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

| Care, Podcast

Our understanding of the soil food web has increased rapidly in the 21st century as microscope technology improves and soil biology research continues, and this opens new doors for gardeners and farmers to employ organic solutions for healthier, more vigorous crops. To explain how soil bacteria play an irreplaceable role in our gardens, my guest this week is gardening columnist and author Jeff Lowenfels.

Jeff has written a weekly garden column for the Alaska dispatch for more than four decades, plus he’s a retired natural resources attorney who earned the title “America’s Dirtiest Lawyer.” He also previously hosted a gardening radio show and Alaska public television’s most popular show, “Alaska Gardens with Jeff Lowenfels.” He’s a former president of the Garden Writers Association of America (now known as GardenComm) as well as a GWA fellow and Hall of Famer. Jeff’s new book is “Teaming with Bacteria: The Organic Gardener’s Guide to Endophytic Bacteria and the Rhizophagy Cycle,” the fourth volume in his “Teaming” series. 


Jeff Lowenfels

Jeff Lowenfels continues his “Teaming” series of books with “Teaming with Bacteria.” (Photo by Judith Hoersting courtesy of Timber Press)


Jeff grew up in Scarsdale, New York, where he planted, weeded, mowed and picked fruits, flowers and vegetables on his father’s 8-acre “gentlemen’s farm” until he left for Harvard College in Cambridge, Massachusetts, where he studied geology. He continued his studies in Boston, Massachusetts, at Northeastern University School of Law, where he earned a Juris Doctor in environmental law.

Jeff is also the founder of Plant a Row for the Hungry, a public service program he began in Anchorage that has since gone national and has resulted in millions of pounds of garden produce being donated to feed the hungry every year. He was a guest on my public television program “Growing a Greener World®” during the show’s second season to talk about Grow a Row for the Hungry for an episode all about how gardeners can help the needy.

Jeff is an old friend, though it’s been a long time since we caught up. He was a guest of the “Growing a Greener World with Joe Lamp’l” podcast — the predecessor to “The joe gardener Show” podcast” — way back in 2010 to discuss his book “Teaming with Microbes.” I am a big fan of the book; in fact, it’s one of my “Must-Have Books for Every Gardener.” A lot has changed how we understand the soil food web since “Teaming with Microbes” was first published in 2006, Jeff points out. That’s among the reasons why he continues the “Teaming” series with books on fungi, nutrients and, now, bacteria.


Jeff Lowenfels and Joe Lamp'l

Jeff and I go way back, and he’s been a guest on my public television program “Growing a Greener World” to discuss his initiative Plant a Row for the Hungry.


Before proceeding with my conversation with Jeff about “Teaming with Bacteria,” I want to take a second to remind you that I have a new book of my own that was released last month. It’s titled The Vegetable Gardening Book: Your complete guide to growing an edible organic garden from seed to harvest” and can be found both online and at local bookstores. It’s chock full of insider tips and new-to-you information that will help you step up your gardening game and tackle challenges. 

And on tap for 2023 is my new Online Gardening Academy™ premium course, Organic Vegetable Gardening. Sign up for the waitlist here.

What We’ve Learned Since ‘Teaming with Microbes’

Between the publication of “Teaming with Microbes” in 2006 and today, soil science has made strides. We knew then that plants take photosynthetic energy and use about 30%, 40% or even 50% of that energy to produce exudates that drip out of their roots.

“The exudates are designed by the plant to attract bacteria and fungi,” Jeff explains. These microorganisms, or microbes, eat the exudates, and then nematodes and protozoa come along that eat bacteria and fungi. The waste that they excrete is in the form of nutrients that plants can easily absorb through their roots.

“What they poop out turns out to be plant nutrients in usable form,” Jeff says. “In other words, the microbes put a charge on it. And if you read my second book, ‘Teaming with Nutrients,’ you’ll see that that charge is necessary for these things to go inside the plant.”

It was years after “Teaming with Microbes” was published that the important role of mycorrhizal fungi was confirmed. Now we know that 90% of plants form a symbiotic relationship with mycorrhizae.

“The fungus feeds the plant in return for getting these nutrients,” Jeff says.

The system that he described back in 2006 was a soil-mediated nutrient system. He says the idea is that nutrients went into the soil, and from the soil, they moved into the plant.

The mycorrhizal system that soil scientists later discovered works by nutrients going from the soil into the fungi, and then the fungi trading those nutrients with roots for exudates.

More recently, Jeff says, scientists gained a greater understanding of rhizobia, a type of nitrogen-fixing bacteria, which forms a relationship with legumes. The plant attracts the bacteria, which create a home in a folded up root hair. As the bacteria take up residence there, they pull nitrogen from the air for the plant’s benefit. 

Not all of the nitrogen stays put.

“Some of it leaks out. Some of it ends up going into the soil,” Jeff says. “And when the plant dies, all of it ends up going into the soil and feeding future generations of plants nitrogen.”


green bean plant

Beans are one of the classic examples of legumes, which work with nitrogen-fixing bacteria to gain nutrients.


