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At least 19 recordsLinked to original sources
PubMed2026

Elevation-structured viral ecological strategies along glacier-fed rivers on the Qinghai-Tibet Plateau.

The Qinghai-Tibet Plateau, a climate-vulnerable source of Asia's major rivers, harbors underexplored viral communities critical to ecosystem functions. By integrating 597 metagenomes from the Yangtze, Yellow, Lancang, and Yarlung Tsangpo rivers with 85 public available glacial metagenomes (Tibetan Glacier Genome and Gene catalog), we built the Glacier-to-River Virome Catalogue, encompassing 36,358 vOTUs and 897,250 viral protein clusters, to decode viral adaptation and ecological influence across elevation gradients. Our results reveal that high-altitude conditions favor viruses with elevated Guanine-Cytosine content, larger genomes and more cold-adaptation genes. A central finding is a systematic viral lifestyle shift from temperate in glaciated regions to lytic viruses downstream, accompanied with decline of pathogens carrying antibiotic resistance genes along the glacier-to-river gradients. Further, viral auxiliary metabolic genes transition from glacier nutrient scavenging (e.g., nitrogen and sulfur transporters) to downstream mineralization processes (e.g., denitrification) in plains highlights their role in biogeochemical cycling. These findings position viruses as pivotal regulators of microbial community structural and functional dynamics to glacier-to-river gradient change and biogeochemistry in the Qinghai-Tibet Plateau, providing critical insights into climate response in vulnerable Asian water towers.

Ice Cover↗
PubMed2026

Magnetite facilitates phage-bacteria interactions and phage-associated metabolic coordination for medium-chain fatty acid biosynthesis under ammonia stress.

Medium-chain fatty acid (MCFA) production from waste activated sludge (WAS) is considered to rely on the syntrophic interactions among distinct functional microorganisms. Whether phages represent an overlooked ecological component involved in MCFA biosynthesis remains unclear. MCFA production is often inhibited by high total ammonia nitrogen (TAN). Conductive materials have been proposed as effective strategies to enhance or recover MCFA production under TAN stress. Therefore, the inhibition-recovery system could provide a useful framework for investigating whether viral ecological responses are associated with MCFA-related metabolic processes. In this study, magnetite (Fe3O4) was selected as the recovery strategy of MCFA production under TAN stress. Results showed that a total of 3915 vOTUs and 118 metagenome-assembled genomes were recovered from the anaerobic bioreactors subjected to three conditions: Control (without TAN stress), TAN stress, and TAN stress with Fe3O4 presence. Under high TAN environment (∼5 g/L), MCFA production reduced by 49% (1.3 g COD/L) in comparison to that without high TAN stress. The ecological coupling between temperate phages and MCFA-related bacterial hosts was weakened, accompanied by substantial decreases in the abundance and transcriptional abundance of phage-associated auxiliary metabolic genes (AMGs) related to MCFA synthesis (e.g., fatty acid biosynthesis, acyl-chain metabolism). In the presence of Fe3O4 (i.e., 10 g/L), MCFA production was four and two times higher than those with and without high TAN stress. In addition to enhanced phage-bacteria ecological coupling and increased the abundance and transcription of AMGs related to MCFA formation, Fe3O4 increased the abundance and expressions of electron-transfer-related AMGs (e.g., cbb3-type cytochrome c oxidase, type IV pilus assembly genes) and QS-related LuxR-family and HTH-type regulators, indicating that such indirect pathway could be largely overlooked during MCFA synthesis. This is also the first-time reporting that phages could represent an ecological layer responsive to iron oxide. Analyses of publicly available metagenomes collected from MCFA-oriented anaerobic systems further confirmed that phages could be broadly associated with the metabolic processes involved in MCFA biosynthesis. Taken together, this study reveals that phages could serve as an overlooked ecological layer associated with MCFA metabolism and provide a viral-ecology perspective for understanding TAN inhibition and iron oxide-mediated recovery during WAS-to-MCFA bioconversion.

Ammonia inhibition↗
PubMed2024

Diverse RNA viruses discovered in multiple seagrass species.

