Written by Logan Hailey

Horticulture review by Sarah Jay


  1. What is a Soil Microbiome?
  2. Members of the Soil Food Web
  3. Garden Benefits of a Healthy Soil Microbiome
  4. 6 Steps to Create Microbially-Rich Soil
    1. Add Organic Matter
    2. Minimize Disturbance
    3. Ditch Synthetic Fertilizers and Chemicals
    4. Aerate (Introduce Oxygen)
    5. Plant Cover Crops
    6. Try a Tea or Inoculant 
  5. Final Thoughts

If you thought rainforests were diverse, you’ll be amazed to discover that soil actually hosts the most biodiverse ecosystems on the planet. Garden soil is far more complex than what meets the eye. Crawling between all the minerals, sand, and fragments of rock are billions of microscopic organisms that fuel the plant life in your garden. Collectively called the soil microbiome, these organisms are the secret to bigger yields, fewer plant diseases, and healthier plants.

Microbes like bacteria, fungi, protozoa, and nematodes often get a bad reputation. Many mistakenly think that they are only the cause of destructive plant diseases. The truth is that less than 1% of microbes on Earth cause diseases in plants or humans. The rest are neutral or beneficial to plant growth and crucial for cycling nutrients and minerals through the dirt.

Let’s dig into the basics of the soil food web and how you can use it to your advantage as a gardener with six simple steps.

What is a Soil Microbiome?

The soil microbiome, or food web, is the collective communities of biota, including bacteria, fungi, protozoa, oomycetes, nematodes, and organisms that are visible to the naked eye, such as earthworms, spiders, and ground-dwelling mammals. These organisms are like the external digestive system and immune system of a plant. 

The soil microbiome is crucial for:

  • Making nutrients available to plants
  • Transforming minerals into nutrients that animals and humans can digest
  • Facilitating water and nutrient uptake by plant roots
  • Decomposing dead plant and animal materials
  • Protecting plants from pathogens (disease-causing organisms)
  • Ensuring long-term structure and health
  • Fueling plant growth and healthy crop yields

Much like the human gut microbiome, the soil microbiome is crucial for digestion and immunity. Healthy soil can reduce or eliminate the need for fertilizers and protect plants from harmful diseases. Microbes help plants “digest” nutrients like nitrogen, potassium, and phosphorus. Without microbial mediators, these nutrients would remain in forms unavailable to plants.

A single teaspoon of healthy soil can contain over one billion microorganisms! Biodiversity is the key to success, so beneficial organisms can work in our favor and outcompete harmful organisms.

Problems With Reduced Diversity

Unfortunately, not all soils have a healthy microbiome. Without the vital communities of microorganisms, the ecosystem suffers from the smallest to largest scale. Globally, soil is being destroyed and degraded at an unprecedented rate due to tillage (plowing and disturbance), herbicidessynthetic fertilizers, and a lack of organic matter.

If you imagine the complex underground ecosystem like a giant city, you can visualize how all the microbes need homes and infrastructure just like humans. The habitats and poor spaces between particles are where microbes hang out, absorbing water, decomposing organic matter, and breathing oxygen. 

Tilling and soil disturbances would be the equivalent of a Godzilla-sized tractor raging through Manhattan and churning it all to pieces. Chemical applications are like planes dropping poison over the entire city. This is what happens to underground “microbial cities” when the soil is degraded, and it can wreak havoc on our garden plants.

The reduced biodiversity of organisms leads to major problems with plant health, which can make gardening more difficult. Microbes are a gardener’s best friends, and if we enhance the beneficial communities, they do most of the hard work for us. When their numbers are reduced, the “bad guys” easily out-compete the “good guys,” and we are left with more challenges.

Common problems caused by a poor microbiome include:

  • Lower crop yields
  • Unhealthy plants
  • Poor seed germination rates
  • Nutrient deficiencies
  • Heavy reliance on synthetic fertilizers and fungicides
  • More weed problems
  • More plant diseases and root rot issues
  • Compaction and hardpans
  • Poor structure and texture (it’s hard to dig)
  • Poor water absorption (more drought injury)
  • More erosion degradation
  • Loss of organic matter
  • Stunted, slow growth

If you want to supercharge your gardening efforts without breaking your back, it’s time to boost your microbial activity so the beneficial organisms can do the heavy lifting for you. In just a single season, you can radically transform your garden into a thriving oasis, starting from the ground up.

