Compost application more strongly shapes soil fungal than bacterial communities across arable fields

Abstract

Organic amendments such as compost are widely promoted for enriching soil microbial communities and supporting key soil functions, yet their effects across diverse farming systems and pedoclimatic conditions remain poorly understood. Most evidence originates from controlled experiments that cannot account for the variability inherent in real agronomic settings. Here, using data from 56 commercially managed wheat fields under different fertiliser regimes (compost, solid digestate, or manure) across Switzerland, we show that compost application reshapes soil microbial communities under real farming conditions. Compost increased fungal diversity, shifted fungal community composition, and markedly enhanced fungal network complexity (+50%), exceeding effects of the overall management system (organic versus conventional). While compost effects were strongest for fungal communities, 13 bacterial and nine fungal taxa also increased in abundance following frequent compost application. We further identified a distinct microbial cluster enriched with compost-responsive taxa, including thermophilic taxa from both bacterial (Thermoactinomycetaceae) and fungal (Thermomyces) lineages characteristic of composting processes, suggesting establishment of compost-derived microbes in agricultural soils. In contrast, solid digestate from biogas plants had weaker and more variable effects on soil microbial communities. Structural equation modelling suggested that compost was associated with higher soil respiration mediated primarily through soil physicochemical properties and to a lesser extent microbial community traits. Together, the results provide evidence that compost application structures soil microbial communities across a wide range of pedoclimatic conditions and management backgrounds within Swiss agroecosystem, supporting its role as an effective practice for strengthening microbially mediated soil processes and promoting sustainable soil management.