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Microbially Friendly Farming

Controlling plant pathogens and increasing plants’ ability to withstand stress

By Dr. Judith Fitzpatrick

Editors note: This is an article printed in the August 2022 Issue of the AcresUSA magazine.

Imagine that you were intelligent enough to diagnose a disease, proscribe the correct antimicrobial and manufacture it. Plants with a healthy microbiome do this!

In this article we will explain how the plant and microbe work together to perform this miracle and why organic farmers use 97 percent less of any kind of pesticide than those using mineral fertilizers, which are genocidal for the soil microbes that protect the plant from pathogens and adverse conditions, produce nutritionally deficient food, and pollute the environment.

Parsley Roots

In organic or regenerative farming, which we will refer to as Microbially Friendly Farming (MFF) — in which growers seek to maintain microbial populations above 250 ug microbial biomass carbon per gram of soil and a F:B (fungal to bacterial) ratio above 0.5 — the plant secretes about 30 percent of its photosynthate to generate the specific microbial population that it requires for nutritional needs and health. The major stimulation for the plant to build this population is the plant’s hunger for the N, P, K and other soil minerals that the microbes can deliver. When the plant is provided mineral N, it does not nourish this microbial population, and the plant loses the ability to protect itself from pathogens and stresses such as drought.

The microbial population in the rhizosphere is controlled by the organic molecules that the plant exudes and the nutrients available in the soil. Microbes are the pickiest of eaters — they can only dine on very special diets and require the support of a population of other microbes that supply some of their dietary needs. This is why we can only grow about 1 percent of soil microbes in the lab — we know about the other 99 percent only because we can detect their DNA, see them microscopically and measure some of their metabolism.

Like us, plants receive their initial microbiome from the seed of the mother plant. It is as important for a plant to establish a healthy microbiome as is it for us; children born by caesarian birth have different microbiomes than those born vaginally and have immune deficits that are attributed to not being inoculated with their mother’s vaginal and fecal microbes.

The microbial population in the rhizosphere descends from the seedling population and expands with plant/root growth and recruitment from the surrounding soil. The seedling feeds the microbes with root exudates, and the microbes send chemical growth molecules to stimulate plant growth; these microbes are therefore called “plant-growth-promoting bacteria.” As with humans, the overall health of the plant is a critical component of disease resistance.

The interaction between the microbes and the plant is very similar to how the microbes in our guts stimulate our immune system, which also doesn’t develop in the absence of microbes. Microbes enter the plant through root tips via a process called rhizophagy. The plant extracts 40 percent of the N it requires, as well as other nutrients, before it releases these microbes back into the soil via root hairs. Some of these microbes enter the plant’s circulation system and interact with receptors that appear on all plant cells called Microbe Associated Molecular Patterns (MAMPs), which recognize and bind to common structures on the surfaces of microbes. This binding leads to an intracellular molecular chain reaction that stimulates the cell to produce more MAMPs and many protective antioxidants. Thus, it produces a cell that is more alert to microbes and is more prepared to respond to infection.

In addition to MAMP receptors, the plant has Pathogen Associated Molecular Patterns (PAMPS) that recognize and bind to structures that are unique to pathogens. Binding to a pathogen receptor stimulates the cell to make more PAMPs, making the plant more sensitive to the pathogen and producing large amounts of antioxidants that are harmful to pathogens; it also sometimes causes the cell to commit suicide (apotosis) to save the spread of the disease.

This exposure to pathogens also stimulates the plant root to up the production and secretion of the foods that attract the microbes that make the antibiotic to combat the particular pathogen. The microbes making this antibiotic then multiply in the root area, making the antibiotic available to the plant. Thus, with MFF, a plant in partnership with microbes develops a strong immune system by upping the number of MAMPs and PAMPs and is more resistant to disease and requires much less pesticide.

Perhaps the biggest wins for MFF is that these healthy plants produce thousands of essential nutrient antioxidants, which are not plentiful in conventional farm produce and are not currently listed as nutrients by the USDA. These antioxidants provide protection against cancer, inflammation, etc., and they are what give fruits and vegetable texture and flavor, leading to better eating habits.

Microbes also stimulate the production of Damage Associated Molecular Patterns (DAMPs), which recognize and bind components of damaged cells, especially those of leaves, and promote healing. Moreover, it has been demonstrated that the chemical odors produced by these damaged cells are specific to the insect causing the damage and that these odors attract insects that antagonize the attacker.

Microbes make antimicrobials in large part to protect their territory from other microbes. So, the microbes surrounding your plant are big defenders against pathogenic soil bacteria — e.g., good nematodes are the best protectors against pathogenic nematodes. Interestingly, it has also been observed that a proper F:B ratio results in a bacterial population that is more prepared to defend itself from predators. The proper ratio varies depending on soil and crop; for agricultural crops it is usually between 0.4 and 1. The proper ratio also tells you that you are not decreasing your soil fertility (organic carbon).

Mycorrhizal fungi, which colonize approximately 90 percent of all plants, are fungi that are totally dependent on the plant for nutrition. A plant root exudate awakens the fungal spore that has only a day to grow to the plant, where it enters a cell and is fed. When established, the fungi send out hypha to collect P, N, K, S, and water, which it brings back to the plant cell and trades for carbon and amino acids. The fungal hypha of a colonized plant can increase the root area as much a 1,000 percent, making significantly more water and nutrients available. The hyphae are also able to form a network connecting trees and are known to send immune signals from diseased trees to other trees in the network to up their resistance to the disease. These fungi also very efficiently protect plants from drought by modifying the root structure, allowing it to absorb more water. Protecting a plant from the stress of drought makes a plant that is more disease resistant and increases yield.

The current best indicator of a healthy soil microbial community is a  

healthy microbial biomass and F:B ratio.

The soil microbial community and economy has thrived for 3 billion years. It has checks and balances and has adapted to soil and water conditions all over the globe. Like our own society, it contains opportunists who take advantage when a defense system is poor and/or the society is weakened. The current best indicator of a healthy soil microbial community is a healthy microbial biomass and F:B ratio: it tells the nutrient level and nutrient balance of the soil and can tell if it is improving. It provides information that chemical tests cannot; e.g., most soils have plenty of P, but it is in a form that only fungi are able to make available to the plant.

A soil test tells you N is low, but it doesn’t tell you that MFF can increase the number of microbes that can deliver N and fix N from the air.

As you can imagine, creating and maintaining a healthy immune system requires plant energy — which is probably why the yields of MFF practices are on average about 10 percent less than those of mineral fertilized farming. But studies show that when microbially friendly farming is optimized, the yield loss is compensated for by tastier produce; lower fertilizer, water and pesticide costs; and better resistance to drought.

MFF also offers the potential to increase financial return by building soil structure, which increases water holding capacity, decreases erosion and water costs, increases drought resistance and increases soil carbon; these benefits have in turn has been shown to increase yield and, over time, decrease fertilizer needs. Understanding the plant health microbial synergy is even more critical now that the cost of mineral N is up as much as 400 percent and pesticides costs are also rapidly rising.

Dr. Judith Fitzpatrick was a microbiologist who designed a number of on-site diagnostic tests and held 13 patents. She was founder and principal scientist at microBIOMETER.