Craig Liddicoat from Flinders University speaks to AZoMining about his team's work on effective rehabilitation in post-mining ecosystems and whether it can set up a predictable trajectory of recovery. We also ask why ecosystem recovery is important in mining operations and the current limitations affecting its success.
Can you tell us about your role at Flinders University and how you began researching the rehabilitation of ecosystems in mining operations?
I am a post-doctoral Research Fellow in Restoration Genomics and my role involves the use of DNA-based assessments to better understand how soil microbial communities may be indicating and possibly facilitating the progress of post-disturbance restoration and recovery of biodiverse ecosystems. Since late 2020 I have worked in the Frontiers of Restoration Ecology research group led by Dr Martin Breed, within Flinders University’s College of Science and Engineering.
Our new paper, which focuses on the use of soil microbial data to track and predict the timing of post-mining ecosystem recovery, arose from collaborative work between restoration practitioners and researchers in the mining industry (Alcoa, Iluka Resources and South32), the Perth-based Kings Park Science (Western Australia Department of Biodiversity, Conservation and Attractions), Flinders University, and a number of other research partners connected to the Australian Research Council linkage project 'Optimising seed sourcing for effective ecological restoration'.
Siegy Krauss from Kings Park Science and Martin Breed from Flinders University were instrumental in setting up this particular study, as they had earlier proposed the use of a DNA-based survey of soil microbes to study the progress of long-term restoration sites at the mines. The data was collected as part of separate stand-alone Honours research projects undertaken with Murdoch University, Flinders University, and supported by CSIRO and the Australian Microbiome initiative.
As the data covered long-term examples of best practice mine site rehabilitation, they provided an ideal opportunity to develop and demonstrate a new alternative assessment approach that I had been working on to visualize and model the progress of recovery in soil microbial communities from disturbed or degraded states towards natural reference states.
Why is ecosystem recovery important in mining operations and what steps are common practices to achieve this?
Mining is a temporary activity, so following mine completion, it is important to reinstate a stable, resilient, and self-sustaining landscape.
Rehabilitation regains the value of the land for the desired post-mining land use and minimizes any ongoing environmental impacts. If the appropriate land cover cannot be established, there may be costly erosion and sedimentation impacts on downstream waterways, or dust emissions which can impact local communities.
In many cases, the goal will be to return former mining sites to locally appropriate biodiverse native vegetation. Such post-mining ecosystem restoration also forms part of the social license to operate.
These days, it is accepted best practice for rehabilitation and ecosystem recovery to be embedded in mine planning from the initial approval stages, within day-to-day operations (e.g. management and movement of soil materials), right through to relinquishment of the site.
Mining typically involves the removal of the overburden to gain access to the mineral ores, but surface soil layers, which are more fertile and biologically active, are critical to plant growth.
Soil layers may be stockpiled separately and are often moved as quickly as possible in the practice termed ‘direct return’ to areas that are undergoing rehabilitation.
Earthworks may be required to reconstruct locally appropriate landforms and drainage patterns, subsoil and topsoil layers are returned, and then deep-ripping and soil amendments may be required to enhance the soil’s physical and chemical conditions. Revegetation can then occur with the aim to recreate natural reference plant communities.
The below images were captured in 2016.
Alcoa Huntly mine site: rehabilitation in 2014 (2 years old). Image Credit: Siegy Krauss WA DBCA
Alcoa Huntly mine site: rehabilitation in 1987 (29 years old). Image Credit: Siegy Krauss WA DBCA
Alcoa Huntly mine site: Reference (undisturbed vegetation). Image Credit: Siegy Krauss WA DBCA
What are the current limitations and challenges surrounding ecosystem recovery in mining?
Mining companies are among the best informed and equipped restoration practitioners to be found anywhere. However, some mining environments can occur in naturally harsh climates and/or soil conditions.
Natural vegetation communities may have established and evolved in the landscape over long periods of time, with the support of beneficial interactions from other plants and a host of soil microorganisms. The process of restoring a near-natural, functioning ecosystem can be slow.
