Herbicides are among the most widely used agrochemicals in modern agriculture, with primary applications in weed control. Beyond their intended targets, herbicides have far-reaching impacts across agroecosystems, influencing the composition and function of microbial and viral communities inhabiting the rhizosphere and phyllosphere. Recent advances reveal that these complex consortia—the plant microbiome and virome—are fundamental to plant health, regulating disease resistance, nutrient acquisition, and stress resilience. As mounting evidence highlights the interconnectedness of these biotic factors with herbicide applications, new questions arise regarding the unforeseen consequences for plant vigor and ecosystem stability. Improved understanding of these dynamics is essential as global agriculture faces escalating pressures of food security and sustainability.

This Research Topic aims to unite contributions at the frontier of herbicide, microbiome, and virome research, clarifying how these interactions collectively shape plant health and system-wide ecological outcomes. We invite original research articles, reviews, methods, case studies, and perspectives that address the effect of herbicides on the structure and function of plant-associated microbial and viral communities. Submissions exploring mechanistic insights, community-level shifts, or the downstream consequences for plant productivity and disease susceptibility are encouraged. We especially welcome studies employing genomics, metagenomics, metabolomics, and integrated field or laboratory-based approaches. In addition, we seek discourse around innovative technologies, risk mitigation strategies, and the advancement of sustainable practices that capitalize on beneficial microbiome and virome functions in agroecosystems. Interdisciplinary approaches bridging plant pathology, microbiology, virology, ecology, and agricultural sciences are highly valued.

To foster progress and actionable insights, we welcome manuscripts addressing, but not limited to, the following themes:

o Effects of herbicides on microbiome and virome diversity and function

o Mechanisms underlying herbicide-microbe-virus interactions

o Impacts on plant disease resistance, growth, and productivity

o Multi-omics approaches for ecosystem-level assessment

o Strategies for restoring or harnessing beneficial microbiota in herbicide-treated systems

o Risk assessment, safety, and regulatory perspectives

By drawing together foundational and innovative research in this domain, this collection aims to illuminate the complex web of interactions that underlie plant responses to herbicides, informing the development of resilient cropping systems and evidence-based policies for sustainable agriculture.

Are you interested in contributing a manuscript to this Research Topic?

Herbicides, Microbiomes, and Viromes: Emerging Plant Health Dynamics