Soil DNA chronosequence analysis shows bacterial community re‐assembly following post‐mining forest rehabilitation

Abstract

Mining activities modify both aboveground and belowground ecological communities, presenting substantial challenges for restoration. The soil microbiome is one of these impacted communities and performs important ecosystem functions but receives limited focus in restoration. Sequencing soil DNA enables accurate and cost‐effective assessment of soil microbiota, allowing for comparisons across land use, environmental, and temporal gradients. We used amplicon sequencing of the bacterial 16s rRNA gene extracted from soil samples across a 28‐year post‐mining rehabilitation chronosequence to assess soil bacterial composition and diversity following rehabilitation at a bauxite mine in Western Australia's jarrah forest. We show that while bacterial alpha diversity did not differ between reference and rehabilitated sites, bacterial community composition changed dramatically across the chronosequence, suggesting strong impacts by mining and rehabilitation activities. Bacterial communities generally became increasingly similar to unmined reference sites with time since rehabilitation. Soil from sites rehabilitated as recently as 14 years ago did not have significantly different communities to reference sites. Overall, our study provides evidence indicating the recovery of soil bacterial communities toward reference states following rehabilitation. Including several ecological reference sites revealed substantial natural variability in bacterial communities from within a single mine site. We urge future restoration chronosequence studies to sample reference sites that geographically span the restored sites and/or are spatially paired with restored sites to ensure this variability is captured and to improve any inferences on recovery.

Integrating soil microbial communities into fundamental ecology, conservation, and restoration: examples from Australia

“…Soil microbiota are fundamentally linked to the restoration of degraded ecosystems; therefore, DNA‐based methods to characterise shifts in soil bacterial community composition have been developed to track restoration progress. Successful restoration of postagricultural landscapes back to biodiverse, functional, and self‐sustaining ecosystems is often hampered by legacies that linger from decades of unsustainable land use (Lem et al ., 2022; Peddle et al ., 2023). Developed from restoration chronosequence study datasets, a new ‘rehabilitation trajectory assessment’ (Liddicoat et al ., 2022) offers promise to help monitor and inform adaptive management practices and predict the ecological progress of restoration sites towards reference states (Craig Liddicoat, Flinders University).…”

Cradle-to-cradle mining: a future concept for inherently reconstructive mine systems?

“…In addition to integrating genomic sequencing technology into the EBS ecological and biodiversity assessment approaches, the same techniques can be used through the mining cycle to monitor the impact of the operations and their legacy sites on agroecosystems, forests, and freshwater habitats, thereby informing any future restoration processes (e.g. Liddicoat et al 2022;Peddle et al 2022). In sites that are seriously degraded prior to mining, the post-mining landscape could actually have a trajectory towards a strongly net-nature-positive outcome and there are good examples where post-mining or quarrying landscapes have been engineered to be beneficial to the environment (Mineral Products Association 2021).…”