Biology subjects

Moniruzzaman, M.

Publications and source records attributed to Moniruzzaman, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Expansive Diversity and Temporal Dynamics of Emerging Polinton-like Viruses in a Marine Ecosystem

Polinton-like viruses (PLVs) are an emerging group of double-stranded DNA viruses of microbial eukaryotes whose ecological roles in marine ecosystems remain poorly understood. Using a five-year monthly viromic time series from the San Pedro Ocean Time-series (SPOT), we investigated the diversity, temporal dynamics, and functional potential of PLVs in a coastal marine ecosystem. We identified 2,355 distinct PLV populations, revealing PLVs to be a highly abundant and diverse component of the marine virosphere. Phylogenetic analyses resolved multiple major PLV clades, including abundant Group X/Trimcap PLVs characterized by triplicate major capsid proteins, supporting the widespread occurrence of this unusual viral architecture in marine PLVs. Approximately half of PLV populations exhibited significant repeatable seasonal dynamics, partitioning into numerous chronotypes that reflect highly modular temporal niches. PLV abundance correlated positively with multiple productivity-linked environmental variables, including nitrate, particulate organic carbon, and primary productivity, suggesting close coupling between PLVs and seasonal ecosystem productivity. Functional analyses further identified diverse auxiliary metabolic genes in many PLV genomes involved in carbohydrate, lipid, redox, and nucleotide metabolism, with strong phylogenetic structuring across PLV clades. Together, these findings demonstrate that PLVs are abundant, functionally diverse, and ecologically dynamic members of marine viral communities, and suggest they are important yet underappreciated regulators of protist ecology and evolution in marine ecosystems.

microbiology↗

bioRxiv2026

Widespread Genomic Islands in Giant Viruses Shape Genome Plasticity and Mosaicism

Giant viruses in the phylum Nucleocytoviricota possess exceptionally large and mosaic genomes, yet the mechanisms underlying their remarkable genomic plasticity remain poorly understood. Genomic islands are large dynamic genomic regions that are major drivers of genome diversification and adaptation in bacteria. However, their contribution to genome evolution in giant viruses remains largely unexplored. Here, we systematically characterize the genomic island landscape of giant viruses using 369 high-quality genomes spanning cultured isolates and long-read metagenome-assembled genomes. We identify 307 genomic islands across >50% of the genomes, demonstrating that these regions are pervasive across Nucleocytoviricota diversity. Giant virus genomic islands are frequently associated with genomic hypervariability and enriched in genes involved in host interaction, particularly surface adhesion proteins, suggesting key roles in host adaptation during virus-host arms race. Comparative analyses further reveal these islands to be major hotspots of genome diversification, exhibiting frequent gain, loss, and rearrangement even among highly similar genomes, with evidence that entire island regions can be exchanged among closely related viral populations. Notably, 37% of genomic islands are enriched in bacterial homologs, and several exhibit striking synteny with genomic regions recovered from environmentally co-occurring bacterial genomes, supporting large-scale genetic exchange between bacteria and giant viruses. Together, these findings identify genomic islands as pervasive and dynamic drivers of giant virus genome evolution, providing a mechanistic framework for genome plasticity, mosaicism, and adaptive potential of giant viruses.

ecology↗

bioRxiv2025

Genes on the Move: Exploring the Resistome of Viable Isolates from a First Nation Community in Manitoba

