Whole-Systems Orcharding

Healthy, profitable orchards require a holistic, multi-pronged strategy for disease and pest control

Orchard crops may receive the most pesticide and chemical applications of all crops. Some varieties will receive 20 or more pesticide applications per year. This has become one of the main tasks for an orchardist: sitting in a tractor and spraying. 

One of the most powerful arguments for regenerative agriculture is thus the potential to greatly reduce or eliminate toxic pesticide applications. 

After decades of proven examples in many crops in many climates, it is undeniable that regenerative farming methods — agroecological farming — can lead to farms and crops that are completely free of disease. What these farms all have in common is healthy soil, abundant farm biodiversity, and optimal plant nutrition, supported by the soil and plant microbiome. 

My farming career began more than 20 years ago on small, highly diversified, bio-intensive, organic farms, with an emphasis on agroecology. On those mixed vegetables and small polyculture orchards, disease and pests did not cause catastrophic crop damage. Using external inputs to control outbreaks was not in my farming paradigm. At the time I took this privilege for granted. I did not completely understand the mechanisms at play leading to crop and farm resiliency — I just trusted the process of a non-conventional chemical approach, focused on natural farming techniques, producing nutritious food for the community. 

Over the years, though, I have farmed and consulted on many large farms with less diversity and have witnessed incredible disease and pest pressure, both on organic and conventional farms. I have spent a lot of time obsessing over organic and biological controls and have learned from many pioneering experts — and from the lessons of hard knock on the fields. I’ve learned that there is no silver bullet — there are many ways to skin the cat to achieve natural resistance against disease, and control over pests. 

What needs to be well understood, and embraced, is a multi-pronged, adaptive approach rooted in a foundation of healthy soils and farm-ecosystem function. Let’s begin by remembering the fundamental reasons disease and pests often prevail.

The Root Cause of Disease

The are certainly many factors at play as to why a disease or pest becomes extreme or prevalent in a specific crop and region. Naturally, there is more potential for fungal disease in humid climates, or adaptation and mutation of a pathogen over time due to fungicide resistant and monocrop farming. But in all circumstances where disease and pests are abundant, the major issue is soil dysfunction, or poor soil health — i.e., soil that is devoid of a healthy microbiome. 

This underground problem is expressed aboveground: dysfunction exists in farms that lack biodiversity, where ecosystem processes are broken. The crops generally have poor nutritional health and a weakened immune system, only surviving on chemical life-support, achieving merely the yields required to offset farming costs. 

I can’t emphasize this next point enough: if you want to build true disease and pest resistance in your field, you must start with a foundation of intentionally farming by the principles of soil health. This requires being brutally honest about the current condition of your soil health and being willing to recognize the core management decisions that are causing excessive soil disturbance — whether from chemicals or from equipment. 

Disease-Suppressive Soils

A disease-suppressive soil is pretty simple by my definition: it is a soil that is well aggregated, down to at least 12 inches for most soil types, with abundant pore space that allows for optimal gas flow and exchange, water infiltration, and water retention. A well-aggregated soil has the ability to cycle gases, water and nutrients. It abounds in diverse soil microbes, which support much of the plant’s nutritional requirements while regulating and balancing the soil ecosystem. 

A disease-suppressive soil — i.e., a well-aggregated soil — will exhibit both anerobic and aerobic conditions, or pockets, down to the micro-aggregate level. In my experience, if soils are not well aggregated down to at least six inches, its biological nutrient cycling and disease-suppressive properties will be poor. Well-aggregated soils also reflect the abundance of saprophytic fungi on the soil surface, which play a critical role in pathogen regulation.

The Profound Role of Fungi in Perennial Crops

I have unfortunately found that most operators of large orchards and vineyards are not well educated in regard to the life support and plant immunity role of fungi for perennial crops.

All orchard crops — whether fruit trees, nut crops, grapes or berries — have a strong symbiotic relationship with fungal life, both in the soil and in the plant canopy (the phyllosphere). Without an abundance of fungi, perennial crops cannot develop a strong immune system or natural defense mechanisms against disease and pests. The physiology of trees — including photosynthesis, the uptake of nutrients, the synthesis of proteins and carbohydrates, and the ability to resist disease and pests — relies heavily upon mycorrhizal and saprophytic fungi, among many other soil microbial species. 

Soil microorganisms, specifically mycorrhizal fungi, are key players in the availability and transport of micronutrients to the tree. Micronutrients, or trace elements, are critical in the function of plant disease protection. Research has also found that mycorrhizal fungi have a supporting role in the populations of nutrient-solubilizing bacteria, which support the availability of many macro- and micronutrients. Without a robust population of mycorrhizal fungi in the orchard, trees exist in a state of poor health.

