5 Steps to Building Healthy Soil: Increasing the Biodiversity of Your Soil Food Web, Part 1

5 Steps to Building Healthy Soil, Increasing the Biodiversity of Your Soil Food Web | Heirloom Soul | heirloomsoul.com

“And the scientists, no matter how much they investigate nature, no matter how far they research, they only come to realize in the end how perfect and mysterious nature really is.  To believe that by research and invention humanity can create something better than nature is an illusion.” – Masanobu Fukuoka in The One-Straw Revolution.


When we garden we revitalize an heirloom heritage that has been lost over time.. We are stewards of the earth and treading lightly and having compassion for our gardens is a necessary practice.

Best part is:  The opportunity for us to restore land back to its fertile origination lies in our own lawns and gardens, and perhaps even more so, by sharing with others how we’ve done it. 

From my personal perspective, I’m going to be frank and show you how modern agricultural practices have depleted our soils.  Then I’ll introduce you to the Soil Food Web –  the living, breathing life force that grows our plants and sustains life on this planet as we know it.  In Part 2, I will present a 5 step plan for you to build a healthy, balanced, fertile garden the soil food web way.

Please note there are affiliate links present in this post, which means if you click on a link and buy something I’ll get like 4 cents for it.  All recommendations are humbly my own, at no extra cost to you.



Modern Agricultural Practices and Soil Degradation

Across the board, this is an extremely controversial, well-documented subject.  Perhaps the most concise account I’ve read on it is the Organic Manifesto: How Organic Farming Can Heal the Planet, Feed the World, and Keep Us Safe by Maria Rodale, CEO of Rodale Institute.  I suggest reading that for anyone who struggles to make a strong point when arguing for organic food.

Onto my first-hand experience…

In the summer of 2012, I worked for a non-profit food distribution center where I helped farm nine different plots of land throughout Metro Detroit.  It was the most gratifiying, amazing job I’ve ever had!  There was one farm that I worked on, about 40 miles north of Downtown Detroit (so, a baby farm in the sticks).  It was a small 1-acre rectangle on the edge of a huge conventional cornfield, donated by the farmer for us to grow organic food for the hungry.

Conventional agricultural practices have degraded the soil on this farm.
Conventional agricultural practices have degraded the soil on this farm.

This girl was a 12-hours-a-day sun garden, and she was hotter and drier than any land I’ve ever worked.  The soil surface, not unlike a battered cement parking lot, had long spider cracks in it that stretched from one end of the field to the other.  Moisture was devoid in the top four inches, except when it rained – that field had an impressive ability to hold a lake’s worth of standing water.  The soil structure was so compacted that I had to use all my weight plus force just to dig a spade halfway down.  

Where vegetable seedlings suffered, thistle grew rampant.  Insect infestations were so bad that for days at a time I would meticulously squish cucumber beetle and squash bug eggs with my fingers, to no avail.  Everything that did grow donned foliage in a yellowy shade of green (see photo), stems and root systems stunted by a lack of nutrients and zero porosity in the soil.  

This plot of land was my first experience with serious soil degradation caused by modern agriculture.  

What happened to this land is eventually what happens on every monocropped conventional farm that uses pesticides and tilling machines – the soil dies.  And when your soil is completely dead, a myriad of serious problems occur.


The Dirtiest Part of Farming Isn’t the Dirt

Utilizing machines to till soil is very common practice, even on organic farms.  Tilling is quick – far quicker than human labor – and for a farmer that has continuously degraded her soil by tilling year after year, it may seem like the only way to aerate in the new season.  

Problem is, though:  Tilling causes the entire soil structure (including cavities created by living organisms that hold water and air) to break apart into individual particles that are very fine in texture.  The particles settle and compact.  When it rains, the soil compacts even more, to the point where the particles are so tight together they don’t allow water to drain, much like concrete.  This is the reason why we have major flooding events during massive rainstorms.

Ever noticed a flooded soybean or cornfield before? Wouldn’t it make sense for all this water to just drain? It’s all soil after all, right? Due to tilling and microbial genocide due to pesticide and herbicide use, this soil is about as tough as concrete.

Meanwhile, another complex problem occurs while the soil structure is broken.  By turning the soil over and exposing it to air, all of the living microorganisms in the soil become oxidized and die.  Miles of fungal hyphae are ripped apart.  Earthworms are shredded to bits.  Habitats of other beneficial bugs are ruined.  So all of the living creatures that created the soil structure in the first place no longer exist.  These creatures are the same ones that provide all of the nutrients for our plants – so if they are extinct from our fields, how do plants get the nutrition they need to grow, and how do we get the nutrition we need from our food?

All plants, whether you’re growing food or not, need nutrients from the soil to grow properly.  Plants that are denied nutrient intake have weak immune systems and are incredibly susceptible to insect infestation and diseases.  The relationship plants have with the soil is not unlike our own relationship we have with food – if our food is devoid of nutrients, so too will we be.

