Pests and Diseases

Common Fungal Diseases and How to Control Them

If using foliar sprays to combat mold issues sounds a bit far out of whack, then you should definitely read on! The appearance of powdery mildew on your leaves during the vegetative stage or finding botrytis (flower rot) as you’re harvesting is something every grower dreads. However, after a successful battle with botrytis or mildew you invariably become a more skilled and confident, grower. It’s all too easy to panic and reach for the chemicals but there are many effective biological products on the market for both prevention and cure of plant fungal diseases. Bacillus subtilis and Bacillus pumilis are a specific group of naturally-occurring bacteria that can be used to prevent and control fungal infections.

What Is Powdery Mildew?

The classic signs of a powdery mildew infection.

Powdery Mildew is a fungal disease that is easy to spot. Look for what/grayish powder on leaves (either side), stems, fruits or flowers. Itlooks like powdered sugar was sprinkled on the plant. Some plants are more susceptible to PM than others. When plants are early in their vegetative stage (when leaves are expanding) this can be a time of high risk. Plants exposed to high levels of nitrogen in the vegetative state are at great risk of PM infection as well. PM thrives in cool, damp, stagnant conditions making it the bane of many greenhouse and indoor gardeners who have not invested in adequate atmospheric solutions.

What is Botrytis?

Botrytis eating away at this tender leaf.Botrytis (aka 'gray mold') is a fungal disease that can devastate annuals and perennials alike. Botrytis cinerea is the most common strain. Cool and humid conditions (such as rainy springtime seasons and early summer weather - around 60 F/15 C) are perfect for gray mold to take hold. This can happen if your indoor garden suffers from long periods of high relative humidity as well. Botrytis can affect any part of the plant above the roots.


It sounds obvious, but always select healthy plants in the first place - fungus preys on the weak! Full sun (or grow lights with a ultraviolet (UV) component) is nature's natural antifungal agent. If growing indoors, be sure to allow adequate space between plants and plenty of oscillating fans to provide air movement in your grow space. Maintain a high level of cleanliness in your garden and never keep trash bags full of dead plant material in or near your garden. Avoid long periods of high humidity. Also, avoid large temperature swings in the garden. Run lights at night through the use of thermostatically controlled block heaters and/or dehumidifiers when your grow lights are off.


Remove diseased leaves and throw away in garbage, not the compost. Also remove any yellowing or dead leaves hanging on the bottom of the plant. Carefully cover the moldy item with a plastic bag and gloves to help prevent the spreading of spores. Never keep piles of old leaves and trash bags in or near your indoor garden. This can be a breading ground for fungal and bacterial diseases.

Fungal Control Options

Left: healthy fungal spore on the surface of a leaf. Right: Destroyed fungal spore after foliar application of the beneficial bacteria Bacillus subtilis strain QST713.

Photo courtesy of Agra Quest inc.

Take care if choosing a chemical control product. Some chemical controls are not to be used on edible crops. Read label directions for specific application and harvest times. Bear in mind that some diseases can become resistant to certain chemicals over time.

If you prefer a more natural route, try beneficial bacterial, specifically Bacillus subtilis or Bacillus pumilus -both are endemic in soil and are well established horticultural techniques and GRAS (Generally Recognized as Safe) by the EPA (United States Environmental Protection Agency)

Some strains of B. subtilis are the active ingredient in broad-spectrum contact fungicides. B. subtills QST713 produces Lipopeptides that kills fungal spores by puncturing the cell membrane. Lipopeptides are highly stable, offering resistance to elevated temperatures and even pH extremes.

What Type of Bacillus subtilis?

Check the exact name of the active ingredient in your chosen B. subtilis product. Keep an eye out for B. subtilis QST 713 or MB1600. Some B. subtilis strains also elicit plant health and growth promotion in treated plants. When applied, these strains can trigger your plant's internal defenses and physiological responses. The effect is systemic - this means that responses are triggered throughout the plant even when just a small area is treated.

Bacillus subtilis Products

  • Broad spectrum control of fungal diseases
  • Little potential for infection to create resistance to treatment
  • No temperature restrictions for use
  • Non-toxic to beneficial insects (including honey bees)
  • Safe to use up to and including the day of harvest
  • Some products based on B. subtilis are approved for organic production.
  • Safe to use with predatory insects.

Bacillus pumilis Products

Products based on B. pumilus instead focus on fungal cell walls rather than membranes. The compounds produced by B. pumilus compete with fungal diseases for amino sugars needed to build cell walls, effectively making it impossible for fungal cells to build and grow.

B. pumilus does not control bacterial diseases. Instead, it's strongest against rust and mildews. B. pumilus is typically used by a gardener when targeting a specific type of fungal infection that is better controlled by this specific bacteria over the more broad spectrum approach of B. subtilis. Also, B. pumilis strains, like those of B. subtilis, have been shown to trigger plant's natural defenses.

Powdery mildew has taken hold on this cucumber leaf due to over-fertilization creating overly tender, vulnerable growth.

When Do I Use It?

Most B. subtilis and B. pumilis products should be sprayed as a preventative measure or be used as a curative control. They can be applied early on in the plant's lifecycle on established cuttings or seedlings, and as late as the day of harvest on mature plants. Most growers freak out at the mere idea of spraying mature flowers or ripe fruit, but these natural Bacillus products are safe for human consumption and actively retard fungal growth.

Spray Timing

When using outdoors, it's best to spray in early morning or late afternoon when light intensity is not too strong. Sunlight contains a natural broad spectrum microbe inhibitor, Ultra Violet light. If applied during strong sunlight, the UV may prevent some Bacillus products from working effectively.

When spraying indoors, it's also good practice to spray in low light. This may mean raising your grow lights up high before spraying, or spray just before the lights come on or go off.

The damage has already been done to this cucumber leaf by Powdery Mildew.

Spray Timing

The best fungal control is achieved when the plants are thoroughly wet, and run-off spray is dripping from the leaves. It's a good idea to use a wetting agent or surfactant for increased coverage and a decrease of surface tension in the foliar application.

Avoid adding other foliar additives or nutrients as this may interact negatively with the beneficial bacteria. Spray the underside and top of the leaves as well as any exposed stems. Applications can be repeated every 3-4 days if plants are heavily infected, or every 7-10 days as a preventative measure. Always read and follow label directions of any products used in the garden. When applying either type of bacteria as a foliar spray one should spay the leaves, shoots and new growth until the plant is dripping wet. Run-off spray will not affect beneficial soil fungi like mycorrhizae. When a gardener is planning to use beneficial bacteria or an organic gardening product to prevent or control fungal and bacterial diseases they should scout the garden often to look for any signs of disease. Strains of these beneficial bacterial can also be found in some compost teas since it can promote plant health and growth promotion.

Serenade uses the patented Bacillus subtilis strain QST 713

What products contain Bacillus subtilis or pumilus for foliar fungal disease control?

Most good quality compost teas will contain some B. subtilus and B. pumilus strains, so regular spraying can help with disease prevention. For a more targeted fungal control, there are patented strains of Bacillus subtilis that have specific MOA (Modes of Action). Bacillus subtilis strain QST 713 can be found in the commercial product SERENADE ASO. Bacillus subtilis strain MB1600 can be found in the commercial product Subtilex NG.

Some B. subtilus and B. pumilus strains can also be found in substrates, beneficial bacteria packs and soils.

WORDS: Emily Walter. A Girl and a Garden. Visit Emily's blog!