Seagrasses are marine angiosperms that form highly productive and diverse ecosystems. These ecosystems, however, are declining worldwide. Plant-associated microbes affect critical functions like nutrient uptake and pathogen resistance, which has led to an interest in the seagrass microbiome. However, despite their significant role in plant ecology, viruses have only recently garnered attention in seagrass species. In this study, we produced original data and mined publicly available transcriptomes to advance our understanding of RNA viral diversity in Zostera marina, Zostera muelleri, Zostera japonica, and Cymodocea nodosa. In Z. marina, we present evidence for additional Zostera marina amalgavirus 1 and 2 genotypes, and a complete genome for an alphaendornavirus previously evidenced by an RNA-dependent RNA polymerase gene fragment. In Z. muelleri, we present evidence for a second complete alphaendornavirus and near complete furovirus. Both are novel, and, to the best of our knowledge, this marks the first report of a furovirus infection naturally occurring outside of cereal grasses. In Z. japonica, we discovered genome fragments that belong to a novel strain of cucumber mosaic virus, a prolific pathogen that depends largely on aphid vectoring for host-to-host transmission. Lastly, in C. nodosa, we discovered two contigs that belong to a novel virus in the family Betaflexiviridae. These findings expand our knowledge of viral diversity in seagrasses and provide insight into seagrass viral ecology.

RNA Viruses↗
PubMed2026

Viral communities from long-term anaerobic alkane-oxidizing enrichment cultures encode predicted cell surface adhesion functions.

The anaerobic oxidation of methane and C2+-alkanes is a dominant metabolism within hydrocarbon-rich deep-sea sediments and is largely mediated by alkane-oxidizing archaea in metabolic partnership with syntrophic sulfate-reducing bacteria. Although these processes fuel a diverse ecosystem, the viral component of alkane-rich sediments has historically been overlooked. We analyzed the viral assemblages in long-term sediment-free cultures of alkane-degrading organisms and found that abiotic factors such as incubation temperature had a greater correlation with community composition than with the phylogenetic patterns among individual viral species. No auxiliary metabolic genes (AMGs) directly involved in hydrocarbon oxidation or sulfate reduction were found, but the presence of candidate AMGs involved in heme synthesis pathways common in methane oxidizers hints at a possible viral impact on alkane degradation. We also examined potential host-virus pairs using CRISPR- and tRNA-based methods. Lastly, we identified the presence of nosD-like proteins in viruses from sediment-derived systems that are not present in water column datasets; their distribution, genomic context, and lack of canonical nosD characteristics suggest an alternate adhesion-related role in sediment communities. The number of new viruses obtained from these multi-year enrichment cultures and their potential roles in mediating host physiology illustrate the importance of studying the viral component in laboratory and environmental systems.

Geologic Sediments↗
PubMed1977

Isfahan virus, a new vesiculovirus infecting humans, gerbils, and sandflies in Iran.

The characteristics and ecology of Isfahan virus, a new vesicular stomatitis virus (VSV) serotype, are described. Two strains of the agent were isolated from pools of Phlebotomus papatasi collected in Iran in 1975. Its animal pathogenicity, growth rate, cytopathic effect, and plaque morphology are similar to those of the other VSV serotypes. Electron microscopic examination of the virus demonstrated a bullet shape, the presence of truncated particles and maturation at plasma membranes. Antigenic relationships between Isfahan virus and three other VSV serotypes (Cocal, Piry, and Chandipura) were demonstrated by complement fixation or neutralization tests. A high prevalence of Isfahan neutralizing antibodies was found in human sera from several regions of Iran, suggesting that the virus may be of some public health importance. All of the residents over 5 years of age in the village where the virus was isolated had been infected. Neutralizing antibodies to Isfahan virus were also found in sera of Iranian gerbils but not in domestic animals. Results of this study suggest that the ecology of Isfahan virus is distinct from the other VSV serotypes and involves chiefly humans, gerbils, and sandflies, a pattern also observed with cutaneous leishmaniasis and sandfly fever in Iran.

Animals↗
PubMed2026

Viral community structure in New Zealand's aquatic birds is associated with scavenging behavior.

Wild migratory birds play a major role in the global spread of viruses, yet the ecological drivers underpinning viral diversity and transmission, particularly host behavior, remain poorly understood. Aotearoa/New Zealand provides a powerful system to address this, including unique species that reflect its geographical isolation, yet with international connections provided by migratory birds across the East Asian-Australasian Flyway and Antarctic regions. Herein, we conducted a large-scale metatranscriptomic survey of wild birds across New Zealand and its subantarctic islands, in which we collected 1,348 samples from 690 individuals across 31 host species spanning four avian orders. We identified 118 avian viruses from 17 families, including 107 novel species, expanding our knowledge of avian viral diversity. Notably, viral community composition was most strongly associated with bird scavenging behavior, which explained more variation than host taxonomy, geography, or migratory status. Scavenging birds and opportunistic scavengers harbored more diverse viromes than non-scavengers, consistent with increased viral exposure across trophic levels. This was supported by the detection of 12 mammalian-associated viruses, primarily in scavengers, including hedgehog hepatovirus, rabbit hemorrhagic disease virus 2, and sea lion astroviruses, with host sequence data confirming dietary origin. We also detected viruses of epidemiological and evolutionary interest, including a low-pathogenic avian influenza A(H1N9) virus from red knots (Calidris canutus) and a divergent tobanivirus from Auckland Island teal (Anas aucklandica), which represented the first putative avian member of the Tobaniviridae. These findings suggest that virome structure in wild birds is associated with scavenging behavior, thus highlighting the importance of incorporating host ecology into viral surveillance and risk assessment.

