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Types of Microbes in Living Soil

Soils are ecosystems tirelessly bustling with microscopic life. A single teaspoon of it can hold more organisms than there are people on the planet. It can contain billions of bacteria, meters of fungal hyphae, millions of protozoa, and a fury of nematodes. 


Electron scanning microscope image of sulfate reducing bacteria. Photo by Pacific Northwest National Laboratory - PNNL (CC BY-NC-SA 2.0). 


In this minuscule world, things are measured in microns. This is a unit of measurement seventy times smaller than the width of human hair. Plant roots and decaying leaves form biomes of continental proportions on this microscopic scale. A single grain of pollen becomes a gigantic feast for swarms of fungi and bacteria. Nematodes move through soils grazing on bacteria like whales feeding on krill. Networks of fungal hyphae intertwine vast volumes of soil; bifurcating, entangling, and connecting the biotic and abiotic life that exists there.


In the soil, diverse biogeographical landscapes of miniature proportions are continuously shifting through ecological succession. A single centimeter in distance hosts an array of microsites with different pH, oxygen levels, nutrient content, and biological diversity. While we won’t ever experience these realms, they are worlds equally as exciting and diverse as those we see on the human scale. In this article we will take a dive into the microscopic domain and discuss the marvels of soil microbes and their plants interactions. 


Object Average Size
Atoms 0.0001 micrometers
Proteins 0.003 micrometers
Humic Acids 0.025 micrometers
Viruses 0.02 to 0.5 micrometers
Smoke Particles 0.4-0.7 micrometers
Bacterias 1 micrometer
Actinomyces 1-2 micrometers
Clay <1-2 micrometers
Fungal Hyphae (diameter)  2-8 micrometers
Plant Root Cell 15 micrometers
Silt 2-50 micrometers
Protozoa 5-100 micrometers
Grain Of Pollen 30 micrometers
Human Skin Cell 30 micrometers
Human Hair (diameter) 75 micrometers
Sand 50-2000 micrometers
Nematodes 300-5000 micrometers
Fruit Fly Larva 2500 micrometers
Average sizes of different objects. 1 micrometer = 0.001 millimeter. Darker green shows the most common soil organisms discussed in this text. Light brown shows the average size of sediments in the soil. 

The Soil Food Web, Nutrient Cycling, and Plant Health

Microorganisms are of paramount importance to soils and the plants that reside in them. They alter soil properties in innumerable ways, ranging from the physical structure to nutrient availability. While there is no doubt harmful disease-causing microorganisms in the soil, there are many more beneficial organisms that are obligatory for keeping the “bad guys” in check. 


It is also important to mention that plants don’t just passively interact with microbes. They are actively employing, exchanging with, and utilizing them. These are not just nitrogen-fixing bacteria and mycorrhizal fungi many people have heard about, but plants work with an elaborate and interlaced network of organisms. Modern science is barely beginning to scratch the surface of how intimate the plant-microbe interactions are. 

The Soil Food Web

Soil ecology is often described by a concept known as “The Soil Food Web”. This concept describes the network of organisms that live in the soil and their relations to each other. It is fueled by photosynthetic plants which provide the carbon that is then disseminated throughout the web. 


In a simplistic linear explanation the Soil Food Web goes as follows;

  1. Plants produce energy-rich carbon compounds such as simple sugars, cellulose, lignin, and other polysaccharides.
  2. Primary decomposers like bacteria and fungi consume plant-based carbon. 
  3. Secondary decomposers such as protozoa and nematodes then prey on the bacteria and fungi.
  4. Tertiary decomposers feed on protozoa and nematodes.


In reality, these processes are more complex than the linear model described above. That's because instead of being a linear process, it is an interconnected web. Organisms can form a myriad of connections and non-linear relations.  

Nutrient Cycling in Soils

Nutrient cycling refers to the movement of nutrients through an ecosystem. It is related to the food web described above because a large portion of nutrients exists within the organisms that make it up.


In fact, healthy soils hold most of their nutrients in the living or once-living organisms that reside there. Nitrogen, phosphorus, potassium, and all the other important nutrients exist within the tissues that make up these organisms, be they leaf litter or bacteria. While many of these nutrients aren't directly available to plants, they do become available via the biological processes that occur there. 


