High stochasticity in rare bacterial community assembly in rice-wheat rotation soils at a regional scale

A growing body of evidence highlights the important role of both abundant and rare microorganisms in agroecosystem for their respective ecological functioning. However, the ecological processes that govern the assembly of abundant and rare taxa microbial communities in rice-wheat rotation soils at a regional scale have not yet been elucidated. Here, we conducted a comprehensive investigation of bacterial diversity, community structure, and assembly in samples from 238 sites under rice-wheat rotation in eastern China. Soil pH was the most important edaphic factor shaping bacterial diversity and community structure. The Shannon diversity of both abundant and rare bacterial taxa had a parabolic relationship with soil pH, with diversity reaching its peak at pH values of 7.50 and 7.31, respectively. Abundant bacteria displayed greater sensitivity to soil pH than rare taxa. Stochastic processes, especially dispersal limitation, predominantly governed assembly for both abundant and rare bacteria, explaining 80% of observed variation. Remarkably, stochastic processes contributed >90% of variation in the assembly of rare taxa communities, surpassing its importance in abundant taxa community assembly. Moreover, the assembly of specific bacterial phyla was predominantly governed by stochastic processes in the rice-wheat rotation soils. Overall, our findings provide the first data that although soil pH can make an initial assessment of the variation of bacterial communities, the high level of stochasticity in rare taxa community assembly would make them highly unpredictable during agricultural managements in rice-wheat rotation soils. These findings contribute new perspectives to understanding the main processes underpinning the observed bacterial communities, with implications for soil sampling, biodiversity conservation and ecosystem functionality in rice-wheat rotation soils.