change in ocean ecosystems.

microbiology↗

bioRxiv2024

An expanded metabolic pathway for androgen production by host-associated bacteria

A growing body of literature implicates host-associated microbiota in the modulation of circulating androgen levels in the host, which could have far-reaching implications for androgen-mediated diseases. However, the microbial genetic pathways involved in androgen production remain unknown. Here, we report the first host-associated microbial gene (desF) encoding an enzyme that catalyzes conversion of androstenedione to epitestosterone (epiT) in the gut bacterium, Clostridium scindens. Despite current dogma that epiT is a nuclear androgen-receptor (AR) antagonist, we demonstrate that epiT is a potent androgen, as assessed by its ability to promote prostate cancer cell growth and expression of prostate specific antigen (PSA). We then quantified the desF gene in fecal samples collected from individuals with advanced prostate cancer (rising blood PSA) undergoing androgen deprivation therapy combined with abiraterone acetate and prednisone (AA/P). Strikingly, fecal desF levels were elevated in a subset of individuals progressing on AA/P versus samples taken during AA/P response (stable). Importantly, we observed that AA does not inhibit the bacterial desmolase enzyme that is analogous to the human drug target of AA. We then determined that bacterial isolates from urine or prostatectomy tissue are capable of androgen production. From these isolates we detected 17{beta}-hydroxysteroid dehydrogenase (17{beta}-HSDH) activity, which has not been previously reported in urinary tract bacteria, and discovered the desG gene in urinary isolates encoding 17{beta}-HSDH that catalyzed conversion of androstenedione to testosterone. Applying advanced artificial intelligence and molecular dynamics, we predict the structures and ligand binding to DesF and DesG. Using a novel bioengineered microencapsulation technique, we demonstrate that urinary androgen-producing bacterial strains can also promote prostate cancer cell growth through steroid metabolism. Taken together, our results are a significant advance for steroid microbiology in humans and suggest that these microbial biotransformations should be further studied in the context of androgen-mediated physiological processes and diseases.

microbiology↗

bioRxiv2024

vClassifier: a toolkit for species-level classification of prokaryotic viruses

As the most abundant and diverse biological entities, prokaryotic viruses play pivotal roles in ecological systems. Their taxonomic classification has been instrumental in elucidating their diversity and ecological functions. However, determination of viral taxonomy remains a considerable challenge. Recently developed approaches succeed in assignment of viral taxonomy at higher ranks, such as at the family level and above, but struggle at the subfamily level and below to the genus and species resolutions. Here, we describe the vClassifier toolkit, a phylogeny-informed methodology to provide species-level taxonomic assignments of viruses. We used single-copy marker genes relevant to specific taxa and reference phylogenetic trees for these groups which facilitates direct comparisons with the taxonomic framework of the International Committee on Taxonomy of Viruses (ICTV). Our method demonstrated significant congruence with the ICTV taxonomy, showing 84-91% alignment at the subfamily and genus levels. For species-level classification, our strategy was integrated with average nucleotide identity, yielding a high congruence rate of over 92% with the taxonomic data from the NCBI Virus database. Benchmarking comparisons revealed that vClassifier matches or surpasses other available tools regarding precision and classification success rates. By achieving objectivity and high levels of consistency, vClassifier streamlines the taxonomic categorization of prokaryotic viral genomes. Accurate assignments at the subfamily, genus, and species levels will significantly refine the taxonomic resolution of viruses, fostering a deeper understanding of viral diversity in microbiomes and ecosystems.

evolutionary biology↗

bioRxiv2024

Discarded diversity: Novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills

BackgroundViruses are the most abundant microbial entity on the planet, impacting microbial community structure and ecosystem services. Despite outnumbering Bacteria and Archaea by an order of magnitude, viruses have been comparatively underrepresented in reference databases. Metagenomic examinations have illustrated that viruses of Bacteria and Archaea have been specifically understudied in engineered environments. Here we employed metagenomic and computational biology methods to examine the diversity, host interactions, and genetic systems of viruses predicted from 27 samples taken from three municipal landfills across North America. ResultsWe identified numerous viruses that are not represented in reference databases, including the third largest bacteriophage genome identified to date ([~]678 kbp), and note a cosmopolitan diversity of viruses in landfills that are distinct from viromes in other systems. Host-virus interactions were examined via host CRISPR spacer to viral protospacer mapping which captured hyper-targeted viral populations and six viral populations predicted to infect across multiple phyla. Virally-encoded auxiliary metabolic genes (AMGs) were identified with the potential to augment hosts methane, sulfur, and contaminant degradation metabolisms, including AMGs not previously reported in literature. CRISPR arrays and CRISPR-Cas systems were identified from predicted viral genomes, including the two largest bacteriophage genomes to contain these genetic features. Some virally encoded Cas effector proteins appear distinct relative to previously reported Cas systems and are interesting targets for potential genome editing tools. ConclusionsOur observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for diverse viruses and atypical virus-host dynamics.

