Crop rotations alter bacterial and fungal diversity in paddy soils across East Asia

• The cosmopolitan taxa might play key-species roles in the ecological networks.
• Fungal slope of distance–decay was steeper than bacterial at the continental scale.
• Soil pH was more important than total nitrogen in predicting microbial diversity.
• Crop rotations remarkably altered microbial diversity, community composition and network.

Rice ecosystems are distributed broadly from temperate to tropical regions, but little is known about the underlying mechanisms shaping microbial communities and their network structure in paddy soils at the continental scale. Soil samples were collected from paddy fields across East Asia representing four types of crop rotations: single rice, rice–wheat rotation, double rice, and rice–legume–rice rotation. Here, we describe the roles that crop rotations, environmental heterogeneity and geographical distance play in determining the spatial distribution of microbial communities in paddy soils across East Asia. Our survey revealed remarkable differences in the diversity and composition of microbial operational taxonomic units (OTUs) among four crop rotations. The shared cosmopolitan OTUs Rhizobiales bacterium (genus Bradyrhizobium) and Hypocreales fungus played key-species roles in the ecological networks. A steeper slope of distance–decay for the fungal samples compared with the bacterial samples implies a faster turnover in fungal OTU composition across geographical zones. Bacterial communities were affected by soil environmental heterogeneity to an extent that overwhelmed the effect of geographical distance, whereas fungal communities were better predicted by geographical distance. The diversity and composition of bacterial and fungal communities corresponded strongly to soil pH but less strongly to total nitrogen. Remarkably, crop rotations played a key role in determining the changes in microbial diversity, community composition and networks. Taken together, these results provide a baseline ecological framework with which to pursue future research on soil microbial function in paddy soils.

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