Digging Into the Basics of Soil Biology – Episode 12

Soil is Alive!

Today we talk about the basics of soil biology including:

• Understanding soil as a living ecosystem
• The “players” in soil biology
• Soil organic matter and nutrient cycling and their importance to soil biology
• The principles of soil health

I also go through the January gardening calendar.  It is a great time for planning in the garden.  

• WSU publications on Soil Health
• USDA Natural Resources Conservation Service on Soil Health
• Permaculture approach to soil health by Andrew Millison (Oregon State University)
• WSU Soil Health
• August 2022 issue of Seeds For Thought page 5. A fun article about soil health called “Soil Your Undies” on page 5.

Welcome to episode 12 of the Evergreen Thumb. Today we’re going to be digging into the basics of soil biology. But first, we want to go over the January gardening calendar.

January is another pretty slow month, but it’s my favorite time to kind of take stock of what went well and what didn’t work last year, to inventory my seeds, and prepare an order. Um, it’s a good time to order summer bulbs like begonias and lilies, uh, for your spring delivery and to evaluate areas of bare soil or chronic weeds and consider. Planting ground covers in those areas. Ground covers can offer weed suppression and soil protection to prevent erosion.

Um, it’s a good time to check on your overwintered annuals. So like I keep my, fuchsias in our little greenhouse. So it’s a good time to check on them, water them. Check bulbs and shrubs under protected eaves and overhangs to make sure that they’re getting water. And spring bulbs can still be planted as long as the ground isn’t soggy or frozen.

So if you didn’t get your bulbs in time or you never got around to putting them in in the fall, you can still do it as long as your soil isn’t soggy or frozen. Um, they may not bloom this year, they’ll be in the ground and preparing for bloom for next year. Check sheltered annuals for insects particularly aphids, and treat if necessary.

Uh, if you’re interested in forcing blooms, you can bring in flowering quince, forsythia, or witch hazel to force the blooming. Soak the branches in tepid water.

Trim amaryllis stems to the bulb once the flowers drop their petals.

Um, be sure to rinse or wipe dusty house plants with tepid water, but don’t fertilize, uh, indoor plants or house plants uh, they need kind of downtime in the winter as well, so, refrain from fertilizing, uh, and monitor house plants for Insects and treat as necessary.

I know in the winter, we bring in our Meyer lemon and it tends to have scale. Because it’s out of sight, it’s in our well house where it’s protected from frost, it’s easy for the scale to get out of control because I’m not seeing the tree every day and monitoring the scale and dealing with that as it happens. If you need help diagnosing a pest issue. Be sure to contact your local extension office and they will get you in touch with local Master Gardeners.

That sums up the January calendar. It’s pretty minimal still, there’s not a whole lot going on, but it’s a big planning month. Especially for me, I love to plan. I also plan out when I’m going to do my pruning. I plan out what type of garden projects we have for this year. We’re going to be building six more raised beds in our vegetable garden and, hopefully, we will also get some cross-fencing done in the back half of our property.

So, this is a good time for planning because it’s rarely decent enough weather to get outside and get anything done. My other goal for January is to get the, uh, garden beds that I didn’t get cleaned up in the fall and get those cleaned up and ready for spring. I’ll cut the corn stalks off at the ground and leave roots. Leave the roots in the ground whenever you can. So yeah, that pretty much covers January. All right, so let’s jump into today’s episode.

So today I am going to talk about how to understand soil as a living ecosystem, including an overview of the soil food web and some of the organisms that are present in soil. Then I’ll talk about more specifics about the players in soil biology and their different roles in soil health. Then we’ll move on to organic matter and nutrient cycling, and the importance of organic matter in soil, and how organisms affect nutrient cycling for plant uptake. And finally, we’ll talk about building healthy soil and the principles of soil health. 

So in drier climates, ants, or termites, or other invertebrates will serve similar functions that worms perform in wetter climates. But in most ecosystems, More life and diversity lives below soil level than lives above. And one cup of soil can contain as many bacteria as there are people on Earth.

So organisms are integral to the cycling of nutrients and they drive the functions of decomposition, mineralization, storage and release of nutrients, filtration and degradation of pollutants, carbon cycling and sequestration, and nitrogen cycling, including nitrogen fixation. Most biological activity takes place in the top 8 to 12 inches in the soil profile, and this is called the rhizosphere or the rooting zone. This is an area of intense microbial activity that is integral to plant and soil relationships.

Um, just as a side note here, keep an eye out. Uh, we hope to have an upcoming episode specific to carbon sequestration, as that’s kind of a, a hot topic, especially in regenerative agriculture and permaculture circles, so we’ll talk more about carbon sequestration in a later episode.

