Seeking soil microbial degraders and enzymatic genes for efficient biomass recycling

Biodegradation is the most sustainable biomass recycling strategy, yet the absence of efficient microbial degraders remains a critical bottleneck. While soil microorganisms can decompose diverse biomass, their functional specificity for distinct agricultural by-products remains inadequately characterized. To address this, five agricultural by-products, including fish skin, soybean meal, shrimp shell, corn straw and chicken feather, were individually or combinatorially incubated in soil. Comparative analysis of 16 S rRNA amplicons and metagenomics from actively degrading microbial communities versus native soil identified key functional degraders. Declines in Chao1 and Shannon indices within biomass-amended soil groups indicated community simplification, driven by the dominance of novel utilizers over indigenous taxa. Genera enriched in native soil were replaced by divergent taxa across biomass types, revealing substrate-dependent community succession. LEfSe analysis identified biomass-specific utilizers at multiple taxonomic levels. Co-occurrence network analysis showed strong positive co-occurrence patterns between significantly enriched operational taxonomic units (OTUs), suggesting potential co-occurrence patterns and shared responses to biomass amendment. FAPROTAX revealed enhanced C/N/S metabolism during biomass utilization. Metagenomic screening identified markedly higher numbers of biomass-degradation genes encoding hydrolases (e.g., proteases, cellulases, chitinases), consistent with significantly elevated enzyme activities in amended soils compared to undetectable levels in controls. Among six candidate OTUs substantially enriched in chicken feather-amended soil, three species demonstrated efficient feather degradation, with some exhibiting multi-substrate capability. This study elucidates substrate-dependent biomass cycling in soil and provides candidate degraders, including Vicinamibacterales-related OTUs, unclassified Enterobacteriaceae, Sphingobacterium paludis, Sphingobacterium griseoflavum, and Lysinibacillus mangiferihumi, as well as enzymatic gene resources for engineered biomass recycling.