Plant - Microbe Synergies

In a Permaculture System

The rhizosphere, or plant root zone, is a happening place. In Permaculture, we’re always talking about the action at the edges. But in this case, the action is focused on a narrow space filled with plant roots.

What’s the Deal Between Plants and Soil Microbiology?

Sunlight is the Key Power Broker

Soil microbes have evolved with plants (and vice versa) to create efficient nutrient-cycling zones in the soil. This activity is beneficial for the plant and fuels microbial activity.

So, what’s happening between these different life forms?

Without sunlight, plants can’t photosynthesize or share the bounty of the sun’s energy with soil microbes. It is an amazing partnership between plants and soil biology. In the rhizosphere, beneficial bacteria and fungi such as AMF (arbuscular mycorrhizal fungi) are busy bringing nutrients and water to host plants. The plants send chemical signals of their nutrient needs to the microbial population, and the microbes go in search of them. The microbiology is rewarded with plant root exudates, manufactured and shared by the plant through photosynthesis.

A mycorrhizal fungal network can stretch up to 20 centimeters (8 inches) beyond a plant’s root system. That doesn’t sound like a lot, but the fungi increase a plant’s root system reach by 100 - 1000%. 

Plants create energy from the sun through photosynthesis, and that takes chlorophyll. The reason we see leaves as green most of the year (an explanation of fall colors will come in another article) is that the chlorophyll reflects green light. Some microbes, in extreme conditions, use bacteriorhodopsin, a purple pigment, to harvest nutrients from the light in extreme environments. 

But after a few millimeters into the soil, all light is lost. It is as dark as a dungeon for those beneficial microbes. But they’re hardly captives. The soil is a place where life doesn’t vanish; it reorganizes. For microbes, it’s a home base, a laboratory, trade routes, and a concert hall all in one.

And the sun is still the main power broker, even when it’s no longer seen. That’s because of the plant-microbe synergies.

How Do Plants and Microbes Help Each Other?

The soil is a hidden kingdom of shadows. Nothing vanishes, it just changes form. There is no waste in the soil. In the loamy, clayey, or sandy darkness of your soil, there is a lot of activity.

• Microbes assemble in chambers and corridors carved not of stone, but of root hairs, mineral clusters, and worm-bored tunnels.

• Fungal networks stretch like secret passageways, foraging and ferrying phosphorus through the gloom with the precision of a well-trained courier guild.

• Exudates drip like coded messages from plant roots, summoning allies, suppressing invaders, and fueling tiny revolutions in chemistry.

• There’s no warden here—just collaboration. 

Mycorrhizal fungi aren’t prisoners; they’re co-conspirators, wrapped around roots like ancient scribes trading knowledge for sugar.

And like any self-respecting fortress, this dungeon defends its own:

• Microbes shield their leafy partners from drought and disease,

• fix nitrogen under siege,

• Rebuild the structure after floods, all in the damp dark.

Yes, it’s dark as a dungeon in the soil. But it’s not a prison. The rhizosphere, or plant root zone, It’s a biological speakeasy, a root-lit realm of strategy, exchange, and resilience.

What Soil Building Practices Foster This Kind of Cooperation?

Permaculture practices aren’t just passive. We can actively support and develop these plant-microbe synergies. The 5 basic principles of Permaculture are:

1. Keep living roots in the soil

1. Keep soil covered with mulch and organic matter

2. Plant for biodiversity

3. Use minimal disturbance of the soil

4. Manage soil moisture and harvest water

The first one, “keep living roots in the soil,” is a hard one for Midwesterners to wrap their heads around. We see winter as a time when everything goes dormant. But does it?

What’s Alive Under All That Snow?

The layer between the snow and the ground is called the subnivium; it’s a thriving world all winter. Small mammals such as voles, mice, and shrews tunnel through the snow feeding on seeds, roots, and their stored food. In the spring, we see these tunnels as indents in the soil surface.

Humans have a love/hate relationship with voles and mice. But in a permaculture mindset, we have to look at the bigger picture. Those rodents not only nibble the roots of plants, but they also eat insects, spiders, and other small invertebrates. They’re part-time pest control allies. Their foraging behavior is beneficial in many landscapes, especially as we encounter more extreme weather conditions. AKA: warmer winters that don’t take out as many insects.

We wouldn’t have vole and mouse activity if it weren’t for the living roots in the soil. They may take out a few plants, but overall, they’re beneficial. And we wouldn’t have food for owls without the voles and mice. It is a positive feedback loop.

