Responses of Soil Microbial Communities to Biogas Slurry Irrigation in Paddy Fields: Interactions with Environmental Factors

Biogas slurry (BS), a nutrient-rich byproduct of anaerobic digestion, is increasingly utilized in agriculture to enhance soil fertility and crop productivity. However, the long-term effects of BS on soil microbial communities in paddy fields have not been thoroughly investigated. This study investigated the impacts of continuous BS irrigation over 0–3 years on soil microbial diversity, community composition, and their relationships with environmental factors in southeastern China. The results showed that bacterial diversity (Shannon index) significantly decreased from 6.96 (0 year) to 6.58 (3 years) (p < 0.05), while fungal diversity displayed a U-shaped trend, initially declining to 4.13 (1 year) and subsequently recovering to 4.86 (3 years) (p < 0.05). Dominant bacterial phyla such as Chloroflexi and Bacteroidetes increased in abundance under BS treatment, whereas Gemmatimonadetes decreased. Fungal communities shifted, with Mortierellomycota replacing Basidiomycota as the dominant phylum. Redundancy analysis (RDA) accounted for 91% and 74.9% of the variance in bacterial and fungal communities, respectively. Correlation analysis further indicated that soil available nitrogen and Cr were the primary drivers of bacterial community composition (p < 0.001), whereas soil available potassium and Cd were the key factors influencing the fungal community structure (p < 0.001). This study highlights that BS application alters microbial dynamics, favoring anaerobic bacteria and suppressing pathogenic fungi like Fusarium, thereby supporting sustainable soil management in rice cultivation systems.