Despite wastewater treatment plants (WWTPs) and oxidation lagoons (OL) being designed for pollutant and pathogen removal, these systems can also serve as environments conducive to the exchange of mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) among microorganisms. This context facilitates the dissemination of antimicrobial resistance (AMR) among both pathogenic and non-pathogenic environmental bacteria, as well as phage populations, within these facilities. To enhance understanding of AMR dynamics in wastewater, our study examined the resistome of bacterial isolates recovered from a OL in a First Nation (FN) community in Manitoba, Canada. Thirty-five samples were collected from all OL stages, including raw sewage, lagoons, submerged attached growth reactor (SAGR), UV-treated effluent, and an upstream control site, from September 2022 to April 2023. Whole genome sequencing of 58 viable isolates was performed using Oxford Nanopore MinION, with genomes reconstructed via de novo assembly. The isolates corresponded to the following genera: Aeromonas 50.87% , Serratia 15.78%, Pantoea and Escherichia 7.01% each, Lelliottia 5.26%, Rahnella, Enterobacter and Buttiauxella 3.50% each, and finally Acinetobacter, Yersinia and Citrobacter 1.75%. Furthermore, a total of 32,559 elements were classified as ARGs. MGEs carrying ARGs were detected in 72.72% of the isolates. ARGs conferring resistance to macrolides, tetracyclines, and fluoroquinolones demonstrated a notable presence within MGEs (plasmids and bacteriophages) identified throughout the facilitys stages. This research represents a non-invasive approach, enabling an in-depth exploration of AMR dynamics by discerning the resistome profiles of bacteria residing within a rural OL facility from a FN community. ImportanceOLs commonly found in rural and Indigenous communities in Canada, are crucial for mitigating environmental hazards and safeguarding public health. Paradoxically, these systems can also serve as hotspots for the dissemination of ARGs and MGEs, thereby exacerbating AMR. The persistence of ARGs within both pathogenic and non-pathogenic bacteria, often carried on MGEs including phages, in treated effluents raises significant concerns about the environmental impact and public health. This study offers fundamental insights into the unique dynamics of AMR within OLs serving a First Nation community in Manitoba. Understanding these specific dynamics is crucial for developing robust monitoring frameworks and implementing targeted, sustainable strategies to mitigate the public health and environmental risks posed by AMR in these often-underserved remote settings.

microbiology↗

bioRxiv2025

Giant viruses specific to deep oceans show persistent presence and activity

Giant viruses (GVs) of the phyla Nucleocytoviricota and Mirusviricota are large double-stranded DNA viruses that infect diverse eukaryotic hosts and impact biogeochemical cycles. Their diversity and ecological roles have been well studied in the photic layer of the ocean, but less is known about their activity, population dynamics, and adaptive strategies in the aphotic layers. Here, we conducted eight seasonal time-series samplings of the surface and mesopelagic layers at a coastal site in Muroto, Japan, and integrated 18S metabarcoding, metagenomic, and metatranscriptomic data to investigate deep-sea GVs and their potential hosts. The analysis identified 48 GV genomes including six that were exclusively detected in the mesopelagic layer. Notably, these mesopelagic-specific GVs showed persistent activity across seasons. To investigate the global deep-sea-specific GV distribution, we compiled GV reference genomic data from the OceanDNA MAG project and other resources, and analyzed 1,890 marine metagenomes. This revealed 101 deep-sea-specific GVs, distributed across the GV phylogenetic tree, indicating that adaptation to deep-sea environments has occurred in multiple lineages. One clade enriched with deep-sea-specific GVs included one GV identified in our Muroto sampling, which displayed a wide geographic distribution. Seventy-six KEGG orthologs and 74 Pfam domains were specifically enriched in deep-sea-specific GVs, encompassing functions related to the ubiquitin system, energy metabolism, and nitrogen acquisition. These findings support the scenario that distinct GV lineages have adapted to hosts in aphotic marine environments by altering their gene repertoire to thrive in this unique habitat. IMPORTANCEGiant viruses are widespread in the ocean surface and are key in shaping marine ecosystems by infecting phytoplankton and other protists. However, little is known about their activity and adaptive strategies in deep-sea environments. In this study, we performed metagenomic and metatranscriptomic analyses of seawater samples collected from a coastal site in Japan and discovered giant virus genomes showing persistent transcriptional activity across seasons in the deep-sea water. Using a global marine dataset, we further uncovered the widespread existence of deep-sea-specific giant viruses and characterized their unique gene repertoire, which likely facilitates adaptation to the limited availability of light and organic compounds in the aphotic zone. These findings expand our understanding of giant virus ecology in the dark ocean.