New Zealand↗
PubMed2026

Evaluating sampling strategies for the detection of avian influenza viruses in the environment.

Highly pathogenic avian influenza (HPAI) viruses pose an increasing threat to wildlife, livestock and human health, underscoring the need for scalable and early-warning surveillance systems. Environmental RNA (eRNA) monitoring offers a non-invasive, cost-effective alternative to traditional host-based sampling by detecting viral genetic material shed into the environment. Despite its utility, the relative performance of different environmental sampling approaches for avian influenza virus (AIV) detection remains poorly resolved. Here, we conducted a longitudinal study with monthly sampling over approximately one year across two urban waterfowl ponds in Aotearoa New Zealand to evaluate four eRNA sampling strategies - fresh faeces, sediment, active-filtered water and passive-filtered water - for their ability to detect AIV. Using a combination of metagenomic sequencing and RT-qPCR, we show that all sample types can detect AIV, although detections were highly inconsistent across sampling methods, locations and time points. While metagenomic sequencing provided valuable genomic data, including subtype identification and phylogenetic context, RT-qPCR exhibited greater sensitivity, with active-filtered water yielding the highest detection rates, and is currently the more cost-effective approach for large-scale surveillance. Notably, AIV detections were asynchronous among sample types and frequently lacked temporal concordance, suggesting that environmental heterogeneity, RNA persistence, and methodological detection limits strongly influence surveillance outcomes. Despite these inconsistencies, phylogenetic analyses revealed that detected viruses belong to established Australasian lineages, highlighting the ability of environmental surveillance to capture ecologically relevant viral diversity. Our findings demonstrate that while eRNA-based surveillance holds substantial promise as a complementary tool for AIV monitoring, its effectiveness is highly dependent on the environmental sampling strategies and laboratory detection methods used.

Ducks↗
PubMed1975

Ecology of California encephalitis viruses on the Del Mar Va Peninsula. I. Virus isolations from mosquitoes.

The ecology of California encephalitis viruses was studied on the Del Mar Va Peninsula. Adult mosquitoes were collected weekly from May to October of 1971 and monthly from May to October of 1972, using CDC miniature light traps with Dry Ice. Floodwater mosquitoes were assayed for virus in suckling mice or cell cultures. In 1971 over 77,000 mosquitoes were processed, resulting in 33 virus isolations. In 1972, over 106,000 were processed and 63 virus strains were recovered. Of the 1971 strains, all but one were recovered from Aedes atlanticus mosquitoes, and of the 1972 strains all but two were recovered from A. atlanticus. All A. atlanticus strains were neutralized by Keystone virus mouse hyperimmune ascitic fluid (MHAF). All other strains were recovered from A. canadensis mosquitoes. The single 1971 strain, and one strain from 1972, were neutralized by Jamestown Canyon MHAF. The remaining strain was neutralized by Keystone MHAF. The rate of virus recovery from A. atlanticus remained approximately the same, both between years and during each year studied, even during periods when large numbers of adults were emerging, suggesting that these mosquitoes had emerged infected.

Animals↗
PubMed1976

Influence of temperatures corresponding to those of the host animals on Tahyna virus.

The influence of temperature of 36.5 and 39.2 degrees C on uncloned low passage Tahyna virus in chick embryo cell cultures was studied in the course of 10 passages. At a high multiplicity of infection, the virus titres showed a considerable variability, especially at 39.2 degrees C. The cytopathic effect (CPE) apparent at both temperatures started later and was of lower intensity at 39.2 degrees C than at 36.5 degrees C. The temperature of 39.2 degrees C intensified the thermostable character of the virus. Changes in plaque size and virulence were connected mainly with the cultivation substrate of the virus.

Animals↗
PubMed1979

[Influenza in man and animals].

A review of references found in World literature concerning the present day problem of grippe virus participation in man's and animals' pathology is made. New aspects of the relations between grippe viruses in man and in the animals, strain circulation, changes in their antigenic structures and the arisal of spontaneous mutations as well as the possibility for preserving human grippe strains in animals during interepidemical periods are revealed. Various hypotheses confirming this possibility are discussed. Results obtained in this field are summed up and an attempt to compare and analyse them is made in view to construct all-round conceptions and elaborate a strategy related with the study of grippe viruses also in animals and birds as their eventual biological reservoir. Data presented are of interest not only for etiology and epidemiology but also for the ecology of viral infections. Conclusions concerning the need to study grippe virus interrelations in man and animals in an all-round aspect, including the participation of various specialists, are made.