Saprophytic fungi may be of equal importance to tree and vine health, and are often less talked about. This family of fungi are the primary decomposers of dead organic matter, such as residues, leaves, woody material, and other dead organisms. They are responsible for breaking down lignin and cellulose, turning organic matter into carbon sources that the lower trophic soil level can feed on, and for unlocking further nutrients for the plant. 

But the most powerful thing about saprophytic fungi is their role in pathogen regulation, both in the soil and in the plant canopy. Many of the common orchard fungal pathogens that cause huge economic stress are saprophytic by nature. In nature, or in a healthy soil ecosystem, pathogen outbreak is kept in check and regulated by other saprophytic species. 

Ecological research has revealed an abundance of saprophytic fungi and bacteria in and on the bark and leaves of a tree’s canopy. The microbiome of the tree canopy, including the trunk, is known as the phllyosphere. The organisms in the tree regulate and suppress disease pathogens. They also help solubilize atmospheric nutrients and support the function of stomata and moisture regulation. 

If there is immense pressure from an insect or fungal pathogen, there is a deep imbalance within the farm ecosystem. This is often a problem that no product can solve. When conventional (and many certified organic) fungicides are applied, the tree microbiome is greatly disturbed. Systemic fungicides have a lasting effect on the ecosystem, regulating the regrowth of many fungi for two to three weeks. Conventional fungicide chemistries are great at what they were designed to do — wiping out saprophytic fungi, including the good guys. Spray mist also settles to the soil surface, killing more fungi and bacteria. 

So, what can we do about this? We can’t just stop spraying, naively wishing that the good guys will control the bad guys, right? The transition can be a challenge.

Measuring Soil Biology

Most conventional orchards and vineyards that bring me in to consult have very little soil fungi, as measured in the soil Phospholipid Fatty Acid tests (PLFA). These tests give me a ballpark understanding of the soil’s biological health and diversity, and potential biological support, both from a nutrient cycling and disease-suppression perspective. As I see fungi levels building in the PLFA tests I can become confident in reducing and eliminating conventional fungicides. 

I have found that a total fungal biomass of 500 ng/g on the PLFA is a good benchmark for a healthy level of fungi for most soils. I have seen it much higher, and I believe that values of 1,000 ng/g indicate a strong state of soil health. In the regenerative transition, once the fungal numbers are high, we can begin controlling disease, while greatly reducing or eliminating pesticides, by optimizing complete nutrition. 

Optimizing Plant Nutrition and Systemic Acquired Resistance

We have been greatly miseducated about plant nutrition by universities and fertilize sales companies. When it comes to understanding how and why balanced plant nutrition leads to optimizing disease and pest resistance, we can give big thanks to experts such as John Kempf and Dr. Kristine Jones, just to name a few. 

We may have always intuitively understood that a healthy, nutrient-dense plant has more immune support — but how do you get there? As I mentioned before, soil biology plays a critical role in the transport and availability of micronutrients. Micronutrients play a crucial role in enhancing plant immunity and protecting against diseases. They are often the missing link in plant nutrition and are not well understood in most fertility programs. 

If the soil biology is poor, then most micronutrients are low in the plant. Micronutrients such as iron, zinc, manganese, copper, molybdenum and boron are involved in many plant functions. As an example, many are involved in activating enzymes that drive the formation of secondary metabolites. Secondary metabolites include compounds such as phenols and terpenoids, critical metabolites with plant-defense mechanisms and antioxidant properties that support plant immunity. 

Many of these micros also serve in key functions such strengthening the leaf cell wall, making it harder for pathogen hyphae to penetrate and invade the plant. In addition, micronutrients are critical for production and storage of carbohydrates to the plant organs — a mandatory mechanism for plant survival, longevity and consistent fruit set.

When plant secondary metabolites are being produced, then the plant can develop what is called Systemic Acquired Resistance. This means that when a plant is attacked by a pathogen or insect pest, the plant sends out signals and develops an immune response to protect itself. A healthy, nutritionally balanced plant, grown in healthy soil with proper nutrition — and lots of it from the biology — can better defend itself. And guess what? Perennial crops are really good at defending themselves — after all, many species have figured out how to outlive humans!

Another nutritional discussion worthy of mentioning is preventing excessive nutrient loading in the soil and plant. This can create antagonistic responses that weaken plant immunity. As an example, it is well understood that high nitrates in plant tissue results in the plant being much more susceptible to leaf-feeding insects and pathogen colonization. Leaf-piercing insects can digest amino acids but cannot digest leaves high in proteins. High rates of synthetic nitrogen lead to reduced protein synthesis in the plant, which opens the doors for more insect and disease pressure. 

