Novel RNA viruses in oysters revealed by virome

Novel viruses discovered in metatranscriptomic analysis of farmed barramundi in Asia and Australia

Barramundi aquaculture is at risk of severe disease outbreaks and massive production losses. Here we used bioinformatics to screen 84 farmed barramundi transcriptomes to identify novel viruses that could threaten barramundi aquaculture and to establish a barramundi aquaculture virome. We discovered five novel viruses: latid herpesvirus 1 (LatHV-1) from the Alloherpesviridae family, barramundi parvovirus 1 (BParV1) from the Parvoviridae family, barramundi calicivirus 1 (BCaV1) from the Caliciviridae family, and barramundi associated picorna-like virus 1 and 2 (BPicV1 and BPicV2) from the Picornaviridae family. LatHV-1, BCaV1, and BParV1 are closely related to pathogenic viruses found in other fish species that can cause mass mortality in farms. To aid in future viral surveillance, we also designed and successfully tested an RT-PCR assay for the detection of BCaV1. Overall, we discovered a range of pathogenic viruses in barramundi aquaculture, paving the way for developing effective detection methods to assist early outbreak management.

Enormous diversity of RNA viruses in economic crustaceans

Crustaceans are important food sources worldwide and possess significant ecological status in the marine ecosystem. However, our understanding of the diversity and evolution of RNA viruses in crustaceans, especially in economic crustaceans, is still limited. Here, 106 batches of economic crustaceans including 13 species were collected from 24 locations in China during 2016-2021. We identified 90 RNA viruses, 69 of which were divergent from the known viruses. Viral transcripts were assigned to 18 different viral families/clades and three unclassified groups. Among the identified viruses, five were double-stranded RNA viruses, 74 were positive-sense single-stranded RNA (+ssRNA) viruses, nine were negative-sense single-stranded RNA (-ssRNA) viruses, and two belonged to an unclassified RNA virus group. Phylogenetic analyses showed that crustacean viruses were often clustered with viruses identified from invertebrates. Remarkably, most crustacean viruses were closely related to those from different host species along the same food chain or ecological aquatic niche. In addition, the genome structures of the newly discovered picornaviruses exhibited remarkable diversity. Our study significantly expands the diversity of viruses in important economic crustaceans and provides essential data for the risk assessment of the pathogens spreading in the global aquaculture industry.

IMPORTANCE

The study delves into the largely uncharted territory of RNA viruses in crustaceans, which are not only vital for global food supply but also play a pivotal role in marine ecosystems. Focusing on economic crustaceans, the research uncovers 90 RNA viruses, with 69 being potentially new to science, highlighting the vast unknown viral diversity within these marine organisms. The findings reveal that these viruses are often related to those found in other invertebrates and tend to share close relationships with viruses from species within the same food web or habitat. This suggests that viruses may move between different marine species more frequently than previously thought. The discovery of such a wide variety of viruses, particularly the diverse genome structures of newly identified picornaviruses, is a significant leap forward in understanding the crustacean virology. This knowledge is crucial for managing disease risks in aquaculture and maintaining the balance of marine ecosystems.

Identification and classification of the genomes of novel microviruses in poultry slaughterhouse

Microviridae is a family of phages with circular ssDNA genomes and they are widely found in various environments and organisms. In this study, virome techniques were employed to explore potential members of Microviridae in a poultry slaughterhouse, leading to the identification of 98 novel and complete microvirus genomes. Using a similarity clustering network classification approach, these viruses were found to belong to at least 6 new subfamilies within Microviridae and 3 higher-level taxonomic units. Genome size, GC content and genome structure of these new taxa showed evident regularities, validating the rationality of our classification method. Our method can divide microviruses into about 45 additional detailed clusters, which may serve as a new standard for classifying Microviridae members. Furthermore, by addressing the scarcity of host information for microviruses, the current study significantly broadened their host range and discovered over 20 possible new hosts, including important pathogenic bacteria such as Helicobacter pylori and Vibrio cholerae, as well as different taxa demonstrated different host specificities. The findings of this study effectively expand the diversity of the Microviridae family, providing new insights for their classification and identification. Additionally, it offers a novel perspective for monitoring and controlling pathogenic microorganisms in poultry slaughterhouse environments.