So, plants leak energy-rich carbon compounds like sugars and amino acids. These are called exudates because they are exuded from the roots of the plants. Every plant species leaks a unique signature of compounds from their roots, and different microbes are attracted to different chemical exudates, so the plants grown play a large role in determining the microbial community in the soil.

So, if you look at an image of the Soil Food Web, which I will share on the website. The levels of the Soil Food Web range from the plant shoots and roots and the organic matter that they create waste and from those plants, bacteria, fungi, nematodes, arthropods, protozoa, all the way up to birds and larger mammals are considered part of the soil food web. They all have an impact on the health and the overall biology.

So the first one we’ll talk about are the larger invertebrates or earthworms, ants, beetles, and similar, creatures. Um, I’m not going to talk about larger ones like birds and moles and things like that, because they’re generally not residing in the soil, but larger invertebrates, especially earthworms, ants, beetles create macro pores. So larger pores that allow water to percolate into and through the soil. Some of these invertebrates feed on plant roots and some feed on each other. 

Earthworms are probably the most recognizable of these soil animals. They eat plant material and organic matter and then exude, excrete worm castings, which become food for other organisms. Similarly, beetles break down organic matter and ants as well, take it deeper into the soil from the surface and bring it down. 

So the next, segment of organisms is bacteria. And these Bacteria continue to break down the organic matter. They are the smallest and the most numerous organism in soil. They live on root exudates and plant material. So again, the plant material that the earthworms and ants and beetles are bringing deeper into the soil, the bacteria can get at those and break those down even further. 

Rhizobium are the nitrogen-fixing bacteria. Many people are probably aware that certain classes of plants, particularly legumes like beans and peas, and clover, are considered a nitrogen-fixing plant. But what allows those plants to fix nitrogen is the bacteria, and the bacteria form symbiotic relationships with those plants. They infect the host plant and convert atmospheric nitrogen into a plant-available ammonium, and then in return, the plant provides simple carbohydrates to feed the bacteria. And many of those rhizobium are plant species specific. So there is a specific species of bacteria that will be hosted on a specific species of plant.

So clovers have a specific species of bacteria that allow those plants to fix nitrogen, whereas beans have a different species. You can inoculate soil with plant species-specific rhizobium. I know of a couple of seed vendors. If you’re buying like a cover crop seed, clover seed, things like that, you can buy them inoculated, um, or you can buy inoculants separate. This is more usually done on a commercial scale, and it’s not strictly necessary because many of the bacteria are already present in the soil. But if you do inoculate your soil or inoculate the seeds before you plant, that usually only has to be done once because the bacteria persist in the soil.

The next major class of organism in the soil are fungi. And they are nature’s recyclers, and they are symbiotic partners with the plants. Now there can be both beneficial and pathogenic fungi in the soil, but most are beneficial. And as the plants provide sugars and B vitamins and other important chemicals to the fungal partners, The fungus, with its long, thin hyphae, which are the strands of fungus, are better able to find water and minerals, particularly phosphate, which is often immobile in soils, and the mycorrhizae solubilize the phosphate and then share that with the plant along with water and other nutrients.

The added water and nutrients allows the plant to thrive rather than merely survive as its counterpart without a mycorrhizal partner would. And until recently, uh, it was believed that mycorrhizal relationships were unusual, but now, um, scientists have confirmed that they occur in as much as 95 percent of plants have some strain of fungi that partners to help provide Water and nutrients to the plants.

Beneficial fungi are also known to increase resistance of the plant host to root diseases. So they can actually form a barrier in the soil between, um, a pathogen and the root. 

Let’s see, the next class are protozoa, and these are microscopic predators that regulate bacterial populations. So they help keep the bacteria levels in check in the soil. They consume the bacteria and then they release nitrogen. Protozoa are also a food source for the next class we’re going to talk about, which are nematodes.

So nematodes can be beneficial or pathogenic. These are microscopic worms that live in the soil and if you look back to the soil food web, they show three different type of nematodes. There’s root feeders, they actually feed on the roots. There are fungal and bacterial feeders that help keep the bacteria and fungi populations in check. And then there are predatory nematodes. Beneficial nematodes eat protein, including protozoa, and small insects, like some, um, arthropods, but they also can serve as a biological control for root weevils and cutworms, Japanese beetle, and more than 250 other soil pests by predating on those pests. So, and then they excrete nitrogen, which is also available to plants. 

So, you see, nitrogen is a common theme. A lot of these are providing nitrogen to the plants. 

