Plant Viromes in the Age of Metagenomics: Diversity, Ecology, and Implications for Crop Health

High-throughput sequencing and metagenomic approaches have fundamentally changed what it means to study plant viruses. For most of the history of plant virology, knowledge of viral diversity was shaped by what caused visible disease — the pathogens that destroyed harvests, triggered epidemics, and drew the attention of diagnosticians. That picture is now understood to be a narrow window onto a far richer reality. Metagenomic surveys of wild plants, agricultural soils, and crop root systems are consistently revealing vast numbers of novel virus species, genera, and entire families with no cultivated representatives and no described host interactions. The gap between estimated and known plant viral diversity is large and widening with each new study. Many of the viruses being discovered are cryptic or apparently symptomless, raising fundamental questions about what plant viruses actually do in their hosts and in ecosystems, and what role they play in shaping plant fitness, microbiome composition, and community ecology beyond the disease paradigm.The concept of the plant virome — the full complement of viruses associated with a plant, its rhizosphere, and the broader agroecosystem — is becoming central to plant biology in the same way the microbiome transformed our understanding of plant-microbial interactions. Soil-borne viral communities are now recognized as dynamic components of the plant pathobiome, with the potential to influence disease suppression, nutrient cycling, and the ecology of fungal and bacterial co-inhabitants. Mycoviruses, which infect plant-pathogenic fungi, add a further layer of complexity: their presence can modulate fungal virulence and persistence, with direct but poorly understood consequences for crop health. Wild plants represent untapped reservoirs of viral diversity that may seed agricultural systems as host range expands under climate change or changing land use. Taken together, these discoveries demand a more ecological and systems-level framework for plant virology — one that positions the virome not as a list of threats to be catalogued, but as a dynamic community with functional significance.Realizing this requires confronting substantial methodological challenges. Reference databases for plant virus identification from metagenomes remain incomplete, making robust taxonomic assignment difficult and leaving much discovered diversity unclassified. Bioinformatic pipelines vary widely in their handling of RNA virus assembly, contamination filtering, and host attribution. Standards for distinguishing genuine plant-associated viruses from environmental background, transient contaminants, or viruses of co-infecting organisms are still being developed. Geographic sampling is also highly uneven, with most large-scale virome studies concentrated in a small number of temperate agricultural systems, leaving tropical agroecosystems, native vegetation communities, and subsistence crop systems largely uncharacterized.This Research Topic aims to bring together the metagenomics, ecology, and plant pathology communities to advance the field on all of these fronts.We welcome Original Research, Review, Mini Review, Methods, Hypothesis and Theory, Perspective, and Opinion articles addressing, but not limited to, the following themes:- Metagenomic discovery, genome characterization, and taxonomic placement of novel plant-associated viruses across agricultural, wild, and managed ecosystems- Ecology and spatiotemporal dynamics of plant viromes across host species, growth stages, environments, and seasons- Soil virome composition and the interactions between soil-borne viruses and root-associated bacterial and fungal microbiomes- Wild plant and non-crop host viromes as reservoirs for emerging agricultural pathogens- Cryptic, endogenous, and symptomless plant viruses: prevalence, persistence, transmission, and potential functional roles in host biology- Mycovirus diversity, ecology, and their effects on the virulence and fitness of plant-pathogenic fungi- Functional significance of plant-associated viruses in host fitness, plant community dynamics, and ecosystem processes- Bioinformatics pipelines, reference databases, and analytical standards for plant virome characterization from metagenomic and metatranscriptomic data- Interactions between the plant virome and co-occurring microbial communities, including bacteria, fungi, and oomycetes- Implications of virome diversity for crop disease emergence, host range expansion, and biosecurity risk assessment- Geographic surveys of plant viromes in underrepresented regions, cropping systems, and native plant communities- Integration of virome data with epidemiological, ecological, and climate models to anticipate future disease risk Topic editors: Anurag Yadav, Edgloris Elena Marys Saravia, Jayanta Tarafdar Source: https://www.frontiersin.org/research-topics/82669/plant-viromes-in-the-age-of-metagenomics-diversity-ecology-and-implications-for-crop-health