genomics↗

bioRxiv2024

BEREN: A bioinformatic tool for recovering Giant viruses, Polinton-like Viruses, and Virophages in metagenomic data

Viruses in the kingdom Bamfordvirae, specifically giant viruses (NCLDVs) in the phylum Nucleocytoviricota and smaller members in the Preplasmiviricota phylum, are widespread and important groups of viruses that infect eukaryotes. While viruses in this kingdom such as giant viruses, polinton-like viruses, and virophages have gained large interest from researchers in recent years, there is still a lack of streamlined tools for the recovery of their genomes from metagenomic datasets. Here, we present BEREN, a comprehensive bioinformatic tool to unlock the diversity of these viruses in metagenomes through five modules for NCLDV genome, contig, and marker gene recovery, metabolic protein annotation, and Preplasmiviricota genome identification and annotation. BERENs performance was benchmarked against other mainstream virus recovery tools using a mock metagenome, demonstrating superior recovery rates of NCLDV contigs and Preplasmiviricota genomes. Applied to a real-world dataset from the Baltic Sea, BEREN identified diverse Bamfordvirae members, giving insight into viral interactions and metabolic functions in this region. Overall, BEREN offers a user-friendly, transparent bioinformatic solution for studying the ecological and functional roles of these eukaryotic viruses, facilitating broader access to their metagenomic analysis.

microbiology↗

bioRxiv2024

Latent infection of an active giant endogenous virus in a unicellular green alga

Latency is a common strategy in a wide range of viral lineages, but its prevalence in giant viruses remains unknown. Here we describe the activity and viral production from a 617 kbp integrated giant viral element in the model green alga Chlamydomonas reinhardtii. We resolve the integrated viral region using long-read sequencing and show that viral particles are produced and released in otherwise healthy cultures. A diverse array of viral-encoded selfish genetic elements are expressed during GEVE reactivation and produce proteins that are packaged in virions. In addition, we show that field isolates of Chlamydomonas sp. harbor latent giant viruses related to the C. reinhardtii GEVE that exhibit similar infection dynamics, demonstrating that giant virus latency is prevalent in natural host communities. Our work reports the largest temperate virus documented to date and the first active GEVE identified in a unicellular eukaryote, substantially expanding the known limits of viral latency.

microbiology↗

bioRxiv2024

Phylogenetic proximity drives temporal succession of marine giant viruses in a five-year metagenomic time-series

Nucleocytoplasmic Large DNA Viruses (NCLDVs, also called giant viruses) are widespread in marine systems and infect a broad range of microbial eukaryotes (protists). Recent biogeographic work has provided global snapshots of NCLDV diversity and community composition across the worlds oceans, yet little information exists about the guiding rules underpinning their community dynamics over time. We leveraged a five-year monthly metagenomic time-series to quantify the community composition of NCLDVs off the coast of Southern California and characterize these populations temporal dynamics. NCLDVs were dominated by Algavirales (Phycodnaviruses, 59%) and Imitervirales (Mimiviruses, 36%). We identified clusters of NCLDVs with distinct classes of seasonal and non-seasonal temporal dynamics. Overall, NCLDV population abundances were often highly dynamic with a strong seasonal signal. The Imitervirales group had highest relative abundance in the more oligotrophic late summer and fall, while Algavirales did so in winter. Generally, closely related strains had similar temporal dynamics, suggesting that evolutionary history is a key driver of the temporal niche of marine NCLDVs. However, a few closely-related strains had drastically different seasonal dynamics, suggesting that while phylogenetic proximity often indicates ecological similarity, occasionally phenology can shift rapidly, possibly due to host-switching. Finally, we identified distinct functional content and possible host interactions of two major NCLDV orders-including connections of Imitervirales with primary producers like the diatom Chaetoceros and widespread marine grazers like Paraphysomonas and Spirotrichea ciliates. Together, our results reveal key insights on season-specific effect of phylogenetically distinct giant virus communities on marine protist metabolism, biogeochemical fluxes and carbon cycling.

