Microbial Generalists Contribute More to Co-Occurrence Network Stability than Specialists in Soils with Citrus (Citrus junos)

Microorganisms respond to changes in habitat resources by regulating their community structure. However, the variation in characteristics of microbial communities in soils with citrus cultivating for different durations remains unclear. We investigated the effects of the duration (3–5, 5–10, 10–15 and >15 years) of continuous citrus cultivation on the diversity and composition of bacterial and fungal communities, and the co-occurrence patterns of generalists and specialists in the orchard soils. The cultivation duration had no significant effect on fungal alpha diversity, but it increased the dissimilarity levels in both bacterial and fungal communities between the minimal 3–5-year duration and each subsequent duration. The top three most abundant generalists identified in the soils were Gammaproteobacteria, Subgroup_2 and Bradyrhizobium, for the bacteria, and Tremellales, Fusarium and Kernia, for the fungi. In total, 17–21% of generalists (e.g., Subgroup_2 and Candidatus_Nitrosotalea) and none of the specialists were found in bacterial networks, and 12–14% of generalists (e.g., Fusarium and Kernia) and 1.1–2.9% of specialists (e.g., Mortierella and Trechispora) were observed in fungal networks. The results highlighted that resource availability and environmental factors played a crucial role in shaping microbial communities. Our results provide insights into the roles of specific microbes in maintaining the stability of microbial co-occurrence networks and contribute to the exploration of microbial resources for the management of citrus orchard soils.