A novel birnavirus identified as the causative agent of summer atrophy of pearl oyster (Pinctada fucata (Gould))

The Akoya pearl oyster (Pinctada fucata (Gould)) is the most important species for pearl cultivation in Japan. Mass mortality of 0-year-old juvenile oysters and anomalies in adults, known as summer atrophy, have been observed in major pearl farming areas during the season when seawater temperatures exceed about 20 °C since 2019. In this study, we identified a novel birnavirus as the pathogen of summer atrophy and named it Pinctada birnavirus (PiBV). PiBV was first presumed to be the causative agent when it was detected specifically and frequently in the infected oysters in a comparative metatranscriptomics of experimentally infected and healthy pearl oysters. Subsequently, the symptoms of summer atrophy were reproduced by infection tests using purified PiBV. Infection of juvenile oysters with PiBV resulted in an increase in the PiBV genome followed by the atrophy of soft body and subsequent mortality. Immunostaining with a mouse antiserum against a recombinant PiBV protein showed that the virus antigen was localized mainly in the epithelial cells on the outer surface of the mantle. Although the phylogenetic analysis using maximum likelihood method placed PiBV at the root of the genus Entomobirnavirus, the identity of the bi-segmented, genomic RNA to that of known birnaviruses at the full-length amino acid level was low, suggesting that PiBV forms a new genus. The discovery of PiBV will be the basis for research to control this emerging disease.

Short-, long-read metagenome and virome reveal the profile of phage-mediated ARGs in anoxic-oxic processes for swine wastewater treatment

Phages are among the most widely spread viruses, but their profiles and the antibiotic resistance genes (ARGs) they carry in swine wastewater remain underexplored. The present study investigated the distribution characteristics of phages and their ARG risk in anoxic/oxic (A/O) wastewater treatment processes of swine farms using short- and long-read metagenome and virome. The results demonstrated that the virome could extract more phage sequences than the total metagenome; thus, it was more suited for studying phages in wastewater settings. Intriguingly, phages had significantly lower abundance of ARG than ARGs harbored by total microorganisms (P < 0.01). Eleven ARGs co-occurred with phages and bacteria (R > 0.6 and P < 0.05), with Siphoviridae being the phage co-occurring with the most ARGs (5). Horizontal gene transfer (HGT) events were observed between Proteobacteria and the major phyla except for Bacteroidota. Furthermore, there were prophage sequences and ARGs on the same contig in bacterial MAGs. These data strongly demonstrate that phages promote horizontal transfer of ARG between bacterial hosts in A/O processes for swine wastewater treatment. Therefore, the risk of phage-mediated horizontal transfer of ARGs cannot be overlooked despite the low abundance of phage ARGs (pARG).

Unveiling CRESS DNA Virus Diversity in Oysters by Virome

Oysters that filter feed can accumulate numerous pathogens, including viruses, which can serve as a valuable viral repository. As oyster farming becomes more prevalent, concerns are mounting about diseases that can harm both cultivated and wild oysters. Unfortunately, there is a lack of research on the viruses and other factors that can cause illness in shellfish. This means that it is harder to find ways to prevent these diseases and protect the oysters. This is part of a previously started project, the Dataset of Oyster Virome, in which we further study 30 almost complete genomes of oyster-associated CRESS DNA viruses. The replication-associated proteins and capsid proteins found in CRESS DNA viruses display varying evolutionary rates and frequently undergo recombination. Additionally, some CRESS DNA viruses have the capability for cross-species transmission. A plethora of unclassified CRESS DNA viruses are detectable in transcriptome libraries, exhibiting higher levels of transcriptional activity than those found in metagenome libraries. The study significantly enhances our understanding of the diversity of oyster-associated CRESS DNA viruses, emphasizing the widespread presence of CRESS DNA viruses in the natural environment and the substantial portion of CRESS DNA viruses that remain unidentified. This study's findings provide a basis for further research on the biological and ecological roles of viruses in oysters and their environment.

Compensatory response of Hong Kong oysters to co-occurring stressors: Zinc oxide nanoparticles and low salinity exposure

