The Various Pests of an Apple Tree

This is Part 2 of a series on Indian agriculture relevant to North India, especially Himachal Pradesh. The cover image for this post has been taken from the Pesticides Atlas, 2022 (licensed under a Creative Commons Attribution License).

Horticulture i.e. cultivation of fruits and flowers, plays a crucial role in Himachal Pradesh’s economy. Key horticultural products of the state include apples, pears, peaches, plums, nectarines, apricots, mangoes, and oranges. Together, fruit crops cover approximately 234 lakh hectares of land in the state, and contribute an annual revenue of over ₹5,000 crores while providing employment to over nine lakh people. Among these fruit crops, cultivation of apples stands out, with the fruit accounting for over 48% of total area under fruit crop cultivation, and over 82% of the total fruit produced in Himachal during the FY 2022-23. These numbers are not only impressive but also hold a lot of potential in transitioning Himachal’s current agricultural landscape. Growing demand for “farm-to-fork” produce has already caught the attention of private investors and with the right policies, infrastructure, community participation, and entrepreneurial spirit it holds a lot of potential to boost rural incomes, and provide employment while driving economic growth.

However, the ongoing planetary crisis of climate change and global warming are a persistent threat to crops, especially those in the Himalayan range. Melting glaciers, erratic rainfall patterns, and increasing temperatures have been positively correlated with crop loss in the past. In addition, monocultures lead to unhealthier soils, weakening the ability of crops to withstand the impact of such rapid changes. Apple production in particular, has already suffered significant setbacks in 2024 due to lack of snow during the winter, coupled with untimely hailstorms and flash floods as the fruit began to develop. Furthermore, outbreaks of fungal infections and insect infestations further jeopardize the health of apple trees making dependence on the crop unsustainable in the long run. This poses a direct threat to the lives and livelihoods of many residents of Himachal, especially those in Kinnaur for whom apple cultivation remains a primary source of income.

In this post, I want to highlight some of the common pests—both fungal and insect—that orchardists in India may encounter. While I won't delve into the detailed biology or management of these pests (as these topics are thoroughly covered here, here, here and even here), I will only provide a brief overview for those who are curious. Instead, I would like to address broader, long-term challenges linked to monoculture practices, and the excessive use of chemical pesticides and fertilisers, and why they are fundamentally unsustainable. I hope to start a conversation on the experiences of our community members, and therefore want to focus on how pesticides, particularly fungicides of different types, are creating a vicious cycle of soil degradation, pest resistance, biodiversity loss, and environmental harm. It’s important to also  acknowledge that the ideas I share are not solely my own; and are drawn from the insights of scientists, researchers, and orchardists in and around Himachal Pradesh. I have made every effort to credit these sources wherever possible to ensure their valuable contributions are recognised.

Pests of Apple

Fungal Pests

1) Alternaria leaf blight (Alternaria mali)

Alternaria is a family of pathogenic fungus that is distributed across most apple growing regions of the world. Alternaria mali, in particular, is a significant threat to apple production in India, causing diseases like Alternaria leaf blotch, fruit spots, and premature defoliation. This fungus has become a major issue in Himachal Pradesh’s apple orchards, with a noticeable increase in infection rates over the past four years. The fungus initially manifests as small, round, purplish or blackish spots on leaves in late spring or early summer. As the infection progresses, the spots grow larger and develop a characteristic purplish border. These lesions can form irregular, darker, frog-eye-like symptoms, leading to premature defoliation. Impact on Apples: Severe defoliation can result in premature fruit drop, reducing both the quantity and quality of apples. Moisture in storage can also cause the fungus to spread, leading to rot in damaged fruits.

Alternaria infested apple leaf and fruit (Image: Madhu et al., 2020)

2) Apple Scab (Venturia inaequalis)

Apple scab, caused by the fungus Venturia inaequalis, has been another prominent issue over the last few years. It typically appears during the wet spring months, with the first symptoms seen as olive-green spots on leaves. If left unchecked, the fungus spreads rapidly, causing significant defoliation, reduced fruit size, and lesions on fruit, making them unmarketable.

Impact on Apples: Apple scab reduces fruit quality, causing blemishes that lower marketability. Severely infected trees may also have stunted growth.

Apple scab infestation on apple leaf and fruits (Image: Shafi et al., 2019)

3) Powdery Mildew (Podosphaera leucotricha)

Powdery mildew is another fungal pest that has affected apple orchards in Himachal Pradesh, with a rising incidence over recent years. This fungus appears as a white, powdery growth on leaves, shoots, and buds. Infected trees may show distorted growth, with leaves curling and turning yellow.