microbiology↗

bioRxiv2024

Systematic genome-wide discovery of host factors governing bacteriophage infectivity

Bacterial host factors regulate the infection cycle of bacteriophages. Except for some well-studied host factors (e.g., receptors or restriction-modification systems), the contribution of the rest of the host genome on phage infection remains poorly understood. We developed PHAGEPACK, a pooled assay that systematically and comprehensively measures each host genes impact on phage fitness. PHAGEPACK combines CRISPR interference with phage packaging to link host perturbation to phage fitness during active infection. Using PHAGEPACK, we constructed a genome-wide map of genes impacting T7 phage fitness in permissive E. coli, revealing pathways previously unknown to affect phage packaging. When applied to the non-permissive E. coli O121, PHAGEPACK identified pathways leading to host resistance; their removal increased phage susceptibility up to a billion-fold. Bioinformatic analysis indicates phage genomes carry homologs or truncations of key host factors, potentially for fitness advantage. In summary, PHAGEPACK offers valuable insights into phage-host interactions, phage evolution, and bacterial resistance.

synthetic biology↗

bioRxiv2024

Characterization of sediment and granite hosted deep underground research laboratories reveals diverse microbiome functions, limited temporal variation and substantial genomic conservation

Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts on nuclear waste, CO2 and H2 stored in the subsurface. We carried out the first multi-year study of groundwater microbiomes sampled from defined intervals between 140 and 400 m below the surface of the Horonobe and Mizunami URLs, Japan. We reconstructed draft genomes for >90% of all organisms detected over a four year period. The Horonobe and Mizunami microbiomes are dissimilar, likely because the Mizunami URL is hosted in granitic rock and the Horonobe URL in sedimentary rock. Despite this, hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds and sulfate reduction are well represented functions in microbiomes from both URLs, although methane metabolism is more prevalent at the organic- and CO2-rich Horonobe URL. High fluid flow zones and proximity to subsurface tunnels select for candidate phyla radiation bacteria in the Mizunami URL. We detected near-identical genotypes for approximately one third of all genomically defined organisms at multiple depths within the Horonobe URL. This cannot be explained by inactivity, as in situ growth was detected for some bacteria, albeit at slow rates. Given the current low hydraulic conductivity and groundwater compositional heterogeneity, ongoing inter-site strain dispersal seems unlikely. Alternatively, the Horonobe URL microbiome homogeneity may be explained by higher groundwater mobility during the last glacial period. Genotypically-defined species closely related to those detected in the URLs were identified in three other subsurface environments in the USA. Thus, dispersal rates between widely separated underground sites may be fast enough relative to mutation rates to have precluded substantial divergence in species composition. Species overlaps between subsurface locations on different continents constrain expectations regarding the scale of global subsurface biodiversity. Overall, microbiome and geochemical stability over the study period has important implications for underground storage applications.

microbiology↗

bioRxiv2024

A 20-year time-series of a freshwater lake reveals seasonal dynamics and environmental drivers of viral diversity, ecology, and evolution

Long-term ecological studies are powerful tools to investigate microbiomes and ecosystem change but have mostly ignored viruses. Here, we leveraged a 20-year time-series of a freshwater lake to characterize 1.3 million viral genomes over time, seasonality, and environmental factors. We identified 578 auxiliary metabolic gene (AMG) clusters representing over 150,000 AMGs, the most abundant of which, including psbA for photosynthesis, pmoC for methane oxidation, and katG for hydrogen peroxide decomposition, were consistently represented in viruses across decades and seasons. We observed positive associations and niche differentiation between virus-host pairs during seasonal change including in keystone taxa, Cyanobacteria, methanotrophs, and Nanopelagicales. Environmental constraints, specifically inorganic carbon and ammonium influenced viral abundances over time, and highlighted roles of viruses in both "top-down" and "bottom-up" interactions. Key evolutionary processes shaping gene and genome-wide selection included favored fitness genes, reduced genomic heterogeneity, and dominant sub-populations carrying specific genes. Overall, our study advances understanding of diversity, ecological dynamics, and evolutionary trajectories of viruses in Earths microbiomes and ecosystems.

microbiology↗