Building Better Forests From The Ground Up: How Soil Microbial Diversity Is Powering Sustainable Eucalyptus Plantations In South Africa
SOUTH AFRICA’S plantation forestry sector powers a major part of the economy, supplying pulp, paper, packaging, timber, poles, and biofuels. With some of the most intensively managed Eucalyptus plantations in the world, our operations are efficient and productive – but potentially vulnerable in ways we’ve overlooked for decades.
The unseen biological engine that sustains our plantations, the soil microbiome, is under increasing pressure. And unless we start managing it as carefully as we manage tree genetics or harvest cycles, the long-term health and productivity of our plantations could be hampered.
After seven years of collaborative fieldwork with Sappi and colleagues, we are beginning to understand not just what’s going wrong, but how we can fix it.
“After seven years of collaborative fieldwork with Sappi and colleagues, we are beginning to understand not just what’s going wrong, but how we can fix it”
MICROBIAL NETWORKS: THE INVISIBLE WEB HOLDING FORESTS TOGETHER
Recent work using microbial network analysis published in Forest Ecology and Management (2025) showed that fungal communities are especially sensitive to management practices. Unlike bacterial networks, fungal interactions collapse when post-harvest residues are removed, but flourish when biomass is retained.
These fungal networks are the biological equivalent of insurance. They regulate nutrient flows, support the tree’s immunity, and maintain good soil health. When we break these networks, we expose trees to environmental stress and pathogen attack. When we preserve them, we build resilience.
Network-based diagnostics gives foresters a powerful new tool: the ability to measure ecosystem readiness before symptoms appear. With the rise of molecular monitoring, we can now evaluate soil function, not just soil chemistry.
This matters because microbial collapse is not just a short-term concern – it can accumulate silently over successive rotations.
Repeatedly planting the same tree species, especially without microbial restoration or species rotation, leads to a rise in soil pathogens (e.g., Phytophthora, Fusarium) and a decline in beneficial fungi and nitrogen-fixing bacteria. The result: reduced tree vigour, lower yields, and in some cases, complete crop failure.
Our 2023 review in Current Forestry Reports drew attention to an emerging but under-recognised threat: the buildup of harmful soil microbes in continuously replanted shortrotation plantations. Like “replant disease” in agriculture, this phenomenon is now being documented in forestry systems around the world.
“If left unaddressed, this silent degradation could undermine the productivity gains of decades of genetic and silvicultural optimisation”
Our findings align with patterns seen in China, Brazil, and Zimbabwe – declining soil microbial diversity, deteriorating physical and chemical soil properties, and increased pathogen pressure. If left unaddressed, this silent degradation could undermine the productivity gains of decades of genetic and silvicultural optimisation.
A strategy to offset the ill effects of repeated planting and to improve microbial networks is the proper management of post-harvest residues.
Traditionally, post-harvest residues in Eucalyptus plantations are burned. It’s cheap, fast, and familiar, but it’s also destructive. Burning depletes organic matter, reduces moisture retention, and sterilises much of the microbial life of soil. Our field trials in KwaZulu-Natal, published in Applied Soil Ecology (2025), show that these effects lead to long-term declines in productivity.
By contrast, mulching, where residues are shredded and redistributed across the site, is highly beneficial. Mulched soils were up to 7°C cooler at peak temperature and held twice as much water. These conditions allowed diverse fungal communities to flourish, especially saprotrophs and mycorrhizal fungi that support decomposition and nutrient uptake.
What’s more, these improvements– likely driven by a combination of factors such as enhanced soil moisture, nutrient availability, and microbial activity – translated directly into tree performance. After four years, Eucalyptus trees on mulched plots had 25% more stem volume than those in burnt plots. That’s not just a marginal gain, it’s a compelling case for rethinking what we do with biomass after harvest.
Perhaps the most counterintuitive result of our work was this: doing nothing, at least for a while, can be a powerful intervention. In plots where planting was delayed for six months after mulching, we saw not just better fungal recovery, but healthier and faster-growing trees.