Okay, so now we’re going to talk about soil organic matter and nutrient cycling. So organic matter in the soil can be living or dead and the, um, soil food web and the organisms that create it are part, are the living part of Soil organic matter. The living portion represents approximately 15 percent of the soil organic matter and those microorganisms, including insects and earthworms, get their energy and nutrients by breaking down organic residues in the soil.

And at the same time, much of the energy stored in those organic residues is used by organisms to make new chemicals as well as new cells. The dead organic matter, or the fresh residues, consists of recently deceased microorganisms, insects, earthworms, etc., old plant roots, crop residues, and recently added manures. This is the part of the soil organic matter that is active or easily decomposed and is the main supply of food for various organisms living in the soil.And then there’s also what is sometimes called the very dead, soil organic matter, um, sometimes called humus. And that is the stable organic matter that resists decomposition. Mainly because its chemical structure makes it hard for the soil organisms to utilize. So, they can be partially decomposed residue, including the remains of microorganisms. They can be in spaces too small for organisms to access.

When these aggregates are broken up by freezing and thawing cycles or by tillage and can be made accessible to microorganisms, then they are readily decomposed. But because much of soil organic matter is so well protected from decomposition, its age in soil can be as high as hundreds of years. Even though it is protected from decomposition, it is an important part of the soil. It holds onto essential nutrients and stores them for slow release to plants.

Another type of organic matter that has gotten a lot of attention lately is often referred to as carbon or char. Biochar or charcoal has become a very popular soil amendment. Charcoal is a very stable form of carbon that helps maintain high cation exchange capacity but does not provide soil organisms with readily available food sources like fresh residues or compost does. 

Adding biochar to soils is not likely to be economical on a large scale, so if you have a large vegetable garden or a large ornamental garden, the costs may outweigh the benefits.

Soil carbon is sometimes used as a synonym for organic matter, although it also includes nutrients and other chemical elements. Soil organic matter is so important because it is the very foundation for healthy and productive soils. It’s true that you can grow plants in soils with little organic matter. Though it becomes increasingly difficult because of problems with fertility, water availability, etc., And it affects the health and yield of gardens and requires even higher levels of input such as fertilizers and irrigation and pesticides.

Most of the nutrients in soil organic matter can’t be used by plants as long as those nutrients exist as part of a large organic molecules. As soil organisms decompose that organic matter, the nutrients are converted into simple inorganic forms that plants easily use. This process is called mineralization and provides much of the nitrogen that the plants need by converting it from organic forms.

So, like I said, the proteins are converted to ammonium, which then can be used by another organism and then converted to nitrate. And most plants take the majority of their nitrogen from soils in the form of nitrate. 

Organic molecules are produced that hold and protect the number of micronutrients such as zinc and iron, and some organisms make mineral forms of phosphorus more soluble, like I said, with phosphate, um, that other organisms or plants can use.

Indirectly, the substances produced by microorganisms promote better root growth and healthier roots, allowing the plants to take up nutrients more easily. And organic matter improves soil structure, which results in increased water infiltration, like I talked about with the, um, the macropores, allowing the water to flow through, it increases the water holding capacity of the soil, which results in better plant health. And allows movement of mobile nutrients, like nitrates to the root zone.

Human influence tends to have the greatest impact on soil organic matter. Erosion has drastically reduced the amount of total organic matter stored in many soils, especially agricultural soils. Um, that topsoil is the most fertile layer, and erosion, whether it’s from wind or rain, um, takes those topsoils and and removes them. 

Tillage is another major factor in not only erosion but also in the decomposition of organic matter. By plowing or tilling, it stimulates nutrient release by enhancing organic matter decomposition. It’s exposing that organic matter to oxygen so that it breaks down faster, which gives you a short boost in your nutrient release and therefore a boost in your growth, but leaves the soil depleted. And also because it breaks down the soil aggregates, it actually makes it more susceptible to erosion.

Some ways to increase organic matter in your soil are to, um, use cover crops and allow those to break down on the soil surface, for like your vegetable gardens, um, mulching with leaves, adding manure and compost, top dressing, you really don’t need to till it in. If you just top dress it, those, um, larger soil organisms like earthworms and beetles and ants will pull a lot of that necessary organic matter down into the soil for you. Let them do the work. 

If you listened to my last episode on an Introduction to Permaculture, a lot of permaculture concepts rely on letting nature do the work for you. And this is kind of one of those areas that, where this is, is really, um, evident is that those soil organisms will pull the organic matter that they need down from the surface.

So finally, I want to talk about building healthy soil and the principles of soil health. The USDA’s Natural Research Conservation Service, um, has a four-pronged approach to soil health. And also, there’s a great book by Gabe Brown, Dirt to Soil. throughout the book, he talks about his experiences and working closely with USDA to improve overall soil health for, um, cropping systems. But there’s a lot in this book that you can take to using in your home gardens as well.

