339-Microbe Science for Gardeners, with Robert Pavlis

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If you have been practicing organic gardening for a while, you probably observe the mantra “feed the soil and let the soil feed the plants,” though to get even more precise, my returning guest this week, chemist and gardening author Robert Pavlis, explains that what gardeners are actually doing is feeding the microbes in soil, and it’s the microbes that are feeding the plants.

Using his background as a chemist, biochemist and Master Gardener, Robert is a gardening myth-buster who runs the popular website He challenges conventional wisdom and explains what the science supports and what it doesn’t support. Robert’s newest book is “Microbe Science for Gardeners: Secrets to Better Plant Health,” the latest in his “Science for Gardeners” series, which started with books on plant science and compost science.


Robert Pavlis

Robert Pavlis has experience as a chemist and biochemist and he applies that background to gardening. He busts some of the most persistent garden myths. (Courtesy of Robert Pavlis)


Robert has been on the podcast several times before to discuss houseplant myths, garden products you don’t need, plant science and compost science. Robert believes that when gardeners learn a little more about science, they’ll understand what they’re doing and will be able to better interpret what they see and hear. 

He writes in his new book: “Learning about plants only takes you so far. If you take the time to understand the underlying basis of nature, growing any plant becomes easy.”

He encourages gardeners to spend less time trying to figure out what a specific plant needs and more time understanding the biology and how nature works. “We solve that, then the plants all grow,” he says.

Robert has a 6-acre botanical garden known as Aspen Grove Gardens in southern Ontario, Canada, packed with more than 3,000 species of plants, trees and shrubs. It’s located in zone 5 and is mostly dedicated to ornamentals with a focus on really interesting plants, and he also has a small vegetable garden.

What We Don’t Know About Microbes 

“On the one hand, we have gardeners saying, ‘Oh, you need to do this and that for microbes.’ The reality is that scientists don’t really know that much about microbes,” Robert says.

For instance, scientists have no clue how many different species of microbes exist, he says. “We’re still guessing at that number. What we do know is that we haven’t identified most of them.”

Scientists believe they have only identified 20 to 25% of all the species that are out there. With advances in electron microscopes and new resources that we have on hand that were unavailable 10 or 20 years ago, we do know a lot more now about microbes — even though there is still much to learn.

Robert says DNA research is key to identifying species because many microbes look the same under a microscope. 

“They do have characteristics, but they’re small and a thousand species could look the same to us,” he says. “But when we look at them with DNA analysis, then we say they have different DNA structures, so we know they’re different species.”

As small as a microbe is — you can put hundreds of thousands on the tip of a pen — we can still use DNA processing to get within it to determine that it’s different from its neighbor. It’s mind-blowing science.


Drechslerella anchonia

Electron microscopes enable scientists to see microbes in new ways. (Photo Courtesy of Robert Pavlis)


Why Learn About Microbes

There are two main reasons gardeners should understand microbes: One, microbes are the source of the plant diseases that gardeners inevitably confront, and two, microbes do wonderful and necessary things for plants.

“If you take pure soil with no microbes in it and you put plants in it, they’re going to struggle,” Robert says. “The soil is important, but it’s really the microbes that are turning the soil over and releasing the nutrients from soil so that plants can use it. And I think it’s that association that we don’t appreciate enough — that it’s the microbes, and the living things they do, that’s actually making the plants grow.”

You may be thinking, “What about hydroponics?” In hydroponics, or aquaponics, there is no soil involved, yet plants still grow. In hydroponic systems, plants get nutrients from nutrient solutions parsed out by a hydroponic farmer. 

When growing outdoors in soil, a gardener is not just growing plants but also growing the microbial community that helps take care of plants.

“In hydroponics, we basically take the chemicals plants need and give it to them directly,” Robert says. “In the garden, what we’re really doing is we’re taking care of microbes. Gardeners don’t realize that. They think they’re taking care of plants, but what they’re really doing in the soil is taking care of the microbe population. And if they do that, the plants just grow automatically.”

For example, adding compost to the garden to feed plants isn’t really feeding the plants — at least not directly.

“We put compost on the garden to feed the microbes so the microbes can feed the plants,” Robert says. 

 How Microbes Help Aggregate Soil

Soil is sand, silt, clay and organic matter, plus water and air. When sand, silt, clay and organic matter clump together into soil aggregates, they provide a good environment for plants to grow in. This crumbly soil, like the kind naturally found in forests, allows roots to easily grow through the spaces around these aggregates. 

“Soil aggregation is really critical for creating good soil,” Robert says. “And how do we get soil aggregation? Well, it’s all the microbes. Soil aggregation does not happen on its own.”

As microbes live in soil they create chemicals, waste products and slimes. These organic compounds around sand, silt and clay cause the soil particles to clump together. 