Sap analysis is an important tool for measuring nutrients to manage for plant nutritional balance. Addressing key micronutrients and making sure nitrates are not high in the plant is a good start for beginning to enhance disease suppression and wean off the harsh pesticides. However, I strongly suggest not to get too obsessed with the numbers on a sap spreadsheet. Use them as a general guide. If you don’t optimize soil health practices first, then you will chase your tail on sap testing.

The Role of Bioinoculants and Biostimulants

Biostimulants provide a food source for microbes. Most also help chelate nutrients and help the plant utilize them more efficiently. It is standard in my work to always fertilizer with a biostimulant. This allows me to greatly reduce the quantity and rate of the product being used — and to get better results. Products like kelp and yucca extract also enhance plant immune response and reduce plant stress. Using these sorts of products can get us another step closer in reducing the detrimental disturbances of hard pesticide chemistries.

The most available biostimulants include fish and soy hydrolosates, humic acid, fulvic acid, kelp and seaweed, molasses, and yucca extract. A little goes a long way, and a combination can provide exceptional synergies, both as soil applied and foliar applications. A combination of biostimulants can serve as a means of mimicking root exudates or other humic substances in the soil. 

Bioinoculants in combination with biostimulants can be very powerful. I am mainly talking about those made on the farm, such compost teas and extracts that are brewed with biostimulants. You can also brew with a low dose of the nutrients your trees need. I call this bionutrient brewing — it creates a solution that is rich in organisms, carbon and nutrients. Be sure to make compost teas and extracts from high-quality compost, such as that from a Johnson-Su bioreactor, or allow the compost to cure for a while to build a good fungal component.

Biopesticides

Do biopesticides work? “I hear they don’t work.” “They are so expensive.” “If I’m going to spray, I want to know it works.” I have this conversation all the time. 

The short answer is that biopesticides are extremely effective — when applied at the right time, when they are well understood, and when the farm has some decent soil health and ecosystem function. There are some products that are actually more effective than their conventional counterpart. But many biopesticides have mixed or even poor results when applied to a highly conventional farm. 

When combined with proper soil health management and farm ecosystem function, and when addressing balanced plant nutrition, biopesticides are a strong tool. But they are not a product-for-product replacement strategy. 

Some biopesticides even enhance Systemic Acquired Resistance. There many effective bacillus products on the market now to control fungal pathogens such as apple scab, alternaria and mildews. Trichoderma products are effective at reducing root rot pathogens such as phytophthora, pythium, and rhizoctonia. There are many plant-extract-based insecticides, such as neem oils, pyrethrin, thyme, cinnamon and spinosad. 

Some of these products are very expensive, though. In order to get the most out of any product, you have to become a master at scouting and understanding the lifecycle of the species you are managing. Do not think for a moment that if you spend the money to spray, things will be fine. Precise timing is critical. 

The Flaws and Fallacies of Orchard Sanitation

Sanitation practices — the act or blowing, sweeping, shredding, or tilling-in fallen leaves, sometimes including applying nitrogen in order to reduce pathogenic inoculum — is a major expense in many orcharding systems. Yet I believe these practices often actually increase disease. I almost always recommend eliminating sanitation practices with my clients.

Back to the phyllosphere for a moment. The decomposition of leaves begins before the leaves fall and hit the ground. A healthy tree is loaded with decomposing organisms in the canopy. They play a role in leaf color change. When there is an abundance of fungi and bacteria thriving in the canopy, the decomposition process is enhanced. Of course, standard fungicide programs eliminate this. 

Leaf mulch is critical for tree health. This is a tree’s natural cycle to replenish nutrition and feed the soil around the trunk. Decomposing leaf mulch enhances beneficial saprophytic fungi, and when the leaves fall with a bunch of organisms on it, the leaf mulch, of duff microbiome, is immense. Worms love leaf mulch. Perennial crops will only thrive when there is significant mulch built up around the base of the plant. Applying woody mulch is also beneficial.

Fallen fruit or nuts that have overwintering larvae decompose faster. On top of that, we see more birds in unsanitized orchards, scratching around and feeding on insects and soil larvae in the leaf mulch. This is free nutrients and pest control. We refer to this sequence of events as “positive compounding.” 

But when sanitation practices with tillage occur, we are creating negative compounding effects, which contribute to farm ecosystem dysfunction, leading to more reliance on fungicides and other inputs. This is one reason why the economics are failing in many orcharding industries across the U.S. We have literally created more work and expenses for ourselves.