For example, when leaves fall on the soil surface soil organisms begin decomposing them immediately. 

  • Some nutrients get released directly into the soil during decomposition where they are bioavailable for plant roots. 
  • The rest become absorbed into the tissues of the decomposers. From here nutrients can follow various pathways. 
    • They may be released into the waste products of the decomposers.
    • They may end up finding their way into the soil food web as the organisms become consumed by predators, parasites, and secondary decomposers. From here nutrients will be released in the waste products of these organisms or continue cycling through the soil food web.

Plant-Microbe Interactions

The Rhizosphere

The Rhizosphere is the biological community that occurs in and around plant roots. It is essentially the "root microbiome". It is stimulated by root exudates, decaying roots, leaf litter, and all of the biological activity that occurs in these regions. The rhizosphere is generally a fertile region rich in biological activity and crucial to the health of plants.


A magnified view of Arabidopsis plant roots and associated microbe.  Photo by Pacific Northwest National Laboratory - PNNL (CC BY-NC-SA 2.0). 

Another intricately structured microbe associated with the roots of Arabidopsis. Photo by Pacific Northwest National Laboratory - PNNL (CC BY-NC-SA 2.0). 

Arabidopsis root enrobed in microbial colony. Photo by Pacific Northwest National Laboratory - PNNL (CC BY-NC-SA 2.0). 

Root Exudates

Root exudates are organic compounds secreted into the soil by plant roots. These are intended to nourish, stimulate, or signal certain microbes in the soil. Root exudates can be sugars, amino acids, polyphenols, flavonoids, organic acids, and a whole slew of different compounds. 


In some cases, they provide an extra boost to decomposers in the soil to speed up nutrient cycling. This is a process known as "rhizosphere priming". In other cases, they secrete compounds that signal mycorrhizal fungi, nitrogen-fixing bacteria, and other beneficial microbes to approach the root zone and form a symbiosis. Root exudates have even been shown to signal microorganisms to produce the enzymes neccesary for the uptake of specific nutrients needed by the plants.


Endophytes are microorganisms that live within the tissues of plants. They are most known for improving the plant's defense system by helping against herbivores, pests, and diseases. Endophytes such as nitrogen-fixing bacteria also help provide nutrients to the plants. Certain endophytes also help in the resistance against environmental stresses. Some endophytes live strictly within plant tissues but others will also occasionally be free living within the rhizosphere. Certain endophytes like Trichoderma have been shown to go from the rhizosphere, into plant roots, and travel up into aboveground tissues.

The Rhizophagy Cycle

The Rhizophagy cycle is a phenomenon that occurs in the soil and describes how plant roots consume soil-borne bacteria for nutrients. It’s a bit wild and complex, but endlessly fascinating. The concept is less than a decade old and likely will continue to evolve as research continues. 


A simplified version of this concept is as follows;

  1. Free-living bacteria enter plant roots near the growing tip of the roop.
  2. Plants induce an oxidative process that breaks down the cell walls of bacteria, causing the cytoplasm (the insides of the cell) to “spill out”. Here plants absorb nutrients from the bacterial cytoplasm.
  3. The cell walls of microbes are reconstructed and the microbes are released alive back into the soil.


Diagram by James F. White from “Rhizophagy cycle: an oxidative process in plants for nutrient extraction from symbiotic microbes


Bacteria are arguably the most important and abundant of all soil organisms. They are extremely diverse and fulfill any niche conceivable. They exist almost everywhere in nature, not excluding all different types of soil. This makes sense as they are some of the simplest and oldest life forms on our planet. 

What exactly are Bacteria?

Bacteria are the simplest of all organisms. They are single-cell organisms and differentiated from other unicellular life forms because they lack organelles and a nucleus. They are usually about 0.5 to 2 microns in size and of various shapes. They are about the same size as clay particles.

Gram-positive bacterial cell. Image by Ali Zifan (CC BY-SA 4.0)


There are photosynthetic bacteria but most rely on obtaining energy and nutrients from their environment. Bacteria largely “feed” by absorbing nutrients through their cell walls. They usually do this passively via diffusion (movement of nutrients from areas of high concentration to low concentration) but may conduct active transport. Bacteria often release enzymes into their environment to break down complex compounds before absorbing them.


