To fight climate-triggered cacao fruit rot, this farm turned to soil, not pesticides
A regenerative farm in Dakshina Kannada is preventing fruit rot through soil inoculation, by using a consortium of microorganisms to counter disease-causing pathogens, writes Vijayalakshmi Sridhar
“Instead of using rat poison, get a cat to check a rat infestation…that is essentially what bio-control is,” says Dr Varanashi Krishna Moorthy, a microbiologist. “It is close to nature’s own solution.”
Dr Varanashi’s analogy captures a central problem in modern agriculture - related to pests and diseases in crops. Crop diseases are biotic stresses caused by pathogens—bacteria, fungi and viruses—that thrive when ecological balance breaks down. Chemical pesticides remain the most common response, but they are systemic and disrupt the health and ecology of the soil.
Bio-control, by contrast, relies on living organisms to keep pathogens in check and works within the ecosystem rather than overriding it.
We were speaking with Dr Varanashi and Dr Ashwini Krishna Moorthy, soil macrobiologist — at Surya Kanti, one of the cottages in the 100-acre Varanashi Farms in Adyanadka, a village on the foothills of the Western Ghats, about 50 kilometres south-east of Mangaluru, close to the Kerala border. Dr Varanashi inherited the land from his maternal grandmother, Thirumaleeswari Amma, a descendant of the Chakrakodi family.
In 1991, after attending a workshop on alternative farming systems, Dr Varanashi began converting the estate into a regenerative farm. By then, chemical farming at Varanashi Farms had already begun to show its limitations: a flush of vegetative growth without corresponding yields, alongside rising pest and disease pressure in arecanut, cacao, paddy and black pepper—the farm’s main commercial crops and staples of the region.
The problem was particularly acute in cacao. In and around Adyanadka, cacao crops are routinely attacked by two fungi—Phytophthora parasitica and Fusarium—which cause young fruits to blacken and fall off. During severe years, such as the rapid outbreak in 2024, nearly 60% of the cacao crop turned black and dropped at the flowering stage.
To address this, Dr Varanashi shifted focus from treating the plant to strengthening the soil. “The enemy of your enemy is your friend,” he says, explaining the logic behind bio-control.
Through continuous soil analysis carried out at Varanashi Farms since the early 1990s—such as tracking micro- and macro-nutrients, organic matter, organic carbon content, electrical conductivity and soil pH—he identified four “good guys” or good microorganisms that consistently co-existed in healthy soils.
When present in higher numbers, Trichoderma, Pseudomonas, Bacillus megaterium and Bacillus circulans, were found to suppress the “bad guys” or the disease-causing pathogens.
“This is not a hundred-per-cent solution, but it helps save about 80% of the crop,” Dr Varanashi says.
Unlike chemical compounds, these natural agents need time to multiply and establish themselves in the soil before they can counter pathogens, which spread rapidly and can devastate cacao plantations within weeks.
Putting bio-control to work
For bio-control to work, beneficial microorganisms must be isolated from the soil, tested, multiplied and then reintroduced along with compost and mulch. It is a slow, labour-intensive process, but a critical one.
Around three months after the monsoon and the annual manuring cycle, Dr Varanashi and his team dig vertical pits about a foot away from selected trees, choosing spots exposed to adequate sunlight. Soil samples from these pits are taken to the laboratory for analysis. Samples are drawn from a depth of 20 centimetres and 40 centimetres, and tested for nutrient content, acidity or alkalinity, and carbon-holding capacity. From a plot of up to six acres, as many as six samples may be collected.
Once microorganisms are multiplied under sterile laboratory conditions, they are introduced into the soil. For this, about 250 grams of soil is sliced from the side of each pit. The microbe-rich soil is then mixed with compost and mulch and returned to the ground. Freshly cultured strains, Dr Varanashi says, are more active and effective in competing with pests and pathogens.
To standardise the process, he developed a bio-based inoculant called Trichoplus, which contains a consortium of beneficial microorganisms mixed with compost and mulch. Dr Varanashi first encountered the disease-suppressing properties of Trichoderma during earlier research on mushroom cultivation.
The application process, referred to as inoculation, by analogy with vaccination, involves spreading about 30 grams of Trichoplus around the tree bed twice a year: once before the monsoon, typically in March along with irrigation, and once again after the monsoon. Repeated inoculation over time, Dr Varanashi says, improves soil fertility and builds resistance to recurring disease attacks.