Some plants may be particularly hard to establish. It may be difficult to detect if certain critical components are missing, or if the disturbed soil’s physical, chemical, or biological parameters are holding back the new plantings from approaching the local reference natural states.
In some cases, new lines of evidence, such as analysis of soil microbial communities, can help provide additional information to help guide, adapt, or confirm rehabilitation strategies.
The below images were captured in 2019.
Iluka Eneabba mine site: rehabilitation in 2012 (7 years old). Image Credit: Siegy Krauss WA DBCA
Iluka Eneabba mine site: rehabilitation in 1981 (38 years old). Image Credit: Siegy Krauss WA DBCA
Iluka Eneabba mine site: Reference (undisturbed vegetation). Image Credit: Siegy Krauss WA DBCA
What is the significance of microbes and soil bacteria following revegetation at mine sites?
Soil bacteria, fungi, and other organisms play critical roles in decomposing organic matter, recycling nutrients to plants, and generally conditioning soils to create more favorable physical and chemical conditions.
They may even help suppress soil-borne plant diseases. Some microbes may be followers (i.e., supported by plant growth), while others may be facilitators (i.e., enabling or smoothing the way for certain plant species to thrive).
Gaining a better understanding of the soil microbial communities, and their shifting composition associated with revegetation can only add to our knowledge of the entire system that is involved with ecosystem recovery.
Can you outline your study, including the methods taken and key findings?
In our recent paper, we demonstrated a new method – based on high-throughput sequencing of soil eDNA and characterization of soil bacterial communities – to monitor and predict the progress of ecosystem recovery towards natural reference states.
At three case study mine sites in southwest Western Australia, with long-term restoration chronosequences (these are a series of study sites with varying rehabilitation ages), we measured the ecological similarity of soil bacterial community samples from rehabilitation sites to a number of corresponding reference samples that represented the desired target ecosystem.
A key step was recognizing that natural ecosystems from just a single location can be quite variable, and that variation needs to be accounted for if we are monitoring the progress of ecosystem recovery towards a target outcome.
Our method did not follow any particular taxonomic group, as individual community members or groups can vary greatly with site-specific conditions. Instead, our measures were based on the entire soil bacterial communities undergoing rehabilitation, and in the context of those local target reference conditions.
After quite a complex analysis, we saw simple patterns emerge. Over time, the rehabilitation sites were increasing in their similarity to the target ecosystems. We were able to visualize the results in simple plots and apply logarithmic slope models, or trend lines, to approximate how the measured ‘similarity to references’ were increasing with rehabilitation age. This approach provided a predicted timeframe for achieving recovery of the soil bacterial communities to a similar condition as found in the references, while also allowing for variability in those reference conditions.
Our research showed that effective rehabilitation can set up a predictable trajectory of recovery, and in these post-mining examples it can take 40-60 years to reach the target.
What is required to ensure more success in restoration?
Restoration project teams are typically highly skilled and experienced. Where necessary, and particularly in new or difficult restoration environments, we would suggest that additional measures to help understand what is happening in soil microbial communities may help expand the evidence and knowledge base to support restoration decisions and adaptive management.
It may be beneficial to trial soil inoculations, which aim to help speed up the supporting contributions of natural (reference ecosystem) soil microbial communities, and other researchers have previously suggested the embedding of such experiments into restoration works. If benefits are found from a particular soil biology treatment, then they can be applied at scale.
The images below were captured in 2019.
South32 Worsley mine site: rehabilitation in 2017 (2 years old). Image Credit: Siegy Krauss WA DBCA
South32 Worsley mine site: rehabilitation in 1996 (23 years old). Image Credit: Siegy Krauss WA DBCA
South32 Worsley mine site: Reference (undisturbed vegetation). Image Credit: Siegy Krauss WA DBCA
How does your research represent a vital step forward in quantitative microbiota-based metrics development for measuring rehabilitation success?