Bacteria feed and grow in size until a fixed point. Afterwhich they typically reproduce asexually through a process called binary fission where one cell is split into two. There are other modes of reproduction and much to say about bacteria but for this text, we will leave it here. 


Bacteria tend to be most abundant in soils with high levels of disturbance and carbon sources that are rich in nitrogen (such as manure, hot compost, etc.). After tilling or other soil disturbances, bacterial populations quickly spike. Soils that are rich in bacterial activity can be referred to as bacterially dominated soils. These tend to be best suited for weedy, quick-growing, and annual plant species.

Roles of Soil Bacteria

  • Soil Aggregation and Structure

Bacteria help with the development of healthy soil structure. This is the physical fabric and arrangement of soil particles that are important for drainage, water-holding capacity, gas exchange, and other important soil properties. Bacteria help create soil structure by producing a variety of polysaccharides and glycoproteins that act as natural glues that cement soil particles together 

  • Nutrient Cycling

Bacteria are aggressive decomposers who grow quickly and can swiftly increase their numbers. Some bacteria can double their population size in mere hours given adequate conditions! This way they can help release nutrients found in complex organic compounds. Bacterial decomposers tend to predominate in conditions where nitrogen is abundant. In contrast, fungi dominate in soils/composts where carbon is abundant and nitrogen is limited. 

  • Mutualists

Many bacteria are mutualists and form intimate relationships with plants. Rhizobia found in nitrogen-fixing plants is one example of this. 

  • Protection From Disease

Populations of beneficial soil bacteria produce antibiotics and other compounds that can help protect plants from disease and organisms. They can also cause direct competition with some of these organisms. 

Lactic Acid Bacteria (LAB)

Lactic Acid Bacteria are a group of bacteria that you may be familiar with. They prevail in your gut and form an important part of your microbiome. They are also probiotics found in fermented foods like sauerkraut, yogurt, sourdough, and lacto-fermented pickles. They are ubiquitous in the environment and play an important role in the soil food web.


Lactic Acid Bacteria are well known in agriculture as bio-fertilizers, plant growth stimulators, and biological control agents. They are voracious decomposers that are active wherever healthy decomposition is taking place. They are facultative bacteria meaning they can survive in both oxygenated and anaerobic environments. 


The term Lactic Acid Bacteria is used to describe a large diversity of bacteria within the order Lactobacillales. This includes but is not limited to those in the genus lactobacillus. These bacteria are known for transforming carbohydrates into lactic acids. 


1000x magnification of Lactobacillus in microscope. Photo by shok (CC BY-NC-ND 2.0).


Culturing Lactic Acid Bacteria

  • You can find these organisms in unpasteurized milk whey, sauerkraut juice, and in almost all fermented foods. These can be used as starters.
  • You can start a Lactic Acid Bacteria culture by fermenting vegetables under saline water using about 2% salt of total weight. 
  • Alternatively, rice wash water can be left to ferment for 2-3 days in a closed container. 
  • Anaerobic ferments with slightly acidic contents also tend to promote lactobacilli. 
  • You can identify a good Lactic Acid Bacteria culture by a sweet, tangy, and mild dairy-like odor. If your ferment smells foul, this is not a good sign!
  • Lactic Acid Bacteria can be applied onto composite, soils, or on plants as a foliar spray. 


Bacillus is a genus of bacteria that are well known to have many health benefits for plants. They are commonly found in the rhizosphere and are known as plant growth-promoting rhizobacteria (PGPR). One of the most famous and well-studied of these is Bacillus subtilis. This is a bacteria common in soils and is produced commercially for use as an organic fungicide. Other species are also used as bacterial fertilizers and contribute other uses.


They provide benefits including;

  • Solubilizing and mineralizing nutrients such as phosphorus.
  • Producing phytohormones that stimulate plant growth.
  • Production of antimicrobials that can ward off pathogens.
  • Induce resistance to environmental stresses. 
  • Fixation of nitrogen.


This is an extremely diverse group of organisms whose functional niche ranges from plant pathogen to mutualist. Some species even infect humans! Even though there are some harmful species, Pseudomonas is considered the second most important growth-promoting mycobacteria after Bacillus. It is known for vigorously colonizing the rhizosphere of plants and producing a swath of antifungal compounds that can help prevent disease. 

