Biogas slurry, the liquid effluent generated during anaerobic digestion, has long been valued as a nutrient-rich amendment in agricultural systems. Recent advances in microbial ecology reveal that biogas slurry is not only a carrier of nitrogen, phosphorus, potassium, and organic compounds but also a reservoir of diverse and metabolically active microbial communities. These microorganisms—including methanogens, cellulolytic bacteria, nitrifying–denitrifying groups, and plant growth–promoting taxa—may influence soil structure, nutrient turnover, crop productivity, and even disease suppression. However, their ecological functions, survival dynamics after field application, and interactions with native soil microbiota remain poorly understood. As sustainable agriculture intensifies global attention, understanding microbial biodiversity, ecological safety, and functional potential of biogas slurry becomes crucial for optimizing its use and advancing circular agricultural practices.

The central goal of this Research Topic is to address the current gap in understanding how microbial communities present in biogas slurry influence soil ecosystems and agricultural productivity. Although biogas slurry is widely recognized for its nutrient value, its role as a biological input containing diverse, active, and potentially beneficial microorganisms remains underexplored. Key challenges include clarifying how these microbial populations survive, transform, or interact with indigenous soil microbiota after field application, and how these interactions affect nutrient cycling, plant growth, and soil health. Additionally, concerns regarding ecological safety, pathogen transmission, and the stability of functional microbes require systematic investigation.

To address these issues, this Research Topic encourages studies that characterize biogas slurry microbiomes under different feedstocks and digestion conditions, elucidate their ecological functions in soil–plant systems, and assess their potential in promoting crop productivity and reducing chemical inputs. Integrating metagenomics, microbial cultivation, soil ecology, and agronomic trials will help build a mechanistic understanding of biogas slurry–mediated microbial processes. Ultimately, these efforts aim to guide the development of safe, efficient, and sustainable utilization strategies for biogas slurry in modern agriculture.

This Research Topic focuses on the microbial ecology of biogas slurry and its functional implications in agricultural systems. We welcome studies that explore:
• Microbial community structure and functional potential in biogas slurry derived from diverse feedstocks and digestion conditions;
• Fate, survival, and ecological interactions of slurry-derived microbes in soil environments;
• Impacts of biogas slurry application on soil microbiome dynamics, nutrient cycling, and plant growth;
• Roles of beneficial or antagonistic microbes in promoting crop health and suppressing soilborne diseases;
• Assessments of environmental safety, ecological risks, and sustainable utilization strategies including antibiotic resistance gene dynamics and horizontal gene transfer potential.

We particularly encourage studies employing systems-level approaches, including microbial network analysis, genome-scale metabolic modeling, community assembly frameworks, and predictive ecological models that move beyond descriptive profiling toward mechanistic understanding. We encourage submissions of Original Research articles, Reviews, Mini Reviews, and Methods papers. Studies integrating multi-omics, microbial cultivation, soil ecology, or field agronomy are particularly welcome, as they contribute to a comprehensive understanding of the microbial functions and agricultural value of biogas slurry. Submissions should demonstrate clear links between microbial community features and measurable functional outcomes.

Studies relying solely on amplicon sequencing or shotgun metagenomics without experimental validation, functional assays, or integration with agronomic/ecological data will not be prioritized.

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Microbial Communities in Biogas Slurry and Their Functional Roles in Sustainable Agriculture