Zinc Oxide nanoparticles (ZnO NPs), due to their ubiquitous use in industrial and consumer applications, present potential risks to marine ecosystems and biota, especially oysters. The physiological and immunological health of marine species is highly dependent on salinity levels. However, the combined impact of lowered salinity and exposure to ZnO NPs, particularly on key marine species like oysters, is an area that requires more research. Our study aimed to examine these concurrent stressors' impacts on phenotypic markers, gill and hepatopancreas physiological indices, and hemocyte immune parameters of Crassostrea hongkongensis. We subjected six oyster cohorts to varied ZnO NPs concentrations and salinity levels over 21 days. Our findings reveal that individual exposure to ZnO NPs or diminished salinity disrupts oyster physiology, impacting metabolism, antioxidant capacity, immune response, and energy distribution through distinct mechanisms. Remarkably, low salinity constituted a more significant threat than isolated ZnO NPs. However, when confronted with combined stressors, oysters exhibited a compensatory response, attenuating individual stressors' detrimental effects. This adaptation was characterised by reduced apoptosis rates, increased calcium ion concentration in mature hemocytes, and a restoration of conditioned indices, hepatopancreas alkaline phosphatase, and gill catalase activity to baseline levels. Principal Component Analysis and Integrated Biomarker Responses validated this compensatory phenomenon. Partial Least Squares Pathway Model analysis underscored these stressors' profound implications on oyster health, primarily driven by stressor exposure rather than mere zinc concentrations, despite acknowledging zinc's immunosuppressive impact on oyster immunity. Our research emphasises the importance of assessing multiple stressors' cumulative effects on aquatic species' ecological resilience, accentuating the need for comprehensive analyses incorporating functional specificity among diverse organs and immune components, including gill, hepatopancreas, and the critical hemocytes.

Viral Diversity in Samples of Freshwater Gastropods Benedictia baicalensis (Caenogastropoda: Benedictiidae) Revealed by Total RNA-Sequencing

Previously, the main studies were focused on viruses that cause disease in commercial and farmed shellfish and cause damage to food enterprises (for example, Ostreavirusostreidmalaco1, Aurivirus haliotidmalaco1 and Aquabirnavirus tellinae). Advances in high-throughput sequencing technologies have extended the studies to natural populations of mollusks (and other invertebrates) as unexplored niches of viral diversity and possible sources of emerging diseases. These studies have revealed a huge diversity of mostly previously unknown viruses and filled gaps in the evolutionary history of viruses. In the present study, we estimated the viral diversity in samples of the Baikal endemic gastropod Benedictia baicalensis using metatranscriptomic analysis (total RNA-sequencing); we were able to identify a wide variety of RNA-containing viruses in four samples (pools) of mollusks collected at three stations of Lake Baikal. Most of the identified viral genomes (scaffolds) had only distant similarities to known viruses or (in most cases) to metagenome-assembled viral genomes from various natural samples (mollusks, crustaceans, insects and others) mainly from freshwater ecosystems. We were able to identify viruses similar to those previously identified in mollusks (in particular to the picornaviruses Biomphalaria virus 1 and Biomphalaria virus 3 from the freshwater gastropods); it is possible that picorna-like viruses (as well as a number of other identified viruses) are pathogenic for Baikal gastropods. Our results also suggested that Baikal mollusks, like other species, may bioaccumulate or serve as a reservoir for numerous viruses that infect a variety of organisms (including vertebrates).

Adaptive response of triploid Fujian oyster (Crassostrea angulata) to nanoplastic stress: Insights from physiological, metabolomic, and microbial community analyses

Triploid Fujian oyster (Crassostrea angulata) is crucial to aquaculture and coastal ecosystems because of its accelerated growth and heightened resilience against environmental stressors. In light of the increasing prevalence of nanoplastic pollution in the ocean, understanding its potential impact on this organism, particularly its adaptive responses, is of paramount importance. Despite this, the effects of nanoplastic pollution on the physiology of C. angulata remain largely unexplored. In this study, we explored the responses of triploid Fujian oysters to nanoplastic stress during a 14-day exposure period, employing an integrative methodology that included physiological, metabolomic, and 16S rRNA sequencing analyses. Our results demonstrate that the oysters exhibit a strong adaptive response to nanoplastic exposure, characterized by alterations in enzyme activity, metabolic pathways, and microbial community composition, indicative of an adaptive recovery state as opposed to a disordered state. Oysters subjected to elevated nanoplastic levels exhibited adaptive responses primarily by boosting the activity of the antioxidant enzyme catalase and elevating the levels of antioxidants such as adenosine, 3-(4-hydroxyphenyl)pyruvate, D-sorbitol, d-mannose, and unsaturated fatty acids, as well as the functional amino acids l-proline and l-lysine. Nanoplastic treatment also resulted in increased activity of succinate dehydrogenase, a key component of energy metabolism, and increased contents of intermediate metabolites or products of energy metabolism, such as adenosine monophosphate, adenosine, guanosine, creatine, and thiamine. Nanoplastic treatment led to an increase in the abundance of certain advantageous genera of gut bacteria, specifically Phaeobacter and Nautella. The observed adaptive response of triploid Fujian oysters to nanoplastic stress provides valuable insights into the mechanisms underpinning resilience in marine bivalves.