Search for: All records

Abstract “Jumbo phages” are tailed phages with genome sizes >200 kbp and physical dimensions reaching up to 0.45 μm. Although jumbo phages represent only a small fraction of the isolated phages to date, metagenomic surveys have shown that they are broadly distributed in a wide range of environments. In this study, we surveyed metagenomic data from aquatic systems and identified 25 genomes from a heretofore-undescribed lineage of jumbo phages with genomes reaching up to 307 kbp. We refer to these phages as “moraphages”, from the Gaelic word ‘mór’, for large. Moraphages represent a diverse lineage with inter-genome average amino acid identity (AAI) ranging from 39 to 95%, and our pan-genomic analysis identified only 26 viral orthologous groups (VOGs) found in at least 80% of the genomes. Our phylogenomic analysis suggests that moraphages are distant relatives of a recently described lineage of huge phages from marine sediment. Moraphages lack much of the genetic machinery found in other lineages of large phages, but they have a range of genes that may be used to take over host cellular machinery and subvert host defenses, such as glutamine synthetases, antitoxin genes, and chaperones. The predicted hosts of most moraphages are members of the phylumBacteroidota, and some encode homologs of the chaperones DnaK and DnaJ that bear evidence of recent gene transfer from members of the orderFlavobacteriales. Our work sheds light on the emerging diversity of large phages that are found across the biosphere. 

ABSTRACT Members of the phylumNucleocytoviricota, which include “giant viruses” known for their large physical dimensions and genome lengths, are a diverse group of dsDNA viruses that infect a wide range of eukaryotic hosts. The genomes of nucleocytoviruses frequently encode eukaryotic signature proteins (ESPs) such as RNA- and DNA-processing proteins, vesicular trafficking factors, cytoskeletal components, and proteins involved in ubiquitin signaling. Despite the prevalence of these genes in many nucleocytoviruses, the timing and number of gene acquisitions remains unclear. While the presence of DNA- and RNA-processing proteins in nucleocytoviruses likely reflects ancient gene transfers, the origins and evolutionary history of other proteins are largely unknown. In this study, we examined the distribution and evolutionary history of a subset of viral-encoded ESPs (vESPs) that are widespread in nucleocytoviruses. Our results demonstrate that most vESPs involved in vesicular trafficking were acquired multiple times independently by nucleocytoviruses at different time points after the emergence of the eukaryotic supergroups, while viral proteins associated with cytoskeletal and ubiquitin system proteins exhibited a more complex evolutionary pattern exhibited by both shallow and deep branching viral clades. This pattern reveals a dynamic interplay between the co-evoluton of eukaryotes and their viruses, suggesting that the viral acquisition of many genes involved in cellular processes has occurred both through ancient and more recent horizontal gene transfers. The timing and frequency of these gene acquisitions may provide insight into their role and functional significance during viral infection.IMPORTANCEThis research is pertinent for understanding the evolution of nucleocytoviruses and their interactions with eukaryotic hosts. By investigating the distribution and evolutionary history of viral-encoded eukaryotic signature proteins, the study reveals gene transfer patterns, highlighting how viruses acquire genes that allow them to manipulate host cellular processes. Identifying the timing and frequency of gene acquisitions related to essential cellular functions provides insights into their roles during viral infections. This work expands our understanding of viral diversity and adaptability, contributing valuable knowledge to virology and evolutionary biology, while offering new perspectives on the relationship between viruses and their hosts. 

Abstract The details surrounding the early evolution of eukaryotes and their viruses are largely unknown. Several key enzymes involved in DNA synthesis and transcription are shared between eukaryotes and large DNA viruses in the phylumNucleocytoviricota, but the evolutionary relationships between these genes remain unclear. In particular, previous studies of eukaryotic DNA and RNA polymerases often show deep-branching clades of eukaryotes and viruses indicative of ancient gene exchange. Here, we performed updated phylogenetic analysis of eukaryotic and viral family B DNA polymerases, multimeric RNA polymerases, and mRNA-capping enzymes to explore their evolutionary relationships. Our results show that viral enzymes form clades that are typically adjacent to eukaryotes, suggesting that they originate prior to the emergence of the Last Eukaryotic Common Ancestor (LECA). The machinery for viral DNA replication, transcription, and mRNA capping are all key processes needed for the maintenance of virus factories, which are complex structures formed by many nucleocytoviruses during infection, indicating that viruses capable of making these structures are ancient. These findings hint at a diverse and complex pre-LECA virosphere and indicate that large DNA viruses may encode proteins that are relics of extinct proto-eukaryotic lineages. 

Abstract Polinton-like viruses (PLVs) are a diverse group of small integrative dsDNA viruses that infect diverse eukaryotic hosts. Many PLVs are hypothesized to parasitize viruses in the phylum Nucleocytoviricota for their own propagation and spread. Here, we analyze the genomes of novel PLVs associated with the occlusion bodies of entomopoxvirus (EPV) infections of two separate lepidopteran hosts. The presence of these elements within EPV occlusion bodies suggests that they are the first known hyperparasites of poxviruses. We find that these PLVs belong to two distinct lineages that are highly diverged from known PLVs. These PLVs possess mosaic genomes, and some essential genes share homology with mobile genes within EPVs. Based on this homology and observed PLV mosaicism, we propose a mechanism to explain the turnover of PLV replication and integration genes. 