Impact on Apples: While powdery mildew doesn’t directly affect fruit but it weakens the tree, making it more susceptible to other diseases and pests. In severe cases, it can lead to reduced fruit quality and size.

 Powdery mildew infestation on apple leaf and young shoots (Image: Rather et al., 2015)

4) Sooty Blotch and Flyspeck

Sooty blotch and flyspeck are fungal diseases that cause cosmetic damage to apple fruit, making it unappealing to consumers. These fungi thrive in humid, wet conditions, and the symptoms appear as dark, blotchy spots on the skin of the apples. While these fungi don't directly harm the fruit’s internal quality, they do significantly reduce marketability.

Impact on Apples: While not affecting the fruit’s internal quality, sooty blotch and flyspeck can lead to significant cosmetic damage, reducing the commercial value of apples even though they are perfectly fine for human consumption.

Sooty Bloch (right) and Flyspeck (left) infestation (Image: KhanLab on X.com)

5) Marssonina Leaf Blotch (Marssonina coronaria)

Marssonina leaf blotch, caused by Marssonina coronaria, has emerged as a significant fungal pest in apple orchards in Himachal Pradesh this year. This disease typically appears as dark brown to black lesions on leaves, often surrounded by a yellow halo. Infected leaves eventually turn yellow and drop prematurely due to lack of chlorophyll and inability to photosynthesize affecting the overall health of the tree. Impact on Apples: Marssonina leaf blotch causes early defoliation, leading to weakened trees, reduced photosynthesis, and poor fruit development without attacking the fruit directly. This results in smaller, lower-quality apples and reduced yield.

Marssonina leaf blotch (Image: Dr Shahzad's Horti Clinic, Srinagar, India)

6) Core Rot / Bitter Rot / Fruit Rot (Fusarium spp. and Other Fungi)

Core rot, also known as bitter rot or fruit rot, is caused by a variety of fungi, including Fusarium species, which infect apples through wounds or during the ripening process. The symptoms often include soft, sunken lesions at the core of the fruit that cause it to rot internally, sometimes accompanied by a foul smell.

Impact on Apples: This rot leads to significant post-harvest losses, rendering affected fruits unsuitable for sale. It can spread quickly in storage, further damaging large batches of apples.

Management Tip!: Good orchard hygiene, careful handling of fruit to prevent injury, and optimal storage conditions are essential to minimize the risk of core rot and fruit rot. 

Core rot in apples (Image: Tribune India, 2018)

Insect Pests

1) Woolly Apple Aphid (Eriosoma lanigerum)

Apple orchards in Himachal Pradesh face significant challenges from woolly apple aphids (Eriosoma lanigerum), particularly during prolonged dry spells like those recently reported in Chamba. These pests appear as cotton-like clusters on tree trunks and branches, weakening trees and reducing yields. Natural predators like ladybird beetles and parasitic wasps play a crucial role in controlling aphid populations, and maintaining their populations is essential to combat the rise of aphids. Closely monitoring the trees and pruning of infested branches is generally advised alongside the application of insecticides during the dormant season. However, indiscriminate spraying of insecticides often eliminates beneficial and “friendly” insects too, disrupting the natural cycle of pest control and starting a perpetual cycle of dependency on chemical interventions. 

Woolly Apple Aphid infested branches and leaves (Image: Tamil Nadu Agricultural University)

2) Codling Moth (Cydia pomonella)

Codling moths (Cydia pomonella) are another major pest, with larvae that bore into apples, causing internal damage and making the fruit unmarketable. In Kashmir, codling moths complete three generations during the apple-growing season. To manage this pest, farmers generally use pheromone traps to disrupt mating cycles, apply insecticides during critical periods, and remove infested fruit to break the pest’s lifecycle.

Sting, deep entries, and calyx entries of Codling Moth larvae (Image: Disket Dolkar)

3) Apple Clearwing Moth (Synanthedon myopaeformis)

The apple clearwing moth (Synanthedon myopaeformis) poses a serious threat by boring into the trunks and branches of apple trees, potentially leading to tree death. Using pheromone traps, and applying trunk coatings such as lime or cottonseed oil to deter egg-laying, along with encouraging natural predators and parasitoids to control moth populations are generally seen as traditional ways of pest control.

