Soil properties and agricultural practices shape microbial communities in flooded and rainfed croplands

Understanding the dynamics of soil microbial communities and the factors that affect those dynamics is crucial for comprehending the processes affecting soil fertility in agricultural ecosystems. Here, we used shotgun DNA sequencing to characterise 29 soil microbial communities in flooded paddies in China's Yangtze River Basin, and comparatively analysed the composition and function of microbial communities with 132 communities from North and South America's rainfed cropland. We hypothesised that soil microbial community diversity and functional composition are predominantly determined by edaphic properties and land-use history, rather than by spatial distance and climate. We revealed significant differences in taxonomic structure and functional composition among the microbial communities collected from a 2000 km transect along the Yangtze River and found that taxonomic diversity and genomic functional composition of the soil microbial communities were predominantly defined by soil pH. The significant correlation between soil pH and microbial community diversity can be extended to soils from different continents. Microbial communities in flooded paddies in China differed significantly from those in rainfed croplands in North and South America, while the communities from rainfed croplands in North and South America were similar despite their significant differences in geographic distance. Together with available evidence, our results suggest that soil microbial diversity is controlled primarily by edaphic variables rather than by climate, which differs fundamentally from the global biogeography of macro-organisms. The predominant element of soil properties (soil pH in particular) and the response of particular taxa to changing pH provides insight for the selection of agronomic practice. Agronomic practice and fertilisation may change soil pH and therefore alter soil microbial diversity and composition, which could have an impact on soil nutrient supply in agricultural ecosystems. Significance: Traditional methods may underestimate the microbial diversity. Metagenome analysis using whole genome sequencing allows quantification of the diversity more accurately and characterisation of the function of the mega-diverse soil microbial communities simultaneously. Using metagenome analysis on 141 soil microbial communities collected from global agriculture soil system with 32 from flooded paddies in China and 129 from rain-fed farmland in North and South America. We found that the significant correlation between soil pH and diversity of microbial communities can be extended to soils from different continents, which is fundamentally different from the diversity and community structure of macro-organisms. Moreover, we revealed that land use and cultivation history have shaped the taxonomic and functional composition in the soil microbial community. Our study deepens our understanding of the structure and function of the soil microbial community in general, and have particularly important implications in agricultural practice.