Dr. Chanyarat Paungfoo-Lonhienne at the University of Queensland in Australia and her graduate students made another important discovery in 2010: bacteria living inside root cells. She called these bacteria “rhizophagy.”

The next stride came from the lab of Dr. James White, a plant biologist at Rutgers University in New Jersey. Jeff compares James White to Dr. Elaine Ingham, the microbiologist and soil biology researcher who originally visualized the soil food web. 

In a series of experiments with his grad students, James White showed that roots somehow convince bacteria that there is something inside their cells that they want. Rhizophagy bacteria enter through the cell wall of a meristem cell at the root tip, but they don’t go through the cell membrane that holds in the meristem cell’s cytoplasm. They stay in the periplasmic space between the cell wall and membrane.

Jeff says the bacteria live in a slime colony, and when the butyric acid level increases, the bacteria push up against the meristem cell and eventually enter through the cell wall.

“It’s unclear whether it’s the bacteria or the plant itself that opens up the cell to let them in,” he says.

Once the rhizophagy bacteria are inside the periplasmic space, the plant sprays them with reactive oxygen, or RO, a superoxide. “It’s a super-oxygenated oxygen, and it strips the cell walls off of the bacteria, and the plant cell absorbs those nutrients that are in that cell wall, and wow, get something to eat,” Jeff says.

The bacteria with no cell walls move around the periplasmic space and continue to multiply. To protect themselves from any more destruction by the plants, they produce nitrite, which turns into nitrate, which feeds the plant. The plant gives the bacteria carbon in return. 

The rhizophagy bacteria also produce ethylene to cause the plant cell to stretch out a little bit.

“If they stop producing the ethylene, the plant won’t give them the carbon that they need,” Jeff says. “And eventually, they get to be so plentiful that they back up against the cell wall of the plant. And because of the ethylene, the cell wall where they backed up forms a tube, and it turns out to be root hair. This is how root hairs form. These bacteria produce ethylene, which causes all root hairs to form. If you don’t have the bacteria, no root hairs.” 

The bacteria live inside the root cells for a couple of days before they are released. Once outside the root and back in the soil, they re-nutrify and regrow their cell walls — and start the process over again. It’s called the rhizophagy cycle.

“Up to 40% of the nitrogen of a plant can come from this system,” Jeff says. “A bunch of the metals that the plant needs for nutrients come from these bacterial walls. This is a major, major new section of the soil food web. It is absolutely amazing.”

People tend to think of plants as stupid, inanimate objects, he says, but the reality is there is a lot of chemical signaling going on between plants and microbes and among the plants themselves.


root hairs and exudates

Plants release exudates through their root hairs to attract beneficial bacteria and fungi. (Photo Courtesy of Timber Press)


Endophytic Bacteria

Bacteria that live inside plants for at least part of their lives and benefit the plants with their presence are called endophytic bacteria. They help plants produce hormones to form leaves, set fruit, drop fruit, etc. 

There are even endophytic bacteria that will jump off one plant, say a grass, onto another, say a dandelion, and kill the dandelion before jumping back onto the grass. “Those kinds of things are being developed as well,” Jeff says. “It’s just a whole new frontier.”

One of the ways that endophytic bacteria persist is by living in seeds. They end up in the flower of a plant and get sealed into the seed coat as the flower forms the seeds. 

“Then when the seed germinates, they hop back into the soil, and they’re available to help the plant,” Jeff says. “The same bacteria that infected — if that’s the right word — corn 400 years ago, exists on corn today because it’s in the seed, and it jumps back out again.”

An exception to this longevity is cotton because of how the seeds are treated to kill bacteria. 

There are also endophytic (endo=inside, phytic=plant) mycorrhizal fungi and endophytic yeast. 


bacteria on roots

The endophytic bacteria that plants pass to new generations through seeds are not always present in cuttings, so seed propagation beats propagation through cutting in this respect. (Photo Courtesy of Timber Press)



James White and his students have done some phenomenal work, Jeff emphasizes. 

Another example is their work with trichomes, the hairs found on certain plants, including tomatoes and cannabis. Cannabinoids, including Cannabidiol, or CBD, are found on cannabis specifically in the trichomes.

Jeff says it was theorized that because trichomes look like hairs, they are formed the same way. But that’s not the case. Trichomes contain bacteria that produce nitrogen that feeds the plants and they help populate the phyllosphere (the area around the aboveground part of a plant) with the right kind of bacteria.

“In the case of cannabis, the RO that’s sprayed on the bacteria to keep them in check is cannabinoids, which is what you are trying to grow,” Jeff says.

How Bacterial Mixes Vary Between Seeds, Cuttings 

The difference in local bacteria contributes to differences between heirloom seeds.

“So your heirloom tomato is different from my heirloom tomato or your heirloom cannabis or whatever because the seeds’ bacterial mix is just a little bit different,” Jeff says.

