Mangrove roots harbor a repertoire of microbial taxa that contribute to important ecological functions in mangrove ecosystems. However, the diversity, function, and assembly of mangrove root-associated microbial communities along a continuous fine-scale niche remain elusive. Here, we applied amplicon and metagenome sequencing to investigate the bacterial and fungal communities among four compartments (nonrhizosphere, rhizosphere, episphere, and endosphere) of mangrove roots. We found different distribution patterns for both bacterial and fungal communities in all four root compartments, which could be largely due to niche differentiation along the root compartments and exudation effects of mangrove roots. The functional pattern for bacterial and fungal communities was also divergent within the compartments. The endosphere harbored more genes involved in carbohydrate metabolism, lipid transport, and methane production, and fewer genes were found to be involved in sulfur reduction compared to other compartments. The dynamics of root-associated microbial communities revealed that 56–74% of endosphere bacterial taxa were derived from nonrhizosphere, whereas no fungal OTUs of nonrhizosphere were detected in the endosphere. This indicates that roots may play a more strictly selective role in the assembly of the fungal community compared to the endosphere bacterial community, which is consistent with the projections established in an amplification-selection model. This study reveals the divergence in the diversity and function of root-associated microbial communities along a continuous fine-scale niche, thereby highlighting a strictly selective role of soil-root interfaces in shaping the fungal community structure in the mangrove root systems.

红树林根部含有大量微生物类群，这些微生物类群有助于红树林生态系统的重要生态功能。然而，沿着连续的小规模生态位的红树林根部相关微生物群落的多样性、功能和组装仍然难以捉摸。在这里，我们应用扩增子和宏基因组测序来研究红树林根的四个区室（非根际、根际、表层和内层）之间的细菌和真菌群落。我们发现所有四个根室中细菌和真菌群落的分布模式不同，这可能很大程度上是由于沿根室的生态位分化和红树林根部的渗出效应。隔室内细菌和真菌群落的功能模式也有所不同。与其他区室相比，内层含有更多涉及碳水化合物代谢、脂质运输和甲烷产生的基因，并且发现涉及硫还原的基因较少。根相关微生物群落的动态表明，56-74%的内圈细菌类群来源于非根际，而在内圈中没有检测到非根际的真菌OTU。这表明与内圈细菌群落相比，根在真菌群落的组装中可能发挥更严格的选择性作用，这与扩增选择模型中建立的预测一致。这项研究揭示了沿着连续的精细尺度生态位的与根相关的微生物群落的多样性和功能的差异，从而强调了土壤-根界面在塑造红树林根系真菌群落结构中的严格选择性作用。