Ecological Fate of Anaerobic Digestate Microorganisms and Their Impact on the Indigenous Soil Microbiome in Field-Grown Maize

The expanding application of anaerobic digestate as a biofertilizer has prompted concerns regarding the ecological fate of exogenous microorganisms introduced to agricultural soils. However, the mechanisms governing the survival of the anaerobic digestion (AD) microbiome in aerobic soil environments remain poorly understood. This study evaluated the structural dynamics and persistence of prokaryotic and fungal communities in a maize field trial following digestate application. High-throughput amplicon sequencing (16S rRNA and ITS) revealed that the soil microbiome exhibited high resistance, with no significant alterations in alpha-diversity or community structure observed between treated and reference soils. Microbial source tracking (FEAST) confirmed that the digestate contributed a negligible proportion (<0.5%) to the established soil community. A rigorous differential abundance filtering approach identified a distinct "transferred" fraction overwhelmingly dominated by prokaryotes, while fungal transfer was virtually absent. The persistence of digestate-derived taxa appears driven by two distinct ecological mechanisms: (1) deterministic survival, characterized by the enrichment of spore-forming Firmicutes capable of enduring oxidative stress; and (2) stochastic persistence, evidenced by the detection of non-spore-forming strict anaerobes likely preserved in anoxic soil microsites or detected as non-viable relic DNA. These findings suggest that the aerobic soil environment acts as a severe abiotic filter, eliminating the majority of the AD microbiome, while biotic resistance from indigenous taxa plays a secondary role restricted to facultative anaerobic microbes.