ecology↗

bioRxiv2024

Expansion of the genomic and functional diversity of global ocean giant viruses

Giant viruses (GVs) play crucial roles in the global ocean microbial food web and biogeochemistry by infecting protists. Traditionally, insights into GV ecology and functions have been limited to culture-based studies. However, recent metagenomic advances have uncovered over 1,800 new GV genomes from the worlds oceans. While this rapid increase in genomic information marks an impressive advance for the field, it is nowhere close to the extensive genomic information available for other marine entities - e.g., prokaryotes and their virome. Addressing this gap, we present 230 novel, high-quality GV genomes and 398 partial genomes from nine global ocean datasets using an open-source bioinformatic workflow we developed. Notably, we identified numerous GV genomes from the Baltic Sea, offering insights into their phylogenomics, metabolic potential, and environmental drivers in one of the largest brackish water ecosystems. We discovered new GV functions, including photosynthetic proteins, and identified a significant functional divide between the Imitervirales and Algavirales orders. Additionally, we evaluated best practices for GV genome recovery from metagenomic datasets through a case study on the Baltic Sea dataset. Our study significantly expands the marine GV genomic and functional diversity, broadening our understanding of their roles in the food web and biogeochemistry.

microbiology↗

bioRxiv2024

Active prokaryotic and eukaryotic viral ecology across spatial scale in a deep-sea brine pool

Deep-sea brine pools represent rare, extreme environments that focus biodiversity at bathyal to abyssal depths. Despite their small size and distribution, brine pools represent important ecosystems to study because they provide unique insight into the limits of life on Earth, and by analogy, the plausibility of life beyond it. A distinguishing feature of many brine pools is the presence of thick benthic microbial mats which develop at the brine-seawater interface. While these bacterial and archaeal communities have received moderate attention, little is known about the viral communities and their interactions with host populations in these environments. To bridge this knowledge gap, we leveraged metagenomic and metatranscriptomic data from three distinct zones within the NEOM brine pool system (Gulf of Aqaba) to gain insights into the active viral ecology around the pools. Here, we report a remarkable diversity and activity of viruses of all nucleic acid types and genome sizes that infect prokaryotic and eukaryotic hosts in this environment. These include giant viruses (phylum: Nucleocytoviricota), RNA viruses, jumbo phages, and polinton-like viruses (PLVs). Many of these appeared to form distinct clades showing the possibility of untapped viral diversity in the brine pool ecosystem. Zone-specific differences in viral community composition and infection strategy were also observed with lysogenic phages seeming to dominate the bacterial mat further away from the pools center. Through host matching, viruses infecting metabolically important bacteria and archaea were observed - including a linkage between a jumbo phage and a key manganese-oxidizing and arsenic-metabolizing bacterium. Our findings shed light on the role of viruses in modulating the brine pool microbial community dynamics and biogeochemistry through revealing novel viral diversity, host-virus associations, and spatial-scale heterogeneity in viral dynamics in these extreme environments. These results will provide crucial foundation for further investigation into the adaptations of viruses and their microbial hosts in extreme habitats in the marine ecosystem.

microbiology↗

bioRxiv2023

In vivo and in silico experiment on Mitragyna speciosa offers new insight of antidiabetic potentials

