Effects of Differential Tobacco Straw Incorporation on Functional Gene Profiles and Functional Groups of Soil Microorganisms

Straw returning is a critical practice with profound strategic importance for sustainable agricultural development. However, within a comprehensive soil health evaluation framework, research analyzing the impact of tobacco straw returning on soil ecosystem health from the perspectives of microbial taxa and functional genes remains insufficient. To investigate the effects of tobacco straw returning on virulence factor genes (VFGs), methane-cycling genes (MCGs), nitrogen-cycling genes (NCGs), carbohydrate-active enzyme genes (CAZyGs), antibiotic resistance genes (ARGs), and their host microorganisms in soil, this study collected soil samples from a long-term tobacco-rice rotation field with continuous tobacco straw incorporation in Shaowu City, Fujian Province. Metagenomic high-throughput sequencing was performed on the samples. The results demonstrated that long-term tobacco straw returning influenced the diversity of soil VFGs, MCGs, NCGs, CAZyGs, ARGs, and their host microorganisms, with richness significantly increasing compared to the CK treatment ( p < 0.05). In the microbially mediated methane cycle, long-term tobacco straw returning resulted in a significant decrease in the abundance of the key methanogenesis gene mttB and the methanogenic archaeon Methanosarcina, along with a reduced mtaB / pmoA functional gene abundance ratio compared to CK. This suggests enhanced CH 4 oxidation in the tobacco-rice rotation field under straw returning. Notably, the abundance of plant pathogens increased significantly under tobacco straw returning. Furthermore, a significantly higher norB / nosZ functional gene abundance ratio was observed, indicating a reduced capacity of soil microorganisms to convert N 2 O in the tobacco-rice rotation field under straw amendment. Based on the observation that the full-rate tobacco straw returning treatment (JT2) resulted in the lowest abundances of functional genes prkC , stkP , mttB , and the highest abundances of nirK , norB , malZ , and bglX , it can be concluded that shifts in soil physicochemical properties and energy substrates drove a transition in microbial metabolic strategies. This transition is characterized by a decreased pathogenic potential of soil bacteria, alongside an enhanced potential for microbial denitrification and cellulose degradation. Non-parametric analysis of matrix correlations revealed that soil organic carbon, dissolved organic carbon, alkaline-hydrolyzable nitrogen, available phosphorus, and available potassium were significantly correlated with the composition of soil functional groups ( p < 0.05). In conclusion, long-term tobacco straw returning may increase the risk of soil-borne diseases in tobacco-rice rotation systems while potentially elevating N 2 O and reducing CH 4 greenhouse gas emission rates. Analysis of functional gene abundance changes identified the full-rate tobacco straw returning treatment as the most effective among all treatments.