Soil Pathobiome in agroecosystems and forests

Abstract

The soil pathobiome comprises complex communities of plant pathogens and their interactions with beneficial microorganisms and the surrounding microbiota, collectively influencing plant health and disease development. Climate change, land-use change, and intensive management practices contribute to pathogen transmission, expansion into new ecological niches, and disruption of native microbial communities, promoting the accumulation of pathogenic organisms within the soil pathobiome. These anthropogenic disturbances raise important questions about the long-term consequences of human intervention for ecosystem functioning and plant health. This review synthesises current knowledge on the soil pathobiome across agricultural cropping systems (including monocultures and intercropping), horticultural production systems, and forest ecosystems, focusing on its definitions, ecological interactions, environmental drivers, and methodological approaches. We evaluate how management practices, including intensive monoculture, crop diversification through intercropping, crop rotation, soil amendments, and microbiome-based interventions, influence pathobiome assembly, disease development, and soil health. Overall, this review proposes an integrated framework linking environmental change, management practices, microbial interactions, and soil pathobiome dynamics, highlighting soil health as a central component of resilient ecosystems.