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

Shawn Peddle, Flinders University
Ryan Borrett, Murdoch University
Paul Bullock, South32 Worsley Alumina
Mark Tibbett, University of Reading
Michael Gardner, Flinders University
Craig Liddicoat, University of Adelaide
Martin Breed, Flinders University
Siegfried Krauss, The University of Western Australia

Mining activities highly modify both above- and below-ground ecological communities, presenting substantial challenges in their rehabilitation. One of these impacted communities is soil microbiota, which has crucial functional roles in ecosystems but often receives less focus in rehabilitation than aboveground communities. Sequencing DNA from soil enables accurate and cost-effective assessment of these microbial communities, allowing for comparisons across land use, environmental, and temporal gradients (e.g. across a restoration chronosequence). Here, we use high throughput amplicon sequencing of the bacterial 16S rRNA gene from DNA extracted from soil samples across a 30-year post-mining rehabilitation chronosequence to assess soil bacterial composition and diversity following rehabilitation at a bauxite mine in Western Australia’s northern Jarrah Forest. We show that while bacterial alpha diversity did not differ between reference and rehabilitated sites, bacterial community composition was severely impacted by mining but 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 Bray-Curtis similarity to reference values compared to reference sites. We identified a significant association between Bray-Curtis ecological distance and geographic distance; however, we found this to be driven by three sample sites that were spatially separated from the main sampling area. This highlights the need to account for spatial influences in chronosequence studies assessing rehabilitation trajectories through an appropriate experimental design such as ours that incorporates multiple reference sites embedded within suitably replicated rehabilitation sites. Overall, our study shows how mining activities initially impact soil biota, but these communities appear to be on a trajectory towards recovery after rehabilitation.