(WARNING: Long post.)

Conventional thinking and agronomy about soil and how plants grow has been dominantly chemistry-based for quite a long time, as pointed out in Soil Story: It’s the Biology.

So, when we turn tables and take a biologically focused perspective on growing food and beautiful flowers, many will undoubtedly find the following content seemingly unscientific and heretical.

At the surface, it will sound counter-intuitive to conventional thinking about how plants grow and how to grow plants. But if you stop and think about it and dig a little deeper, it starts to make sense.

You won’t find this in your standard gardening books and magazines… yet.

What we’ll discuss

While we love gardening for growing plants, it still starts with the soil, regardless of where you live or what plants you’re trying to grow.

First, we’ll discuss how the tiniest of the tiny helps your plants and vice versa.

I’ll then talk briefly about the impacts of using fertilizers, pesticides, and tillage. I will also talk about “anaerobic” versus “aerobic” soils, what this means for your garden and it relates to using the above inputs.

Finally, I’ll discuss (very briefly) things you can start doing to help you get your tiny-but-mighty army going in your soil, and to keep them there.

There’s so much to discuss, and many, many rabbit holes to go down. I plan to write more about these in future posts!

Let’s talk soil biology.

Soil life is fueled by plants. Plants drive soil life through photosynthesis.

Photosynthesis is where plants turn sunlight energy plus carbon dioxide (CO₂) and water into oxygen, water vapour, and simple sugars. Oxygen and water vapour are released by the stomata in the plants leaves (and stems, to some extent). The plant also uses some simple sugars, but most… and this is where science takes a “unknown/grey area” approach.

Previously, it was thought that the sugars were stored in the roots as energy reserve. And, that plants simply leak these sugars out randomly. Now, we’re finding that the latter prediction is incorrect, and the former is half-right.

These sugars are, instead, used to feed microbes. Further, and we’ll get to this soon, they are used as a way for plants to–get this–farm microbes.

But first, what role do these microbes play in the soil?

Bacteria and fungi “eat” crushed rock and break down organic matter into tinier particles and compounds using special acids and enzymes. They keep minerals in their bodies and release gases such as CO₂. They also “glue” different tiny particles together to make larger soil particles called “aggregates.” Where bacteria create small soil aggregates, fungi create even bigger particles called “macro-aggregates.”

Fungal hyphae attach themselves to root hairs and exchange nutrients and sugars with the plant in this manner. Some hyphae can insert themselves right into the root hairs, whereas others surround the roots.

Fungal hyphae are very good at reaching water and nutrients were root hairs are too big to do so because they’re so much tinier in diameter. They can get in between soil particles where root hairs fail. They’re best known as major highways, transporting nutrients from particles and organic matter to plants. They also house and support bacteria, making it easy for bacteria to move around in the soil.

Fungi are considered most important for supplying plants with phosphorus (P), as they are best suited for unlocking natural sources of P in the soil and making it available for plants to take up. As we’ll talk about later, phosphorus fertilizers is a good way to “kill off” your fungal populations.

Bacteria and plants have just as fascinating relationships with each other. Before less than a decade ago, we assumed that plants got their nutrients from bacteria through “passive” means; in other words, bacteria would, basically, “give up” certain nutrients plants needed if the plant gave what it needed in simple sugars. (Even before then, we thought that plants would passively, without reason, release simple sugars into the soil.)

Now, thanks to Dr. James White of Rutgers University, who discovered that plants farm bacteria in the same manner we farm livestock for meat and milk. Take a look at the illustration below, and allow me to explain!

Root exudates are what the plant releases through its roots into the soil. Remember the products of photosynthesis mentioned above? One of the most important is simple sugars, which are like sweet treats to bacteria and fungi.

Dr. Elaine Ingham came up with a great analogy to better understand what root exudates actually are, like cookies and cakes. These exudates contain lots of sugar, a little bit of protein, a little bit of carbohydrate, a little bit of fat, and a tiny bit of vitamins. Basically, everything needed to make cookies and cakes:

• Sugars = brown sugar and white sugar.
• Protein = eggs and milk. If it’s vegan, then vegan eggs and nut milks.
• Carbohydrates = flour.
• Fat = butter or margarine.
• Vitamins = whatever is in the above ingredients.