Members of the Soil Food Web

In the tiny world of the soil microbiome, spiders and earthworms are the giants. There are billions of other organisms at work that we cannot see without a microscope. But you will know they are there once you start seeing your plants flourish to new heights. These loyal food web members work 24/7 to provide nutrientswaterroot support, and immunity to our garden plants

Imagine the food web of a forest, which may include plants, insects, frogs, snakes, birds, deer, wolves, and bears. The microbiome acts in a similar way, with some species operating at the bottom of the food chain and others eating them until they reach the top of the food chain and the cycle restarts. The key difference is that the microbiome is microscopic and includes lots more decomposers that break down dead plant and animal matter. 

While many of the microbes on Earth still haven’t even been identified, we know that the bulk of organisms fall into these key categories:






Thankfully, you don’t have to memorize all of these soil dwellers to enjoy their benefits. But it is helpful to know who is acting in your favor beneath the surface of your garden beds.

Garden Benefits of a Healthy Soil Microbiome

The list of benefits from a healthy soil food web may sound like a ridiculous marketing commercial, but they are backed by a robust volume of peer-reviewed scientific studies.

A healthy food web can lead to:

  • Higher yields, plant vigor & crop productivity: A healthy soil food web can increase yields by 30-50% or more.
  • Reduced issues with plant disease. The “good guys” outcompete the “bad guys,” so you don’t have to worry about as many plant diseases.
  • Less erosion: Microbes help to keep soil in your garden so it doesn’t blow away in the wind.
  • Less water runoff. After heavy rains or irrigation, water stays in the soil and infiltrates downward instead of flooding or puddling on the surface.
  • Prevent compaction: Microbes make a fluffier texture that is easier for plant roots to penetrate.
  • Lower fertilizer costs: With a healthy soil microbiome, you eventually may not need fertilizer at all.
  • Optimized input use: Fertilizers are used more efficiently when microbes are in action.
  • Greater resilience to drought: Beneficial microbes aid in plant uptake and create structure to hold onto more water.
  • Healthier, faster-growing plants: Crops grow better when they have their symbiotic root partners.
  • Carbon sequestration: Fungi and other microbes help conserve carbon for climate-friendly agriculture.

Here’s more detail about these benefits and how you can enjoy them with very little effort.

Improved Crop Yields

If you’re tired of measly strawberries or pathetic tomatoes, improving the soil microbiome can boost your yields and the quality of your garden crops. The “good guy” bacteria, fungi, and nematodes are particularly important for underground nutrient cycling. They will enhance the overall nutrition of your plants and act like personalized nutritionists at the roots of your crop. 

Believe it or not, microbes can communicate with plant roots. When the plant is producing leaves, it can “ask” its symbiotic partners for more nitrogen. When the plant shifts to flowering and fruiting, it will change its requests for more phosphorus and potassium.

Most gardeners don’t realize that fertilizers need microbial aid to break down. The process works similarly to what we see in a compost pile, except it doesn’t require heat or a perfect balance of “browns” to “greens.” 

Instead, the soil food web constantly decomposes whatever biodegradable material you put in the garden bed. You can put manure, bone meal, kelp, oyster shells, or coffee grounds in the soil, but these materials will do absolutely nothing for your plants unless microbes are present to decompose them. The microbial decomposition process extracts the nutrients and transforms them into forms that plants can “eat.” 

Reduced Need for Fertilizer

Microbial nutrient cycling does all the hard work, so you don’t need to apply as many fertilizers to the garden. The compost, rock minerals, mulches, and other biodegradable materials that you add are slowly transformed into natural fertilizer.

You may think you can bypass this natural digestive system by simply applying quick-release synthetic fertilizers. However, to create built-in fertility that withstands the test of time, you may want to avoid chemical fertilizers.

These lab-made products are instantly plant-available, but they come with many risks, including the destruction of many beneficial microbes. While synthetic fertilizers can provide a short-term boost, they actually degrade your soil’s fertility over the long term.