Tilling also destroys the mycorrhizal networks that are connecting the fungi to the plants and the, and those, um, networks actually also connect plants together. It actually, they actually provide a channel of communication for plants. When a plant is attacked by insects, it can actually send a signal to a neighboring plant via the mycorrhizae that warns it of the attack and allows it to trigger a release of volatile organic compounds that attract that insect’s predators. So by with tilling, you’re breaking up those mycorrhizae and um, preventing that communication and then the protection that the fungi provide to the roots from pathogens as a physical barrier.

The second principle of soil health is armor. I kind of joke that, um, Mother Nature is modest. She likes to stay covered. So bare soil is a vector for erosion, whether it be, you know, heavy rainfalls or wind, kind of like we talked about, but using cover cropping and green manures help to hold soil in place.

Um, Woody mulches are another great way to cover the soil to help with erosion. Those wood chips also make a good environment for fungal spores. we had wood chips brought in one time that, uh, we had put under some apple trees and the following year morel mushrooms come up, and that’s the first, that was the first time we’d ever seen morels on our property. So we think that it actually came in on the wood chips, but because the spores of the morels actually do really well in the leaf litter of apple trees, it created a perfect environment for those morels to proliferate.

So, the third principle of soil health is allowing for a diversity of plant and animal species. So, um, using fungicides and bactericides on your soil, um, kill those soil organisms. They will kill the beneficial bacteria that assist the mycorrhizal activity to form the nitrogen nodules on legumes. They will kill the beneficial nematodes that ward off different pests.

The use of chemical inputs for long-term soil health can be detrimental. Fertilizers are often applied at much higher rates than are needed by plants which means wasted money for the gardener. But also creates water pollution and runoff. 

Maximize the biodiversity in the soil by not using chemicals, And by integrating animals into the system; pollinators, predatory insects, um, using livestock on homesteads and farms, um, like chickens or ducks, in your gardens. Ducks are great at eating slugs, um, and then their manure also helps fertilize the soil. so when you have a diversity of plants, you have a diversity of soil organisms and, pollinators and, so, avoiding Unnecessary chemical usage helps protect not just the soil food web, but pollinators, predatory insects, and things like that as well.

And then finally, maximize the presence of living roots. So, using living mulches is another way to think of it. Um, low ground covers like strawberries or, uh, kinnikinnick are great ways to cover the soil. Like I mentioned before, you know, avoid, um, uncovered soil., those ground covers facilitate the mycorrhizal networks between plants, um, but also keeping living roots in the soil helps to create those macropores for water to infiltrate.

So cover cropping, you’ve got those live roots in the soil and you know, when you cut them down, the roots do die, but then they leave the macropores. Um, they leave food sources for the microorganisms and, create just more activity and, uh, organism activity in the soil. 

So in summary, the USDA’s four principles of soil health are minimize disturbance using no-till practices. Maximizing biodiversity is the second principle, improving, pollinator habitat and rotating crops and those kinds of things. The third one is maximizing soil cover. So, using woody mulches, um, cover crops to help maximize soil cover, um, living ground covers. There’s a lot of overlap between maximizing soil cover and maximizing diversity. Then the fourth principle is maximizing living roots. So that, um, helps to increase water infiltration and increases the, uh, available food for microorganisms.

So, that kind of wraps up the basics of soil biology. I hope it was not too technical. , sometimes I forget what other people don’t know. So if there is a principle or a term or something that I’ve used, feel free to email me at hello@theevergreenthumb.org and I’m happy to answer your questions.

So just to kind of review our key takeaways; soil is alive. It is a living ecosystem. The, the key players in soil biology include large invertebrates, such as earthworms and beetles; bacteria, including the rhizobium that allow the symbiotic relationship of fixing nitrogen; fungi, which improve, resistance of the host plant to root diseases and form mycorrhizal relationships that help, um, share water and other nutrients with the plant; protozoa consume bacteria and release nitrogen. They keep bacterial populations in check. And they feed the last category, which are nematodes. Not only do they eat protozoa, but they eat small insects and can be biological control for over 250 soil pests.

Organic matter is what feeds the microorganisms. So use cover cropping, mulches, compost to add organic matter to the soil. And finally, the four principles of building healthy soil are limited disturbance, maximizing biodiversity, maximizing living roots, and maximizing soil cover.

I hope this has been useful for you. Thanks for tuning in and I would like to invite you to share this episode with fellow gardeners who are interested in soil health and soil biology. Thanks for listening.