Community structure and co-occurrence network analysis of bacteria and fungi in wheat fields vs fruit orchards

Soil microorganisms play a vital role in biogeochemical processes and nutrient turnover in agricultural ecosystems. However, the information on how the structure and co-occurrence patterns of microbial communities response to the change of planting methods is still limited. In this study, a total of 34 soil samples were collected from 17 different fields of 2 planting types (wheat and orchards) along the Taige Canal in Yangtze River Delta. The structure of bacterial and fungal communities in soil were determined by 16S rRNA gene and ITS gene, respectively. The dominated bacteria were Proteobacteria, Acidobacteriota, Actinobacteriota, Chloroflexi, Bacteroidota, and Firmicutes. The relative abundances of Actinobacteriota and Firmicutes were higher in the orchards, while Chloroflexi and Nitrospirota were more abundant in wheat fields. Ascomycota, Mortierellomycota, and Basidiomycota were the predominant fungus in both soil types. Diversity of bacterial and fungal communities were greater in the wheat fields than in orchards. Statistical analyses showed that pH was the main factor shaping the community structure, and parameters of water content (WC), total organic carbon (TOC) and total nitrogen (TN) had great influences on community structure. Moreover, high co-occurrence patterns of bacterial and fungal were confirmed in both wheat fields and orchards. Network analyses showed that both wheat fields and orchards occurred modular structure, including nodes of Acidobacteriota, Chloroflexi, Gemmatimonadota, Nitrospirota and Ascomycota. In summary, our work showed the co-occurrence network and the convergence/divergence of microbial community structure in wheat fields and orchards, giving a comprehensive understanding of the microbe–microbe interaction during planting methods’ changes.