223-How Soil Microbes Make Good Soil Great

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Soil microbes are the microscopic life in soil that work in concert with roots to feed plants. To help us better understand the symbiotic relationship between microbes and healthy plants, my guest on the podcast this week is David Stark, an expert in molecular biology.

David is an Indiana resident with a doctorate in molecular biology from Washington University in St. Louis, Missouri. He’s currently the president of Holganix Agriculture, which produces an organic plant probiotic that contains more than 800 species of beneficial soil microbes to improve plants’ uptake of nutrients, minerals and water.  Before entering the innovative field of soil microbes for agriculture, David was on a much different path — he worked in corporate affairs for Monsanto, the global agrochemical and agricultural biotechnology corporation.


David Stark

David Stark has a doctorate in molecular biology and is an expert on soil science. (Photo: Courtesy of David Stark)


I should give you a heads-up right now: This week’s conversation requires a major Geek Alert because we go deep on the science behind soil microbes and why they are vital to raising healthy, vigorous, more productive plants. 

From Monsanto to Microbes

Before getting into the meat of this week’s discussion, a bit more about David and his interesting career journey.

“My career, I could have never plotted out to save my life,” he says.

David went to college with no clue as to what he wanted to do, but he discovered he loved science. He went from pre-med to a genetics major and found that he enjoyed working on plants more than animals. Around 1983, he started cloning genes. “That’s about as early as it gets,” he says.

While at Washington University to pursue his doctorate, he wrote a dissertation on how to engineer plants to be resistant to virus infection. “This was groundbreaking work,” he says. “I was part of the first field trial on the planet of a genetically engineered plant in 1987.”

The university lab was funded by Monsanto, and it was a natural fit to go work for the company, he says. He ran the potato business — potatoes were Monsanto’s first biotech crop — and because he excelled in communicating science in a way that most people could understand, he entered management. He worked in global corporate affairs and government affairs and says he’s answered more questions on GMOs than anyone.

After 25 years at Monsanto, he was ready to move on. However, when he retired in 2014, he found himself at home, in his mid-50s with no plan. “I went nuts,” he says.

So he became a consultant to help companies understand agriculture and the related technology, trends and opportunities. It was a friend from his Monsanto days who turned him on to Holganix. The friend wanted him to offer mentorship to the folks at the start-up business. When he learned the assignment was microbials, he didn’t want to do it, he admits. He thought microbials were “bugs in a jug” and lousy science that didn’t work — but he reluctantly agreed anyway.

So why would a molecular biologist turn his nose up at soil microbes? “Soil biology is a new field of study,” David says. Scientists know more about the genetics of the seed being planted than they know about the biology of the soil it is planted into. Also, he adds, almost everybody at Monsanto and in the industry stuck to the old agriculture paradigm of needing a single microbe, with a defined mode of action, that could be patented.

While a single gene or a single chemical could be beneficial in seed production or disease resistance, it’s just not the way soil works, David says. It’s the diversity of life — bacteria, fungi, actinomycetes, protozoa, amoebae and nematodes — that is important in soil. A biome applied to soil finds food sources that individual species can’t and fights pathogens that individual species can’t. 

Holganix piqued David’s interest when it shared a story of a Pennsylvania Dutch Country Amish farmer who, after 10 years, beat his cousin in the watermelon-growing contest. David learned that applications of soil microbes lead to bigger, sweeter, more flavourful produce. Additionally, microbe applications on turf fields lead to grass with better color and better playability, all while requiring less water and less fertilizer. Big-name stadiums and top golf courses have reported that microbe applications cut their fertilizer needs in half. The seeds also germinate right away and the facilities’ water use is reduced 10-30 percent because the grass has better roots. Sod sprayed with “biology” firms to the ground just five days later, according to David.



Microbe applications on turf fields lead to grass with better color and better playability, all while requiring less water and less fertilizer. (Photo: David Stark)


How Diverse Soil Microbes Benefit Plants

A teaspoon of healthy soil can have thousands of species of microbes and over a billion individuals, David points out. Adding one or two species to soil won’t change a thing, he notes. Many species working in concert is how a vibrant soil food web functions. “It is an elegantly complex system,” he says.

Plants invest up to 30 percent of their photosynthetic energy into secreting food sources into their root zones — the rhizosphere — to attract nutrients. In exchange for that food, the microbes bring the plant nitrogen, potassium, phosphorus, sulfur and numerous micronutrients, like metals and boron. Those nutrients are in chemical forms that the plants can’t access but the microbes can, David says.

