Microorganisms in Agricultural Soil: Advances and Challenges of Biological Health, Vol II

This is the second edition of a series of Research Topics and you can explore the first edition here.Soil microorganisms play pivotal roles in organic matter decomposition, nutrient cycling, disease suppression, and pollutant transformation. They form the essential foundation for soil health, global food security, and human well-being. As the core of the soil microbial food web, they drive ecosystem multifunctionality through energy flow and matter transformation. However, intensive agricultural practices, including the mismanagement of agricultural wastes such as crop residues and livestock manure, continue to degrade soil microbial communities. This leads to rising soil-borne pathogens, disrupted nutrient cycling, accelerated organic carbon loss, and elevated pollution risks from waste accumulation or improper disposal. These pressures are further intensified by climate change and emerging contaminants, severely compromising the integrity of the soil microbial food web, reducing energy-flow efficiency, and impairing overall ecosystem multifunctionality.At the same time, rapid advances in metagenomics, microbiome engineering, multi-omics integration, and AI-driven microbial ecology are transforming our capacity to decipher the complexity of soil microbial communities and their functional dynamics under environmental stress. Despite notable progress, critical knowledge gaps persist regarding the drivers of microbial degradation, its long-term ecological consequences for the soil microbial food web, ecosystem multifunctionality, and energy flow, as well as effective restoration strategies.To address these challenges, this Research Topic seeks to close key knowledge gaps by elucidating the causes and dynamics of soil microbial degradation and clarifying its impacts on ecosystem services, multifunctionality, energy flow, and microbial food-web structure. We will emphasize innovative pathways to restore soil biological health and integrate the latest advances with current challenges to support evidence-based strategies for sustainable agriculture. As a sequel to the first volume, this second Research Topic aims to build upon prior contributions and further advance the field by inviting Original Research, Review, and Perspective articles on “Microorganisms in Agricultural Soil: Advances and Challenges of Biological Health”. The subtopics include, but are not limited to:• Drivers and dynamics of microbial ecological degradation: mechanisms of pathogen proliferation, nutrient imbalance, and soil-borne disease outbreaks driven by intensification and climate change.• Carbon and nitrogen cycling and greenhouse gas emissions: microbial-mediated soil organic matter depletion and the mechanisms regulating CO₂ and CH₄ fluxes.• Pollutant stress and microbial responses: community dynamics and transformation functions under heavy metals, antibiotics, microplastics, and other emerging contaminants.• Novel strategies for soil health regulation: microbial technologies that enhance nutrient availability, suppress pathogens, and mitigate organic matter loss and pollution.• Resource utilization and valorization of agricultural wastes: microbial conversion of by-products (e.g., crop residues, manure) into biofertilizers, soil amendments, or biochar to restore microbial communities, reduce pollution, and enhance soil multifunctionality.• Design and application of synthetic communities (SynComs): rational engineering of SynComs and their use in remediating soil constraints, boosting fertility, controlling crop diseases, environmental cleanup, and carbon mitigation-to strengthen soil multifunctionality and microbial food-web stability.We especially encourage submissions that deliver mechanistic insights and hypothesis-driven studies, along with practical aspects of SynComs deployment, new evaluation frameworks, and technological innovations. Through this collection, we aim to accelerate the translation of microbiome science into actionable solutions, fostering resilient, multifunctional, energy-efficient, and microbial food-web-stable sustainable agricultural systems. Topic editors: Yanlong Chen, Lucas Pecci Canisares, Duntao Shu, Yangquanwei Zhong, Xiaomeng Wei Source: https://www.frontiersin.org/research-topics/79760/microorganisms-in-agricultural-soil-advances-and-challenges-of-biological-health-vol-ii