Images of an adult Clearwing Moth, infested tree trunk, and Clearwing Moth Larva (Image: BC Tree Fruit Cooperative)

4) Tent Caterpillar (Malacosoma spp.)

Tent caterpillars (Malacosoma spp.), active in the spring and early summer, can defoliate trees and weaken their health. Effective control measures include manually removing caterpillar tents, applying insecticides during early infestations, and supporting natural predators like birds and parasitic wasps to manage their populations.

Tent Caterpillars infested peach plant (Image: Vikaspedia)

5) Burr Knot Borer (Saperda candida)

Burr knot borers (Saperda candida) target apple tree roots, leading to weakened trees and reduced yields. Control strategies involve soil treatment with insecticides after harvest, maintaining orchard hygiene by removing and destroying infested plant parts, and encouraging natural predators to keep the pest in check.

Apple trees infested by burr knot borers (Image: Rashmi ER et al., 2024)

6) Red Mites

Apple mites, including the European red mite (Panonychus ulmi) and the two-spotted spider mite (Tetranychus urticae), are common pests in apple orchards of Himachal Pradesh, with recent infestations reported in Shimla and Lahaul and Spiti. These mites feed on the undersides of leaves, causing yellowing, stippling, and reduced photosynthesis, which weakens trees and lowers fruit yields. Control strategies include the use of miticides during dormant and active growth periods, regular monitoring of mite populations to determine threshold levels, maintaining orchard hygiene by removing weeds that act as alternate hosts, and encouraging natural predators like ladybird beetles and predatory mites to manage infestations biologically.

Adult European Red Mite (Image: Ahmed et al., 2018, Qadir and Qamar, 2019)

In addition, there is a growing concern of other pests like Leafminer, San Jose Scale, Fire Blight, Stem borer, and others in the state, making it important for all stakeholders to find long-term solutions to manage these direct threats. More often than not fungicides play a vital role in combating these pests. Typically, contact fungicides (sprayed only on the infected part), systemic fungicides (sprayed throughout or in the soil for the plant to uptake), or a combination of the two are used to deal with these pests. I list some advantages and disadvantages of each, along with examples of fungicides used in the table below:

Table 1: Different types of fungicides

Type of Fungicide	Mode of Action	Advantages	Disadvantages	Examples	Criticisms
Contact	Directly kills the fungus upon contact. Not absorbed into plant tissue.	Fast action. Effective for controlling existing infections.	Easily washed away by rain, hence shorter duration of control. Only protects the plant where the spray is deposited.	Mancozeb, Captan, Propineb (Antracol), Sulfur, Copper salts	Repeated applications are needed. Relatively ineffective. Residues can remain on food. Some are dangerous to human health.
Systemic	Absorbed by the plant and distributed through the xylem vessels, i.e. from the roots to all water carrying tissues of the plant.	Longer-lasting protection. Controls both existing and potential infections.	May leave residues, hence are not recommended for crops close to harvest.Some systemic fungicides move to all parts of a plant. Some are locally systemic, but some move upward.	Carbendazim, Propiconazole, Tebuconazole, Diamethomorph,Metalaxyl, Bupirimate	The fungal pathogen can develop resistance more easily.Can increase sensitivity to a different chemical class (negative cross-resistance)*.
Trans - laminar	Redistributed from the upper, sprayed leaf surface to the lower, unsprayed surface.	Protects both sides of the leaf.Effective against fungi infecting the underside.	Less common	Trifloxystrobin	Some may be toxic to mammals, bees, and birds.
Contact + Systemic	Combination of both contact and systemic modes of action.	Offers a more comprehensive protection.	Disadvantages of both types of fungicides apply to this category.	Trade names: Saaf, Indofil, Amistar Top, Joint, Avatar	Criticisms of both types of fungicides apply to this category.

*negative cross-resistance: Once a pest develops widespread resistance to a particular pesticide, the chemical (or even the entire chemical class) loses its utility to act as a pesticide. In such cases, the pest that has developed resistance to one pesticide may become hypersensitive to another pesticide or toxin (single chemical or entire chemical class) called negative cross resistance toxins (NCR toxins). Theoretically, it becomes easier to eradicate pests that are resistant to one class of chemical pesticides with these NCR toxins, however,  research on NCR toxins is limited to academic laboratories at the moment. They are rarely developed by industries due to the extensive time and resources required for research, making these chemicals virtually inaccessible to the general public. This book chapter discusses the concept of NCR toxins in detail, in case you are interested. For detailed information on some of these fungicides, please refer to the table provided in a previous post.