Diabetes Mellitus (DM) is a serious metabolic disease with several treatments available for managing it, however, they can be expensive and have side effects. Medicinal plants have been used for many years to treat numerous diseases. Mitragyna speciosa (M. speciosa) plant has been shown to have anti-diabetic properties in preclinical studies. Hence, this study aimed to investigate the phytochemical compositions and anti-diabetic effects of M. speciose, using both in vivo and in silico approaches. In the in vivo study, experimental diabetes was induced in Swiss albino mice using the drug alloxan (150 mg/kg). Four groups of diabetic mice were taken. Two of the groups were given extracts at doses of 200 mg/kg and 400 mg/kg respectively. Diabetic mice treated with the reference drug, glibenclamide (5mg/kg) were chosen as a positive control, and mice with only vehicles were considered as a negative control. The Oral Glucose Tolerance Test (OGTT) and the acute toxicity test were performed. In the in silico study, molecular docking and dynamics were performed for the identification of the plant compounds that could effectively bind with the DPP4 receptor. Analysis of the study suggested that the lethal dose (LD50) values were greater than 2000 mg/kg, indicating that a dose below this level can be selected. The OGTT results showed that both doses of M. speciose extracts significantly reduced blood glucose levels (P<0.0001). However, neither dose exhibited a significantly higher blood glucose reduction compared to glibenclamide (5 mg/kg) (P > 0.05). Phytochemical screening and the ADMET profile analysis suggested four key compounds: Mitragynine, Corynantheidine, Corynoxine, and Speciociliatine in M. speciosa. The molecular docking analysis revealed these four compounds as potential antidiabetic agents considering their high binding affinity to the DPP4 receptor. These compounds were also found to be stable in the DPP4 binding pocket, as evidenced by the molecular dynamics simulation. Lastly, it can be demonstrated that the in silico experiments confirmed M. speciosa extracts to be capable of reducing blood glucose levels because of the presence of compounds.

pharmacology and toxicology↗

bioRxiv2023

Widespread Occurrence and Diverse Origins of Polintoviruses Influence Lineage-specific Genome Dynamics in Stony Corals

Stony corals (Order Scleractinia) are central to vital marine habitats known as coral reefs. Numerous stressors in the Anthropocene are contributing to the ongoing decline in coral reef health and coverage. While viruses are established modulators of marine microbial dynamics, their interactions within the coral holobiont and impact on coral health and physiology remain unclear. To address this key knowledge gap, we investigated diverse stony coral genomes for endogenous viruses. Our study uncovered a remarkable number of integrated viral elements recognized as Polintoviruses (Class Polintoviricetes) in 30 Scleractinia genomes, with several species harboring hundreds to thousands of polintoviruses. We reveal massive paralogous expansion of polintoviruses in stony corals, alongside presence of integrated elements closely related to Polinton-like viruses (PLVs), a group of viruses that exist as free virions. These results suggest multiple integrations of polintoviruses and PLV-relatives, followed by their paralogous expansions shaped stony coral genomes. Gene expression analysis reveals all polintovirus structural and non-structural hallmark genes are expressed, strongly supporting free virion production from polintoviruses. Our results revealing a significant polintovirus diversity across the Scleractinia order open a new research avenue into their possible roles in disease, genomic plasticity, and environmental adaptation in this key group of organisms.

genomics↗

bioRxiv2023

Phylogenetic diversity and functional potential of large and cell-associated viruses in the Bay of Bengal

The Bay of Bengal (BoB), the largest bay in the world, provides valuable ecosystem services such as fishing and recreation to millions of people living along its coast and has a significant economic value. The BoB is impacted by various environmental factors such as seasonal monsoons and multiple freshwater inputs, and this region is particularly vulnerable to sea-level rise and increased frequency of devastating cyclones that are predicted to be exacerbated due to global climate change. These factors are also compounded by anthropogenic influences from tourism and development, making it an important ecosystem to understand and study from a global change perspective. Despite its importance, microbial diversity and ecology have remained largely understudied in this region. In this study, we describe the diversity and putative functional importance of large and cell-associated (that is, originating from the cellular size fraction) viruses from two coastal sites in the BoB, with an emphasis on giant viruses and large phages. Sites chosen for this study include Coxs Bazar, a populated beach with multiple freshwater inputs, and Saint Martin Island, a resort island that has considerably less human influence compared to Coxs Bazar. Through metagenomic sequencing, we were able to identify a more abundant and more diverse viral community at Coxs Bazar consisting of many viruses that are indicators of freshwater intrusion and runoff. Overall, 1962 putative phage genome bins were obtained ranging from 10 - 655 kilobase pairs (kbp) in sizes. Of these genomes, 16 from Saint Martin were found to be larger than 100kbp which we deemed "large" phages, and we were able to reconstruct a phylogeny of these large phages using the TerL gene as a marker. This phylogeny revealed clades enriched in large phages and a high diversity of large phage candidates in the Bay of Bengal coast. Protein annotation analysis showed a wide variety of functionality from both sites with more auxiliary metabolic genes (AMGs) found in the Coxs Bazar viral community. Five giant virus (Phylum Nucleocytoviricota) genomes were also reconstructed from Coxs Bazar and identified as belonging to the orders Imitervirales and Pandoravirales. These genomes ranged from 83 - 876 kbp in size and contained a wide range of encoded functionalities. To the best of our knowledge, our study represents the first insights on the phylogenetic and functional diversity of viruses in the Bay of Bengal. These results thus provide an important foundation for further studies on the impact of host-virus interactions on biogeochemical cycles and microbial food web in this understudied marine environment.