“The more microbes you have, the more of this activity that takes place, the better the aggregation,” Robert says. “And the better the aggregation, the better the plants grow.”

You will notice aggregation by the porosity of soil and the sticky substance microbes create. 

“You can tell right away,” Robert says. “You can take your hand and you push it into aggregated soil and it just goes in easily. You don’t need to jump on a shovel to try and move the soil.”

Of all the microbes in soil, fungi are crucial.

“Fungi play an important role here because the fungi create these long filaments, these hairs,” Robert says. “And so they hold the aggregate together. They’re really important for that structure to take place.”

Once an aggregate is created, it is not stable. If the microbes were to all die, the aggregate would come apart. What keeps it together is the ongoing presence of microbes.


great soil

Great soil is made up of soil aggregates — sand, silt and clay clumped together by microbes while leaving enough room for air and water to circulate.


Does The Kind of Organic Matter, Matter?

All organic matter, on a molecular basis, is really the same thing, Robert says. 

A bacterium, a banana peel and cow manure are all made of the same components on the molecular level. 

“A bacteria is about the same as a human cell,” Robert says. “There isn’t a lot of difference. We all have proteins, we have carbohydrates, we have enzymes. The nutrients that both of us need are the same. So bacteria need nitrogen and phosphorus and potassium and so on. We need all of those things. We both have DNA in our cells. There are certainly differences, but there are many, many similarities.”

“We get too hung up on trying to figure out which of these are the best and which are not. They’re all organic matter. They all decompose.  They all go through very similar chemical changes as that decomposition happens, and so they have the same effect on soil.”

I use the terms “organic material” and “organic matter” when talking about creating compost and improving soil. I think of “material” as the inputs gardeners use, such as straw, leaves and manure, and “matter” as what’s left of these inputs once they decompose. Really, it’s all organic matter, even before it has broken down into finished compost.

Robert points out in his book that a living tomato and a dead tomato look the same under a microscope, at first. Over time, the dead tomato decomposes, breaking down chemically into small molecules and becoming indistinguishable from other decomposed organic matter.

“Once the cells break apart and all the molecules come out, there is no difference between a tomato and a bacteria,” he says. “They both have proteins. Now, the types of proteins may be slightly different, but in fact, there are proteins that are identical between a bacteria and a tomato plant. Both have starches, they both have sugars. They both have ATP [adenosine triphosphate], which is the thing that provides all the energy for living matter. So as we break these molecules down, they’re identical. It doesn’t matter where they came from. It could come from animals, from plants, from microbes, from fungi, doesn’t matter. At some point, you cannot tell where those things came from.”


Buckets full of plant material

Compost inputs are all essentially the same once they decompose. Organic material is made up of the same components, and composting breaks the material down to its parts.


Covered in Microbes

A plant’s leaves may look “clean” but they are covered in millions of microbes that can be crucial to how well the plant performs. There are thousands of species in a community of microbes populating a leaf.

“They’re breathing, they’re surrounded by water, they’re breeding, they’re making babies, they’re eating each other,” Robert says. “There’s this whole world going on there.”

Bacteria in Soil

Bacteria are the most common microbes in soil. Robert points out that while we think about bacteria living in soil, they live in water. 

“Bacteria live pretty much everywhere, wherever they can find the resources they need, and bacteria need a couple things,” he says. “They need water … and I think it’s very beneficial for us to think of these as water organisms.”

When soil gets too dry, bacteria can’t live, he says. They either die or go into a state of inactivity, like hibernation, during which they stop metabolizing. Dormant bacteria shrivel up and basically stop living, with no need to eat. They will remain this way until moisture returns and the temperature is favorable again. 

Fungi in Soil

Bagged soil and potting mix products often tout that they contain mycorrhizae, or mycorrhizal fungi.

The mycorrhizae may be present, but not currently active, in dry soil.

“Each organism has a mechanism for going dormant,” Robert says. “So when the environment is too harsh for itself,  one of two things happen: They either go dormant or they die. And it will depend on the species.”

This is true of both bacteria and fungi, as well as other microbes. In the case of fungi, they make spores. “I equate those to plant seeds,” Robert says. “They’re a little capsule where all the DNA’s in there. They can just sit around for long periods of time, and then when conditions get right, they sprout.”

Most mycorrhizal species are hard to cultivate and will die once bagged up. They can’t survive hot temperatures, and somewhere on the line of being bagged, stored and shipped, the fungi will overheat and die. However, Robert says other species are quite easy to cultivate, and those are the ones that manufacturers like to use in their bagged products.

Fungi are much larger than bacteria. Think of them like long filament hair, Robert suggests. 

“What’s really important with fungi is that they actually make an association with plants,” he says. “So the two actually join together, and the fungi filaments actually burrow into plant roots.”


