Canopy gaps can result in abiotic heterogeneities and diverse niches from gap borders to centers, potentially affecting fine root decompositions mediated by soil fungal communities. Despite extensive discussions on the relationship between soil fungi and fine root decomposition, the mechanism by which gap locations regulate fine root decomposition through the soil fungal community remains elusive. Here, we conducted an in situ field decomposition experiment of Chinese Toon (Toona senensis) fine roots in a low-efficiency weeping cypress (Cupressus funebris) plantation forest across three microhabitats: gap centers, gap borders, and closed canopy areas. Soil fungal communities were determined using internal transcribed spacer (ITS) sequencing after two years of field incubation. Results showed that soil properties and nutrient content in residual roots varied across the three microhabitats, with the gap borders exhibiting the highest decomposition rates. While fungal α-diversity remained relatively consistent, taxonomic compositions differed significantly. Decomposition rates did not show significant correlations with soil properties, observed fungal ASVs, or overall community composition. However, they positively correlated with the relative abundance of saprotrophic Sordariomycetes, which in turn positively correlated with soil total nitrogen (with a highest correlation), peaking at the gap borders. Overall community variations were primarily driven by soil temperature and magnesium content in residual roots. Further analysis revealed high fungal community similarities and low dispersal limitations between the gap borders and closed canopy areas, with more phylogenetically clustered communities at the borders. These results demonstrate that the gap borders possess a high decomposition rate, likely due to the centralization of functions driven by soil fungi such as saprotrophs existing in the “microbial seed bank” or migrating from closed canopy areas. These findings highlight the key role of soil fungi, especially saprotrophic fungi, in fine root decomposition at the gap borders, stressing the importance of soil fungi-driven mechanisms in nutrient cycling, and also informing sustainable forest management practices.
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