Soil 101: How to Create a Healthy Soil Microbiome

A healthy soil microbiome can enhance crop yields, prevent plant diseases, and make gardening easier. Soil expert and former organic farmer Logan Hailey explains the science behind beneficial soil microbes and how you can create a thriving microbiome in your garden.

Close-up of a hand pouring healthy soil through its fingers against the background of soil in the garden.


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 healthy soil appears dark and crumbly, with a rich texture.
Healthy microbiomes fuel plant growth and nutrient uptake.

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

Close-up of a male farmer plowing the soil in his garden using a cultivator.
Soil degradation harms plant health by destroying vital microbial communities.

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), herbicides, synthetic 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

Close-up of soil with a crumbly, slightly clumpy texture and light brown color.
Invisible microbes work tirelessly, ensuring plant health and growth.

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 nutrients, water, root 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:


Bacteria are the most abundant soil microbes, and the majority are beneficial. Thousands of species of bacteria work to transform minerals into plant-available forms. These are the workhorses of nutrient cycling. The most well-known bacteria belong to the genus Rhizobium, and they live in the root nodules of legumes, transforming atmospheric nitrogen into plant-available ammonium so crops can use it to grow.


Not all fungi cause nasty diseases, nor do they all produce mushrooms! Fungi are the decomposers of the ecosystem, helping to break down dead plants and woody materials. Perhaps the most underrated and neglected members of the food web, fungi are the threads that tie the entire food web together with their long strands called hyphae. Beneficial fungal networks improve structure, water uptake, plant immunity, nutrient availability, and more, but they are the quickest to be destroyed by tillage or disturbance. Most garden soils lack fungi because the annual crops are constantly uprooted.


Root-knot nematodes are the “bad guys” of this group, but there are thousands of other beneficial nematodes that we actually want in our gardens. They are like the “cows” of the soil food web and are considered grazers. They are the middlemen that graze on the minerals mined by bacteria and fungi and turn them into plant-accessible food. Any time you apply manure or an organic fertilizer like bone meal or feather meal, nematodes are crucial for helping break it down into plant-available forms.


These may sound like weird alien organisms that cause diseases, but protozoa are also helping gardeners, even though most people have never heard of them. Like nematodes, protozoa aid in the nutrient transformation process by eating bacteria and fungi, creating a food-web effect. Every time they eat another microbe, they extract the nutrients and make them available to feed plants. Protozoa include organisms like ciliates, amoebas, and flagellates. They hang out in a water film that coats particles, so it is very important that your soil holds onto moisture to keep them alive.


As opposed to microorganisms, macroorganisms include visible soil dwellers like mites, earthworms, spiders, beetles, and burrowing rodents. They interact with the microbes and move through the soil at a larger scale, often creating tunnels and aeration for water and oxygen. While spiders benefit the web by keeping things like mites and ants in check, the guts of earthworms help create organic matter. This is why earthworms are often used for composting! Additionally, there are predatory arthropods (like centipedes and beetles) that munch up dead plant and animal matter to get it ready for microbes to break down.

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

Close-up of young tomato seedlings growing in a bed of loose, dark brown soil.
A healthy food web boosts yields and disease resistance.

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

Close-up of a woman's hand harvesting ripe strawberries in a garden bed.
Enhancing the microbiome improves crop quality.

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

Close-up of a farmer's hands throwing fresh, loose, dark brown soil into the air in a sunny garden.
Nutrient cycling reduces the need for synthetic fertilizers.

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

Close-up of a cluster of plump, ripe cherry tomatoes nestled among a backdrop of lush, verdant green foliage in a well-tended garden bed, with the vibrant red fruits shining brightly against the backdrop of healthy leaves.
Healthy soil yields nutritious food, enriching your homegrown harvests.

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 

Close-up of a woman's hands gently sifting through the soil, feeling its texture and moisture content as sunlight streams through the garden.
Microbes transform hard soil into rich, crumbly loam.

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



Particles from 0.002mm to 0.05mm


Layered particles smaller than 0.002mm

Organic matter

Carbon-based decomposed matter from dead animals or plants

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

Close-up of female hands planting a young sapling consisting of a thin stem and a pair of oval green leaves with pointed tips among loose, moist soil in the garden.
Beneficial microbes act as a natural defense against plant diseases.

