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Abstract Microbes, similar to plants and animals, exhibit biogeographic patterns. However, in contrast with the considerable knowledge on the island biogeography of higher organisms, we know little about the distribution of microorganisms within and among islands. Here, we explored insular soil bacterial and fungal biogeography and underlying mechanisms, using soil microbiota from a group of land-bridge islands as a model system. Similar to island species-area relationships observed for many macroorganisms, both island-scale bacterial and fungal diversity increased with island area; neither diversity, however, was affected by island isolation. By contrast, bacterial and fungal communities exhibited strikingly different assembly patterns within islands. The loss of bacterial diversity on smaller islands was driven primarily by the systematic decline of diversity within samples, whereas the loss of fungal diversity on smaller islands was driven primarily by the homogenization of community composition among samples. Lower soil moisture limited within-sample bacterial diversity, whereas smaller spatial distances among samples restricted among-sample fungal diversity, on smaller islands. These results indicate that among-island differences in habitat quality generate the bacterial island species-area relationship, whereas within-island dispersal limitation generates the fungal island species-area relationship. Together, our study suggests that different mechanisms underlie similar island biogeography patterns of soil bacteria and fungi. 

Abstract Plant microbiomes are known to influence host fitness and ecosystem functioning, but mechanisms regulating their structure are poorly understood.Here, we explored the assembly mechanisms of leaf epiphytic and endophytic bacterial communities using a subtropical forest biodiversity experiment.Both epiphytic and endophytic bacterial diversity increased as host tree diversity increased. However, the increased epiphytic diversity in more diverse forests was driven by greater epiphytic diversity (i.e. greaterα‐diversity) on individual trees, whereas the increased endophytic diversity in more diverse forests was driven by greater dissimilarity in endophytic composition (i.e. greaterβ‐diversity) among trees. Mechanistically, responses of epiphytes to changes in host diversity were consistent with mass effects, whereas responses of endophytes were consistent with species sorting.Synthesis. These results provided novel experimental evidence that biodiversity declines of plant species will lead to biodiversity declines of plant‐associated microbiomes, but the underlying mechanism may differ between habitats on the plant host.