Urban Worm Interview Series: Soil Biology 101, Part I

I kind of always thought of soil as just “dirt”, the stuff under the grass, the brown substance plants just magically grow out of. And it wasn’t until embarrassingly recently that I learned of the level of complexity that ecosystem that exists, or at least should exist under the surface in order for our plants to grow healthy and strong.

I became familiar with Dr. Elaine Ingham’s work (and her rabid following on SoilFoodWeb.com) soon after I began my worm journey here and was taken aback by the entire body of knowledge surrounding soil biology and the interplay of microbes, humus, soil, critters and other goodies that comprise lively soil.

The vermicomposting and vermiculture world can be an echo chamber at times, so it’s important to get out and learn about the larger ecosystem of which earthworms are only a part.

I am the farthest thing from a reliable source on soil biology, so I’m going to rely on the expertise of my friends and fellow Worm Farming Alliance members, Heather Rinaldi of the Texas Worm Ranch and Nina Folch-Torres of Microbes in My Soil to help educate me – and possibly you as well – on this fascinating topic. Heather owns the Texas Worm Ranch, a mid-scale, but high-end-quality vermicomposting operation near Dallas, TX while Nina owns a soil testing service and online store at Microbes in My Soil in Santa Fe, NM (Update: Nina has closed her lab as of 2020).

I’m going to ask my dirt girlfriends some basic questions that will help bring me up to the 101 level on soil biology and what we can do to promote soil health.

My preamble ends here and the learning begins! Enjoy this interview, AKA “Soil Biology for Dummies, Part I!”
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A Primer on Healthy Soil

UWC: If I were to give you guys a handful of healthy soil and asked you to observe it, both with and without a microscope, what would you expect to see?

Heather: I start my classes asking that same question: “What does healthy soil look like?”

According to Dr. Ingham, “healthy soil is the color of a high-dollar, 70% cocoa bar.” (Good reason to go buy some good chocolate!). It should feel moist and crumbly, and as you walk across it, it should be quiet and feel spongy underneath your feet.

It should smell earthy, like a forest floor, and you should be able to taste a higher sweetness and mineral taste in crops grown in healthy soil.

An example of a nematode

Under the microscope, I want to see thousands of bacteria and diversity of bacteria, many strands of dark and segmented beneficial fungal hyphae (minimum of 1 in every 5 views), no or low ciliates, but lots of other protozoa (at least 1 in every 5 views), and at least one beneficial nematode per slide sample.  Evidence of humic and fulvic acids is also a good sign.

UWC: Of all the various microbes, is there one that is harder to culture?

Nina: Fungi are finicky organisms that only thrive when the conditions are just right, and temperature, moisture, and food requirements can vary greatly between species – which is why diversity is so important.  Not only are fungi susceptible to predation, sometimes they are simply outcompeted by other organisms that eat the same food sources, but maybe just a little faster, like molds and bacteria.  This is the reason mushroom growers do everything they can to work in controlled and sterile environments.

Nematodes are probably the second hardest to encourage, in my opinion.  Their population numbers are directly related to their environment; temperature, moisture, and oxygen levels will all work together to determine incubation period, growth rate, and survivability.

Both organisms are also quite sensitive to soil disturbance.  This is why tilling and sifting can become a bit of a problem if not managed correctly.

Heather: Bacteria are everywhere.  Protozoa eat bacteria, and so they are fairly common.  Pathogens are easy to grow in anaerobic conditions.  Fungi and nematodes depend on inoculation of a source of the microbes, no disturbance, proper food sources, and appropriate moisture levels.

UWC: Is the point to grow healthy microbes? Or to maintain the conditions where those microbes can thrive?

In other words, should we be concerned with playing God when it comes to soil and take an active role, or just do a few things here and there to make sure the ecosystem grows itself?

Heather: Bacteria were the first organisms on this planet and can thrive in the most inhospitable conditions. However, without the appropriate habitat, you are going to have a hard time growing anything but bacteria and you may actually be growing pathogens.

This gets complicated.