Mycorrhizal fungi infecting a root

An illustration of how mycorrhizal fungi penetrate a root. (Photo Courtesy of Robert Pavlis)


‘Adding’ Microbes to Soil

Robert does not agree with the notion that a new garden needs an application of microbes from a bottled product, such as bioinoculants. 

“That’s actually not how this thing works,” he says. “The microbes are already there. They’re not really active because their conditions aren’t great.”

Loosening up compacted soil, so the microbes can get air, and keeping the garden watered, so the microbes have plenty of moisture, will encourage the microbes that are already present to proliferate. If the soil lacks organic matter, then adding compost will provide the microbes with the food they need.

“The thing about microbes is they change very quickly,” Robert points out. “So literally within hours they start multiplying and growing, and they’re very quick to adapt to changes in the environment.”

Robert recalls reading a book on composting that advised throwing some soil in with the compost inputs to add some microbes. However, now he knows that every leaf and stem he throws into a compost pile is already covered with millions and billions of microbes.

“You don’t have to add any,” he says. “They’re already there. All we have to do as gardeners is to take care of them.”

If gardeners give microbes air, water and food, their population will explode. “In fact, we can’t stop them from exploding,” Robert says. “They will just start growing.”

When buying a bottle of microbes, there is no way for the gardener to know if the microbes are living or dead, because the product will look exactly the same either way. 

“This could have sat in a hot greenhouse for a couple of years and everything’s dead, or it might have just arrived and was kept cooler,” Robert says. 

Even a gardener with a microscope is at a disadvantage.

“Under a microscope, you may still see the particles. That doesn’t mean they’re necessarily alive and growing,” Robert says. “So you’d have to take that and culture them and grow them first and see if something grows.”

Laboratories have done this test with some surprising results.

“There was a study done where they went out and bought something like 20 products and analyzed them,” Robert says. “They found that about half of them did not have the DNA in there for the microbes that are on the label.”

And when they measured which microbes were alive versus dead, they found a large percentage were dead.

How and What Bacteria ‘Eat’

Bacteria don’t have mouths, but they still “eat.” 

“You can think of this round blob, and the skin’s fairly porous, and they have to nuzzle up to their food and, and suck it in through their skin,” Robert explains. “But they can only do that for smaller molecules.”

If a molecule is too big for bacteria to absorb, they exude an acid to digest it into smaller molecules, the way we digest food with stomach acid. Once the molecule has broken down adequately, the microbe can absorb it.

“Bacteria are constantly excreting these digestive juices,” Robert says.

Some bacteria have little hairs, or flagella that act like tails or propellers to help them move toward food. 

“There’s not much intelligence here. There’s no brain or anything. This is all just chemical reactions that’s making them do this,” Robert says.

As bacteria make acid to digest protein, starches and sugars in soil, the bacteria only use some of the molecules. The rest become available for plants to use.

“Remember, plants can’t use proteins either,” Roberts points out. “They are too big. So they have to wait until that protein molecule degrades and the nitrate comes out, and then plants can take it.”

Many microbes will sit right near plant roots as they constantly digest organic matter and create nutrients that plants need. The process by which microbes decompose organic matter into plant-available nutrients is known as “mineralization.”


"Microbe Science for Gardeners"

Robert Pavlis’s “Microbe Science for Gardeners” explains how different microbes interact with soil and plants, and does so in a way that is easy for gardeners to understand. (Photo Courtesy of Robert Pavlis)


How and What Fungi Eat

Fungi have a similar diet to bacteria and can send out digestive juices to break down things around them, as bacteria do. They also eat bacteria.

Fungi can also use their branching filaments, called ​​hyphae, to go into mineral particles in soil. “They’re better at digesting something like phosphate in the soil particles than other organisms,” Robert says.

“The nice thing about these filaments is they’re kind of like a highway,” he adds. “So we’ve got some phosphate in minerals at one point, and the fungi digest that and bring it inside — they basically eat it — and that phosphate molecule now travels along that highway to the other end of the fungi. So they’re moving molecules along these filaments.”

That phosphate molecule leaves the fungi and goes into the plant. In return for the fungi giving the plant the molecules that it needs, the plant gives the fungi sugars. 

“Fungi do not photosynthesize,” Robert points out. “They can’t use light to make food. They have to get their sugar source from some other place, and one place they get it is from the plant.”

However, if a plant is given lots of water-soluble phosphate fertilizer by a gardener, the plant won’t form that relationship with fungi because it already has what it wants. The plant also won’t make as many roots because it doesn’t need to explore to find phosphate.

Temperature and Microbes

Different bacteria species prefer different temperatures. When the temperature is ideal, they will more readily reproduce.

