Author: Shawn Peddle
Peddle, Shawn, 2025 Harnessing the soil microbiome to improve ecosystem restoration in a global biodiversity hotspot, Flinders University, College of Science and Engineering
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The effective restoration of degraded ecosystems is essential in addressing the twin global crises of biodiversity decline and climate change. However, restoration success is elusive, and the development of innovative methods is needed to address these shortcomings. Soil – our planet’s most biodiverse habitat – is home to at least 60% of Earth’s species yet it is inadequately integrated into the practice and science of restoration. The soil microbiome is a crucial component of healthy ecosystems. Improved integration of the soil microbiome into the restoration of biodiverse, functional and resilient ecosystems has the potential to improve restoration success and help address the global crises of biodiversity decline and climate change.
In this thesis, I take on exploring current and emerging practical uses of the soil microbiome in the restoration of functional and resilient ecosystems in southwest Western Australia – a global biodiversity hotspot. In chapter one, I present a comprehensive forward-looking review that covers current knowledge and future directions for the practical application of soil microbiota to improve ecosystem restoration (published in Biological Reviews). The review highlights how soil microbiota are currently integrated in ecosystem restoration, identifies knowledge gaps constraining their integration and suggests research to address these knowledge gaps. In chapter two, I use amplicon sequencing techniques in an observational study to assess the state of recovery of soil bacterial communities following landscape-scale revegetation across six restoration sites in southwest Western Australia (published in Biological Conservation). I identify key persistent agricultural land-use legacies that have inhibited the recovery of these important ecological communities. In chapter three, I use shotgun metagenomic sequencing approaches to explore how expanding from taxonomic-based metrics by examining functional potential can provide a more ecologically informative picture of the recovery of specific microbial-mediated ecosystem functions. In this chapter, I show that both taxonomic and functional gene compositions have not entirely recovered following restoration efforts and land-use legacies associate with these altered compositions. While results may indicate incomplete recovery, they do not necessarily mean dysfunction but likely reflect functional adaptations to altered conditions. In chapter four, I embed a soil translocation experiment into active restoration sites in southwest Western Australia to assess the effectiveness of three different soil translocation methods on the establishment of beneficial soil microbiota. I show that retaining soil structural integrity through intact soil translocations is important in achieving successful inoculation. By contrast, mixed soil translocations and surface spreading – the predominant method of soil translocation – saw microbial communities diverge away from the microbial profile of donor sites. Together, these thesis components employ novel methods to identify, address and close knowledge gaps towards improving ecosystem restoration outcomes through improved integration of the soil microbiome.
Keywords: ecosystem restoration, soil microbiome, restoration monitoring, restoration genomics, soil translocation, microbiota, soil inoculation
Subject: Environmental Science thesis
Thesis type: Doctor of Philosophy
Completed: 2025
School: College of Science and Engineering
Supervisor: Martin Breed