Boosting the below-ground microbiome can save you a lot of money because you won’t need to buy as many fertilizers. Eventually, many gardeners can stop fertilizing altogether. This is because the soil becomes rich in organic matter and microbes to transform the nutrients into natural fertility.

More Nutritious and Flavorful Food

Modern food is far less nutritious than it was just a few decades ago. Many gardeners are growing their own food for greater flavor and nutrition than what we find at the grocery store. The increased nutrition and flavor are directly correlated to a healthy soil food web. 

Perhaps you’ve heard stats like, “You have to eat 8 oranges in the modern day to get the same amount of Vitamin A as your grandfather’s oranges”. The depletion of minerals from industrially farmed soils is causing widespread nutritional deficiencies in humans. It turns out that artificial plant supplements like synthetic fertilizers aren’t quite the same as nature’s built-in nutrients.

How Soil Health Impacts Taste

Researchers at the University of Texas compared USDA nutritional data from vegetables between 1950 and 1999. They found major reductions in all the key nutrient categories, including calcium, protein, iron, phosphorus, vitamin C, and riboflavin (vitamin B5). Modern vegetables may not provide the same nutrition that they used to. This link goes straight back to the soil that the food is grown in. A solution to nutrient deficiencies could reside in enriching your garden soil!

There is growing evidence that healthier soil yields more nutritious food. When the microbiome is thriving and active, plants can uptake a wider range of macronutrients, micronutrients, and minerals. If your kale’s roots have a connection with beneficial microbes, it has a huge range of juicy natural vitamins. As a result, its leaves are filled with more minerals and provide more nutrition when you eat them. 

Intriguingly, a diversity of microbes is linked to more aromatic oils and flavorful compounds.

These make the vegetables and fruits taste better

Basically: More beneficial soil microbes = more naturally-occurring nutrients. This means less fertilizer needs and more microbially-rich plant roots. This results is more nutritious and flavorful food for humans.

You can see how boosting your soil creates a very positive feedback loop of benefits for human health, ecological health, and overall garden rewards. Obviously, we want our food to taste amazing, and this phenomenon likely explains why a homegrown tomato is so much more flavorful than those cardboard-flavored tomatoes at the supermarket.

Better Texture 

If you dream of plunging your hands into rich, loamy soil rather than hard, packed clay, soil microbes can help with that, too. Plant roots have a very difficult time pushing down into hardpan soil, yet so many are compacted due to poor texture, plowing, construction, machinery, and repeated stomping. 

Instead of working all day with a shovel or churning a big rototiller through packed soil, you can use the soil food web to bust up the cracks and enrich the texture, eventually creating a crumbly loam that is a joy to garden with.

Soil Components

Soil texture is made up of four physical components:

Particles from 0.05mm to 2mm in size



Organic matter

While the first three parts are mineral-based (non-living), living microbes are the key to that final component— organic matter. Sometimes called humus, this is the secret sauce to a thriving garden and it is the reason we add so much compost to our soil. However, compost is not the only form of organic matter. Mulches like leaves and straw are an amazing source of carbon to “feed” microorganisms. As they break down the material, they slowly bring the decayed particles down deeper into the soil, loosening it over time. 

As the organic matter is added, the microbes work even harder to enrich the soil texture. They create air spaces between sand, silt, and clay particles, allowing roots to plunge deeper. The added oxygenation bursts through the compaction and makes it harder for harmful organisms like root rot fungi to thrive. The beneficial fungi use their root-like hyphal webs to hold the structure in place and bring water into the compacted cracks, opening those spaces up, too. 

Eventually, a functioning microbial web can loosen hard soil and create a support system to prevent future compaction. This has a ripple-effect of benefits, like better water retention (more drought resilience) and  improved water infiltration (no more puddling up on the surface!)

Immunity to Plant Disease

Microbes have an unfortunate reputation as major causes of disease. While some bacteria and other microbes can destroy plants, the vast majority of them are beneficial. In fact, a healthy microbiome is like a built-in free security system for your garden.

A diverse underground food web provides a protective layer of disease-fighting organisms. Like protective armor, this microbial barrier coats leaf and root surfaces, preventing all types of plant diseases, including root rot, damping off, blight, and botrytis. 