If you propagate plants by taking cuttings — rather than gathering their seeds —  the same bacteria won’t be transferred to the next generation of plants, he points out.

“If you are taking a cutting, you’re getting a good plant. They root, but they may not have that great setup that you want to have, which you definitely have when you use a seed plant.”

How Understanding Bacteria Will Improve Agriculture

By understanding how plants can fix their own nitrogen, agriculture can use less of the harmful chemicals that are often relied on. 

“Research has shown that if you’re using chemical nitrogen, you are reducing your nitrogen produced by bacteria,” Jeff says. “And, you know, plants have been doing this for thousands and tens of thousands of years. Why do we think we’ve got a better system?”

When plants are getting chemical nitrogen fertilizer, they don’t have to signal to beneficial, nitrogen-fixing bacteria that they need them around.

To promote good bacteria on and in the plants in your garden, Jeff advises making sure your soil has plenty of organic matter to support a healthy biome. Sterile soil and sterilized seeds disrupt the natural systems of plants.

He notes that regular compost and vermicompost have different bacterial mixes, and one will work better on some plants than the other. The compost inputs affect what bacteria are present.

Jeff’s recommendation is that if you want to grow grass, you should apply compost that you made with grass clippings, and if you want to grow tomatoes, you should use compost you made from composted tomato plants.  (A caveat I’ll add here is that if your tomato plant had a plant disease, you should throw it away rather than compost it, because those pathogens will persist in the compost.)


Sarcina in carrot

Sarcina bacteria in carrots.
(Photo Courtesy of Timber Press)


The Law of Returns

Jeff says the United States, and perhaps the world, has only 60 years of soil left because traditional agriculture is destroying soil structure by using all these chemicals and tilling.

“These bacteria in particular produce a slime that sticks those soil particles together, and the fungi come in and weave them together and hold them in there,” he says. “I mean, the soil food web is a phenomenal system. We have violated the soil food web system, and worse, there’s something called the ‘law of return,’ which we as gardeners are very, very bad on. We violate the law of return almost by definition.”

He explains that the law of returns means that what falls from a plant is supposed to remain where it falls so it can decay and the microbes can feed the nutrients to the plant again. 

But when gardeners harvest lettuce leaves, ears of corn, etc., they are removing that organic material. We can replace the nutrients we take away with different organic materials or with chemical fertilizers

The Future of Gardening and Bacteria

Jeff notes that rhizobia bacteria and Bacillus are already available for sale. They are marketed as inoculants or probiotics to treat plants or soil. He foresees endophytic bacteria coming on the market next.

The challenge with selling bacteria is they are living. They need to be packaged in a way that they will survive storage and shipping. Bacillus forms spores that allow the bacteria to protect themselves, but other bacteria aren’t so easy to work with. They may need to be freeze-dried.

Jeff predicts that we are going to see things in the next five or six years that are going to blow our minds — things that we never would’ve thought would happen, even after 2006, when we learned about the soil food web. 


Teaming With Bacteria Cover

“Teaming with Bacteria” is the fourth book in Jeff’s “Teaming” series. (Photo Courtesy of Timber Press)


I hope you enjoyed my conversation with Jeff Lowenfels on “Teaming with Bacteria.” If you haven’t listened yet, you can do so now by scrolling to the top of the page and clicking the Play icon in the green bar under the page title. 

Have you used inoculum to add microbes to your garden? Let us know in the comments below.

Links & Resources

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

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 184: More Must-Have Books for Every Gardener

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

Episode 281: The Chemical Age: How Tools of War Became Agricultural Chemicals

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

joegardener Online Gardening Academy Organic Vegetable Gardening: My new premium online course membership opens in 2023. Sign up for the waitlist here.

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® 

GGW Episode 220: Gardening for the Hungry

GGWTV YouTube   

Growing a Greener World with Joe Lamp’l” podcast Ep. 029 with Jeff Lowenfels

Plant a Row for the Hungry

Jeff Lowenfels on Instagram: @gardenerjeff

Jeff Lowenfels on Twitter: @gardenerjeff

Jeff Lowenfels | Alaska Gardening and Growing column

Teaming with Microbes: The Organic Gardener’s Guide to the Soil Food Web” by Jeff Lowenfels and Wayne Lewis 

Teaming with Fungi: The Organic Grower’s Guide to Mycorrhizaeby Jeff Lowenfels 

Teaming with Bacteria: The Organic Gardener’s Guide to Endophytic Bacteria and the Rhizophagy Cycleby Jeff Lowenfels

Teaming with Nutrients: The Organic Gardener’s Guide to Optimizing Plant Nutrition” by Jeff Lowenfels

He Wrote a Gardening Column. He Ended Up Documenting Climate Change.” | The New York Times | By Zach St. George

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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, AeroGarden, Milorganite, Soil3, Greenhouse Megastore, PittMoss, Territorial Seed Company, Earth’s Ally, National Wildlife Federation 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.

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