Put them all together, bake them in the oven and voila, pastries!

To compound on Elaine’s lovely analogy, the plant needs to “bake” all sorts of different types of cookies and cakes to entice different types of bacteria and fungi. Some like raisin and oatmeal cookies; others like chocolate chip cookies; some prefer strawberry angel food cake, others like black forest or red velvet cakes. By making different types of cookies and cakes, the plant invites different microbes that hold whatever nutrients that plant needs.

Now, get ready for the interesting part.

These tiny microbes are sucked into (or absorbed) the growing root hair tip. Then, their cell membranes are stripped off. Nutrients they’ve held in their cells are released when the plant subjects them to superoxide.

(Science note: Superoxide is a chemistry term referring to an extremely unstable oxygen molecule that is ready to react to other molecules. Primarily, those other molecules include nitrogen, phosphorus, sulfur, calcium, magnesium, silicon, potassium, iron, zinc, and more. Through some complex biochemistry I won’t get into, the plant uses superoxide to get any one or more of those specific nutrients in a form it can take up and use for growth and/or reproduction.)

(Some microbes may die in this process. Bacterial lifespans are mere minutes long; fungal hyphae live for 5 to 7 days.)

The survivors are then released back through root hairs that are “elongating” or growing, and outside of the root environment they reform their cell membranes and go harvest more nutrients from the soil.

Yet again, the plant’s root exudates entice them, and the cycle starts again.

White and his team called this the Rhizophagy Cycle. Rhizo = root, phagy = eat. In other words, roots are eating microbes. Plants farm microbes.

Pretty neat, huh?

At first, I thought of this almost like Hansel and Gretel with the wicked witch of the woods, only the whole… undressing… thing… just didn’t fit. Plus ew, pedophilia is just vile. In my defense, though, the reason I thought of it was how the plant (the old witch) harvests microbes (children Hansel & Gretel) by killing and eating them. As we’ve seen above, though, not all microbes die and get eaten like what happens in this Grimms’ Brothers fairy tale. Thus, this analogy just isn’t accurate.

A better analogy would be how we raise dairy cows for milk in a pasture-based system. Think of the plant as the human population who drinks milk and certain workers of the plant (the farmers) who raise and use sweet feed (root exudates) that the cows (microbes) really like as a means to bring them into the barn (inside the root tips) to be milked. When they’re done being milked, they’re sent back out to pasture again, and the cycle continues.

Can you think of a better analogy?

Negative Impacts on Soil Biology

Researchers have been trying to answer the question of how plants are so successful at getting nutrients (and being healthy) without man-made inputs. What I described above is the Coles Notes version of what they’ve discovered so far.

What this means in a garden context is that plants, if given the chance, can harvest their own nutrients without much assistance from us. In a garden context, it means we need to create an environment where these microscopic organisms can thrive.

If we don’t, we get a lot of problems with our soil. Many of us don’t (yet) connect those problems with the inputs we decide to use on our plants.

The Problem with Fertilizers & Pesticides

The role of those organisms (and, something I forgot to mention, the other organisms that feed on them and help contribute to the amazing soil food web) is not only to feed the plant, but also keep it healthy.

So, what if I told you that giving things that your plants supposedly “need” severs that relationship?

There’s a myth out there that “fertilizers kill microbes.” No, they don’t.

What fertilizers do is create a sudden, and huge flush in microbe populations. Very little (around 10 to 60% according to some studies) goes to the plant.

That fertilizer always goes through the soil microbe population first before going to the plant. They use up as much as they are able, and feed the plant what it needs.

Once those microbe populations use up that “free” source of fertilizer and they get nothing much else, they crash. Hard.

Mycorrhizae suffer, especially when [too much] phosphorus is applied as fertilizer. The plant will take up what it can and tell the mycorrhizae that its services are no longer needed.

The microbes don’t just pick up afterward. It takes time to rebuild that plant-microbe relationship, especially if the soil is “hooked on drugs,” so to speak.

And we wonder why plants start showing nutrient deficiency signs a while after. And, to counter these apparent deficiencies, why we’re regularly told that the solution is to apply yet more fertilizer. Often the excuse being, “because the soil simply isn’t supplying enough.” The same thing happens yet again, with us not realizing we’re not feeding the plant, we’re feeding the microbes that feed the plant.