In other words, the healthy soil microbes migrate all over the plant to act as a defensive army against potential invaders like powdery mildewblight, or even insect pests. These mechanisms of microbial warfare are becoming increasingly popular with certain biocontrol sprays that use beneficial fungi to combat harmful fungi. 

But you don’t have to apply any products to your plants to reap the benefits. You can support this army of plant-immunity-boosters by incorporating more organic matter, reducing disturbance, and using the methods below for inoculating the soil with a richer diversity of beneficials.

6 Steps to Create Microbially-Rich Soil

All of this information is useless without practical action. Here are the simple steps to help you reap all the benefits we discussed above. 

Add Organic Matter

I once had a college soil science professor who constantly reiterated, “What’s the answer? The answer is always to ADD ORGANIC MATTER!” Organic matter is the secret sauce to healthy soil, and it is where most of the microbiome magic (which is actually science) takes place.

Modern soils are insanely depleted of organic matter because animal agriculture has been removed from plant agriculture. Historically, plants and animals were always grown together, just like in nature. Forests are filled with deer and critters, grasslands were once filled with buffalo, and traditional family farms all over the world incorporate livestock with crops. 

Since most gardeners don’t have cows, sheep, goats, or chickens, we have to import our organic matter from outside sources or make our own with kitchen scraps. But if you have backyard hens or a worm bin, you are already off to a great start!

Organic matter is any carbon-based material that comes from a once-living plant or animal. It is the most important source of “food” for microbes. Microbes eat organic matter and then provide the extracted nutrients to plants. 

Organic matter includes:

  • Animal manure and bedding of any kind
  • Compost
  • Vegetable scraps
  • Crop residues (any part you don’t use)
  • Grass clippings
  • Tree leaves
  • Straw
  • Pine needles
  • Peat moss
  • Wood chips or bark
  • Stems and twigs
  • Plant roots and stubble
  • Animal byproducts (blood, feathers, bones, etc.)

You can add any of these materials directly to your garden beds, or you can allow them to decompose first before applying. For example, autumn leaves can be layered on as mulch right away, or you can rake them in a big pile to let them break down before applying. Similarly, wood logs and twigs can be layered at the bottom of your garden beds while filling them, or you can use wood chips and bark as the carbon source in your compost pile, allowing them to break down before you add to the garden.


Any of these methods work well for fueling the soil food web, but they will differ in the speed of decomposition. High-nitrogen materials like manure, veggie scraps, and grass clippings tend to break down the fastest because bacteria consume them rapidly. However, we don’t typically add these materials to the garden raw because they can carry some pathogens and may be too intense for plants. Nitrogen-rich materials need a balance of carbon-rich materials to soak up excess moisture and nutrients, allowing them to decompose into a more stable compound like compost

Backyard composting is arguably the best way to boost your microbiome because it creates a more closed-loop cycle of localized microbes from your veggie wastes. However, you may need to bring in manure or animal bedding from a local farm or neighbor to boost the fertility of the compost. 

Aeration is the most important part of the composting process because it constantly incorporates oxygen to fuel the “good guy” microbes. Most “bad guy” pathogenic microbes develop in anaerobic (non-oxygenated) conditions, often creating that nasty putrid smell of rotten eggs or a stale, unturned compost pile. 

If you don’t have room for a large compost pile, vermicomposting is the next best option. Worms have an incredible diversity of microorganisms in their guts, and they can rapidly contribute to improving the soil food web in your garden. You can purchase readymade worm castings for a microbial boost or make your own worm compost with an Urban Worm Bag. A Hungry Bin is another compact worm composter that makes it easy to compost food scraps quickly. 

Minimize Disturbance

Soil disturbance is the enemy of the microbiome. Every time you aggressively churn around the soil with a shovel or heavy machinery like a rototiller, you are destroying the fragile structure of the below-ground “city” and all of its microbial inhabitants. Of course, you still need to prepare your beds, plant your crops, and pull up weeds. While a little bit of disturbance is necessary for gardening, you can switch to predominately no-dig or no-till methods to minimize the disruption to the food web.