In healthy, fertile, organic soil, all of the plants’ nutrients are naturally provided by living microbes.  When this natural system is balanced, there is no need for extra fertilizers! (amazing, right?!)

And then there’s pesticides.  We all know they’re bad, but most people only understand the reasons that are directly related to body health.  Most of us know residual pesticides may be on our fruits and vegetables, so food should be scrubbed or the skins removed.  Most of us probably understand that pesticides have required the formulation of Genetically Modified Organisms (GMOs).  GM food is grown from seeds that contain a bit of pesticide in them (famous example: Bt corn) so they won’t die when the chemicals are applied – the plants are resistant.  When you eat the food, you eat the pesticide.  All true, and then some.

Some intense pesticide spraying action.


What we, as gardeners, need to understand about pesticides is that they have seriously degraded our soils and continue to do so.  Pesticides claim to be specifically formulated to kill harmful bugs and pathogenic bacteria, when in fact, they kill everything.  They kill our soil structure-building earthworms, spiders, centipedes and beetles; they suppress the immune and central nervous systems of honeybees, contributing heavily to Colony Collapse Disorder; and they massacre every invisible microorganism in the soil that provides all of the plants’ nutrients.  

Monocropped farms are like death row for bee hives.


Pesticides also contribute heavily to water pollution! As fields flood due to lack of porosity (caused by tilling!), the water that runs off into streams, lakes and oceans is laden with residual chemicals from the soil.

The combination of tillage and pesticide usage is a vicious system that breeds weak plants.  Tons of synthetic fertilizers must be applied just for the plants to receive enough nitrogen to survive, but this is a suboptimal way of providing nutrition and further hinders the natural, biological process.  When fertilizer is added to the soil from an outside source, there is no need for symbiotic relationships to form between plant roots and fungi, nor is there a need for bacterial colonies to hold nitrogen naturally in their bodies.  

Nitrates in fertilizers irritate earthworms’ skin, so they leave.  Meanwhile, harmful insects and soil pathogens quickly evolve because there are no beneficial microorganisms to keep them in check.  This requires new, stronger formulas of fertilizers and pesticides.  It’s really the most ridiculous, destructive cycle we’ve gotten ourselves into.

Synthetic fertilizers irritate earthworms’ skin, so they bolt!


Organic gardeners have so much to learn from the mistakes made by big agriculture.  We might not be farming thousands of acres at a time, but I know people that use rototillers in their backyard gardens.  So many people use chemical fertilizers and weed killers on their lawns, oblivious to the destruction they are causing.  There are easier, completely natural, more mindful ways of dealing with our gardens that save us time, effort, money, and have the ability to prolong life on our planet.  

We must be enlightened by the fact that our soil is the living, breathing part of our gardens where all life is born.  In most cases, the soil actually requires our help to restore its natural fertility.


The Soil Food Web: Nature’s Perfect, Natural System

All forms of life begin with, or are nurtured by, soil.  I was astonished to learn that there are more living creatures in one mere tablespoon of healthy soil than there are people on our planet – 8 billion, approximately!  They include invisible microorganisms and our more familiar, bigger bugs, and altogether as a system, make up the Soil Food Web.  They are responsible for all of the nutrients in our soil and the exchange of those nutrients to our plants.  They are fragile, and require humans to be aware and conscious of their presence and needs, if we are to coexist in the modern world.  The Soil Food Web is a perfect, natural system of microorganisms – and any part of it that has been disrupted with machines and chemicals can be restored.  

Put simply, microbes create soil structure while decomposing organic matter in the soil.  They do so to provide nutrients in useable form for our plants.  Take our beloved earthworm, for example.  Happiest in soil teeming with bacteria, the earthworm slithers through layers of earth, leaving behind her a tunnel of air and water.  She glides to the soil surface to munch on a layer of brown, decaying tree leaves – shredding them to bits and allowing what’s left behind to be decomposed by bacteria, which will happen much quicker with the added surface area the worm has provided.  The bacteria in the earthworm’s digestive tract, paired with gritty sand in her gut, break the leaves down into vermicastings rich in phosphate, nitrogen, calcium and magnesium – nutrients that were otherwise unavailable to plants before the earthworm made her route.

There are hundreds of thousands of different varieties of algae, bacteria, protozoa, fungi and macro- and microarthropods that are constantly working to decompose organic matter in the soil, and to keep the “bad” pathogenic and insect populations in check.  Most of this primary decomposition occurs in the rhizosphere, so nutrients are readily available for plants right at their roots.  Mycorrhizal fungi in particular grow on roots of plants and extend themselves in long strands of hyphae (in old growth forests, uninterrupted hyphae strands have been found to span up to 40 miles! – yes, you read that right).  Just like in forest soils, mycorrhizal hyphae grow laterally to new areas of our gardens to mine nutrients where plant roots can’t physically reach on their own.  When the hyphae die, nutrients that were tied up in the strands become available for all plants, and the strands create amazing structure by leaving behind long tunnels of air in the soil.  