Pesticides are… pretty obvious. They’re chemicals meant to kill living things. Pesticides include all chemicals meant to kill weeds (plants), insects, fungi, bacteria, and other organisms seen as harmful to crops. Some are more “selective” than others.

But, do they kill all microbes? Yes, but completely and totally. No pesticide has ever been known to permanently get rid of any living organism at any time in the past 150 years that pesticides have been invented.

The thing is, if you have already healthy soil, its microbes will detoxify the chemicals that enter it. If you have healthy soil that is “dead,” bare, and prone to runoff and erosion, that’s an entirely different story! It’s what makes synthetic fertilizers and pesticides unquestionably harmful to the environment.

Anaerobic/Compacted Soil Issues?

There’s talk as well that synthetic fertilizers, especially, contribute to anaerobic soils and therefore soil compaction.

The logic is this: Fertilizers encourage soil microbe populations to explode, using up a lot of oxygen in the soil. Then, they crash because they run out of food but, most importantly, oxygen and replace it with carbon dioxide (CO₂). When they die, anaerobic microbes take over.

Anaerobic soil isn’t bad, per se. It does, however, affect the root zone of the plants you want to grow, most which prefer aerobic soil, and can be seen as toxic to those plants. Anaerobic soil is perfectly fine for growing rice or aquatic plants in a natural wetland environment.

Some claim that fertilizers, which supposedly cause soil to go anaerobic, also cause soil compaction. Well, actually, that’s false.

Brief Truths about Compaction

Soil compaction is caused/influenced by four main things: tillage, heavy traffic, soil texture, and depth of soil profile. Tillage is the number one cause for soil compaction in garden soils.

Tillage is seen as having the ability to “fluff up” the soil. However, long-term impacts cause soil particles to smoosh tightly together, lessening gaps for water and oxygen to get into or escape. It also encourages soil microbes to consume the soil’s organic matter, helping decrease soil organic matter levels—something you don’t want.

This is how anaerobic soils occur. Aerobic microbes use up gases like oxygen, while carbon dioxide (and methane) accumulate. This is favourable for anaerobic microbes, so we get anaerobic soils.

So, the verdict is that compaction creates the conditions for anaerobic soil environments. Not the other way around. Nor do fertilizers cause compaction. They’ll exacerbate it, yes. But honestly, you don’t need synthetic (or organic) fertilizers to make anaerobic soils.

However, fertilizers and pesticides make plants more prone to disease. In a nutshell, the dissociation from its microbe population compromises its immune function. It sounds counterintuitive, but just like how we need our gut microbiome to keep our immune systems healthy and functioning, a plant also needs its microbiome to keep itself healthy and functioning in order to fight off pests and diseases.

If a plant isn’t healthy, it attracts pests and diseases. We mistakenly think that we need to spray something to kill that pest or disease when, in fact, that plant is screaming that it needs to re-associate with its microbes.

How Does All This Translate to My Garden?

For your garden, this means finding ways to wean yourself off of using pesticides and fertilizers. I don’t mean stop cold-turkey, but rather find alternate solutions rather than spending money to grab a jug of chemical that could be doing more harm than good.

Use compost. Turn your kitchen scraps into compost you can use for the garden. Be mindful of how you create good compost, which should smell good and be aerated, rather than smell horrible and could potentially be harmful to your plants.

Start a worm farm. They help with the composting methods.

Use mulch, lots and lots of mulch. Lawn clippings, dead leaves, wood chips, garden waste; basically any kind of organic “waste” that most would bag up and throw away would be perfect to put in a mulch pile to use on the garden. Mulch protects the soil and feeds your soil microbe population.

Reduce tillage as much as possible. Tillage, remember, causes compaction. Some soil disturbance is good for plants, but not a whole lot. It exposes soil, which must be covered and protected at all times.

Have a wide diversity. Gardens naturally have diversity, but diversity where plants are closer together–similar to in nature–with different canopies overlapping one another.

Overall, probably the biggest number one rule is to always protect the soil. Don’t allow any bare soil to be exposed. Don’t cover it with plastic landscape fabric; instead, mulch, mulch, mulch.

Your plants (and soil biology) will thank you.