Mining has always been an industry that’s built on measurement. Tonnes, grades, recoveries, energy use and more are tracked with increasing precision, forming the backbone of operational decision-making.
But there has long been a missing layer from this data ecosystem: life itself.
“DNA is essentially nature’s operating system. It’s present everywhere at mine sites. It exists in soils, water, air and waste, encoding how living systems interact with their environment. Until relatively recently, that code was near-impossible to decipher,” said Erin Marshall, Chief Operating Officer at Koonkie, a biological data analytics and software company specialising in DNA and biodiversity data.
Today, advances in DNA testing technology mean that operators can now read DNA at scale. In doing so, they gain access to a new layer of insight that sits alongside variables like geology, chemistry and engineering, to optimise their operations from a biological perspective too.
Environmental DNA and the future of mine closure
One area where DNA is already proving its value is mine closure. Closure has traditionally been a process that’s slow, uncertain and reactive. Operators implement rehabilitation strategies and then wait – often for decades – to see whether ecosystems recover. The problem is not just time, but the lack of early indicators.
Environmental DNA (eDNA) offers a different approach. By analysing DNA that’s present in soil and water samples, operators can track biodiversity from the earliest stages of site recovery. Instead of relying on visible signs such as vegetation or wildlife, they can assess whether the underlying biological systems are returning.
“We’re really excited about the ability to track early biological signs of recovery via eDNA, particularly in the soil,” said Marshall. “Soil health is foundational. It underpins plant growth, nutrient cycling and the broader ecosystem, so if we can understand what’s happening there early, we can get a much clearer sense of whether a site is on the right trajectory.”
This information enables:
- Trajectory tracking: The ability to compare disturbed areas with undisturbed reference sites for benchmarking purposes.
- Earlier intervention and course correction: The ability to identify what’s working and what’s not within years, rather than decades.
- Holistic biodiversity insights: The means to capture information on more of the ecosystem than traditional monitoring methods.
In practical terms, this shifts closure from a reactive process to a proactive one, reducing uncertainty and helping operators to actively manage the outcomes over time.
From monitoring to decision-making
The real test of any new dataset in mining is whether it changes decisions and eDNA is beginning to do exactly that. By comparing DNA signatures across different reclamation treatments, operators can see which approaches are most effective early enough to adjust their strategy.
“We were recently able to go into a site where different reclamation treatments had been applied, and compare them using eDNA data,” Marshall explained. “By looking at how the soil biology in those areas compared to an upstream reference, we could see quite early on which treatments were moving things in the right direction.”
This means that instead of committing years of time and capital before results are visible, operators can refine their interventions in near-real time. This has direct implications for cost, risk and liability.
Closure sites represent long-term obligations on company balance sheets. Any approach that can shorten timelines or improve predictability has immediate value both operationally and financially.
Beyond closure: exploration and safety
While closure is a natural starting point, DNA applications extend across the mining lifecycle. For example:
Exploration with fewer drill holes
DNA in soil reflects environmental conditions, including the presence of certain minerals buried underground. By analysing eDNA signals in surface soils, operators may be able to gain additional insight into the rocks that lie beneath. This does not replace drilling, but it can help to prioritise targets, thus reducing cost and improving confidence in early-stage decisions.
Safer, less invasive sampling
Exploration and monitoring activities often require personnel to operate in remote or hazardous environments. DNA-based sampling, by contrast, can provide meaningful insights from small samples that are easier and safer to collect. Using biological indicators means fewer boots on the ground. That has a direct impact on safety, particularly in confined or unstable environments.
Recovery in a lower-grade reality
Declining ore grades are forcing operators to rethink traditional approaches to metal extraction. If microbes are already facilitating parts of the recovery process, then understanding which communities are most effective, and under what conditions, creates the potential to optimise performance.
“We’re seeing a strong pull from miners to apply DNA insights across the mine lifecycle, particularly to optimise the leaching process in lower-grade ore bodies and waste rock” Marshall said. “There’s a lot of historical waste that still contains valuable minerals and microbial technologies can help unlock that under the right conditions.”
Turning DNA into insight: the role of M-MAP
Collecting DNA is only part of the story. The real value lies in its interpretation. The Mining Microbiome Analytics Platform (M-MAP) was co-created by Koonkie with mining partners Rio Tinto, Teck and others, and was designed to transform raw DNA data into actionable insights.
The platform integrates DNA data from thousands of mine-site samples along with environmental context on factors such as geochemistry, climate and location, using standardised methodologies to allow comparison over time. This creates a continuously expanding, mining-specific reference system that enables operators to benchmark their sites and understand change as it happens.
Rather than starting from zero, M-MAP compares new samples against data from other mine sites around the world, which gives immediate context and accelerates decision-making.
Importantly, M-MAP is not just a database: it’s an analytical layer that connects DNA with other datasets to unlock deeper, more actionable insights at an operational level.
A low barrier, high-impact dataset
One of the most compelling aspects of eDNA sampling is how easily it fits into existing workflows. Most mine sites already carry out routine soil and water sampling. Adding DNA analysis often requires nothing more than taking an additional sample at the same time. This simplicity lowers the barrier to entry, allowing operators to start small and scale their datasets over time.
A new dimension to the life-of-mine
eDNA will not replace traditional mining datasets. But it adds something that has long been missing; a way to understand the living systems that underpin mine performance and environmental recovery.
Seen through this lens, mining is not just about moving rock and managing chemistry. It’s about working within complex, dynamic and living ecosystems. eDNA provides a way to read that system and, increasingly, to act upon it.
For an industry facing growing pressure to improve its sustainability, reduce risk and deliver better closure outcomes, that represents a fundamental shift.
And it brings a new meaning to the phrase “life-of-mine”.
This article is sponsored by Koonkie. If you’ve enjoyed reading it, try this 2025 piece on bioinformatics and mine management, and download this case study from Koonkie and Rio Tinto.