Stover returning practices alter the functional diversity of genes associated with carbon conversion in Mollisol of Northeast China

Stover returning practices influence soil carbon conversion processes, which are critical for soil carbon sequestration and agricultural sustainability. Although studies on functional gene diversity offer valuable insights, the mechanisms linking this diversity to specific carbon transformation pathways in agroecosystems remain unclear. This study investigates the functional diversity of β-glucosidase (BG)-related genes (GH1 and GH3, glycoside hydrolase families 1 and 3) under four tillage regimes: conventional tillage (CT), stover biochar with rotary tillage (BC), direct incorporation of chopped stover with rotary tillage (SD), and stover mulching with no-tillage (NT), in a 3-year field experiment conducted in Northeast China. Our results showed that CT significantly increased GH1 (8586 copies/g) but decreased GH3 gene abundance (2660 copies/g), with BC showing the highest GH3 levels (20701 copies/g). While BG activity showed no significant difference, this indicates that BG coding genes respond more rapidly to external factors than BG activity does. GH1 and GH3 correlated divergently with BG activity, indicating distinct functional strategies in soil carbon cycling. Under NT, the GH1-associated keystone species OTU12 ( Micromonospora ) facilitated cellulose degradation; its abundance was positively correlated with soil organic carbon (SOC) (17.43 g/kg) and microbial biomass nitrogen (73.80 mg/kg) while being negatively affected by nitrate nitrogen (8.43 mg/kg). Notably, GH1 gene abundance (1637 copies/g) decreased under NT, suggesting a decoupling between gene copy number and functional potential. In contrast, the GH3-associated keystone species OTU3093 ( Brevundimonas ) under BC treatment was positively associated with SOC (18.80 g/kg) and particulate organic carbon (4.79 g/kg), suggesting its potential involvement in carbon mineralization processes. Contrary to conventional expectations, biochar paradoxically stimulated BG activity through SOC decomposition mediated by OTU3093, potentially driving its priming effect. These findings highlight the complex relationship between soil enzyme genes and activity, as well as the critical role of low-abundance genes. The study advances the mechanistic understanding of stover carbon conversion by examining functional gene diversity under different stover-returning practices, providing insights into optimizing carbon turnover in agroecosystems.