Leaf litter, manure and compost must be digested by microbes before their nutrients become available to plants. As David put it, those microbes are the stomach of the plants. The process of microbes decomposing organic matter into a form that is easily available to plants is known as mineralization.

Microbes also help plants resist pathogens that those plants cannot defend themselves from.

Likewise, we have learned the importance of microbes to our own health and immune systems. In the 1970s and ’80s when David was in college and a  professor himself, it was thought that the immune system comprised antibodies and white blood cells, he says. But today, we know there is so much more to it. Our microbiome — the microbial life in our gastrointestinal system, on our skin and elsewhere — aids digestion and protects us from threats to our health.  


trees growing on a tree farm

It’s the diversity of life in soil, not one single organism, that helps plants grow more vigorously. (Photo: David Stark)


How Soil Is Destroyed

Overfertilized soil — too much nitrogen, potassium, phosphorus, etc. — creates biochemical feedback that signals plants to stop feeding the microbes. The microbes eat up all the organic matter in the soil instead and deplete it over time from around 5% of the soil composition down to zero. Soil with no organic matter becomes like asphalt, David says.

Soil Needs Air

The aerobic layers of soil are those top-most layers that “breathe.” That’s where aerobic bacteria live. Meanwhile, anaerobic soil has no oxygen, and that’s where anaerobic bacteria are found. 

Aerobic bacteria are plentiful, genetically diverse, and phenomenal degraders, David says, that readily break down grass clippings, leaves and compost. They are attracted to roots so they typically live within a half-inch of them.

Bacteria have a high nitrogen requirement, and bacteria alone can actually tie up nutrients in the soil. Bacteria will hold onto nitrogen until bacteria’s predators — namely, fungi — come in and eat the bacteria. The fungi cycle nutrients so plants can use them.

Bacteria need 1 nitrogen atom for every 3 carbon atoms, but fungi only need 1 nitrogen atom to 10 or 30 carbon atoms. Because the fungi consume more nitrogen than they can use themselves, they cycle it right back into the root zone. 

In a field that’s been tilled and fertilized with nitrogen, bacteria are abundant but fungi are lacking. Tilling introduces more oxygen to the soil, and in the presence of extra nitrogen and oxygen, the bacteria population explodes — doubling every 20 minutes. But tilling also destroys the mycorrhizal pathways used by fungi.  

The mycorrhizal pathways also connect plants to one another, so if one plant in a field or one tree in a forest is attacked by a pathogen or a predator, it can send out a signal to others to kick on their defenses. Fungi eat pathogens that could be attacking plants. As fungi attach to root hairs, they increase the effective surface areas of those root hairs a thousandfold. David also notes that fungi are incredible degraders, which you can see when mulch has white growth on it. 

Experimenting with Soil Microbes

The inventor of Holganix Bio 800+ Agriculture, Stephen Lange, had brewed a lot of compost tea, but he found it inconvenient: It was watery, so it required a lot per acre, and it had no shelflife. It was also inconsistent, sometimes working great and sometimes not so much.

Stephen tinkered with the process of making compost tea by playing with temperatures, controlling the pH, and adding ingredients at different times. The result is a concentrated and consistent product that is stable.

Meanwhile, Barrett Ersek had 100 trucks that sprayed fertilizer on lawns daily. Local laws were passed to reduce fertilizer use to protect the Chesapeake Bay from fertilizer runoff, and fertilizer prices were going up at the same time, so Barrett looked for another way.

When Barrett tried Stephen’s product, he discovered that lawns grew well with reduced fertilizer applications or no fertilizer at all. He fell in love with the product, so he bought Stephen’s company, and Stephen stayed on as a scientist to continue perfecting the product over the last 15 years.

The product today has more than 600 species of bacteria and over 200 species of fungi, plus several dozen protozoa, amoebae, and beneficial nematodes. While the bacteria are grown in a fermentation system, the fungi are added after the fact. It got its name because of the more than 800 oxygen-loving species it contains.

The product is refrigerated from the moment it is produced, including during shipping. Keeping the microbes cold keeps them alive but in stasis. Once they hit the ground and get warm, they get to work. The product also contains molasses and kelp extract so the microbes have what they need once they are applied to soil. The customer can use it right away or store it in a refrigerator for up to a week before using it.