These fungicides, though well-intentioned, can cause a cascade of unwanted negative effects that harm the natural ecology (by eliminating beneficial fungi) and human health (ingestion during spraying or during consumption). The issue of fungicide resistance, where fungi evolve and develop resistance to chemicals, is a serious one. Resistant fungi become stronger and untreatable, leading to further yield losses with greater economic consequences in the long run. In many ways, fungicides designed to protect crops can create new ecological and social problems, warranting constant monitoring and evaluation of their impact. Overuse or misuse of fungicides can accelerate fungicide resistance development, harm non-target and beneficial organisms, and disrupt natural ecosystems. Furthermore, the economic burden on farmers increases as they are forced to invest in newer, more expensive fungicides or alternative control measures. Instead, using integrated pest management (IPM) strategies that combine chemical, biological, and cultural practices to reduce reliance on fungicides while ensuring sustainable crop protection may be of more help. IPM strategies are also useful in dealing with other indirect threats that the apple trees face, as discussed below

Other indirect threats

1) Resistance to Fungicides Overuse of fungicides to control diseases like Alternaria can lead to resistance in the fungal pathogens, making the treatments less effective over time. This increases the need for stronger chemicals or alternate fungicide treatments, driving up input costs and posing environmental risks.

2) Combination Diseases Insects like the woolly apple aphid or codling moth can act as vectors, transmitting fungal diseases such as Alternaria or Marssonina, creating a co-infection of mites alongside fungi. This can exacerbate the symptoms and severity of both diseases in trees, leading to significant crop loss and complicating management efforts.

3) Phytotoxicity (weakened tree health due to chemical spraying) Excessive, inappropriate or indiscriminate use of insecticides and fungicides can damage tree health by causing phytotoxicity. This results in stunted growth and makes the trees more susceptible to secondary infections and environmental stressors, which may further reduce yield and quality (Chandel et al., 2017). It is therefore extremely important to follow guidelines - such as spraying schedules provided by Dr. YS Parmar University of Agriculture and Forestry, Nauni-Solan - and spray only the recommended amount of pesticides and protocols provided.

4) Heatwaves, Snowless Winters and Untimely Rains

The changing weather patterns have significantly impacted apple cultivation in Himachal. Heatwaves may cause early flowering, fruit from, and a poor fruit set in apple trees, adversely affecting the quality and yield. In 2024, a snowless winter followed by untimely rains and hailstorms in the spring led significant losses, particularly in Shimla and Kullu districts.

5) Antimicrobial Resistance in Humans The overuse of fungicides in agriculture can also contribute to antimicrobial resistance (AMR), as evidenced by Candida auris, a drug-resistant fungus that was found in samples of Indian apples. Such resistance makes infections in humans harder to treat and poses significant health risks, highlighting the need for careful management of fungicide applications to prevent unintended consequences for both human health and agriculture. Highly Hazardous Pesticides (HHPs) pose severe risks to human health and the environment, particularly in the Global South (including India and other South Asian countries from where India imports its edible oil and  other consumables). Regulations in this part of the world are also weak and access to protective equipment is limited which has led to CSOs advocating for a global ban on HHPs and the promotion of agroecological alternatives.

As mentioned earlier, it is important to find solutions that are comprehensive and address specific deficiencies in the trees, plants, and the soil. This approach should take precedence over conventional practices that rely heavily on chemicals like NPK fertilisers, that have been associated with reduced soil fertility (as a result of reduced soil organic carbon SOC) in India.

So what is the solution?

As discussed in my first previous post on Indian Agriculture, shifting away from indiscriminate chemical pesticide and fertiliser use while adopting practices like polyculture, intercropping, and agroforestry can be a sustainable solution. These methods protect beneficial insects and microbes, reduce pests naturally, and improve soil health. They also offer the chance to grow additional crops, providing an additional income source or more diverse harvests. In addition to these methods already discussed earlier, some of the following are specifically important to look into. 

1. Cover Crops (such as mustard, strawberries, fenugreek)

   This video from Mr. Pranav Rawat’s YouTube channel explains how planting a winter cover crop of mustard (Brassica family) helped him naturally reduce Alternaria and Marssonina infestations without resorting to indiscriminate spraying of systemic fungicides. Generally, planting legumes (peas, beans), cereals (wheat, barley), and cruciferous crops (cauliflower, mustard) alongside apple trees boosts nitrogen fixation and phosphorus solubilization, improving soil fertility and, in turn, plant health. In his video, Mr. Rawat also mentions that the mustard cover crop helps retain moisture in his orchards and may have contributed to a naturally larger fruit size, even though 2024 experienced droughts during the fruiting phase in Himachal. His channel is dedicated to practices in regenerative farming and offers practical advice and relatable experiences that may serve as a valuable resource. Additionally, researching further to identify suitable cover crops for your orchards, as these may vary with elevation, could be beneficial.
   