Soil microbes and fungi remain active all winter. They slowly decompose organic matter and leaf litter, effectively cycling nutrients. There are very good reasons to leave your leaves all winter and not rake until later in the spring. You’ll have fewer insect issues.

The abundance of soil bacteria and fungi creates food for insects and arthropods. Springtails, rove beetles, emerald ash borers, and ladybugs have all evolved strategies for making it through a cold (as in Minnesota) winter. Many insects enter a state of suspended development, called diapause. They slow their metabolism and wait out the cold. Some mosquito species lay cold-hardy eggs that survive freezing temperatures.  Check out your rain barrel in the middle of winter during a thaw. You’ll see mosquito larvae wiggling around in there. 

What are the Impacts of This “Under Snow” Activity?

All that microbial activity creates heat and carbon dioxide, which is diffused slowly up through the snowpack. The rate depends on the snow density, temperature gradients, wind, and surface soil disturbance. In other words, if we’ve got a pretty good layer of insulating snow and we’ve left crop residue in the gardens, we’ll have more long-term carbon sequestration. The microbial activity leads to the formation of stable soil organic matter, such as humus.

According to a 2020 study in Nature Communications, winter microbial activity plays a subtle but important role in annual carbon budgets. And that’s especially true in northern ecosystems with consistent snow cover.

The under-snow activities of decomposing microbial species lead to the build-up of carbon-rich humus that sequesters carbon for years or decades if the soil is not disturbed. 

Our perennials look like they’re dead in the winter, but the root zone is alive and well. In fact, the microbial allies of plants remain connected to the plant roots and help buffer against freeze-thaw stress. Photosynthesis stops in the above-ground biomass, but the roots remain alive and feed off the carbohydrates and nutrients the plant stored during the growing season. Those sugars and solutes that accumulated in root cells lower the freezing point of the root biomass. They essentially create their own natural antifreeze.

Microbes produce cryoprotectants like glycerol to survive subzero conditions. The adaptations of microbes in our Midwestern winters also apply to glacial microbial life. Adaptations in glaciers to extreme cold, low nutrients, and high UV radiation are being studied by biotech. 

None of These Survival Techniques Work Well With Tillage

Developing a highly diverse biomass is only one piece of the puzzle for efficient plant-microbe synergies. The soil has to be disturbed as little as possible to maintain that positive equilibrium. The relationships between microbes, especially AMF, with their long hypha, are optimally maintained by optimizing all 5 of the Permaculture Principles for soil building.

Tillage breaks up soil aggregates, those crumbly soil clusters held together by fungal hyphae, root exudates, glomalin, and microbial biofilms. When you put your plow, disc, or rototiller in the soil, you collapse microbial habitats, emit CO2 to the atmosphere, and sever mycorrhizal hyphae.

Breaking up the soil creates a negative feedback loop. The quantity and quality of the microbial population are diminished, and your plants have less resilience to pests and diseases.

Fewer aggregates > less microbial habitat > fewer microbes to rebuild structure > less resilience > more inputs > fewer aggregates.

This is, sadly, the formula of conventional agriculture and gardening.

Permaculture Systems: Positive Feedback Loops

With minimal or no-till practices, you preserve microbial networks, enhance nutrient cycling and water retention, and support long-term soil carbon sequestration. You are also creating a future-proof field or landscape by developing redundancies of resilience.

You have to design for plant-microbe synergies, and it starts with observation. Those positive feedback loops are everywhere, and when we act before we’re aware of them, we’re undoing natural systems. 

After observation comes companion planting, if needed. Many weeds are the companion plants of our desired food crops and are more desirable to insects. Take out the weeds, and you’re setting up your landscape for insect and disease damage. 

Weeds tell us what is missing or out of balance in that part of the landscape. Inoculants and compost teas are good microbial jumpstarts for an area that has seen far too many chemical treatments. Biochar inoculated with compost tea, manure, or humates does double duty by sequestering carbon and supplying habitat and food for beneficial microbes. The synergies created in a Permaculture landscape are infinite. 

Permaculture doesn’t just grow plants, it cultivates relationships. The soil is a living, collaborative system. We have an active role in maintaining as many synergies as we can observe, and abstain from pulling weeds, disturbing the soil, or leaving the soil bare. 

As Permaculture Designers, we work with Nature and not against her for the highest good for all inhabitants of our planet. We acknowledge that the sun is the prime mover, and we plan our actions based on the synergies, known and unknown, between plants and soil biology. 

Is this a way of living on the land that you’re interested in? GRLPI is an organization of Permaculture professionals who are always interested in optimizing synergies.