Recovery of soil microbiota in naturally regenerating Acacia mangium ecosystems

Forest ecosystem restoration often focuses on the recovery of tree diversity and carbon stocks, with minimal attention given to soil microbial communities. Given the essential role of soil microorganisms for ecosystem health and recovery, this lack of understanding may limit reforestation success. In this study, we address this gap by analysing the taxonomic and functional characteristics of fungal and bacterial communities in minimally managed Acacia mangium plantations, especially considering their role in carbon sequestration and ecosystem functioning. We sampled naturally regenerating Acacia mangium plantations aged 2, 10, and 24 years, grasslands of Imperata cylindrica as the baseline condition, and remnant forests as reference state. We identified soil fungal and bacterial taxa through high-throughput amplicon sequencing of soil environmental DNA (eDNA), targeting ITS and 16S rRNA metabarcoding markers. Our results showed that microbial community and functional groups composition differed among landcover types, although taxonomic richness did not. Bulk topsoil organic carbon, pH, and total nitrogen were key factors associated with the composition of microbial communities, especially dominant fungal phyla. Symbiotrophic fungi and copiotrophic bacteria generally increased and recovered over time, potentially enhancing carbon (C) sequestration and balancing nutrient cycles. These findings demonstrate that natural regeneration in A. mangium plantations can promote the recovery of soil microbial communities and their associated functions, including those relevant for climate change mitigation. Furthermore, our study highlights the effectiveness of eDNA and high-throughput sequencing in monitoring early ecosystem shifts in soil microbial communities, which could be used to guide reforestation efforts towards desired ecosystem services.