Nitrogen Fixing Bacteria

Nitrogen-fixing bacteria are capable of taking atmospheric nitrogen and converting it into a plant-available form. The most famous of these are the Rhizobia species that form symbiotic relationships with legumes. There are also free-living nitrogen-fixing bacteria such as Azotobacter, Azospirillum, and Clostridium. These free-living species are believed to account for only a minuscule portion of biological nitrogen fixation. 


It is also worth mentioning there are a handful of denitrifying bacteria. These do the reverse and take plant-available nitrogen and convert it into atmospheric nitrogen. These are typically present in low-oxygen conditions where there are high levels of nitrogen. While these are bad in agricultural contexts, they are beneficial in areas with nitrogen pollution.

Sulfur Oxidizing Bacteria

These are bacteria such as Thiobacillus which can oxidize elemental sulfur and turn it into a plant-available form. 


Actinomycetes are technically bacteria but they share many characteristics with fungi. In particular, they produce spores and filamentous mycelia. If you’ve ever seen a thin cloudy white film of what looks like fungal mycelium on an active compost pile, you were actually seeing actinomycetes in action. 


Actinomycetes are responsible for the characteristic “earthy smell” of freshly turned soil. Actinomycetes are important in soils for their roles as decomposers, mutualists, and in the inhibition of plant pathogens. Actinomycetes can account for about 10-50% of microorganisms in the soil.

  • As Decomposers
    Actinomycetes are capable of breaking down some of the most complex organic compounds in nature. This includes lignin, chitin, cellulose, and xylan. Their fast growth and ability to break down what other bacteria cannot make them important in nutrient cycling.

  • Inhibition Of Pathogens
    Actinomyces are astonishing in their ability to produce unique and powerful antibiotic compounds.  Approximately 2/3 of natural antibiotics isolated by man originate from Actinomycetes. While humans use these to treat diseases in the human body, in the soil these antibiotics help in the inhibition of diseases and pests in plants.

  • Mutualists

Certain actinomycetes are capable of fixing nitrogen and forming mutualistic relationships with non-leguminous plants. Actinomycetes have also been shown to be mutualist endophytes which may help in the synthesis of secondary compounds. 


Streptomyces are some of the important and common actinomycetes in the soil. They are famous for their production of antibiotics, some of which are used in conventional medicine. Studies suggest streptomyces are responsible for the production of about 7600 bioactive compounds. Streptomyces can colonize plant roots and are almost always present in plant rhizospheres. 


Electron scanning microscope image of Streptomyces. This image is courtesy of the Actinomycetes Society of Japan (CC BY-SA 4.0). The original authors are S. Amano, S. Miyadoh & T. Shomura.



Frankia is a nitrogen-fixing actinomycete that lives in symbiosis with non-leguminous plants. Plants that form an association with Frankia are commonly known as “actinorhizal”. Actinorhizal plants include Alder, Ceanothus, Sea Buckthorn, Coriaria, Purshia, and a wide range of other genera from various families. Frankia forms nodules directly on plant roots and has strains that are host specific.


Fungi are an extremely diverse kingdom that plays many different roles in the biology of the soil. They range from single-celled yeasts to filamentous fungi and even endophytes living within plant tissues. Some fungi are decomposers while others form mutualistic mycorrhizal relationships with plants. 

Roles of Soil Fungi

    • Decomposition and Nutrient Cycling
      Fungi are BIG players in decomposition and nutrient cycle. They produce unique enzymes capable of breaking down materials most other organisms are incapable of. This allows them to convert tough-to-digest materials into ones readily consumed by plants and other soil organisms.  
  • Soil Structure
    Their intertwining and web-like mycelium help build soil structure. They make specialized glues such as globulin that are highly resistant to degradation.
  • Disease Suppression
    Fungi are important players in the world of plant disease. Beneficial fungi suppress disease via competition, the production of antibiotics, and by directly attacking pathogenic fungi. 
  • Mutualism

Some of the most important organisms on the planet are mutualistic fungi. These include mycorrhizal fungi and endophytes that live within plant tissues. 