Animals↗
PubMed2026

Exploring the ecological drivers of bacteriophage diversity and functional viral potential in the skin of the axolotl Ambystoma altamirani.

Bacteriophages play important roles in shaping microbial community dynamics across diverse environments. In the amphibian skin, most microbiome studies have focused on bacteria and their interactions with the fungus Batrachochytrium dendrobatidis (Bd), leaving other microbial components, including viruses, largely unexplored. Here, we present the first characterization of the viral community in the amphibian skin microbiome, focusing on ecological drivers of bacteriophage diversity and functional potential in the axolotl Ambystoma altamirani. Using public shotgun metagenomes, we found that the viral fraction was dominated by bacteriophages of the class Caudoviricetes. Bacteriophage diversity was significantly associated with local physicochemical parameters at the time of sampling, and showed a strong positive correlation with bacterial diversity, whereas no significant associations were detected with the presence of Bd. In addition, seasonality influenced the composition and properties of bacteria-bacteriophage co-abundance networks. Functional annotation of assembled bacteriophage sequences revealed a diverse functional potential, including putative auxiliary metabolic genes, superinfection exclusion, toxin-antitoxin, and virulence factors. Overall, these findings highlight the ecological relevance of bacteriophages in amphibian skin microbiomes and underscore the need for further studies on their role in the amphibian host's health.

Animals↗
PubMed2026

The Hidden Diversity of Benyviridae and their Polymyxa Vectors: A Comparative Analysis.

The Benyviridae family encompasses multipartite soil-borne phytoviruses characterized by rod-shaped virions and positive single-stranded RNA genomes. The family is mostly known for its type species, the beet necrotic yellow vein virus, the causal agent of rhizomania on sugar beet. However, the recent description of candidate Benyviridae species and "beny-like" sequences suggests a far greater diversity than previously recognized. Also, their increasing relevance in agriculture has drawn attention to this family of viruses. In this review, we provide a comparative analysis of Benyviridae viruses, including newly identified emerging relatives. We highlight recent advances in understanding their diversity, pathogenicity, and interaction with plant hosts and their plasmodiophorid vectors, Polymyxa spp., that remain poorly characterized. Finally, we identify critical knowledge gaps and exciting opportunities-particularly in vector biology, host interactions, and the ecological dynamics of viral spread-that will shape the research ahead.

Plant Viruses↗
PubMed2026

Rumen DNA virome plasticity and viral metabolic potential are associated with seasonal adaptation in grazing yak and cattle on the Qinghai-Tibet Plateau.

BACKGROUND: As a diverse and abundant component of the rumen ecosystem, viruses interact with other microorganisms and are thought to influence microbial metabolism and host productivity. However, how the rumen virome responds to seasonal fluctuations in extreme environments remains poorly understood. Here, metagenomic analyses were used to investigate temporal dynamics of viral diversity, functional potential, and virus-host associations in the rumen virome of yak and cattle on the Qinghai-Tibet Plateau across warm and cold seasons. RESULTS: Rumen viral communities exhibited pronounced seasonal variation in both yaks and cattle, with higher alpha diversity observed during the cold season than in the warm season. Across seasons, the yak rumen virome showed greater alpha diversity and community stability than that of cattle. In total, 27,353 temperate and 31,976 virulent viral operational taxonomic units (vOTUs) were identified, predominantly belonging to the class Caudoviricetes. These viruses were linked to microbial hosts spanning 24 bacterial and 8 archaeal phyla, with Bacteroidota and Bacillota representing the dominant lineages. Virus-host associations were more numerous in the cold season and showed distinct host-specific patterns between yaks and cattle. Cold-season virome exhibited reduced diversity of anti-defense genes and enrichment of auxiliary metabolic genes (AMGs) associated with fatty acid metabolism and hemicellulose degradation. Notably, greater divergence between yaks and cattle was observed during the cold season: the yak rumen virome was enriched in pathways related to amino acid, lipid, and energy metabolism, as well as cellulose-degrading CAZyme families, whereas the cattle rumen virome showed enrichment in general carbohydrate metabolism and replication and repair processes. CONCLUSION: Seasonal plasticity of rumen DNA virome and pronounced interspecific divergence between yaks and cattle provide insight into their distinct microbial processes in the harsh environment of the Qinghai-Tibet Plateau. These findings suggest that the rumen DNA virome exhibits complex ecological and functional responses to seasonal variation and may be associated with host-microbiome interactions and nutrient utilization under environmental stress. This study highlights the ecological relevance of rumen viral genomes in understanding virus-microbiome interactions, microbial adaptation, and nutrient utilization in high-altitude ruminants.

Auxiliary metabolic genes↗