Collimonas: The Fungal-Feeding Bacteria That Keeps Your Soil in Balance
Collimonas is a soil bacterium that can grow by feeding on living fungi. Scientists call this mycophagy. It also dissolves minerals out of rock and makes compounds that hold back some disease-causing fungi. It lives at low numbers in undisturbed, nutrient-poor soils, and it is one small check inside the soil food web that keeps bacteria and fungi in balance. Healthy soil balance comes from a diverse community of microbes, not from any single species.
Every October the first cool rain turns my mulch beds into a mushroom farm. I walk out with my coffee and there they are, little tan caps that weren't there the night before.
The mushroom is just the fruit. The real fungus is underground, a tangle of white threads finer than sewing thread running all through the bed. If you could zoom in far enough, you'd find bacteria crawling along those threads.
A few of them are eating it.
That's Collimonas, this week's microbe spotlight. I'll admit I picked it partly because the name sounds like a cough syrup. Then I started reading, and it changed how I think about what "balanced" soil even means.
What's in this guide
What Is Collimonas?
Collimonas is a group (genus) of soil bacteria in the family Oxalobacteraceae, a word I had to look up twice. Dutch researchers named it in 2004. They called the first species Collimonas fungivorans, and fungivorans means fungus-eating, so nobody was being subtle.
You won't find much of it anywhere. It hangs around in small numbers in some of the stingiest soil on the planet (Leveau et al., 2010):
- Sand dunes and old, unplowed grassland
- Forest floors, especially around tree roots
- Pretty much anywhere easy food is hard to come by
I think that's why it got so creative. If nobody's leaving out snacks, you figure out how to eat the furniture.
Collimonas lives in a crowded underground where bacteria and fungi are always competing for space and food.
Collimonas at a Glance
| Trait | What to know |
|---|---|
| Type of organism | Gram-negative soil bacterium, family Oxalobacteraceae |
| Named | 2004; type species Collimonas fungivorans ("fungus eater") |
| Where it lives | Nutrient-poor, low-disturbance soils: dunes, grasslands, forests, tree root zones |
| Main skill | Mycophagy: grows by feeding on living fungal threads |
| Other skills | Breaks down chitin, dissolves minerals from rock, makes antifungal compounds |
| Abundance | Low numbers; more common in fungal-rich soils than in plowed fields |
| Role in the garden | A small check on fungi inside a diverse soil food web |
| In Elm Dirt Plant Juice? | No. Two relatives from the same family are (see below) |
How a Bacterium Eats a Fungus
Most soil bacteria are scavengers. They live off dead plant bits and the sugars that living roots leak into the dirt. Collimonas goes after fungi that are still alive, which very few bacteria can pull off.
It's slow about it. No teeth. Just chemistry.
- First it latches on to a fungal thread. Scientists call these threads hyphae.
- Then come the enzymes. Chitinases break down chitin, the same tough stuff in a crab shell and the main material in a fungal cell wall. Collimonas throws in some antifungal compounds for good measure.
- Once the thread starts leaking, it eats whatever comes out. A little gross? Sure.
For a while nobody knew whether this only happened in lab dishes. So a team in the Netherlands added fungal threads to real field soil and watched. Collimonas numbers climbed, while most of the other soil bacteria they tracked just sat there (Höppener-Ogawa et al., 2009).
The part that tickled me is tucked into the same paper. Trichoderma, a fungus we've written about before, was feeding on those same fungal threads in the same soil. A bacterium and a fungus both works the same buffet. Nature doesn't care much for our neat little categories.
Researchers are still sequencing new strains to figure out which genes run the whole operation (Song et al., 2015). If the chitin-cutting part rings a bell, that's because Serratia uses the same trick to protect plants from fungal disease.
Collimonas works along fungal threads like these, breaking down chitin and feeding on what leaks out.
Why a Fungus-Eater Helps Keep Soil Balanced
Now, if you love mycorrhizal fungi (I do, probably more than is normal), a bacterium that eats fungi sounds like the last thing you want in your beds.
Relax.
The soil was sorting this out long before any of us showed up with a trowel and a strong opinion about how things ought to go, and it's still pretty good at it when we give it half a chance.