The compost used in Trichoplus is also developed on the farm. Made by converting waste streams into stable, carbon-rich soil systems, it improves the availability of secondary nutrients such as nitrogen, phosphorus and potash. Its production relies on a microbial starter culture developed at the farm, known as the Varanashi composter.
Support systems
Inoculation alone is not enough. At Varanashi Farms, pest and disease control depends on an integrated approach that combines biological inputs with cultural practices.
Adequate irrigation is essential for inoculation to be effective. To reduce exposure to fresh disease attacks, cacao plants are also pruned thoroughly in August, as the harvest season draws to a close. Pruning improves air circulation, limits the spread of fungal spores and reduces conditions that favour infection.
Additionally, cacao at the farm is not grown as a monocrop. Instead, it is inter-cropped within a diverse agroforestry system that more closely resembles a natural forest.
Inter-cropping disrupts pest cycles, prevents diseases from spreading rapidly across the farm, and allows resources such as sunlight, air and water to be used more efficiently. As a result, crops grown this way tend to show greater resilience than those cultivated in monoculture.
Within this multi-layered ecosystem, cacao is better able to withstand climate-triggered diseases such as stem canker, fruit rot, black pod rot and wilting disease.
Farm hygiene is maintained without removing mature trees. New plants are introduced only by filling gaps with saplings rather than by transplanting or cutting existing trees. In regenerative farming, trees are treated as long-term infrastructure.
Large plantations in the region typically prioritise arecanut, given its relatively stable market prices. At Varanashi Farms, cacao has remained a focus despite its vulnerability to disease. Organic dried cacao beans fetch around Rs 1,000 per kilogram, compared to about Rs 350 for conventionally grown produce, allowing the farm to offset risk through quality rather than volume.
For a resilient plantation and sustained yields, nourishment is as important as disease control. While the farm’s compost addresses most nutrient requirements, Dr Varanashi and his team also inoculate water bodies with effective microorganisms. Once every two months, microbial inoculum from the lab is mixed with jaggery and added to the farm’s seven irrigation ponds. When this water is used for irrigation, microorganisms gradually enter the soil.
Another key input is Arbuscular Mycorrhizal Fungi (AMF), a symbiotic soil fungus applied directly to plant roots, including those of weeds. Through its extensive underground mycelial network, AMF redistributes nutrients across plants, suppresses disease, improves soil structure and enhances microbial activity. It also accelerates the breakdown of organic matter, fallen leaves and bark, allowing nutrients to return to the soil.
What does a healthy ecosystem look like?
At Varanashi Farms, the answer stands in the form of a 65-year-old cacao tree. Cacao trees typically live for about 25 years. Planted by Dr Varanashi’s father, the tree is now tilted, its thick trunk resting almost horizontally on the ground, resembling a grandmother in repose. It is the star-attraction in the farm and holds proof that a well-maintained agroforestry ecosystem promotes longer lifespan and tree health. Here, the dry leaves crunching underfoot tell a different story. Beneath them lies a layer of mulch covering black, porous soil alive with organisms, Dr Varanashi explains. Elsewhere, outside the farmed area, the soil is red in colour.
Water, too, behaves differently at the farm. Everywhere there is the sound of trickling or gushing water. While Dakshina Kannada district receives an annual rainfall of about 3,912 millimetres, Adyanadka gets nearly 1,000 millimetres less. The surrounding region faces chronic water stress as rainwater runs off steep slopes, while extensive arecanut cultivation has further depleted groundwater levels.
At Varanashi Farms, catch pits, ponds, check dams, percolation pits and feeding borewells are used to slow, store and sink water into the soil. “The goal is to enable running water to walk, walking water to crawl, and crawling water to stand and sink into the soil,” Dr Varanashi says.
The impact is visible in the harvest. In 2022, the farm recorded a peak cacao yield of 4.5 tonnes. In 2025, production was close to that level at 3.95 tonnes—around double the output reported by many other farmers in the area.
Soil is the currency here
Repeated soil tests at the farm have shown high levels of microbial activity and organic matter, findings that have also formed the basis of several doctoral studies. A soil biome study conducted between 1996 and 1998 analysed 60 soil samples over three years from arecanut and cacao basins at the farm and found dense leaf litter functioning as both mulch and manure.
Compared to forest floors, plantation basins at Varanashi Farms showed significantly higher populations of humifying macro-organisms, including pill millipedes (Arthrosphaera sp.), black millipedes (Jonespelites sp.), red millipedes (Spirostreptus sp. and Julus sp.), and earthworms: all indicators of active decomposition and nutrient cycling.