Fungi are prominent in soils that are relatively acidic, rich in carbon, free of disturbance, and fairly low in nitrogen. These are often described as fungal-dominant soils. These tend to be found in undisturbed environments and are suited for perennial plants and tree species.  

Saprophytic Fungi

This is a large and diverse functional group. Saprophytic means that they obtain their carbon through decomposition. There are countless species, each specialized at breaking down specific substrates under certain conditions. They range from mycellium forming mushroom producing fungi to bread and cheese molds. You find these fungi in abundance within carbon-rich environments like mulch, rotting logs, plant stems, and leaf litter. 


The parasol mushroom is a common decomposer which inhabits prairie and forest soils. Photo by ahenobarbus (CC BY-SA 2.0).


The important role of fungi as decomposers is thanks to special enzymes known as peroxidase. These are non-specific enzymes that break down some of the toughest materials found in nature. This includes the polymer lignin which you find within the woody tissues of plants. This cannot be broken down by most other organisms.


These enzymes are why fungi are also being studied for their use in breaking down human pollution such as oil and even plastic! Once these tough materials are broken down by fungi the nutrients and carbon can enter the soil food web and flow into the nutrient cycle. 


These fungi are also beneficial for their roles in repelling pathogenic fungi and attracting beneficial fungi like Trichoderma. Many filamentous fungi, like Oyster Mushrooms and King Stropharia, also prey on nematodes and mites.


Yeasts are a large group of single-celled fungi. The term “yeast” actually describes the single-celled lifestyle of the fungi as opposed to referring to a genetically related group. For example, some yeasts are more related to your common button mushrooms than to your common bread yeast. 


Yeasts are relatively omnipresent in the environment. They exist in soils, on the surface of plants, and even within their tissues. While their presence in soil has been known for quite some time their roles as soil organisms remain overlooked. 


Like yeast, the term Mold is used to describe a fungal lifestyle as opposed to a genetically related group. Molds are filamentous fungi that produce many asexual spores at the ends of their hyphae. The hyphae give them a white fuzzy appearance while the dustiness is the spores. Most people are familiar with molds from old bread, fruits, and cheeses. Molds are important players in decomposition but are also renowned for their roles in disease suppression. 



Penicillium is most famous for its role in the discovery of the antibiotic penicillin. It is just one example of the powerful compounds produced by these types of fungi. Penicillium is common in soils and one of the most regular inhabitants in the rhizosphere. On top of being important in disease suppression, they also help with phosphorus uptake and produce phytohormones like indole acetic acid and gibberellic acid that improve plant health.


Spore of a penicillum species associated with plant roots.  Photo by Pacific Northwest National Laboratory - PNNL (CC BY-NC-SA 2.0). 




Trichoderma is infamous for this blue-green color that makes the nightmares of mushroom cultivators. Photo by Boobook48 (CC BY-NC-SA 2.0).


Trichoderma is a fungus that plays a key role in soil health, particularly in terms of suppressing fungal diseases. That’s because it is a fungal antagonist, meaning it has aggressive and offensive behaviors towards other fungi. Ask a mushroom cultivator whose biggest pest is and it’s likely to be Trichoderma


It antagonizes fungi by directly competing with them for resources, but also by producing antibiotics and directly predating on their fungal cells. Plants form intimate relationships with Trichoderma and will absorb them through their roots and host them as endophytes within their above-ground plant tissues. 


Trichoderma is a popular biopesticide. Applying Trichoderma to soil or as a foliar spray is commonly used to help remedy fungal pests. It is also applied post-harvest directly to fruit to help prevent the growth of other fungi which shortens the shelf-lives of fruit. 


Thankfully, Trichoderma is pretty much ubiquitous in all soils. Management techniques like applying wood chips and other carbon-rich materials that promote fungal activity are a great way to invite Trichoderma. Using waste from mushroom production is also another great way to promote it. 

Mycorrhizal Fungi

Mycorrhizal fungi are filamentous fungi that form symbiotic relationships with plants via their roots. They essentially become an extension of the plant's root system and help in the absorption of nutrients and water. They also help in disease suppression and the development of soil structure. 


