Exploring the biogeographical patterns and driving mechanisms of microbial communities in four microhabitats of Zostera japonica beds

Understanding the spatial distribution patterns and driving mechanisms of plant-associated microbial communities across multiple scales is essential for uncovering the generation and maintenance of microbial diversity under plant influence. However, large-scale evidence on the biogeographical patterns of seagrass-associated microbes remains scarce. Here, we sequenced microbial communities in four microhabitats (seawater, phyllosphere, rhizosphere, and sediment) of Zostera japonica beds in China, generating 480 amplicon sequencing datasets and 40 metagenomes. Subsequent analysis explored the structure and functional potential of microbial communities in these microhabitats. The microbial community exhibits significant spatial distribution patterns, characterized by latitudinal distribution patterns and distance decay relationships. While the null model results suggest a dominance of random processes in the construction of microbial communities in Zostera japonica beds, NST analysis reveals a transition from stochasticity to determinism in the assembly of rhizosphere bacterial communities with increasing latitude. Response ratio and GAM analysis further demonstrate differential responses of bacterial and fungal communities to environmental factors, indicating selective regulation of microbial groups by specific environmental drivers in different microhabitats. Functional analysis reveals that key genes involved in nitrogen and sulfur metabolism (such as nirS , norBC , cysNDCH , and cysJI ) display latitudinal gradient changes and microhabitat-specific differences in annotated microbes. For example, the cysC gene found in northern sampling points is sourced from Actinomycetota, Bacteridota, and Cyanobacteriota, while in southern sampling points, it primarily comes from Campylobacterota and Pseudomonadota, highlighting the functional adaptability of microbes to environmental heterogeneity. As the first systematic investigation into the biogeographic patterns of microbial communities associated with marine macrophytes, this study not only elucidates the multi-scale distribution patterns of Zostera japonica bed microbiomes but also establishes a theoretical framework for the dual regulation of microbial communities by latitude and microhabitat. The discoveries provide new insights into further investigating the interactions between microbes and seagrasses, as well as the potential for biogeochemical cycling. They contribute to understanding the adaptive strategies of seagrass ecosystems under different environmental pressures and how microbial communities respond to these stressors. This information is crucial for assessing the health of seagrass beds, predicting their response to environmental changes, and formulating effective conservation and management measures based on scientific evidence. Video Abstract