Tillage refers to any mechanical disruption of the soil, namely plowing or rototilling. Tillage is proven to reduce biodiversity in the soil food web. The process also causes:


Loss of Fertility and Organic Matter


Here are a few major steps you can take to reduce disturbance and support an abundance of beneficial bacteria, fungi, and other microbes:

Don’t Garden Naked

Avoid Heavy Machinery

Use Raised Beds

Chop at Soil Level

Ditch Synthetic Fertilizers and Chemicals

Synthetic fertilizers are the enemy of a healthy microbiome. While slow-release organic fertilizers can help feed microbes, synthetic chemical fertilizers are toxic to them. Synthetic fertilizers seem to provide a miraculous boost to plants, but they also pose huge risks for over-fertilization, nitrogen burn, and waterway pollution.

Moreover, synthetic nutrients lead to salt accumulation in the soil. Because most chemical fertilizers are made from petroleum byproducts, they are loaded with mineral salts that damage the soil microbes, reducing overall biodiversity and exhausting the natural fertility of the soil. You can sometimes see a salty crust over the soil surface where lots of fertilizers have been applied. 

If you want to create natural soil fertility without depending on fertilizer products, you first must ditch any synthetic chemicals, including synthetic fertilizers, pesticides, and herbicides. All of these chemicals act like antibiotics in the soil, killing away the microbes you need for long-term plant nutrition. After removing these chemicals from your garden, there may be a recovery period where the ecosystem struggles to get back in balance. Don’t worry, this is normal!

In the early stages of a transition, supplement your garden crops with slow-release organic fertilizers and mineral boosters like liquid fish or kelp meal. These will help soil microbes reestablish their populations and wean your plants off of their dependency on synthetic fertilizers.

Aerate (Introduce Oxygen)

Oxygenation is crucial to healthy soil. If you’ve ever tried growing food in soil that feels hard as concrete, you know firsthand how difficult it is to bring airflow into those hard-packed clay layers. Waterlogged soils and plants that struggle with root rot are also suffering from a lack of oxygen in their root zone. 

Pathogenic fungi thrive in soils with low oxygen, which is why they tend to colonize roots in compacted garden beds. When you introduce more oxygen and fluffy organic matter texture to the soil, root-borne diseases cannot survive. Instead, beneficial fungi and bacteria can flourish.

The best way to oxygenate soil is to use a broad fork. Broadforking is a simple physical action that uses long metal tines to plunge into the soil without tilling it or disrupting the soil texture. Each tine creates a channel for oxygen and water to flow into the deeper layers. Compost and microbes can follow into those channels, working to break up compaction and create a positive feedback loop with more and more aeration. 

Plant Cover Crops

Cover crops are an excellent way to boost soil microbial activity, especially if you choose leguminous (nitrogen-fixing) species. Planting a cover crop over the winter or between your vegetable successions can regenerate the soil and ensure living roots are always in place to fuel the below-ground microscopic workers

Cover crops should always be mowed or incorporated back into the soil to reap their full benefits. I like to chop them back and lay a tarp over them for a few weeks to add extra warmth and boost microbial breakdown. You can also cut down a cover crop and incorporate it into your compost. In cold climates, I recommend winter-kill cover crops like phacelia that die back with frosty temperatures and leave a nice weed-smothering, microbe-supporting mulch on the soil surface. Ensure you’re not planting an invasive cover crop, though. This can alter the soil structure as well.

You don’t have to spend a ton of money to have a healthy soil microbiome, but affordable garden inoculants are helpful for jump starting the process. A compost tea or a microbial inoculant is basically like a soil booster. These products are filled with beneficial microbes to apply directly to the soil as a drench. The microbes can then colonize the ground, start decomposing the organic matter, and form partnerships with plant roots.

The best soil renewal we’ve found is this Inoculant and Bokashi Garden Duo that provides a rapid jumpstart to healthy soil. The blend of over 80 beneficial bacteria and microbes can immediately get into action improving the soil food web in depleted gardens. 

Final Thoughts

Ultimately, microbes are more friends than foes. These organisms have existed on Earth for billions of years before we did. They work in symbiosis with our plants to improve overall garden health and boost soil structure over time

The key to creating healthy soil is to think about your microbial allies before any garden activity. Add lots of organic matter, reduce disturbance, protect the soil from the elements, and avoid synthetic chemicals that can harm the populations. Don’t forget to regularly amend the soil with biodegradable materials to create a positive feedback loop of fertility and biodiversity.