Bacillus pumilus strain PDSLzg-1, an efficient hydrocarbon-degrading bacterium, was isolated from oil-contaminated soil. Here, we present the complete sequence of its circular chromosome and circular plasmid. The genomic information is essential for the study of degradation of oil by B. pumilus PDSLzg-1.

Background: Enhancing soil organic carbon (SOC) sequestration in degraded lands is critical for climate mitigation and sustainable agriculture. While straw amendment combined with microbial inoculants holds great promise, the underlying mechanisms governing its impact on soil microbiome and carbon cycling genes remain poorly understood. Results: Here, we employed metagenomic sequencing to analyze responses in soil carbon (C) cycling genes, microbial community structure, and functional profiles across three degradation levels (severely, moderately, and non-degraded) of cinnamon soils under straw application alone or in combination with microbial inoculants. Results showed that both straw and straw-microbial inoculants treatments significantly improved soil properties, with improvements in available nitrogen and microbial biomass carbon (severe degradation), SOC (moderate degradation), and available nutrients (non-degradation). The combined application notably reshaped microbial communities by enhancing bacterial alpha diversity while reducing fungal diversity, and strengthened the relationship of relevant key soil C genes in severely degraded soils. Soil pH exhibited significant positive correlations with soil C cycling genes. Key bacterial genera ( Sphingomonas , Bradyrhizobium ) showed strong associations with ABC transporters and glycoside hydrolases, and fungal genus ( Chaetomium ) linked to pyruvate and purine metabolism. Importantly, we observed degradation-level specificity: straw addition significantly increased the abundance of the amylase gene K01214 (encoding α-amylase for starch hydrolysis) in severely degraded soils, whereas the straw-inoculant combination enriched the chitinase gene K01207 (encoding chitinase for chitin hydrolysis) in moderately degraded soils. Conclusions: Accordingly, we propose targeted application of straw with a customized chitinolytic-cellulolytic synthetic microbial community (1–5% of straw mass) to restore carbon cycling functions in degraded soils, while adopting optimized agronomic management to preserve microbiome stability in non-degraded soils. Our findings provide novel insights into microbial-mediated carbon cycling and a foundation for targeted soil restoration.