Litter decomposition dynamics are largely governed by microbial interactions. While the involvement of endophytic fungi in early-stage decomposition and microbial succession is well established, their species-specific contributions to decomposer community assembly remain insufficiently understood. This study investigated the effects of single-strain endophytic colonization using dominant species (Tubakia dryina, Tubakia dryinoides, Guignardia sp.) and rare species (Neofusicoccum parvum, Penicillium citrinum) on Quercus acutissima leaf decomposition through a controlled field experiment in a karst ecosystem. Endophytes accelerated decomposition rates across treatments but paradoxically reduced transient CO₂ emissions, linked to intensified microbial carbon and phosphorus limitations in late stages. Contrary to expectations, decomposition efficiency was governed by endophytic fungal species traits rather than colonization abundance, with rare species outperforming dominant taxa. Endophytes induced significant fungal community restructuring, reducing Ascomycota while enriching lignin-degrading Basidiomycota, but minimally affected bacterial composition. Co-occurrence networks revealed endophyte-driven fragmentation of microbial connectivity, with only two keystone fungal hubs (Trechispora sp. and Russula carmesina) identified compared to natural communities. Endophytic colonization improved fungal community assembly, mediated by an increase in lignin-degrading Basidiomycota and the suppression of pathogenic Leotiomycetes lineages. Our findings demonstrate that endophytes hierarchically regulate decomposer communities through phylogenetically conserved fungal interactions, prioritizing functional trait selection over competitive dominance, thereby stabilizing decomposition under nutrient constraints. This mechanistic framework advances predictions of litter decay dynamics in forest ecosystems undergoing microbial community perturbations.

This study examines the role of endophytic microbial colonization on the decomposition of oak leaf litter, a high-quality substrate in forest ecosystems. Over a one-year incubation, we observed a significant reduction in mass loss in colonized litter (46%) compared to non-colonized litter (80%), indicating an inhibitory effect of endophytes on decomposition. Structural equation modeling revealed a bimodal impact of endophytic microbes, with an initial enhancement followed by a pronounced inhibition as decomposition progressed. Extracellular enzyme stoichiometry showed phosphorus limitation became significant, particularly with endophytic colonization, contributing to reduced decomposition rates. Microbial diversity analyses exposed the variable impacts of endophytic colonization on fungal and bacterial communities, with taxa such as Helotiales (order) and Burkholderia–Caballeronia–Paraburkholderia (genus) significantly affected. The identification of 16 keystone species, mostly endophytic bacteria, underscored their pivotal influence on decomposition processes. Despite initial endophytic impacts, abundant carbon resources promoted stochastic colonization, potentially surpassing the effects of early endophytic establishment. This study provides insights into the priority effects of endophytic colonization and niche differentiation, offering a foundation for further research into the mechanisms underlying these processes and their ecological consequences in various ecosystems.