Soil nutrient levels determine the variation of bacterial communities in the rhizosphere of rice under different conditions of climate and genotype

Abstract

Abstract The rhizosphere microbiome, which plays a pivotal role in plant productivity, is shaped by both plant-related and environmental factors. However, few studies have evaluated the effects of plant genotype, soil type, climatic factors, and their interactions on the rhizosphere microbiome of rice (Oryza sativa L.). Here we used Illumina sequencing to investigate the bacterial community in the rhizosphere of two rice genotypes grown in three soil types (Albic, Black, and Chernozem) across three climatic regions in northeastern China. Results showed that soil type, followed by climate, was the primary factor in shaping the bacterial community structure, and their interactions significantly influenced α-diversity. Principal component analysis also revealed that the dispersion of bacterial community in albic soil was much lower than that in black and chernozem soils. Additionally, soil nutrients explained approximately 45% of the variation in bacterial communities, suggesting the effects of climate or genotype on the variation of bacterial communities are associated with soil nutrients. Network analysis revealed that the co-occurrence relationships in albic soil were loosened compared with black and chernozem soils. In three soils, the abundant taxa were more located in central positions within the network than the moderate or rare taxa. Moreover, the closeness centrality of abundant taxa displayed a significantly negative with organic matter, implying a more convergence communities in albic soil probably due to the loose co-occurrence relationship of abundant taxa by high organic matter. Our study revealed the underlying mechanism for the stability of bacterial communities in rice rhizosphere with rich organic matter, and provided a basis for improving the soil quality and maintaining the sustainable development of rice production via fertilization.