Phytoviromes of Agroecosystems: Surveillance, Ecology, and Risk Forecasting

Plant viruses are pervasive across agricultural landscapes, consistently challenging crop yields, stability, and agroecosystem biosecurity. Mounting evidence demonstrates that viral communities, rather than isolated pathogens, underpin virus dynamics, with complex distributions across crops, wild reservoirs, and vectors. Despite the recognized value of considering phytoviromes at field and landscape scales, traditional diagnostics continue to detect only a small slice of viral diversity, limiting our grasp of the mechanisms behind virus emergence and spread. Cutting-edge advances in high-throughput sequencing and viral metagenomics have now uncovered extraordinary genetic diversity, frequent mixed infections, and rapid viral evolution in managed systems. However, these technological leaps have also revealed methodological inconsistencies and highlighted the difficulty of integrating genomic datasets with ecological parameters, such as host composition, agricultural management, and spatial landscape factors; thereby constraining risk assessment and prediction capabilities. This Research Topic aims to overcome these challenges by fostering integrative approaches that unite viral genomics and metagenomics with ecological, spatial, and predictive analyses. The objective is to move beyond descriptive inventories toward predictive and explanatory models, testing how plant virus communities are structured, how they change over space and time, and which ecological and environmental drivers are most influential in shaping patterns of emergence and transmission. Ultimately, this Topic seeks to bridge molecular surveillance with broader ecological understanding, supporting the development of early-warning systems, sustainable crop protection strategies, and more proactive responses to emerging and re-emerging plant virus threats. The scope of this Research Topic includes studies that examine the composition, diversity, and drivers of plant virus communities in agricultural environments, with an emphasis on analyses that integrate viral genomics with ecological or spatial insights. We welcome articles that address dynamic processes across fields, orchards, and landscapes, and that leverage predictive or risk-assessment frameworks. To gather further insights in this integrative domain, we welcome contributions addressing, but not limited to, the following themes: Viral metagenomics and high-throughput sequencing for agroecosystem surveillance. Diversity, structure, and dynamics of plant virus communities Mixed infections and virus–virus interactions. Virus–plant interactions, including genetic and genomic determinants of susceptibility or resistance. Evolutionary and phylogenetic analyses of plant viruses in managed landscapes. Landscape, ecological, and environmental drivers of virus emergence and spread. Integration of genomic data with spatial, ecological, or predictive models for disease risk assessment. This Research Topic welcomes the following article types: Original Research, Reviews and Mini-Reviews, and Data Reports. Topic editors: Dilyara Gritsenko, Nami MINATO, Rachid TAHZIMA Source: https://www.frontiersin.org/research-topics/78271/phytoviromes-of-agroecosystems-surveillance-ecology-and-risk-forecasting