Abstract Phages (viruses of bacteria and archaea) are a ubiquitous top-down control on microbial communities by selectively infecting and killing cells. As obligate parasites, phages are inherently linked to processes that impact their hosts’ distribution and physiology, but phages can also be impacted by external, environmental factors, such as UV radiation degrading their virions. To better understand these complex links of phages to their hosts and the environment, we leverage the unique ecological context of the Isthmus of Panama, which narrowly disconnects the productive Tropical Eastern Pacific (EP) and nutrient-poor Tropical Western Atlantic (WA) provinces. We could thus compare patterns of phage and prokaryotic communities at both global scales (between oceans) and local-scales (between habitats within an ocean). Although both phage and prokaryotic communities differed sharply between the oceans, phage community composition did not significantly differ between mangroves and reefs of the WA, while prokaryotic communities were distinct. These results suggest phages are more shaped by dispersal processes than local conditions regardless of spatial scale, while prokaryotes tend to be shaped by local conditions at smaller spatial scales. Collectively, we provide a framework for addressing the co-variability between phages and prokaryotes in marine systems and identifying factors that drive consistent versus disparate trends in community shifts, essential to informing models of biogeochemical cycles that include these interactions. 

Abstract Viruses of the phylumNucleocytoviricota, often referred to as “giant viruses,” are prevalent in various environments around the globe and play significant roles in shaping eukaryotic diversity and activities in global ecosystems. Given the extensive phylogenetic diversity within this viral group and the highly complex composition of their genomes, taxonomic classification of giant viruses, particularly incomplete metagenome-assembled genomes (MAGs) can present a considerable challenge. Here we developed TIGTOG (TaxonomicInformation ofGiant viruses usingTrademarkOrthologousGroups), a machine learning-based approach to predict the taxonomic classification of novel giant virus MAGs based on profiles of protein family content. We applied a random forest algorithm to a training set of 1531 quality-checked, phylogenetically diverseNucleocytoviricotagenomes using pre-selected sets of giant virus orthologous groups (GVOGs). The classification models were predictive of viral taxonomic assignments with a cross-validation accuracy of 99.6% at the order level and 97.3% at the family level. We found that no individual GVOGs or genome features significantly influenced the algorithm’s performance or the models’ predictions, indicating that classification predictions were based on a comprehensive genomic signature, which reduced the necessity of a fixed set of marker genes for taxonomic assigning purposes. Our classification models were validated with an independent test set of 823 giant virus genomes with varied genomic completeness and taxonomy and demonstrated an accuracy of 98.6% and 95.9% at the order and family level, respectively. Our results indicate that protein family profiles can be used to accurately classify large DNA viruses at different taxonomic levels and provide a fast and accurate method for the classification of giant viruses. This approach could easily be adapted to other viral groups. 

Abstract The phylum Nucleocytoviricota includes the largest and most complex viruses known. These “giant viruses” have a long evolutionary history that dates back to the early diversification of eukaryotes, and over time they have evolved elaborate strategies for manipulating the physiology of their hosts during infection. One of the most captivating of these mechanisms involves the use of genes acquired from the host—referred to here as viral homologs or “virologs”—as a means of promoting viral propagation. The best-known examples of these are involved in mimicry, in which viral machinery “imitates” immunomodulatory elements in the vertebrate defense system. But recent findings have highlighted a vast and rapidly expanding array of other virologs that include many genes not typically found in viruses, such as those involved in translation, central carbon metabolism, cytoskeletal structure, nutrient transport, vesicular trafficking, and light harvesting. Unraveling the roles of virologs during infection as well as the evolutionary pathways through which complex functional repertoires are acquired by viruses are important frontiers at the forefront of giant virus research. 

Abstract 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 m), 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 genes 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. 

Vibrio parahaemolyticus(VP) is a bacterial pathogen found in brackish and marine water that infects many marine organisms, such as oysters and shrimp. Consumption of raw or undercooked seafood contaminated withV. parahaemolyticusis a primary cause of seafood-borne gastroenteritis in humans. Due to increasing ocean temperatures,V. parahaemolyticuscontamination of oyster beds in the United States has spread up the east and west coasts to the northern-most states. Promising new research is exploring the isolation of bacteriophages againstV. parahaemolyticuswith a long-term goal to possibly decontaminate oyster beds, thereby expanding the harvest season and allowing for safer consumption of seafood. In this study, store-bought oysters harvested from the Chesapeake Bay in Virginia were used to isolate four bacteriophages with activity against a specificV. parahaemolyticusstrain. A standard double agar overlay plaque assay was used to identify phage activity. After phage isolation, the genomes were sequenced, and transmission electron microscopy (TEM) was performed to visualize the virions. The genomes and TEM images revealed four distinct phages. Three of the phages are distinct isolates that exhibit podovirus-like morphology with short tails and genome sizes of approximately 43 kbp. One phage has siphovirus-like morphology and is a mid-sized tailed phage with a genome size of 80 kbp. Although spot tests performed with the oyster homogenates on up to 10 differentV. parahaemolyticusstrains recovered activity across a wide range of hosts, plaque assays with the isolated phages showed limited host range. Future work will be necessary to determine the viability of using the bacteriophages for elimination ofV. parahaemolyticusin harvested oysters, treatment of aquaculture seed and spat, and/or the environment.