microbiology↗

bioRxiv2023

Exploring Microbial Diversity and Functional Potential along the Bay of Bengal Coastline in Bangladesh: Insights from Amplicon Sequencing and Shotgun Metagenomics

Although the Bay of Bengal (BoB) is the worlds largest bay, possessing distinct physiochemical properties, it has garnered little research focus concerning its microbial diversity and ecological importance. Here, we present amplicon (16S and 18S) profiling and shotgun metagenomics data regarding microbial communities from BoBs eastern coast, viz., Saint Martin and Coxs Bazar, Bangladesh. From the 16S sequencing data, Proteobacteria appeared to be the dominant phylum in both locations, with Alteromonas, Methylophaga, Anaerospora, Marivita, and Vibrio dominating in Coxs Bazar and Pseudoalteromonas, Nautella, Marinomonas, Vibrio, and Alteromonas dominating the Saint Martin site. From the 18S sequencing data, Ochrophyta, Chlorophyta, and Protalveolata appeared among the most abundant eukaryotic divisions in both locations, with significantly higher abundance of Choanoflagellida, Florideophycidae, and Dinoflagellata in Coxs Bazar. Functional annotations revealed that the microbial communities in these samples harbor genes for biofilm formation, quorum sensing, xenobiotics degradation, antimicrobial resistance, and a variety of other processes. Together, these results provide the first molecular insight into the functional and phylogenetic diversity of microbes along the BoB coast of Bangladesh and lay the foundation for further in-depth assessment of microbial community dynamics and functional potential in the context of global change in this region.

microbiology↗

bioRxiv2023

Assessing the biogeography of marine giant viruses in four oceanic transects

Viruses of the phylum Nucleocytoviricota are ubiquitous in ocean waters and play important roles in shaping the dynamics of marine ecosystems. In this study, we leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to investigate the biogeography of these viruses in marine environments. We identified 330 viral genomes, including 212 in the order Imitervirales and 54 in the order Algavirales. We found that most viruses appeared to be prevalent in shallow waters (<150 meters), and that viruses of the Mesomimiviridae (Imitervirales) and Prasinoviridae (Algavirales) are by far the most abundant and diverse groups in our survey. Five mesomimiviruses and one prasinovirus are particularly widespread in oligotrophic waters; annotation of these genomes revealed common stress response systems, photosynthesis-associated genes, and oxidative stress modulation that may be key to their broad distribution in the pelagic ocean. We identified a latitudinal pattern in viral diversity in one cruise that traversed the North and South Atlantic Ocean, with viral diversity peaking at high latitudes of the northern hemisphere. Community analyses revealed three distinct Nucleocytoviricota communities across latitudes, categorized by latitudinal distance towards the equator. Our results contribute to the understanding of the biogeography of these viruses in marine systems.

microbiology↗

bioRxiv2022

Conformational restriction shapes inhibition of a multidrug efflux adaptor protein

Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system from Escherichia coli, AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and {beta} domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.

biochemistry↗

bioRxiv2021

Endogenous giant viruses shape intraspecies genomic variability in the model green alga Chlamydomonas reinhardtii