Mycorrhizal fungi do not receive their carbon from organic materials like decomposers but instead receive it directly from their plant hosts. Most mycorrhizal fungi don't even have the genetic code needed to produce the enzymes necessary for decomposition.


While there are many classifications of mycorrhizal fungi, the most important for most cultivated plants are known as Arbuscular mycorrhizae. Traditionally these were also known as “endomycorrhizal” but this term now refers to a larger group of fungi to which the arbuscular mycorrhizal fungi belong to. The second most important group of mycorrhizal fungi are ectomycorrhizal fungi which grow almost exclusively with forest tree species like Oak, Pine, Fir, Alder, and Beech. 


This is a colorized scanning electron microscopy image of a pine tree root surrounded by a soil fungus. Photo by Pacific Northwest National Laboratory - PNNL (CC BY-NC-SA 2.0). 


Arbuscular Mycorrhizal Fungi

Also known simply as AM Fungi, these fungi are associated with around 95% of all plant species. They are an ancient lineage and are believed to have existed alongside plants as they first made their way onto land almost one billion years ago. They are omnipresent in vegetated soils and associate with almost all cultivated plants. Members of the mustard family are some of the few plants that do not form these associations (although there are exceptions).


Cross section of root infected with arbuscular mycorrhizal fungi. The red within the plant cells are the mycorrhizal structures known as arbuscules. Image by OCC Biology Department (CC BY-NC 2.0).


The greatest role of AM fungi is generally considered to be their ability to help with phosphorus uptake in soils. They do this by turning fixed phosphorus in the soil and converting it into a plant-available form. This phosphorus is transported within the mycelium of the fungus directly to the root tips of the plants. Here it is exchanged with the photosynthetic sugars produced by the plants. AM fungi also help with the uptake of other nutrients such as nitrogen.


Lastly, AM Fungi are an important component of the “communal mycorrhizal network”. It is also known as the “wood wide web”. This network promotes communication between plants and can aid in the exchange and movement of nutrients. One of the most studied benefits of this network is its ability to help in an “early warning system” against plant pests. In this case, plants will sense when their neighbors are attacked by a pest species and begin producing defense compounds before pests directly attack them. 


Protozoa are single-celled organisms much more complex than bacteria. They are eukaryotes meaning they have specialized organelles such as mitochondria present within their cells. They can be highly mobile and tend to have more sophisticated behaviors than other single-celled life forms. Protozoa often move with the help of slender thread-like organelles attached to the cells known as flagella or cilia. 


Protozoa can be predatory, parasitic, or simply consume organic debris. In the soil food web, Protozoa are important secondary decomposers who consume other soil organisms.  Many Protozoa feed through a process known as Phagocytosis that allows them to engulf and consume food through a specialized mouth-like aperture. Common food sources for Protozoa include algae, bacteria, and microfungi. Waste products of Protozoa are rich in nutrients such as ammonia. 


Ciliated Protozoa at 400x magnification. Photo thanks to Berkshire Community College Image Library (CC0 1.0).


Nematodes are the most important animals people have never paid attention to. They are the most prevalent animals in soils and account for 4/5ths of the animals on our planet. Most nematode species are undescribed and it is believed there may be up to a million different species. While nematodes often have a bad reputation as pests, most species are not bothersome to plants and in fact beneficial to soil health. 


Internal Anatomy of male nematode Caenorhabditis elegans. Diagram by K. D. Schroeder (​​CC BY-SA 3.0)


Types Of Nematodes

There are many functional groups of nematodes that are classified based on their preferred food sources. When looking under a microscope the functional group of the nematode can be easily identified by the structure of their mouthparts. 


Electron scanning microscope image of nematode mouth with teeth. Photo by eLife - the journal (CC BY 2.0).


Nematode populations are directly correlated to the types of organisms they are feeding on. Since they can reproduce extremely quickly (a single individual can lay hundreds of thousands of eggs in a single day), their populations quickly mimic that of their food source. This and their relatively large size make them great indicators when studying soil. 

  • Bacterial Feeding Nematodes
    These nematodes are the most common in agricultural and horticultural soils. That’s because these tend to be bacterially dominated soils rich in nitrogen and experiencing regular disturbance.

  • Fungal Feeding Nematodes
    These are abundant wherever fungi are present. This tends to be in forests, orchards, and less disturbed soils with perennial plants. Also wherever there are abundant sources of carbon with high C:N ratios.