Livestock Integration — The Disease and Pest Management Squad

Integrating livestock is one of the soil health principles that scares many orchardists. Alternatively, it’s even an excuse: “I can’t do soil health because I can’t have animals.” But when a farm commits to the integration of animals, a whole other superpower gets unlocked. Livestock are of course a very powerful tool for enhancing nutrient cycling, but I believe their greatest impact in orchards is in reducing diseases and pests. 

How does this work? First, when managed regeneratively, in particular with adaptive grazing principles, the plant diversity on the land increases. This promotes greater diversity of beneficial insects and birds — i.e., more good insects and less pest pressure. 

The manure, urine and biology from the saliva of animals enhances decomposition in the field. The organisms in their feces and fluids also play a role in enhancing the overall biology, increasing pathogen regulation. Sheep, for example, will increase the decomposition of leaf mulch and reduce the potential of high inoculant loading. They will also eat fallen nuts or fruit, including those that contain overwintering larvae such as coddling moth or naval orange worm. 

Chickens, especially layers, are masters at finding larvae in the soil and from fallen fruit or “mummy” nuts. Chickens are a very powerful tool for controlling moth species, or any insect that lays their eggs and larvae in the soil and leaf litter. They also provide a great source of nutrients from their manure. If you have lots of leaf litter around the tree, the chickens will spend more time around the tree, scratching and scavenging for insects and worms. I have experienced a huge reduction of coddling moth in apples with the introduction of chickens. 

Building Habitat on the Farm

If you do not want to raise livestock, no worries — we can still bring wildlife (i.e., free workers!) to the farm. More plant diversity on the orchard floor increases predatory and beneficial insects and other wildlife. Do not underestimate the significance of this. One hundred percent of the time, when orchard-floor diversity increases, pest pressure declines. Managing the orchard floor like a grassland ecosystem or pasture for some length of time will bring grassland birds species. Just envision what they are doing down there — feeding and fertilizing. 

The Research Institute for Organic Agriculture in Europe has released a publication called “Perennial Flower Strips — A Tool for Improving Pest Control of Fruit Orchards.” It presents a long-term study comparing conventional orchard floor management with organic orchards that managed for lots of plant diversity. The organic orchards, which had no insecticides sprayed, had less apple aphid damage than the conventional orchards using standard insecticide applications. The plant diversity alone in the organic orchards, which brought in more beneficial insects, was more effective at controlling pests. 

Orchards and vineyards that have ecosystems within and outside of the fields always have more birds of prey, including raptors and owls. Barn owls and hawks can significantly control rodents, such as gophers, voles and field mice. A barn owl is a master nocturnal hunter and can consume up to 3,000 rodents in one breeding season. I highly recommend that all orchards install barn owl boxes. They are generally occupied immediately. Be sure to learn how to manage them for success. Also, install raptor perches and bluebird boxes around the farm. Raptors contribute to the control of rodents, and bluebirds feed on insects.

And last but not least, bats. Bats are magical in the orchard. A single bat can consume up to 5,000 insects per night! One colony can eat hundreds of thousands of insects in a single evening. Installing bat boxes is essential in my work — specially in orchards that battle moth or lepidoptera species. Bats love anything that flies. You do not need to install many boxes on your land to make an impact. 

I understand it can seem overwhelming to find time to do all of this, but the addition of raptor, owl, bird and bats boxes makes an incredible difference on pest pressure.

Bird Nestbox Plans The Cornell NestWatch program (nestwatch.org) helps you figure out what species of birds are in your area and what type of nests they prefer — and it offers free downloadable plans to build nestboxes.

Conclusion

I understand this article appears to throw everything at the wall. But a whole-systems approach truly is required to achieve regenerative disease and pest control. Although products and inputs were mentioned as a tool, I want to make sure the reader walks away understanding that you are responsible for the conditions you create on your land. 

In the words of Michael Phillips, the great orchard ecologist, “If there is immense pressure from an insect or fungal pathogen … there is a deep imbalance within the farm ecosystem that calls for immediate action and attention, which no product will solve.” 

Your management determines whether disease and pests are causing uncontrollable damage or not. The foundation of the regenerative approach is farming for soil health within the guidelines of the principles. Manage the ecosystem and utilize all the tools I have mentioned in this article, and you will begin chipping away at a more economical and less toxic approach. What you may also find is that your long-term yields improve or crop quality improves. Disease and pest resilience go hand-in-hand with quality and nutrient density. 

Regenerative orcharding requires more thinking and observation. Over the years, though, more time should open up in your day, and farm economics should improve. It’s just a smarter way to farm. 

Chuck Schembre is a consultant with Understanding Ag.