Bacterial diversity exploring and functional prediction in ancient rice original-producing region of Wannian County, China

Rice (genus Oryza) is the world’s largest food crop, and China has a long history of rice cultivation with widespread rice distribution. This study investigated the unique soil microecological environment of ancient rice-producing regions in China by examining the rice-producing areas around Wannian County. This study analyzed the structure and function of bacterial communities using 16S rDNA high-throughput sequencing technology and FAPROTAX function prediction while exploring the critical factors affecting them. The results showed that while there were no significant differences in physicochemical parameters (including pH, cation exchange capacity, organic matter, total phosphorus, available potassium, available phosphorus, Cr, Pb, Hg, Ni and As) between the ancient rice-producing area and the neighboring regions, this area had higher levels of total nitrogen (2.41 g∙kg ⁻¹), available nitrogen (289.57 mg∙kg ⁻¹) and copper (57.6 mg∙kg ⁻¹). The bacterial community characteristics were primarily different in composition rather than abundance (based on 16S rDNA fluorescence quantitative PCR technology) and alpha diversities (including ACE index, Chao1 index, Shannon index, Simpson index, and PD_whole_tree index) using 51 bacterial phyla found in the study area showed that Proteobacteria (22.17%), Chloroflexi (19.31%), Acidobacteria (16.95%), and Actinobacteria (13.46%) were the most abundant. Specifically, soils in the original rice-producing area contained a higher relative abundance of Firmicutes (5.80%) and Bacteroidota (2.98%), whereas Acidobacteriota (13.83%) and Nitrospirota (2.24%) had low abundances. For the dominant bacterial genera (>1%), soils in the original rice-producing area had a higher relative abundance of Xanthobacteraceae_unclassified (3.44%), Conexibacter(1.79%) and Methylocystis(1.83%), while Acidobacteriales_norank (3.09%), Thermofovibrionia_norank (1.37%), Candidatus_Solibacter(0.08%), Bryobacter(0.88%) and Holophagae_Subgroup_7_norank (0.88%) were low (not significant, P>0.05). In addition, the bacterial taxa in the ancient rice-producing area displayed a higher capacity for carbon metabolism (including methanol oxidation, fermentation, cellulolysis, methanotrophy, hydrocarbon degradation, and methylotrophy) but a weaker potential for nitrogen (such as denitrification, nitrous oxide denitrification, nitrite denitrification, nitrate denitrification, nitrite respiration, nitrate respiration, and nitrogen respiration) and sulfur metabolism (such as anoxygenic photoautotrophic sulfur-oxidizing and dark oxidation of sulfur compounds). Further analysis revealed that soil nutrient elements (e.g., cation exchange capacity, organic matter, total nitrogen, available nitrogen, available potassium, and available phosphorus), pH, and heavy metal elements (e.g., Cd, Cu, Hg, and Ni) influenced the characteristics and functional potential of the bacterial community. In conclusion, the distinctiveness of the soil environment in the ancient rice-producing area stemmed primarily from the higher availability of nitrogen and copper, with the bacterial community showing a higher potential for carbon metabolism than nitrogen metabolism. Our study found that not only were the physical and chemical environments of paddy soil in ancient rice original-producing regions different from those in other study areas, but that the microorganisms enriched there had a higher carbon turnover and nitrogen storage capacity. Together, these factors constituted a unique soil microecological environment in ancient rice-producing regions. This study provides a valuable theoretical reference for high-quality rice cultivation and environment-friendly field management practices.