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Stuart McAlpine runs a mixed cropping and cattle operation at Buntine, in the northern wheatbelt of Western Australia – a semi-arid, Mediterranean-climate region with ancient, highly weathered soils.
Over nearly three decades he has built a reputation as one of WA’s most respected voices in regenerative and biologically driven farming. Stuart tests practices in his own paddocks through long
-term trials, watches what the data tells him, and acts on it.
Taking this approach a step further, one of Stuart’s more recent initiatives is undertaking soil DNA functionality testing through Green Mate Agriculture. This exercise is helping him identify exactly what biology is present in and absent from his soil, what functions it’s serving or inhibiting, and how to act on this information.
At the core of Stuart’s land management is a simple belief: soil biology is the foundation of everything. Without an active, functioning microbiome to build long-term resilience, most interventions are short-lived. The microbiome is what holds gains in place over time, and without that foundation, reliable production and profit simply aren’t sustainable. Stuart does, of course, acknowledge the need for soil biology to be addressed in tandem with other limiting factors.
“A lot of people that say…we’ll never get our soil biology right until we get the physical and chemical property of our soils right. I argue strongly that you need to work on all three at once.”
Where it began: Droughts, data, and a change of direction
Stuart’s interest in on-farm research isn’t new. In 1997 he co-founded the Liebe Group, a grower-driven organisation created to bring research capability into his isolated farming region. One of its earliest projects was a long-term soil health and soil biology trial on Stuart’s own farm, and the group has since flourished by treating farmers as genuine research partners and forming strong ties with the likes of DPIRD, CSIRO, GRDC, and other agribusiness partners.
Before Stuart was awarded WA No-till Farmer of the Year in 1999, he had long been reducing tillage, limiting soil disturbance, and demonstrating an overall progressive approach to producing food. But it was three severe droughts in the 2000s that prompted his most significant shift in land management. Still running a high-input system, Stuart noticed that profitability wasn’t following productivity, leading him to believe that declining soil health was his primary limiting factor. This set him on a path towards understanding soil biology as the missing piece.
The behaviour of Stuart’s cattle provides valuable insights into both the health and nutritional quality of his plants and the soil that supports them.
“What I once considered to be healthy, lush, deep green plants driven by high rates of fertiliser often aren’t at all because they’re the last plants in the paddock the cows choose to eat.”
By observing his cattle’s grazing preferences, Stuart has gained a deeper understanding of nutrient balance and oversupply. He has found that applying too much of any nutrient can disrupt the function of the soil microbiome and lead to inefficiencies, with nutrients either going unused or being supplied in ratios that the plant and soil system simply does not require.
More importantly, plant health is about far more than yield or colour. When soils are biologically active and nutrient cycles are balanced, plants produce a wider range of compounds that nourish both livestock and people. These include amino acids, antioxidants, polyphenols and other secondary metabolites that contribute to nutrient density, improve flavour and support animal and human health. Many of these compounds also play a critical role in the plant’s own defence systems, helping it resist pathogens and insect attack and reducing its reliance on external inputs.
Shifting his system to embrace biology
Today, Stuart’s operation includes cereal cropping (wheat, canola, lupins) alongside cattle. Over recent years he has transitioned away from synthetic fungicides and insecticides, intervening with these chemical controls only occasionally. Stuart has built the use of biostimulants (a blend of 40-50 plant exudates) into his program to support a stronger, more diverse microbial community.
He has also been trialling reduced and more targeted fertiliser use, testing lower and zero-fertiliser strips against his standard program. Following their worst drought financially in 2023, and a similarly tough start to 2024, Stuart planted his entire cropping program without any starter fertiliser at all – a decision backed by nearly 20 years of on-farm trial data. Stuart waited until he was confident that seasonal conditions were optimal (with sufficient rainfall), and opted to apply fertiliser following seeding. This decision was undertaken with the knowledge that any beneficial nutrients previously delivered by this starter fertiliser and taken up by plants would need to be replaced. Even with limited early rainfall to activate soil biology, the results were impressive, underlining the resilience the system had built over time.
The proof is in the paddock
Nearly two decades of trialling and data collection have produced results Stuart can point to directly:
All these outcomes are clear proof that Stuart has built a functional, living, resilient system. What he is still seeking clarity on, however, are the particular organisms and processes driving these. That’s what soil DNA functionality testing was brought in to investigate.
Closing the gap between instincts and evidence with DNA testing
Stuart’s property is now being tested using DNA soil functionality testing through Green Mate Agriculture, who collaborate with Biome Makers in the US to sequence soil samples for DNA and RNA.
A machine-learning model identifies all the organisms it can, then generates a functional map of the soil microbiome. Three key areas are addressed: which pathogens are present or absent and what’s controlling them, what’s helping the plant handle drought, heat, cold and salt stress, and which organisms are converting soil nutrients into a form the plant can actually use.
The composite soil samples used for this testing are usually taken from the same location and at the same time as standard chemical soil tests (usually from the root zone, around 15–20cm deep) so the biological results sit directly alongside the nutrient results, to enable a direct comparison of the chemical aspect of the soil with the biological aspect as well.