Studying ecosystem restoration through the lens of soil microbes represents a growing area of science. Typically, studies of soil microbial communities in a restoration context will present large amounts of information on changes and comparisons between particular taxonomic groups. While it may be possible to interpret certain functions to some of these microbes, many are capable of performing multiple roles and there can be a mixture of both environmental drivers and pure chance (for example, who settled first) that decide the relative abundance of any particular member/group of the microbial community. This means that looking at any particular microbe or group of microbes (and there can be tens to thousands of these depending on the level of taxonomic grouping) may often not provide clear and consistent signals to assess progress towards ecological reference states. Therefore, for the purpose of measuring rehabilitation progress, we avoided focusing on any particular group(s) of bacteria and instead looked at the whole community. From the processing of highly abundant soil eDNA-based data, our algorithm-generated simple numeric measures of ecological similarity to references, that were easily visualized and modeled with a trend line over increasing rehabilitation ages.
Successful and best practice mine closure planning requires specific, measurable, achievable, relevant and time-bound (SMART) completion criteria, such as returning ecological communities to match a target level of similarity to reference sites – and in the case of the fundamental ecosystem component of soil bacteria, our approach provided a measure of rehabilitation progress that is consistent with these requirements.
What challenges has your team faced during your research and how have these been overcome?
From my own experience, while we are supporting restoration practitioners, my work is largely computer-based so I am somewhat removed from the challenges in a hands-on role of working to establish complex plant communities at scale in field conditions. My challenges are largely around trying to handle, analyze, and interpret large and complex datasets. In my work, there are always new software and algorithms to learn, and I am challenged on a daily basis, in developing and debugging my own code for statistical programming and modeling. When writing computer code from scratch, it is inevitable that mistakes can be made, so I am constantly looking for two or three different lines of evidence to check and support the findings of my analyses. I am both challenged and motivated to find better and simpler ways to visualize data and results, as visual communication of findings is critical to building understanding, both for me personally and in communicating with others. That means I am continually learning and looking for better ways to do things.
What are the next steps for this type of research?
In studying ecosystem restoration from the perspective of soil microbes, there are numerous outstanding research questions, but I can probably only highlight a few here. Given the critical role of microbes and the generally slow nature of ecosystem recovery from highly disturbed states such as post-mining, our research group is interested to discover new ways to speed up ecosystem recovery. Perhaps this may be achieved through greater use of soil microbial inoculations, but that probably requires detailed work in a number of different types of environments to understand what type of inoculations may work best (e.g., are they generic or site-specific?). Techniques to study soil microbial communities might also be employed to help understand if there may be missing critical components that are holding back ecosystem recovery. Microbial communities and their patterns of association with soil physical and chemical conditions may also help point to particular adaptive management actions (e.g. soil amendments) that could be applied to help the progress of recovery.
Where can readers find more information?
Link to our paper: Next generation restoration metrics: Using soil eDNA bacterial community data to measure trajectories towards rehabilitation targets (free open access for 50 days): https://www.sciencedirect.com/science/article/pii/S0301479722003218?via%3Dihub
Wider reading from Science Magazine: Soil microbiota as game-changers in restoration of degraded lands: https://www.science.org/doi/10.1126/science.abe0725
For organizations that may be looking for assistance to trial or further develop our soil DNA-based restoration monitoring technique please feel free to get in touch ([email protected])
About Craig Liddicoat
Craig Liddicoat is a post-doctoral researcher at Flinders University focusing on the role of soil microbiomes in supporting ecosystem restoration and ecosystem services such as microbiota-mediated human health, and also a Senior Natural Resource Management Scientist with the South Australian Department for Environment and Water.
Research and career highlights include completion of a Ph.D. in Bioscience in 2019 researching connections between biodiversity, environmental microbiomes and human health.
Craig received a university doctoral research medal and a School of Biological Sciences postgraduate academic achievement award from his Ph.D. studies at the University of Adelaide.
Craig was part of the collaborative team that produced the groundbreaking, continental-scale, fine-resolution predictive mapping products of the CSIRO-led ‘Soil and Landscape Grid of Australia’, and was among a team of researchers presenting to delegates at the United Nations Biodiversity Conference hosted at COP14 Sharm El Sheik in Egypt 2018 on connections between biodiverse environments, microbes, and human health.
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