Mesophilic bacteria prefer moderate temperatures — not too cold and not too hot — and thermophilic bacteria prefer warmer temperatures. If you compost at home, you’ve probably noticed that your compost inputs break down much faster in warm temperatures. That’s because thermophilic bacteria are more active in the summer months, and they create their own heat as they digest organic matter.

“Both in a compost pile and in soil, microbes are most active in the summer when there’s some warmth,” Robert says. “As things cool down, certain microbes go into a dormant stage. Others just become less active. But there are other species now who do best when it’s cool, and so they become more active in the fall.

“There are so many species of microbes that no matter what the condition is, there are some microbes that are really happy in that condition,” he continues. “So if we go to the Arctic, there are microbes that thrive there because it’s so cold, and we bring them down into warm climate, they’re going to die. We can go to a hot spring and there are bacteria in there that love that hot spring because it’s really the right temperature for them.”


Compost thermometer

A compost thermometer will indicate whether thermophilic bacteria are at work decomposing organic materials.


Good Guys and Bad Guys

“In every classification of microbes — bacteria, fungi, nematodes and so on — there are always some good guys and some bad guys,” Robert says. “Now, in general, 80% of them are the good guys, and 10 to 20% are pathogens.”

That means the overwhelming majority of microbes are helping plants or at least neutral. The percentage of microbes that are pathogens is small.

One way plants protect themselves from pathogenic microbes is to exude chemicals from their roots that control the types of organisms that surround the roots. They farm the good bacteria to eat the pathogens. 

Another defense plants have against bacteria and fungi is they can drop infected leaves. They are less successful at surviving infection from a virus and from certain bacterial infections that are particularly deadly.   

Rhizobia and Legumes

Rhizobia are nitrogen-fixing bacteria that form nodules on plants. The plants farm the bacteria, and the bacteria take nitrogen from the air and turn it into nitrite, which the plant then turns into nitrate.

“That’s why we find legumes grow quite well in soil. It has very low nitrogen levels because this bacteria allows them to grow there, but only legumes really have this kind of association with the rhizobium,” Robert says. “And so they can grow in low-nitrogen soil, whereas other plants struggle.”

If planting peas or beans in soil that has not hosted legumes for a number of years, Robert advises inoculating the seed with rhizobia to ensure there is enough of that bacteria present.

Add inoculant powder to a plastic bag with the seed, shake it up to coat the seed, and then plant the seed.


Root Nodules

Root nodules form on legume roots with nitrogen-fixing bacteria known as rhizobia.
(Photo Courtesy of Robert Pavlis)


If you haven’t listened yet to my conversation with Robert Pavlis about microbe science for gardeners, you can listen to this episode now by scrolling to the top of the page and clicking the Play icon in the green bar under the page title. 

Do you consider microbe science while gardening? Let us know in the comments below.

Links & Resources

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

Episode 048: The Simple Science Behind Great Gardening, with Lee Reich

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

Episode 143: Gardening Products You Don’t Need, and Why

Episode 153: The Science Behind Great Soil

Episode 223: How Soil Microbes Make Good Soil Great

Episode 270: Plant Science for Gardeners, with Robert Pavlis, Part I

Episode 272: Plant Science for Gardeners, Part II, with Robert Pavlis

Episode 282: The Vital Role of Soil Bacteria in the Garden, with Jeff Lowenfels

Episode 283: A Soil Chemistry Primer: How Protons and Electrons Influence Soil Moisture and Fertility

Episode 305: Compost Science for Gardeners, with Robert Pavlis

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joegardener Online Gardening Academy Master Seed Starting: Everything you need to know to start your own plants from seed — indoors and out. 

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

joegardener Online Gardening Academy Growing Epic Tomatoes: Learn how to grow epic tomatoes with Joe Lamp’l and Craig LeHoullier. 

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.

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Growing a Greener World®  


Garden Fundamentals on YouTube

Garden Fundamentals Facebook group

“Microbe Science for Gardeners: Secrets to Better Plant Health” by Robert Pavlis

Compost Science for Gardeners: Simple Methods for Nutrient-Rich Soil” by Robert Pavlis

Plant Science for Gardeners: Essentials for Growing Better Plants” “Soil Science for Gardeners: Working with Nature to Build Soil Health” by Robert Pavlis

Building Natural Ponds: Create a Clean, Algae-free Pond without Pumps, Filters, or Chemicals”  by Robert Pavlis

Best Garden Plants for Connoisseurs: The best plants from my collection of over 3,000 garden gems” by Robert Pavlis

Garden Myths: Book 1” by Robert Pavlis

Garden Myths: Book 2” by Robert Pavlis

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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 was 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: Corona Tools, Milorganite, Soil3, Greenhouse Megastore, Territorial Seed Company, Earth’s Ally, Proven Winners ColorChoice and Dramm. 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.

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