The incessant fight over evil
Each spell of rain brings renewed pressure. Disease-causing pathogens thrive in wet conditions, often overwhelming beneficial microorganisms in the soil and weakening their ability to support nutrient uptake. When pathogens destroy food reserves stored in plant roots, beneficial microbes can die off as well. With climate change extending monsoon periods, heavier and more prolonged rainfall has meant longer and more frequent disease attacks.
In such conditions, regenerative farming becomes a matter of timing and judgement—understanding soil cycles, microbial activity and the needs of the moment.
“Our interaction with the Earth never ceases,” says Mahalinga Naik, a 79-year-old farmer who lives with his wife on the farm. He spends most of his day tending to the fields, opening water channels, spreading manure and checking crops.
His preventive remedy against bacterial and fungal attacks is a traditional mixture of copper sulphate and lime, known as Bordeaux mixture. “Natural cultivation methods are the only ones I know,” he says.
For many farmers, however, economics determines what is feasible. Chemical fertiliser costs around Rs 5,000 per bag but is sold at a subsidised price of about Rs 500 and requires only 250 grams per plant. Organic manure costs roughly Rs 1,200 per bag, receives no subsidy and needs to be applied at nearly two kilograms per plant. For small landholding farmers, the expense can be prohibitive.
“The struggle is not knowing how to do it, but how to keep doing it,” says Sundara Naik, a small farmer from Alike village in Adyanadka, one of the 1,800 farmers trained under the Moodambail Movement, a collaborative initiative by the state and central government in 2004 to bring back regenerative farming practises.
Alongside farming, Sundara Naik works as a driver to supplement his income, yet continues to invest in his land. On the way down, he pauses to show jasmine plants grown with poultry manure. “I make at least Rs 500 every day selling the flowers,” he says.
Why intervene at all?
Nearly 95% of a plant’s requirements come from sunlight, carbon dioxide and water; only about 5% comes from the soil. Most of what plants need is already present underground. What they require are microorganisms, the “cooks”, that make these nutrients biologically available. Care for the soil, Dr Varanashi argues, and it will take care of the crop.
Regenerative farming, he says, is a long-term commitment rather than a quick fix, but it is achievable when its principles are understood and applied consistently. At 65, Dr Varanashi visits the farm daily, supervising work and fine-tuning processes. Under his guidance, his son Partha Varanashi, a molecular biologist and international swim coach, has taken on outreach and education. Since 2014, more than 500 volunteers from around the world visit the farm each year to learn about soil microbiology and regenerative agriculture.
Beyond cultivation, the work now extends through training, outreach and the production of organic inputs. Still, Dr Varanashi says regenerative farming will become truly sustainable for most farmers only if bio-fertilisers and organic manure are made affordable. He remains optimistic. “Once voluntary carbon credits are fully established in India, regenerative farming will become more viable and eventually become the only way to farm,” he says.
This story is published as part of the Hands of Transition initiative, which connects communities leading the transformation of food systems in India. Officially launched in 2025, Hands of Transition brings design, storytelling, and ground-up action together to ensure that the people most affected by climate and food insecurity are also the ones shaping the solutions, as both messengers and drivers of change.
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Fascinating how the bio-control approach flips the typical agricultural mindset from treatment to ecosystem managment. The 80% crop salvage rate using microorganism consortiums vs chemical pesticides really hammers home that working with soil biology beats overpowering it. Had a similar experince with composting where letting natural processes dominate produced way better results than trying to control every varaiable.
I’m unclear as to why a 79 yo heritage farmer at the farm itself is quoted as saying he uses Bordeaux mixture there “because it’s all he knows and natural”!
Is this a cautionary tale showing what these innovators are up against? On their own land?
Bordeaux mixture is a very toxic chemical pesticide that is toxic to worker’s lungs and eyes, the forest eco systems and especially persistent in water bodies. NO!
https://pubchem.ncbi.nlm.nih.gov/compound/Bordeaux-Mixture#section=GHS-Classification
I treasure some beautiful antique gardening books, but was told early on by professionals to never ever start using their obsolete unstudied formulas for fertilizer or pesticides!
Lifespans were shorter way back then and science-based diagnostic methods were in their infancy. I can enjoy the engravings, design principles and companion plants recommendations without poisoning myself or anyone’s garden!
I would encourage the writers and publishers here to embrace a ‘fact-checking everything’ mindset towards this fascinating and hopeful story that is reaching all over the world.