There are so many things to consider when setting up compost, vermicompost, or soil habitats to support diverse microbe populations. Here are just a few.

In soil, they need growing plants to release exudates to attract and feed them. In all three of these habitats, you must be aware of appropriate moisture, aerobic conditions, security from UV light and temperature extremes, continual additions of soil organic matter (SOM) for a food source, managing to not collapse numbers with too much food at one time, appropriate foods for the microbes you want to establish, not disturbing the ecosystem to break fungal strands or harm nematode populations, calcium levels in clay soil, higher trophic-level organisms (like microarthropods and earthworms) to assist the decomposition process, and much more.

Most of the vermicompost samples, and almost all hot compost samples I look at are full of bacteria, and not much more. The best value of our clinics are that we cover all the ways to increase your microbe diversity and density in your vermicomposting practices.

UWC: I’ve been hearing a lot about fungi lately and reaaalllllly enjoyed watching this TED Talk on fungi by Paul Stamets. So I know fungi are good, and Stamets’ talk taught me more about why. Can you take a similar stab at explaining, in layman’s terms, why fungi are so beneficial?

Fungal hypha

Heather: Fungi develop mutualistic relationships with your roots.  Plants release exudates that attract and feed fungi.  Fungal hyphae serve several purposes:  Fungi mines minerals, it stores water in the soil, and transports water and nutrients to the plant when the plant needs it.  When beneficial fungi thrive, they are also thought to outcompete pathogens and ensure plant health.

Nina: Paul Stamets is one guy I recommend paying attention to. And this is such a great video.

UWC: What crops respond better to fungal conditions and which ones respond to bacterial conditions?

Nina: The suggestions are somewhere along these lines.

Now, please keep in mind that these are a suggestion of ranges.  Fungal-to-bacterial ratios can vary greatly even within a short distance, so it’s really difficult to work outside of the use of ranges.  Understanding how these ratios correlate to successional plant (and soil) stages, I think, is much more valuable.

Succession really is really just another way to refer to the evolutionary progression of life within an ecosystem. For soil and plants, we look at the progression of barren rocks, to the appearance of early successional plants such as weeds, to more productive ecosystems, such as those found in evergreen forests.

If you look at the table I’ve given you above, you’ll notice that early successional plants require way less fungi than late successional plants, but it’s important to understand that as succession moves upward from weeds to evergreens, we also see an increase in soil biology.  Just as the fungal requirements increase, so does the need for all the organisms to be there – more nematodes, more protozoans, etc.  And with higher biomass, also comes higher diversity.

UWC: What parts of the US natively feature excellent soil? I would imagine the answer depends on “excellent for what purpose?”

For example, I live 45 minutes away from Kennett Square, PA, one of the premium places to find and culture mushrooms, so I would imagine it’s great for fungal soil.

Nina: Generally, undisturbed, warm and humid environments are always going to contain a much higher number of organisms, and organism diversity than dry, disturbed, extreme hot or cold environments.  So, I would tell you to go get acquainted with all your local national forests. If you can find a creek or river, even better.  If you have friends that own large parcels of undisturbed wild land, ask permission to walk the grounds and collect a bit of soil or go mushroom hunting.  Accessibility and location are really going to determine where we and how far we can go.

Heather: Historically, the plains of North America were some of the most fertile soil on our continent.  You had long-rooted prairie grasses being cropped by nomadic herds of bison, elk, antelope, and other herbivores that were harried along by apex predators (namely wolves), so they didn’t overgraze.  So a herd animal would eat about 1/3 of the leaf of those grasses, and their roots would self-prune in response, which would leave behind soil organic matter (SOM) as food for the soil microbes.

A herd would leave behind quite a lot of their own digested organic matter, as well.  This would be picked through by birds, eaten by beetles and other insects, and finally be consumed as soil organic matter by the microbes.  With no bare soil and constant plant interaction, the Great North American prairie was able to establish many feet of fertile, carbon sequestering soil.

Heather’s worm bins are a diverse ecosystem, not just worms, bedding, and food waste.

