Habitat fragmentation is regarded as one of the major causes of species extinction in human-modified landscapes. However, the vast majority of existing fragmentation studies mainly focus on aboveground organisms, even though soil microbes play fundamental roles in maintaining ecosystem functions and services. In particular, the extinction of soil microbes has been largely overlooked because of the “everything is everywhere” assumption. Here we used inundated subtropical land-bridge islands as a model system to test the effects of habitat fragmentation on soil bacterial and fungal communities. We collected 306 soil samples from 29 islands in the Thousand Island Lake, China, as well the nearby mainland, and identified the bacteria and fungi by pyrosequencing.
Habitat fragmentation resulted in the loss of taxonomic and phylogenetic biodiversity for both bacterial and fungal species. Islands showed lower diversity than mainland, and the total OUT richness significantly decreased with decreasing island area. However, the loss of bacterial and fungal diversity was driven by different ecological mechanisms. For bacteria, OUT richness per sample (alpha diversity) was significantly lower in smaller islands, while the dissimilarities among samples within islands (beta diversity) remained constant. In contrast, for fungi, OUT richness per sample were not associated with island area, while dissimilarities among samples within each island significantly decreased in smaller islands, indicating a strong biotic homogenization due to habitat loss. Further, we found that environmental variables, such as soil chemistry, were the primary driver of bacterial community composition and structure. The structure of fungal communities, however, were largely determined by spatial factors (e.g., isolation). These findings suggest that increased habitat fragmentation would increase the extinction risk of soil microbes, but the conservation strategies for bacteria and fungi should be different.