Chlamydomonas reinhardtii is an important eukaryotic alga that has been studied as a model organism for decades. Despite extensive history as a model system, phylogenetic and genetic characteristics of viruses infecting this alga have remained elusive. We analyzed high-throughput genome sequence data of C. reinhardtii field isolates, and in six we discovered sequences belonging to endogenous giant viruses that reach up to several hundred kilobases in length. In addition, we have also discovered the entire genome of a closely related giant virus that is endogenized within the genome of Chlamydomonas incerta, the closest sequenced phylogenetic relatives of C. reinhardtii. Endogenous giant viruses add hundreds of new gene families to the host strains, highlighting their contribution to the pangenome dynamics and inter-strain genomic variability of C. reinhardtii. Our findings suggest that the endogenization of giant viruses can have important implications for structuring the population dynamics and ecology of protists in the environment.

microbiology↗

bioRxiv2021

A Phylogenomic Framework for Charting the Diversity and Evolution of Giant Viruses

Large DNA viruses of the phylum Nucleocytoviricota have recently emerged as important members of ecosystems around the globe that challenge traditional views of viral complexity. Numerous members of this phylum that cannot be classified within established families have recently been reported, and there is presently a strong need for a robust phylogenomic and taxonomic framework for these viruses. Here we report a comprehensive phylogenomic analysis of the Nucleocytoviricota, present a set of giant virus orthologous groups (GVOGs) together with a benchmarked reference phylogeny, and delineate a hierarchical taxonomy within this phylum. We show that the majority of Nucleocytoviricota diversity can be partitioned into 6 orders, 32 families, and 344 genera, substantially expanding the number of currently recognized taxonomic ranks for these viruses. We integrate our results within a megataxonomy that has been adopted for all viruses to establish a unifying framework for the study of Nucleocytoviricota diversity, evolution, and environmental distribution.

microbiology↗

bioRxiv2021

High Transcriptional Activity and Diverse Functional Repertoires of Hundreds of Giant Viruses in a Coastal Marine System

Viruses belonging to the Nucleocytoviricota phylum are globally-distributed and include members with notably large genomes and complex functional repertoires. Recent studies have shown that these viruses are particularly diverse and abundant in marine systems, but the magnitude of actively replicating Nucleocytoviricota present in ocean habitats remains unclear. In this study, we compiled a curated database of 2,431 Nucleocytoviricota genomes and used it to examine the gene expression of these viruses in a 2.5-day metatranscriptomic time-series from surface waters of the California Current. We identified 145 viral genomes with high levels of gene expression, including 90 Imitervirales and 49 Algavirales viruses. In addition to recovering high expression of core genes involved in information processing that are commonly expressed during viral infection, we also identified transcripts of diverse viral metabolic genes from pathways such as glycolysis, the TCA cycle, and the pentose phosphate pathway, suggesting that virus-mediated reprogramming of central carbon metabolism is common in oceanic surface waters. Surprisingly, we also identified viral transcripts with homology to actin, myosin, and kinesin domains, suggesting that viruses may use them to manipulate host cytoskeletal dynamics during infection. We performed phylogenetic analysis on the virus-encoded myosin and kinesin proteins, which demonstrated that most belong to deep-branching viral clades, but that others appear to have been acquired from eukaryotes more recently. Our results highlight a remarkable diversity of active Nucleocytoviricota in a coastal marine system and underscore the complex functional repertoires expressed by these viruses during infection. ImportanceThe discovery of giant viruses has transformed our understanding of viral complexity. Although viruses have traditionally been viewed as filterable infectious agents that lack metabolism, giant viruses can reach sizes rivalling cellular lineages and possess genomes encoding central metabolic processes. Recent studies have shown that giant viruses are widespread in aquatic systems, but the activity of these viruses and the extent to which they reprogram host physiology in situ remains unclear. Here we show that numerous giant viruses consistently express central metabolic enzymes in a coastal marine system, including components of glycolysis, the TCA cycle, and other pathways involved in nutrient homeostasis. Moreover, we found expression of several viral-encoded actin, myosin, and kinesin genes, indicating viral manipulation of the host cytoskeleton during infection. Our study reveals a high activity of giant viruses in a coastal marine system and indicates they are a diverse and underappreciated component of microbial diversity in the ocean.

microbiology↗