2. Nutrition & Moisture Management Addressing nutrient imbalances and deficiencies in trees—particularly micronutrients—and maintaining proper moisture levels are essential for enhancing photosynthetic efficiency. This improves the plant's natural ability to fend off diseases, especially fungal pathogens, while supporting healthy growth and carbon assimilation. Over-reliance on chemical inputs such as DAP, NPK, fungicides, miticides, and insecticides, especially without a thorough understanding of your farm’s soil health through data-driven insights (such as a soil health card that is regularly validated), is widely regarded as an unsustainable agricultural practice that can degrade soil health, harm the environment, and weaken crop resilience over time.
   

3. Organic Inputs Instead of relying solely on harmful chemical pesticides, prioritize organic methods for managing pests and diseases. Natural options such as neem oil and chili-garlic sprays are effective alternatives that not only control pests but also address long-term challenges like insecticide resistance, which can make chemical solutions unsustainable over time. To combat fungal issues, try to make the most of natural sunlight or use ultraviolet lamps (with proper safety precautions) in areas with limited sunlight. These approaches should be your first choice before turning to chemical pesticides, which often only provide temporary solutions and can eliminate beneficial insects as well. Additionally, natural farming practices, such as Subhash Palekar’s Zero Budget Natural Farming (ZBNF), utilize affordable, locally available materials to enhance plant nutrition while maintaining soil health and fertility, promoting a more sustainable and cost-effective approach to farming.
   

4. Soil Health & Fertility Building on our earlier discussion on proper nutrition management, the Soil Health Card plays a crucial role in assessing the overall condition of the soil, including identifying nutrient deficiencies. By addressing these gaps and supplementing the soil with high-quality inputs like magnesium, sulfur, and manganese, you can significantly enhance its fertility. Healthy soil with a balanced nutrient profile is the foundation of tree growth, enabling trees to resist pathogen attacks more effectively and thrive in the long term.
   

5. Hygiene Maintenance & Regular Monitoring

   Maintaining a clean environment around the tree helps prevent the growth of harmful fungi and bacteria. Regularly remove dead or decaying matter and monitor mulching materials like straw to ensure they don’t promote pests or fungal growth. Consistent hygiene and monitoring are vital for tree health.
   

6. Biodiversity

   Finally, and perhaps most importantly, preserving natural biodiversity is crucial. Naturally growing native plants, such as those found in grasslands outside farmlands (commonly known as Ghasnis), can serve as effective cover crops. Even if these plants don’t have an obvious direct use, they play an important role in supporting the soil, other beneficial plants, insects, and animals that indirectly protect (or don't harm) cash crops such as apple trees. Recent reports from Himachal have highlighted the decline of the native honeybee, Apis cerana indica, primarily due to the loss of its natural habitat as forests are cleared for farming. Similarly, the increasing presence of wild animals like bears and langurs in orchards, driven by the lack of natural vegetation, is also concerning and unsustainable. This calls for strategies that focus on preserving forests and natural habitats to protect crops. 
   

7. Involvement with community Additionally, when buying chemicals from local shops, it’s important to ask how they affect local soil health, native pollinators, and cover crops. This can create a positive feedback loop where market demand encourages safer, more sustainable products and drives research into better alternatives.
   

A holistic, thoughtful approach to farming is the most effective strategy for long-term sustainability, as it recognises and honours the interconnectedness of our ecosystem. Maintaining a balanced ecosystem is critical—more so than anything else discussed in this post. Whatever labels these approaches carry—permaculture, regenerative farming, natural farming, or organic farming—their aim remains the same: to restore and regenerate depleted soils, allowing plants to thrive with minimal and thoughtful external inputs. At their core, these methods champion balance, resilience, and a future that is guided by ecological principles. In my next post, I’ll share the inspiring story of a small village in Kinnaur, Himachal Pradesh, that has successfully transitioned from synthetic chemical farming to natural farming. I hope their journey will offer valuable insights and encouragement to those who are still uncertain about adopting natural farming or other low-chemical alternatives. Can you guess the name of the village I’m talking about? Share it in the comments!