Bacteria and fungi are always shoving each other around underground, and a healthy garden needs plenty of both. Trouble usually starts when one side gets way out ahead. Collimonas is one of the little things that shoves back, and the research on it is pretty specific:
- Its effect on the total amount of fungus in soil is small. There just isn't that much Collimonas around.
- It may change which fungi do well. When scientists added it to soil, the fungal mix shifted, probably because it prefers some species over others.
- Some strains make compounds that held back plant-disease fungi in lab tests (Ballhausen et al., 2016).
- Nothing it eats goes to waste, since it all cycles back into the soil.
I wouldn't call it a referee. That gives it too much credit. It's one of thousands of players keeping each other honest, which is the whole reason living soil matters more than the numbers on a fertilizer bag.
Think of it as a circle. Fungi feed your roots through the mycorrhizal network. Collimonas nibbles on the fungi. Protozoa and nematodes graze on bacteria like Collimonas, and around it goes. Nobody wins for long, and that constant push and pull is what balanced soil actually means.
Extension soil scientists put it in plainer terms than I just did. A diverse soil food web crowds out disease organisms by competing with them for food and space, and using fewer chemicals helps keep that web intact (UF/IFAS Extension; WSU Extension).
It Also Pulls Nutrients Out of Rock
Eating fungi would be enough of a party trick for most microbes. Collimonas also dissolves rock. Some strains release acids that pull minerals straight out of sand grains and rock particles (Picard et al., 2020).
The chemical engineer in me loves this one.
A lot of what your plants need starts out locked inside mineral particles where roots can't get at it. Potassium is one. Phosphorus is another, along with trace metals like iron and magnesium. Weathering bacteria are one of the slow, patient ways nature unlocks all that, and they've been at it under our feet since long before anybody sold a bag of anything.
Between eating fungi and weathering minerals, Collimonas keeps nutrients moving through living soil.
Is Collimonas in Plant Juice?
No.
We had Plant Juice independently DNA-sequenced, and the lab named 291 verified species. Collimonas wasn't on the list. I'm writing about it anyway because it's a great way to explain how balance works underground, not because you'll find it in the bottle.
Out of curiosity I went back through the results to see how close we got. Closer than I expected, actually.
- Two Collimonas cousins are in there. Herbaspirillum huttiense and a Massilia species belong to the same family, Oxalobacteraceae, and Massilia happens to be a rock-weathering bacterium too.
- Plant Juice also has five Lysobacter species. They're a different group, but they're known for fighting fungal plant disease.
So no, it's not a Collimonas product, and I won't pretend otherwise. What you get is 291 species that build the kind of crowded, diverse community where a specialist like Collimonas tends to show up.
How to Build a Balanced Living Soil
You can't buy balance in a single microbe. It comes from the whole crowd. The nice surprise is that building that crowd mostly means doing less work, not more.
- Leave the leaves. Compost, shredded leaves, and mulch feed a huge cast of bacteria and fungi, and specialists like Collimonas need that variety to exist at all.
- Dig less. Collimonas turns up more in undisturbed, fungal-rich soil than in plowed fields. No-dig beds keep those fungal threads in one piece.
- Keep something growing after summer. Fall greens, a cover crop, a few perennials. Any living root keeps the microbes fed.
- Add living microbes. Plant Juice carries 291 verified species and Bloom Juice carries 192.
- Worm castings and Ancient Soil add organic matter and microbes in one step.
- Go easy on harsh stuff. Heavy salt fertilizers and broad fungicides thin out soil life. We dug into what gardens on synthetic fertilizer are missing if you want the longer version.
A layer of mulch is one of the easiest ways to feed both sides of the soil, the fungi and the bacteria.
What Gardeners Tell Us
I'd rather you hear it from them than from me.
Cynthia F.
"We live in the mountains n soil is rocky. This is the only fertilizer that keeps my garden alive ❤️"
Linda F.
"Using elm plant food every2-3 weeks alternating with plant bloom. Has given my roses healthy blooms and few diseases of the leaves. Love the product."
Linda W.
