Long-term organic amendments regulate cbbL-harboring bacterial community via soil physicochemical properties and enzyme activities in a paddy soil

Purpose: Organic amendments improve soil physicochemical and microbial properties, but the effects vary by fertilizer type. These amendments also modulate the autotrophic CO₂-fixing microbial community, particularly those harboring the cbbL gene, which encodes the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) form I. Nevertheless, how cbbL-harboring autotrophs respond to different organic amendments and their associations with soil enzyme activities are still not well understood. Materials and methods: A long-term organic amendment experiment was established in a double-cropping rice paddy field in Southern China, including four treatments: without organic fertilizer input (control), green manure (GM), pig manure (PM), and rice straw returning (RS). Soil C-, N-, and P-acquisition enzyme activities were analyzed using a fluorometric method. The cbbL-harboring bacterial community was characterized by quantitative PCR (qPCR) and high-throughput sequencing. Partial least squares path modeling (PLS-PM) was used to determine the relationships among physicochemical properties, enzyme activities, and the cbbL-harboring community. Results and discussion: The organic amendments improved soil physicochemical properties, including pH and soil organic C (SOC). Soil C-, N-, and P- acquisition enzyme activities responded variably to the amendments. Although the cbbL gene number did not significantly change, all organic amendments reduced the diversity of cbbL-harboring bacterial community. Shifts in the cbbL-harboring community composition were also observed: GM enriched Afipia, PM favored Pseudonocardia, and RS exhibited increased abundances of Methylotenera and Sulfuricaulis. PLS-PM indicated that soil pH, SOC, and C- and N-acquisition enzyme activities negatively influenced the diversity and the composition of the cbbL-harboring community, whereas P-acquisition enzyme activity had a positive effect on the community diversity. Conclusions: Our study highlights the complex interactions among soil physicochemical properties, enzyme activities, and cbbL-harboring bacterial community under organic amendments. The results address the critical factors shaping the cbbL-harboring bacterial community, advancing our understanding of CO₂-fixing microorganisms in agricultural ecosystems.