Why? Because the pause gave microbial communities time to recolonise the rhizosphere and begin breaking down organic matter. In fast-rotation systems, where every month is measured in revenue lost or gained, this finding challenges conventional thinking. But when a six-month delay yields a 25% increase in stem volume, the economics speak for themselves.
This strategy doesn’t require new tools, just new timing. And it demonstrates that microbial resilience can be a tangible lever in forest productivity.
Beyond mulching, we also tested how complete residue retention compares to removal (with and without fertilisation). The findings, published in Forest Ecology and Management (2023, 2025), were unambiguous. Plots retaining post harvest residues not only had higher nutrient availability, but they also harboured more diverse and functional fungal communities.
Fertilisation provided a shortterm nutrient boost but did little to rebuild the underlying microbial network. In contrast, retained biomass acted as a slow-release nutrient source and a habitat for beneficial fungi. This matters because it’s not just about nutrients; it’s about sustaining the biological scaffolding that underpins root health, disease resistance, and long-term site productivity.
Globally, fertiliser is often regarded as the go-to fix for poor soils. But you can’t fertilise your way out of microbial collapse. Residue retention coupled with mulching and delayed planting offers a more ecological – and ultimately more sustainable – solution.
FROM PROBLEM TO PRACTICE: WHAT FORESTRY CAN DO RIGHT NOW
It’s easy to feel overwhelmed by microbial complexity. But our research points to five clear, actionable strategies that can begin reversing these trends:
- Retain and mulch postharvest residues. Biomass is not waste—it’s the foundation of the next rotation’s success.
- Delay replanting. Allow time for the microbial engine to rebuild before introducing new trees, although the optimal duration for this pause remains uncertain and warrants further investigation.
- Alternate or intercrop tree genera across rotations. Break pathogen cycles and diversify microbial habitats by alternating or intercropping, such as Eucalyptus with Acacia or Pinus.
- Inoculate seedlings with beneficial microbes. Equip nursery plants with symbiotic fungi and nitrogen-fixing bacteria to improve survival and growth.
- Use fungal network complexity as a monitoring tool. Incorporate molecular diagnostics into site readiness assessments.
These are not speculative ideas. They are science-backed interventions ready for operational deployment.
SOIL IS INFRASTRUCTURE: A NEW MINDSET FOR FORESTRY
Foresters have long thought of soil as passive, a substrate for roots and a container for nutrients. That view is no longer tenable. We must start treating soil as biological infrastructure, just as essential to plantation performance as roads, nurseries, or harvest schedules.
This shift, from extractive to regenerative forestry, is both urgent and achievable. We already have the tools. What’s needed now is the will to use them.
THE FUTURE OF FORESTRY GROWS FROM BELOW
We are at a decision point. Continue managing forests as factories, and we will see diminishing returns, rising costs, and greater biological risk. But manage them as ecosystems, rooted in microbial health, and we unlock a more resilient, productive, and sustainable future.
Soil microbes are not just a curiosity for scientists. They are strategic allies in the forest industry’s future. The question is not whether we can afford to invest in soil health, it’s whether we can afford not to.
“Let’s listen to what the soil is telling us – before it goes silent”.
SOURCES
Bose et al., 2025. Forest Ecology and Management, 586, 122734. https://doi.org/10.1016/j.foreco.2025.122734
Bose et al., 2025. Applied Soil Ecology, 210, 106091. https://doi.org/10.1016/j.apsoil.2025.106091
Bose et al., 2023. Current Forestry Reports, 9, 230.https://doi.org/10.1007/s40725-023-00188-z
Bose et al., 2023. Forest Ecology and Management, 532, 120806. https://doi.org/10.1016/j.foreco.2023.120806
Written By: Dr Tanay Bose (Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa)
Tanay.Bose@fabi.up.ac.za
Source: Tip-Mag
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