Winter 2014-2015
The reproductive conidia of Venturia inaequalis erupting through the cuticle of a crabapple leaf. From the Wikipedia article “Apple Scab,”

By C. J. Walke

As organic farmers and gardeners, we understand the importance of a biologically active soil, where beneficial microbes thrive in the rich organic matter and humus layer, converting mineral nutrients into forms that plant roots can use. Research shows that a handful of healthy soil contains more microorganisms than there are people on the planet. We depend on these microbes and trust in their microscopic activity, but the soil is not the only place where microbes colonize and help nurture our crops, and ourselves.

Healthy plants are typically colonized by numerous microbes (bacteria, fungi, yeasts, algae) that exist in the aerial habitat where the plant meets the sky, and this zone, termed the phyllosphere, is being studied increasingly as research discovers more activity than previously known. Over the past decade, closer examination and study of the phyllosphere has identified new species of bacteria and fungi, demonstrating that this ecosystem is far more complex than previously thought. The majority of this research has focused on the leaf surface, and this is where farmers and gardeners can cultivate these beneficial aerial microbes.

Competitive Colonization

The surface of a leaf is similar to any plot of land or other area with limited space for inhabitants to exist or activities to occur. Only so much can happen in a limited space, especially in nature. When a new apple scab ascospore is discharged from its pseudothecium (fruiting body) home during apple bloom on a rainy day in May, it is seeking residence on the fresh young leaf tissue of the apple tree so that it can penetrate a cell of that leaf, access plant nutrients and initiate a primary scab infection in the tree. But it needs a place to land, and this is where competitive colonization comes into play.

That scab spore “wants” to land on the surface of a leaf, but we now know that numerous other organisms, such as bacteria, filamentous fungi, yeasts and algae, are or could be there already, taking up residence and leaving little space for the young scab ascospore to land. Here’s the interface where organic farmers and gardeners can influence the scene and boost microbial activity in the phyllosphere by adding new beneficial microbes, as well as food sources for these microbes to thrive.  “Effective microbes” are naturally occurring organisms that can be used as a probiotic inoculant to increase species diversity in the phyllosphere and promote ecosystem health.

Effective Microbes

Effective microbe cultures contain three main groups of organisms – photosynthetic bacteria, lactic acid bacteria and yeasts. Photosynthetic bacteria use sunlight to produce sugars, used in amino acids and nucleic acids, all of which feed other microorganisms and promote plant growth. Lactic acid bacteria, which we all know from our sauerkraut and pickles, can suppress pathogenic microorganisms while also helping to decompose lignin and cellulose beneath trees. Yeasts feed on sugars and amino acids produced by the photosynthetic bacteria to synthesize antimicrobial substances. All together these effective microbes live and feed off of one another to create an active ecosystem in the microscopic phyllosphere. They are available from suppliers such as Fedco Seeds, which offers a product called EM-1 and describes its various uses at

The application of effective microbes in the orchard begins in early spring, while the earth is just waking up and tree buds are starting to show a little green. Northern New Hampshire grower Michael Phillips has developed a schedule of four spring sprays that use effective microbes and other whole plant nutrient materials to boost orchard biology, and the timing straddles the primary infection period for apple scab. Timing is key, since we are trying to get these beneficial microbes established in the phyllosphere before pathogenic organisms awake and catch a ride on the wind.

The schedule starts at quarter-inch green, the time to apply microbes as the new plant tissue emerges. A second application occurs at early pink as blossoms are swelling but not yet open. The third is at petal fall, when insect pests are on the rise and other strategies may be integrated, and the fourth is at first cover, seven to 10 days after the petal fall application. The leaf surface is a rather hostile place for microbes due to fluctuating temperatures and moisture levels, so populations can ebb and flow, making these more frequent applications necessary to establish strong competitive colonization in the phyllosphere.

As summer rolls on, applications can be slowed to a monthly timing and may be integrated with other nutrient applications in the orchard. Effective microbes can also be beneficial into fall and after harvest, when they can colonize bud scales and tissues where overwintering diseases such as peach leaf curl may try to settle and wait for the first green of spring. The cycle starts again come spring, and we continue to work to keep pests at bay by outcompeting the pathogens rather than trying to obliterate them with materials that are often not friendly to the beneficial organisms in the orchard, both on the orchard floor and in the phyllosphere.

C. J. Walke is MOFGA’s organic orchardist and librarian. You can address your orcharding questions to him at 568-4142 or  [email protected].

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