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 mildew, blight, 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

Close-up of a red hen walking through a garden bed among loose dark brown soil with growing ground covers.
Chicken manure enriches soil with valuable nutrients and enhances fertility.

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.


Close-up of an elderly woman pouring kitchen waste from an iron bowl into a large wooden composter bin.
Balanced composting fuels soil microbes for healthy decomposition and fertility.

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

Close-up of a large garden shovel stuck into dug up soil in a garden.
Reduce soil tillage to preserve the soil microbiome’s health.

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:


Soil texture is like a mixed stack of bowling balls (sand), golf balls (silt), and marbles (clay). Each of these different particle sizes has spaces of air between them when they are stacked. The airspaces are where plant roots, water, and your trusty microbial friends live. Tilling is like putting all those balls in a blender and grinding them into dust. The resulting material would be fluffy for a moment, but then it would settle and compact into a hard surface with very little air space between. Compaction is the most common way that gardeners destroy their  microbiome.

Loss of Fertility and Organic Matter

We talked earlier about modern soils losing fertility and organic matter. How does this happen? When the soil is tilled or disturbed, a bunch of oxygen is rapidly infused into the layers, causing organic matter to decompose faster than usual. This accelerated breakdown of plant and animal residues basically “burns up” the soil carbon, leading to reduced reservoirs of fertility and a loss of all that fragile organic matter you worked so hard to add.


Soil is our most valuable and expensive garden asset, but tillage and disturbance make it more likely to blow away in the wind or wash away with water. This is why it’s important to mulch your soil because the mulch protects the upper layers from blowing away. It’s also important to keep living roots in the ground so the soil is never left bare, naked, and exposed. Moreover, when you reduce erosion, you can keep your valuable microbes in place to help your plants.

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

You probably wouldn’t stay outside naked for a long period of time, so avoid leaving your garden soil “naked” and exposed to the elements. When one crop comes out, try to put another one in right away or grow cover crops. You can also use mulch to protect barren beds.

Avoid Heavy Machinery

While a tiller may be useful to open up new ground, it’s best to make it a one-time ordeal. It can be tempting to use heavy machinery every time your garden needs preparation, but this will kill the beneficial microbes quickly and create more weed problems with time.

Use Raised Beds

Generally, raised beds require less disturbance because you are building from the ground up, rather than digging into existing soil. The benefits of the soil microbiome in the raised bed will eventually seep into the ground below (as long as your raised bed has an open bottom).

Chop at Soil Level

Instead of yanking out your finished crops, try lopping or chopping them off at the ground level. Leaving the roots intact supports all the microbes and gives them more food to break down, enriching your soil and reducing disturbance.

Ditch Synthetic Fertilizers and Chemicals

Close-up of a gardener's gloved hand carefully applying a vibrant blue liquid fertilizer from an iron bowl onto a bed of growing onions.
Shift away from synthetic fertilizers to nurture a healthy microbiome.

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)

During the broadforking process, a gardener inserts the tool's tines into the soil and leans back, utilizing body weight to break up compacted earth, creating deep, loosened channels for soil aeration.
Enhance soil oxygenation with efficient broad forking techniques.

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

Close-up of flowering lacy phacelia plants in a sunny garden, displaying delicate, fern-like foliage adorned with clusters of small, purple-blue flowers
Boost soil health with cover crops, especially nitrogen-fixing varieties.

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.

Here is more on cover cropping and how it can enhance the soil food web:

YouTube video

Try a Tea or Inoculant 

Close-up of dark brown compost tea being poured from a compost barrel into a white plastic bucket.
Boost soil health affordably with microbial inoculants like compost tea.

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.

Close-up of a gardener's hand in a blue glove pouring synthetic fertilizers onto a plant with large succulent green leaves in the garden. The plant forms a rosette of large, strong, vertical, succulent green leaves with reddish and pointed tips. Fertilizers are granular and white.

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Soil test benefits. Close-up of a woman's hand scooping up soil with a small shovel in the garden to place it in a glass test tube. The soil is slightly moist, dark brown. A small seedling with a pair of smooth cotyledons grows in the soil.

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