In order to explore the distribution of cyanobacteria in paddy soil under different ecological conditions, the composition, diversity, and environmental drivers of soil cyanobacteria communities in rice fields from six regions of Jilin Province (China) were investigated. The results showed that the 16S amplicon high-throughput sequence detected the existence of cyanobacteria of 16 phyla, 33 orders, 60 families, and 113 genera in the soil of rice fields in Jilin Province. The dominant cyanobacteria populations in Jilin Province paddy soils comprised Cyanobium_PCC-6307, Synechocystis_PCC-6803, Planktothrix_NIVA-CYA_15, and Nodosilinea_PCC-7104. Each soil sample included a significant proportion of nitrogen-fixing filamentous cyanobacteria Anabaena and Nostoc according to microscopic analysis. The structural properties and diversity of cyanobacteria communities differed by geography, with soil pH and SOC being the main environmental drivers of cyanobacteria community structure. The alkaline soils S1, S2, and S5 displayed greater diversity than the acidic soils S3, S4, and S6, with S5 displaying the greatest cyanobacteria diversity. This research has crucial implications for developing and utilizing local cyanobacteria resources.

Cyanobacteria, ubiquitous phototrophic prokaryotes, can enhance soil fertility and crop productivity by promoting biological nitrogen fixation, phosphate dissolution, and mineral release. In this study, five nitrogen-fixing cyanobacteria were isolated and purified from paddy soil in Jilin Province. The effects of nitrogen-fixing cyanobacteria on soil fertility and rice seedling growth were examined through a pot experiment to clarify their growth and nitrogen-fixing characteristics. The results showed that the application of nitrogen-fixing cyanobacteria led to a significant increase in soil nitrogen content. GD2 and GD8 have the highest nitrogenase activity, at 75.33 U·mg⁻¹ and 50.34 U·mg⁻¹, respectively. It also enhanced the activities of urease, sucrase, phosphatase, and catalase in rice soil. In addition, it significantly promoted root development and plant height in rice plants. The total number of microorganisms in rice soil increased by 133–366%. Remarkably, the Desmonostoc muscorum GD2 strain was found to exhibit higher growth state indicators, including the growth curve, chlorophyll content, carbon and nitrogen content, and biomass accumulation, compared to other algae strains. The total nitrogen content of rice leaves treated with GD2 increased by 48.73%, and the soluble protein content increased by 52.89%. GD2 has great potential as an excellent nitrogen-fixing cyanobacteria inoculant for rice, suitable for agricultural production. In conclusion, the application of these nitrogen-fixing cyanobacteria significantly increased soil nitrogen levels and activated key enzyme activities involved in plant nitrogen metabolism. Moreover, it improved nitrogen utilization rates and promoted plant growth.