How ecological regimes and emergent macrophytes determine sediment microbial communities: A new insight into typical eutrophic shallow lakes

Abstract Understanding the response of microbial communities to different ecological regimes in eutrophic lakes and the underlying assembly mechanisms is of great significance for revealing the biodiversity maintenance mechanisms of lake ecosystems under alternative stable states. However, our current understanding of the response of sediment microbial communities under emergent macrophytes to regime shifts remains limited. Here, we demonstrated, for the first time, the asynchronous variations of littoral sediment bacterial and fungal communities, regarding the microbial diversities, assembly mechanisms, and inter‐kingdom interactions across three lake regional regimes: macrophyte‐dominated, transitional, and phytoplankton‐dominated. We found the alpha diversities of the bacterial and fungal communities showed opposite trends, as the transitional regime had the highest bacterial but lowest fungal diversities. Stochastic processes, dominated by dispersal limitation, determined fungal community assembly, whereas deterministic processes, especially variable selection, shaped the bacterial community. The highest number of species–environment interactions and proportion of intra‐kingdom interactions were observed in the co‐occurrence network of the transitional regime; however, this network had the lowest proportion of inter‐kingdom (bacteria–fungi) interactions among the three lake regional regimes. Furthermore, the macrophyte‐dominated regime was observed to have the most complex network structure and maintain the highest microbial community stability. The rhizosphere of Phragmites australis enhanced the inter‐kingdom interactions of bacterial and fungal communities. These findings provide a preliminary ecological perspective for understanding the hysteresis of regimes in response to environmental stress at the microbial community level and emphasize the importance of distinguishing ecologically distinct microbial taxa in future studies focused on alternative stable states.