"The plant that was in my granddaughters room, got some kind of a disease or something was going on with it, lost most of its leaves, and my granddaughter was ready to throw it away, and I was bound and determined to save it. … after I started using El dirt the plant fertilizer that it has lots of new growth"
Plant Juice is rated 4.65 out of 5 across 1,793 customer reviews.
Frequently Asked Questions
What is Collimonas bacteria?
Collimonas is a genus of soil bacteria in the family Oxalobacteraceae, first described in 2004. Its type species, Collimonas fungivorans, means "fungus eater" because it can grow by feeding on living fungal threads. It can also dissolve minerals out of rock and make antifungal compounds. It lives at low numbers in nutrient-poor soils such as dunes, grasslands, and forest floors.
How does Collimonas eat fungi?
Collimonas attaches to living fungal threads (hyphae) and releases enzymes, including chitinases, plus antifungal compounds. These break into the chitin-based fungal cell wall. Nutrients leak out and Collimonas uses them to grow. This feeding style is called mycophagy, and it is uncommon among soil bacteria.
Are fungus-eating bacteria bad for my garden?
No. Collimonas lives at low numbers, and field research found its effect on total fungal biomass is likely minor. Its role is a small check within a diverse soil food web. It can nudge which fungi thrive, and some strains make compounds that hold back certain disease-causing fungi. A healthy garden soil still has plenty of beneficial fungi.
Where is Collimonas found?
Collimonas is found in nutrient-poor, low-disturbance soils such as sand dunes, grasslands, forest floors, and tree root zones. Research found collimonads are more common in fungal-rich grassland and forest soils than in fungal-poor plowed farm fields.
Is Collimonas in Elm Dirt Plant Juice?
No. Independent DNA sequencing of Plant Juice identified 291 verified species, and Collimonas was not one of them. Two members of the same bacterial family were found: Herbaspirillum huttiense and a Massilia species. Plant Juice also contains five Lysobacter species, a separate group of soil bacteria studied for antifungal activity.
Healthy Soil Is a Balancing Act
Next time October mushrooms pop up in your mulch, think about what's going on under 'em. There's a whole crowd down there eating each other and breaking down rock, and not one bit of it needs you to manage it.
Feed the soil. Dig a little less. Then let it sort itself out, which is my favorite thing about gardening this way: you're not doing it alone.
Where to go next:
- New to all this? Start with Soil Biology 101: what lives in a tablespoon of dirt.
- Read how microbes protect your garden from disease without spraying.
- Want one small soil win in your inbox each week? The email signup is at the bottom of this page.
- And if you spot mushrooms in your beds this fall, tag us @elmdirt. I love seeing them.
Sources: Leveau JHJ et al., "The bacterial genus Collimonas: mycophagy, weathering and other adaptive solutions to life in oligotrophic soil environments," Environmental Microbiology, 2010 (link). Höppener-Ogawa S et al., "Mycophagous growth of Collimonas bacteria in natural soils, impact on fungal biomass turnover and interactions with mycophagous Trichoderma fungi," The ISME Journal, 2009 (link). Song C et al., "Exploring the genomic traits of fungus-feeding bacterial genus Collimonas," BMC Genomics, 2015 (link). Ballhausen MB et al., "Trait Differentiation within the Fungus-Feeding (Mycophagous) Bacterial Genus Collimonas," PLOS ONE, 2016 (link). Picard L et al., "Draft Genome Sequence of Collimonas pratensis Strain PMB3(1), an Effective Mineral-Weathering and Chitin-Hydrolyzing Bacterial Strain," Microbiology Resource Announcements, 2020 (link). UF/IFAS Extension, "The Soil Food Web" (link). WSU Skagit County Extension Master Gardeners, "What's in Your Soil?" (link).
Founder & Chemical Engineer · Elm Dirt, Kansas City
Lauren started Elm Dirt after her 6-month-old daughter grabbed fistfuls of backyard dirt and ate them. As a chemical engineer and a mom, she dug into the science of what was really in garden soil, and built a fertilizer line around beneficial microbes instead of synthetic chemicals. Today Elm Dirt products are used by home gardeners, rose show champions, and organic growers nationwide.