Fast forward to the eradication of those great herds and apex predators, and their replacement by overgrazing domestic animals in static pastures or even worse, being plowed and left bare season after season.  Much of that humus-rich soil blew away in the Dust Bowl.  Some better practices came about, but now we have added microbe-killing chemical fertilizer, herbicides and pesticides to the mix.  That prairie has become so very degraded.

What was once naturally fertilized by the Soil Foodweb is now treated in a constant bath of chemicals used to maintain low-nutrient crops.  That soil was once a great storage for water (by fungal hyphae), and now those crop fields flood and wash remaining top soil and all the chemicals into our tributaries, into the Mississippi, and finally into the Gulf of Mexico as a source of great pollution.

UWC: Oof. Let’s lighten the topic and talk about humus! Other than a yummy spread you put on pita bread, what is it? (Totally a joke, people!)

Nina: Wait, let’s not get hummus and humus confused!  Hummus is a delicious Mediterranean dish made with chick peas.  Humus, on the other hand, is a complex organic substance that results when microorganisms decompose organic matter – in other words, it’s well-aged compost.

Humus molecules are complex and never the same, but we do know they are made up of mostly carbon and nitrogen (plant and microbe foods).  We also know that it is the most stable form compost is known to take, resisting further decomposition for over a hundred years.

Did you catch the part where I said humus is also microbial food?  Yeah, not only do they make humus, but they use it as well.

UWC: Other than creating food for microbes, why is humification so beneficial?

Nina: It is food for plants, and it is food for soil microbes.  It also improves tilth because it increased porosity, aggregation, aeration and water retention – all of which have a direct effect on soil fertility and productivity.

Cannabis and Soil Biology

UWC: Heather, we’ve spoken about how cannabis growers are the most knowledgeable customers when it comes to buying your worm castings. Do they possess a certain background in order to know this stuff? Or are the economic incentives such that they are simply motivated to self-teach?

Heather: Money talks and the cannabis growers have an incentive to learn.  They also don’t have 75 years of agri-chemical company advertising or lawn treatment advertising to overcome.  There have been several lawsuits against legal cannabis companies selling toxic cannabis.  Medical cannabis growers are dealing with immune-compromised individuals, so they have incentive to grow organically.  Cannabis growers might have more flexibility to “grow with the flow” than conventional crop farmers, since financial institutions won’t typically fund them.

UWC: Is there something about the cannabis plant that responds so well to these micro organisms? If you have personal experience with this, please don’t incriminate yourselves!

Heather: From a microbial standpoint, it isn’t any different than other crops needing a specific microbiome, especially a specific fungal-to-bacterial ratio for its habit of growth.

My hypothesis would be that to get a bunch of leafy growth, high numbers of protozoa could only help.  I really can’t speak to that from a practical standpoint, because I honestly have no personal experience (Yes, really!).

That being said, if one of my family members had epilepsy, Parkinsons or some physical ailment that could be helped by cannabis, I would certainly think about growing it using my knowledge of soil microbes –in a legal-to-grow state.

Anecdotally, I have customers that admit their use of my product to grow cannabis and report the best production they have ever had.

UWC: I never ask the question, but I suspect many of my local customers are cannabis growers. And yes, they love the worm castings! What can farmers – both organic and conventional – learn from cannabis experts?

Heather: If you want to be profitable, learn something besides chemicals!

Soil Biology and Microscopy

UWC: What minimum power of microscope do you need in order to fairly judge the life of your soil, compost, or castings?


Nina: The recommendations for assessing soil biology are pretty basic, you need a compound microscope that has binocular 10x eyepieces and includes 4 objective lenses: 4x, 10x, 20x, and 40x.

To calculate the total magnification, you need to multiply the eyepiece magnification by the objective magnification (10x X 4x = 40X).

This eyepiece and objective lens combination will give you this magnification range: 40X, 100X, 200X and 400X.

UWC: What kind of money would someone expect to spend to buy one of these?

Nina: Expect to spend somewhere around $400 for a brand-new microscope.  You may be able to pay less if you buy a used one, but just remember to consider part replacements, cleaning, maintenance, and comfort.  These things often become an issue with old used microscopes.