For Stuart, gaining a comprehensive understanding of nutrient and carbon cycling in the context of the microbiome is extremely valuable. It allows him to see whether the biology responsible for making nutrients available to plants is active and how it can be improved. Paired with observations like deepening root growth, the testing gives him a way to confirm whether his microbiome is functioning as it should, and where the gaps still are.
A comparable case from Green Mate Agriculture’s work elsewhere makes this point: a site with very high measured potassium levels was still showing potassium deficiency in the plant, because the organisms responsible for solubilising potassium had been crowded out by an overabundance of potassium-consuming microbes. More fertiliser wouldn’t have fixed that – only rebuilding the right biology would. It’s the same logic behind Stuart’s own decision to plant his entire 2024 program without starter fertiliser: the input itself was never really the limiting factor, and nearly 20 years of his own trial data told him so before the DNA results confirmed it.
Stuart first enlisted Green Mate to test his soils in 2024 across two contrasting paddocks – one on heavier soil, one lighter. Follow-up testing was carried out in 2025 after introducing biology that appeared to be missing from the first round of results. Because different crops recruit different microbial communities, Stuart is tracking results across crop types in rotation (cereals, canola, lupins) to build a season-by-season picture rather than relying on a single snapshot – a continuation of his ongoing commitment to building long-term evidence bases that direct his practices.
The report produced by Green Mate offers a suite of tools for helping farmers like Stuart understand their soil function, including a farm-specific microbiome visualisation (searchable by organism, shown as both raw cell count and percentage of the microbiome, to account for seasonal expansion/contraction); a comparison tool for tracking paddocks, trials, or the same paddock over multiple years; and a Venn diagram tool for comparing similarity/overlap between soils.
These tools elevate guesswork to diagnoses, supporting year-on-year tracking that allows farmers to detect whether interventions are working as intended. The report identifies the highest-value next steps within a given budget and set of objectives, rather than applying inputs indiscriminately – an expensive and often counterproductive approach.
Peter Briscoe of Green Mate Agriculture posits that we can rely on nature to slowly bring function back to soils, but costs and timeframes often necessitate interventions to accelerate this process. That’s the role that their customised, context-informed programs and evidence-based products can play.
Confronting challenges and facing realities
Stuart has noticed a flattening yield response curve to synthetic N and P, even in high yielding years, to the point that zero P trial plots are often just profitable as fertilised ones. He notes, however, that this approach may be unsustainable – if you’re not replacing what the crop removes, you’re mining a finite nutrient bank. There is a lot of work that needs to be done in surveying if these nutrients are being cycled from deeper in the profile and helping build more functionality in the soil to a greater depth along with understanding that we cannot exhaust nutrients to critical deficiencies in our soil.
The challenge of finding the “sweet spot” where crops are provided enough energy during cold, dormant periods without oversupplying soluble nutrients is ongoing for Stuart, who is acutely aware of the potential adverse impacts of this oversupply as well as undersupply.
Soil biology varies greatly from one property to another – what works for your neighbour may not work for you, and vice versa. Stuart holds this understanding close when investigating what’s driving his system, learning from others, and considering how his experience is best transferred and communicated.
Questions of energy expenditure and nutrient efficiencies continually come up for Stuart. Plants release carbon-rich compounds from their roots, feeding the soil microbiome that in turn helps nourish the plant. Enormous quantities can be exuded by crops and pastures to feed the soil microbiome, acknowledging that this is difficult to account for when considering return on investment.
“It’s been a long journey,” says Stuart. His system has been steadily developing and improving over decades – testament not only to his dedication but also to the fact that real, long-term shifts take time, trial and error, and endless learning.
Sustaining hope and scaling impact
Stuart recognised that what tools such as soil DNA functionality testing offer extend well beyond his own farm. He is hopeful that by embracing emerging technologies such as DNA soil functionality testing, productivity will improve across our agricultural landscape, and it will improve in conjunction with soil health, water holding capacity in a drying climate, and nutrient density. Through targeted testing and data interpretation, Stuart believes learning will accelerate across the sector and hopes that this information can feed back into local research institutions to compound knowledge.
Stuart sees tools like DNA functionality testing as an important bridge between observational science and institutional research, nature-based solutions and evidence-based science. “To me, it’s an exciting way for us to move back to working with nature and really start delving scientifically into what’s going on…We’ve still got a lot to learn, but we can’t learn unless we start testing and start trying to interpret the data…and hopefully some of that observation can lead back into our institutions and research institutions.”
Stuart’s connection with Green Mate, forged through his trailblazing work in soil biology, has opened the door for four additional farmers to access these services through RegenWA’s Advancing Natural Capital Accounting project. This is helping to remove the financial and access barriers that often keep individual farmers from this kind of testing and directly providing them information required to make informed decisions about practice change. In doing so, it’s building the evidence base for biologically driven farming more broadly, and above all, helping accelerate the adoption of regenerative agriculture practices.