Someone who makes compost tea at home probably has a diverse product, David says, though he stresses that the tea must be aerated. If it’s not, anaerobic bacteria will proliferate, and anaerobic bacteria are more likely to be disease-causers. The compost tea should also be used immediately before the life in the tea dies.

The way to tell if compost tea or Holganix has gone bad is to smell it. If it smells like something died, it went anaerobic. 


comparing corn roots

The difference in root and top growth between corn grown in untreated soil and soil treated with beneficial microbes. (Photo: David Stark)


Do you use soil microbes on your garden or turf? Let us know in the comments below.

Links & Resources

Some product links in this guide are affiliate links. See full disclosure below.

Episode 058: Biochar Basics and More: Digging Deeper Into the Science of Soil

Episode 116: Understanding the Soil Food Web, with Dr. Elaine Ingham

Episode 117: Compost, Compost Tea and the Soil Food Web, with Dr. Elaine Ingham

Episode 153: The Science Behind Great Soil

Episode 194: Easy No-Dig Gardening, with Charlie Nardozzi

joegardener blog: A Guide to Using Cover Crops in the Home Garden

joegardenerTV YouTube: No-Till Gardening: If You Love Your Soil, Ditch the Tiller

joegardenerTV YouTube: How to Prepare Your Soil with Amendments in Fall

joegardener Online Gardening Academy™: Popular courses on gardening fundamentals; managing pests, diseases & weeds; seed starting and more.

joegardener Online Gardening Academy Master Pests, Diseases & Weeds: Learn the proactive steps to take to manage pests, diseases and weeds for a more successful garden with a lot less frustration. Just $47 for lifetime access!

joegardener Online Gardening Academy Perfect Soil Recipe Master Class: Learn how to create the perfect soil environment for thriving plants.

joegardener Online Gardening Academy Beginning Gardener Fundamentals: Essential principles to know to create a thriving garden.

joegardener Online Gardening Academy Growing Epic Tomatoes: Tomato expert Craig LeHoullier joins me in leading this course on how to grow healthier, productive tomato plants and how to overcome tomato-growing challenges. 

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Disclosure: Some product links in this guide are affiliate links, which means we get a commission if you purchase. However, none of the prices of these resources have been increased to compensate us, and compensation is not an influencing factor on their inclusion here. The selection of all items featured in this post and podcast were based solely on merit and in no way influenced by any affiliate or financial incentive, or contractual relationship. At the time of this writing, Joe Lamp’l has professional relationships with the following companies who may have products included in this post and podcast: Rain Bird, Corona Tools, Milorganite, Soil3, Exmark, Greenhouse Megastore, High Mowing Organic Seeds, Territorial Seed Company, Wild Alaskan Seafood Box and TerraThrive. These companies are either Brand Partners of and/or advertise on our website. However, we receive no additional compensation from the sales or promotion of their product through this guide. The inclusion of any products mentioned within this post is entirely independent and exclusive of any relationship.

About Joe Lamp'l

Joe Lamp’l is the creator and “joe” behind joe gardener®. His lifetime passion and devotion to all things horticulture has led him to a long-time career as one of the country’s most recognized and trusted personalities in organic gardening and sustainability. That is most evident in his role as host and creator of Emmy Award-winning Growing a Greener World®, a national green-living lifestyle series on PBS currently broadcasting in its tenth season. When he’s not working in his large, raised bed vegetable garden, he’s likely planting or digging something up, or spending time with his family on their organic farm just north of Atlanta, GA.

0 Responses to “223-How Soil Microbes Make Good Soil Great”

  • Robert E. Forest says:

    Joe, I will be listening to this again, since I know I missed something, but I have a question. I keep worms in my shop for the castings. In the bottom bin of the two bin arrangement, I have the surplus liquid from the process. I believed that it would be beneficial to my garden, yet from what I hear, it contains the anaerobic bacteria, which is not so good. Should I just dump it or will it somehow still benefit the garden? Thanks. Bob Forest

  • LMS says:

    The mycorrhiza you need are already in the soil. There is no need to put them there unless you are killing them off with your other practices (tilling, over-fertilization, over-watering, etc.). Life existed long before Monsanto, and with a little luck it will continue. You don’t need to buy microbes (or anything else) for healthy soil and crops.

  • Bonny Wagner says:

    Now let’s have a show on how to increase or add microbes to the soil without buying product.

  • Pankaj says:

    Thankyou for sharing the information. Website is so easy to use – I am impressed with it.
    Devops Course

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