UWC: Would this make sense to most vermicompost and worm castings producers?

Heather: My opinion is that there are 3 levels of need:

  1. If you are selling vermicompost, and want to maximize the quality and price of  your vermicompost, you need to be testing and practicing continuous improvement of your biological quality.  If you are selling vermicompost to producers of cash crops, and you sell them a product full of pathogens, you could be liable for their crop failure.  You won’t know unless you look under the scope. I would invest in learning how to sample your product for quality.
  2. If you are using your vermicompost yourself on large fields of crops or pastures, you might want  to know exactly what you are doing from a biology perspective, so you aren’t putting bacteria-only vermicompost in areas that need fungi, in which case you would be setting yourself up for soil that encourages weed production (and not the profitable kind).   I would send that to a well-respected soil testing lab.
  3. If you are a small home vermicomposter using your own vermicompost in houseplants or your own garden, and see good results, I wouldn’t worry so much about it.

Nina: Indeed, it’s not the kind of investment I’d recommend anyone make on a whim.  It’s an expensive tool that takes time and practice to get really good at.  Learning to use the microscope itself is relatively easy.  It’s learning how to identify what you are seeing that takes a bit more time, determination, dedication and sometimes a bit of instruction.  If working hard at something doesn’t faze you, then I’d say do it!

But if you think (or know) that that new microscope is going to end up in a corner covered in dust, unused, for months at a time, then why spend that hard-earned money?  It would be way cheaper to simply pay a professional lab for that service.  Now, if you’re curious, determined, and self-driven, then what are you waiting for?!  The microscopic world is quite fascinating.

UWC: I’m trying, I’m trying!!  Now Nina, you run a ridiculously underpriced service where you conduct a biological assessment of soil for your customers. What do you use as a unit of measure when measuring biological health of soil?

In other words, how to you quantify how good – or how sucky – someone’s soil or compost is?

Nina: I measure the total biomass of the four major organism groups found in soil (bacteria, fungi, protozoa, and nematodes). These numbers are reported as μg/g (micrograms per gram) or as #/g (numbers per gram) – depending on the organism being measured.  I also take note of species diversity, and preferred environment.

Bacterial populations provide us with an indicator of abundance of food for predators, nutrient cycling capacity and general diversity.  Fungi populations provide us with further insight into nutrient retention and nutrient transportation.  For fungi, I measure length and width to calculate biomass, instead of counting individual organisms, as is done with bacteria.   I also provide an average of the fungal diameter of fungal hyphae, which are important because they help to determine whether the overall populations are beneficial or not.

Protozoans are broken down into three further groups. These are flagellates, amoebae, and ciliates.  Flagellates and amoebae are true aerobes, which simply means that they must have adequate oxygen to survive.  High numbers of flagellates and amoebae tell us we have a well-aerated environment, with lots of nutrient cycling happening.  Protozoans are voracious bacterial predators, and are therefore key players in the nutrient cycling process.  However, a high number of ciliates tell us that we are now dealing with an anaerobic environment– a key indicator that things aren’t moving in the right direction.

For nematodes, I report the total number per gram and then break down these total populations into individual functional groups (bacterial feeders, fungal feeders, omnivorous or predatory, fungal/root feeders or switchers, and root feeders).  Like protozoa, nematodes are very important in the nutrient cycling process.

By looking at the total populations, identifying their functional groups, and cross-referencing (whenever possible) to the plant being grown, we can get a pretty good picture of productivity.

UWC: When observing under the microscope, do you need to make a solution using water or something? Or can you just slap some soil on the slide and take a look?

Nina: It’s almost impossible to see these tiny organisms just by looking at soil directly under the microscope. Water is an absolute must!  I believe most labs use a 1:10 soil to water ratio, and then dilute further as needed.  Dilution allows us to separate the biology from the solids, pulling them out into a medium that we can observe through.

Organic Matter in our Soil

UWC: What is “soil organic matter?”