Meanwhile, bacteria in the soil stick together and form colonies, secreting a sticky carbohydrate slime that glues particles of soil together as they move.  And get this:  A biodiverse system of bacteria, one that has 20-30,000 species, is the only defense mechanism needed against pathogens in the soil.  And while they are eating and secreting the bad guys, bacteria hold nutrients in their cell membranes which become available when the bacteria die.  While granulated fertilizers just wash away, bacteria hold nitrogen in their bodies – and these nutrients will never go away as long as the bacteria are present.  It’s entirely fascinating.

And after all that, while they are two very important primary decomposers, fungi and bacteria make up only a fraction of the Soil Food Web.  To learn more, I highly recommend reading Teaming with Microbes: The Organic Gardener’s Guide to Building a Healthy Soil Food Web by Jeff Lowenfels and Wayne Lewis.


Organic Food at the Supermarket Just Doesn’t Measure Up 


In 2013, there was a Stanford study that claimed organic food is no healthier than conventional food grown with pesticides.  This was based on evaluations of human health after people ate a certain amount of conventionally- and organically-grown fresh foods.  The actual nutrient content of both types of food was also tested.  

At first I was taken aback and angered – How, in their right, educated minds, could people say that on television so everyone in the world can go along believing it?  I was so, so mad.  Though they were completely wrong and unjustified in their convictions on organic vs. conventional food, it is still the bold truth that large-scale organic farms have depleted their soils just as much as their pesticide-laden conventional counterparts.  How could this be?  

Many large-scale organic farmers mechanically till their soil, use lots of synthetic fertilizers, and have failed to revive their broken soil food webs back to life, thus wiping out their natural source of nutrients.  Buying organic food at the supermarket is surely a way to avoid pesticides, and to support a more ethical agriculture – but the food itself is largely empty of the vitamins and minerals we all assume would be there.  Healthy organic food with optimum nutrient content is only grown in healthy organic soil that has a biodiverse soil food web.  But the beauty of it all is: We can absolutely restore the health of the soil food webs in our own backyards.

Related Article:  6 Reasons Why You Need to Start Your Organic Garden Now


Summarized Benefits of the Soil Food Web, For Every Farm and Garden

Soil organisms have many functions in the garden and their benefits are multitudinous.
  • – All plants, not just vegetables, depend on the soil food web for nutrition and healthy growth.
  • – As microbes decompose organic matter in the soil, nutrients are stored in their bodies until they die.  They are then made available for plant absorption, negating the need for external fertilizers.
  • – As microbes move through the soil, they create porosity for root growth, and increase soil water holding capacity, reducing the need to aerate and water as frequently; increased water holding capacity prevents excessive stormwater runoff.
  • – Some bacteria, particularly those that form on the roots of legumes, have the ability to fix nitrogen from the air and make it available for plants straight at their roots.
  • – A system of diverse microbes will keep pathogenic diseases and predatory insects in check, completely negating the need for pesticides and lessening the need for organic pest management.

The point is that for millions of years nature already had it all figured out!  There is no need for tillers, fertilizers, or pesticides, but because Big Ag is so big and monocropping so rampant and problematic, we’ve been forced into this system.  By growing our own food in our own healthy soils, we move in the other direction.

In the second half of this soil food web discussion, I outline a 5 step plan for you to build your own healthy soil by restoring your soil food web.

Building Healthy Organic Garden Soil - Increasing the Biodiversity of your Soil Food Web, Part 1 | Heirloom Soul | heirloomsoul.com

Building Healthy Organic Garden Soil - Increasing the Biodiversity of your Soil Food Web, Part 1 | Heirloom Soul | heirloomsoul.com


  1. Reply

    This is very fantastic and I thank you. I am new to gardening. My mother is nearly 90 and I am setting up a garden for her. Never had so many bug problems — ever. I am trying so hard to remain organic. I am mindful of bees, birds, and have set up habitats for the lizards. I decided to buy earthworms to help prepare her soil before seeding with EarthTurf grass (she’s never had any grass). I have a very sick (all plants and trees are brand new) nectarine tree and citrus, and have been ordering and then fighting the urge to use sprays that may compromise any of these beings (and now including earthworms). She’s never seen any worms in her yard before. I am more hopeful and newly excited after reading this very informative article. I found I have done some things right and need to do other things differently. In any case, I am very blessed to have found and read this. Thank you for writing it. Marge.

    1. Reply

      Marge! So excited for you and your mom and her new garden! I truly believe the bugs and diseases take care of themselves as long as we cultivate a happy environment for the good ones to thrive. Usually that means leaving them alone! 🙂 And embracing compost – it’s earth’s greatest gift. Best of luck!! Keep me updated on progress throughout the season! 🙂
      – Fran

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