  • Predatory Nematodes
    These are of particular interest because they consume harmful pests such as other nematodes, insects, and protozoa. For this reason, they are valued as a biological control agent. Having a complex soil food web with diverse organisms is the best way to ensure the presence of these predatory nematodes.

  • Plant Parasitic Nematodes

These nematodes primarily feed on plant roots. Aside from the damage they directly cause to the plants they also act as a vector for other diseases. Since many of these nematodes are host-specific, proper crop rotation is important to reduce these populations. 


Juvinile root knot nematode penetrating a tomato root. Photo by William Wergin and Richard Sayre. Colorized by Stephen Ausmus. U.S. Department of Agriculture (CC BY 2.0).

Soy bean cyst nematode.Photo thanks to United States Department of Agriculture (CC0)


Promoting Healthy Soil Biology

  • Avoid tilling, mixing, or excessively disturbing soils.
  • Much heavily and regularly.
  • Use well-finished and healthy compost. Avoid anything with a foul smell, that's still highly active (hot), or has undecomposed vegetation/manure.
  • Use activated biochar.
  • Use compost teas, organic fertilizers, ferments, and other amendments properly and not in excess.

Directing Biology To The Need Of Your Plants

It's important to consider that not all plants require the same biology. For example, most annual crops benefit from the quick and ferocious activity of bacteria while perennials tend to prefer the slow and steady activity of fungi. 


As you develop soil by building structure, increasing organic matter,  avoiding disturbance, and following regenerative practices, soil tends to go from bacterial to fungal. Depending on what you want to cultivate it is important to modify your management strategy accordingly.


Promoting Bacterial Soils Promoting Fungal Soils
  • Tilling and soil disturbance.
  • Compost teas and ferments. Particularly those utilizing molasses and other simple sugars as a food source.
  • Application of composts made with a low C:N ratio.
  • Using mulch with low C:N ratios.
  • Applying liquid nutrients and amendments, particularly anything high in nitrogen.
  • Avoiding soil disturbance.
  • Using fungal composts derived from materials with a high C:N ratio.
  • Using wood mulch or other materials with a high C:N ratio.
  • Not using ferments or compost teas. Compost teas can be brewed with fish hydrolysate to promote fungal populations.
  • Avoiding liquid fertilizers or nutrients.


A Word On Compost Teas and Other Ferments

Compost teas and other ferments make great additions to your management practices but they should be used in the proper context and not in excess. If you have healthy, complex, and living soil already these sorts of biological amendments can be harmful. That's because they cause "boom and bust" spikes in the microbial population that impede the stability and balance of the food web. The same goes for other liquid nutrients and amendments. Not to mention, spraying can be a lot of work if working in large areas of land.


Proper Contexts for Compost Tea and Ferments  

  • When working with highly degraded, diseased, or contaminated soils.
  • To speed up decomposition in compost piles, mulch, and other carbon-rich materials.
  • In some intensive agricultural productions.
  • Near the end of the season to improve harvests, particularly for annual crops.
  • For the treatment of specific diseases and ailments.
  • Other unique contexts where speeding up nutrient cycling or promoting microbial activity is beneficial.


All of this being said, if you are a fan of these products then by all means go right ahead! If you can make it work for you then there is no harm done. It is all contextual and based on your management strategy. Just be aware the more is not always better!


Soil is a complex and diverse ecosystem full of microscopic life. In this article we have barely scratched the surface about the organisms and processes taking place there. This has just been a simplified explanation of some of these concepts. The deeper you dig, the more perplexing it gets.


Thankfully, you do not have to be a microbiologist to be a good farmer or gardener. You don't need to memorize the names of microbes and have a microscope to grow a nice crop. The best horticulturist in history never did.


Yet, learning about this microscopic world does have benefits. It is not only fascinating and inspiring, but it brings insights into management practices. It makes you think twice about your resources and how you use them. It helps you understand why certain practices are beneficial and why others can be harmful. While you don't need to know all the details, the broad concepts are what matters.


In organic agriculture everything ties back to the microbes eventually. Understanding them, even just a bit, will help guide you to making better decisions for healthier and happier plants!