Nina: Soil organic matter (SOM) is the decaying detritus material that is left over by plants and animals as they excrete, wilt, and die and are now in the process of decomposition.  Basically, anything that was once alive, and is now dead and decaying.

UWC: What does soil organic matter actually do in this case?

Nina: It’s the fuel of the system.  It’s what drives the cycle and is the bottom of the food chain.  SOM feeds and houses the biology that is responsible for humus formation, and ultimately the creation of heathy, productive, fertile soils – necessary for plant cultivation and healthy food production.

UWC: What would be an ideal or good number when it comes to the percentage of our topsoil that should consist of organic matter?

Nina: Like fungal-to-bacterial ratios, the percentage of organic matter in soil can be a bit tricky to measure, because the numbers can vary so much, sometimes within a short distance.

According to the University of Florida the ranges of organic matter in soil span between 1% and 90%; and I think it was the University of Michigan that suggested lawns have somewhere between 2-3% SOM, and 4-6% for flowers and herbs.  Of course, the further up the successional stages we move, the more SOM we need; and with higher SOM, the more fungi we get in the system.

UWC: Is it really that big of a deal when the percentage can be that small?

Nina: It’s the difference between a backyard full of weeds, and a backyard that looks like a beautiful luscious garden full of flowers and vegetables, and fruit trees.

The less SOM we’ve got, the less we have of everything.  The less humus, the less biology, the less aggregation, the less water retention, and so on.  You’ll increase compaction issues and erosion problems… and with either an increase in weeds or total desertification.

UWC: Got it. So what’s wrong with tilling? The soil looks so good after I do it!

Heather: Tilling breaks up all your fungal hyphae and exposes other microbes to sun and temps that can kill them too.  Sequestered carbon that increases soil fertility is released instead as carbon dioxide into our atmosphere.   Tilling kills earthworms.  You basically destroy your soil ecosystem.

Nina: Do you remember the movie Honey, I Shrunk the Kids?  What may look like minimal disturbance at our human-size scale, can in fact be catastrophic to soil biology.  Tilling cuts, rips and pulls the earth apart – it’s like an earthquake of 7+ magnitude, but at a smaller scale.  If it takes humans years to recuperate from such horrible destruction, why would we imagine it is any less a struggle for soil biology?

I’m not saying there aren’t reasons for tilling (the jury is still out on that one), I’m saying that the practice doesn’t come without a price.  There’s a huge struggle for life to repair itself again after an event like this, use it wisely or don’t use it at all.

Wrapping It Up

So if you haven’t noticed, one thing we haven’t covered yet are earthworms and how they factor into our maintenance of healthy soil. I really gave Nina and Heather a workout here so I figured I’d give them a break before hitting them with some worm-specific queries. We’ll save that for Part II.

For some reason, it’s really hard for me to get my head around this topic which is why I had to ask them to take me back to the basics and explain soil and the life – or lack thereof –  within it. I have kind of always thought of soil as a mixture of various elemental parts, much like a salad, rather than an interconnected web of living material. While I can’t say I’m sold on considering plants to possess the capacity for cognition or the ability to sense pain, the ecosystems that exist in soil become easier to comprehend when you attribute human – or at least animal – characteristics to them. Pathogens are bullying asshole predators who pick on the weak while fungi are the mensches who feed the homeless, beat back the bullies, and form the basis of a healthy society.

So I thank Heather and Nina for helping bone me up on these basics. They are extremely valued members of the Worm Farming Alliance and are our prime time players when it comes to answering questions about the sorts of things we can’t observe with our own two eyes.

That’s it for now. Part II will feature more worm-specific questions and answers and once I tie up a few loose ends, I’ll get that published!

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4 thoughts on “Urban Worm Interview Series: Soil Biology 101, Part I

  1. This was REALLY good. If I can retain even a small part of it, I’ll be miles ahead next time I try to explain what VC and soil health is all about. Thanks Steve, Heather and Nina!

    1. Hi Susanna,
      Unfortunately, no as this interview was completed over e-mail. However, I’m considering a series of podcasts that will include interviews like this!

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