The Soil Community

The Soil Community

The Soil Community

As I like to say, soil has soul.  It is not simply a lifeless, inert medium in which plants grow in, but a living dynamic system.  I stress the word system here to reinforce the notion that soil is less a thing than it is a process.

Soil scientists have determined that 90% of the functions we expect soil to perform are biologically driven (Stika, 2016).   The numbers here are staggering.  One tablespoon of healthy soil can contain billions of soil organisms.  In a handful of healthy soil, the number of soil organisms outnumbers the human population of the planet by a factor of seven.  In one acre, there can be up to two-thousand pounds of soil organisms, the weight of two cows!

In this post I'd like to offer a brief introduction to our favorite members of the soil community—bacteria, actinobacteria, fungi, protozoa, nematodes, enchytraeids, and arthropods—and discuss the roles each play in maintaining healthy soils.   I am leaving out earthworms intentionally here because I believe they deserve their own post.  It is important to note that a majority of the nutrients necessary for crop production do not exist freely in the soil but are contained within the membranes of these soil creatures.  And once these organisms are consumed (seldomly do they just die) their nutrients become mineralized, made available to plants as waste.   Primarily, these organisms themselves subsist off the sugars and carbohydrates released as exudates.  The continuous recycling of these nutrients through various levels constitute what soil ecologists call the “Soil-Food Web”. 


Bacteria are some of the smallest and most abundant soil organisms found in the soil food web.  As a result, they are the main sources of food for larger soil organisms such as protozoa and nematodes.  As Stika (2016) informs us, bacteria can either exist freely or in symbiotic partnerships with certain plants, such as the rhizobia bacteria residing in the roots of legumes (plants which bear seed pods).    

These rhizobia reside in the plant roots and convert atmospheric nitrogen to plant-available nitrogen.  In exchange for their services, they are first in line for sugars exuded from plant roots.  Because they fix their own nitrogen, legumes generally grow very well in a variety of soil conditions; however, their ability to grow is heavily dependent on how efficiently air is exchanged in the soil.  Although our atmosphere is composed of roughly 80% nitrogen, the lack of air exchange due to poor porosity, compaction, or disturbance will inhibit the growth of legumes. 


Actinobacteria are compact and canonical unicellular organisms, resembling fungi both in function and appearance. Actinobacteria specialize in the decomposition of complex carbohydrates such as cellulose, lignin (that substance that makes wood, woody), and chitin (the main substance found in the exoskeletons of crustaceans and soil-inhabiting arthropods), as well as polysaccharides, proteins, fats, and organic acids, thus playing a number of functions essential to nutrient recycling.

Actinobacteria inhabit a variety of environments, such as soils, rivers, lakes, and deserts.   They are responsible for fresh, earthy smell of healthy soils, as well as produce a variety of metabolites found in many of our most valuable antibiotics.


More and more, research is illuminating the beneficial role fungi play in our agricultural systems, specifically for decomposition, nutrient and water cycling, and aggregate building. Since fungi cannot photosynthesize, they are dependent on the obtaining nutrients locked-in in once-living plant and animal matter, accessed through decomposition.  However, fungi also consume the sugars found in exudates directly, seemingly with voracious appetites.  It is estimated that fungi consume up to 30% of the sugars a plant produces through photosynthesis.  In exchange, mycorrhizal fungi deliver water and other nutrients to their hosts, as well as provide better protection against biotic stresses.

Depending on their mycorrhizae—the symbiotic association between a fungus and a plant, as well as the role the fungus plays within the rhizosphere—fungi acquire and deliver nutrients differently.  As their name suggests, endomycorrhiza contain unique structures known as vesicles and arbuscules (from the Latin arbor, “tree”) and are capable of penetrating the cells of their host. Endomycorrhiza, on the other hand, do not penetrate the cortical cells of their host, instead forming a symbiotic relationship with the plant roots.

As already mentioned, one of the roles fungi specialize in is mining for nutrients and water.  Hyphae can extend the roots of plants up to 100 times, making it possible to deliver water and nutrients from places otherwise inaccessible to plants such as rocks and tiny pores in the soil.  In addition to connecting with plant roots, mycorrhizal networks can communicate with each other, helping to balance out the delivery of nutrients across plant communities. 

 Through the production of glomalin, a sticky gel-like substance functioning to seal hyphae in order to maximize the transportation of water and nutrient, mycorrhizal fungi also contribute to aggregate formation.  It is hypothesized that glomalin also functions as a food source for larger organisms of the soil food web, such as springtails.  Wispy and threadlike, the hyphae of mycorrhizal fungi are extremely delicate and are especially sensitive to soil disturbance.  As Stika (2016) emphasizes, the reparation of mycorrhizal networks is energy intensive, and can delay or rob energy that would otherwise be used to support plant associations to maintain healthy soils.


Depending on health of the soil, as many as 10,000-1,000,000 protozoan can be found with one gram.  Protozoa play critical roles in maintaining ecological balance of soil and nutrient cycling in agricultural soils through bacterial grazing.  For this reason, protozoa are found in high concentrations around the rhizosphere—the area teeming with microbes immediately encircling plant roots, something which David Montgomery cleverly calls a “biological bazaar”.   But, the multitude of exchanges occurring within rhizosphere are also ideal conditions for pathogens to seek out.  An abundant protozoa community helps to control the spread of pathogenic bacteria. 

Protozoa are motile creatures and move rather peculiarly through the soil through tiny hairs, small whip-like structures, or the use of false feet, otherwise known as pseudopods.   While many protozoans are beneficial, many are patristic and are known to cause disease to plant as well as humans.  In fact, some researchers have suggested that protozoa may act as Trojan Horses for pathogens, housing pathogenic bacteria and encouraging their propagation (Barker and Brown, 1994).  Through a phenomenon known as “packaging”, protozoa coat the membranes of bacteria with a protective film helping to make them more resistant to harsh or nutrient poor environments.   


Nematodes are microscopic worm-like organisms that prey on bacteria, protozoa, plant roots, and even other nematodes.  Because of this, they are found in highest concentrations in the upper horizons of the soil where plant roots, microorganisms, and organic matter are most abundant, and contribute to maintaining ecological balance. Nematodes move about in water films and live inside water-filled pore spaces in the soil.

Nematodes are classified based on their feeding habits.  Most research on soil nematodes focuses on plant-parasitic nematodes that target plant roots as their primary food source; however, agriculture soils also shelter bacterial, fungal, omnivorous and cannibalistic-feeding nematodes.  While healthy soils should ideally contain consistent proportions of each, imbalances occur depending on practices.  For instance, we tend to see bacteria-feeding nematodes dominate conventionally tilled soils, while fungal-feeding nematodes occupy undisturbed soils, such as forests or woodlands.    Part of the reason is due to the oxygenation which occurs following the inversion of the soil from tillage.   The increase in air flow not only results in rising aerobic bacteria populations but also leads to an increase in their food source as organic matter, previously stored away in aggregates at various layers, because readily available—setting a feast for bacteria-hunting nematodes.  

Nematodes also play a number of crucial roles in maintaining soil fertility and biological control. Through the consumption of fungi and bacteria, nematodes help convert and maintain plant-available nitrogen in the form of ammonium (Ferris et al., 1998).  This happens as a result of mineralizing the nutrients stored in organisms.   Predatory nematodes can also regulate the populations of bacteria-feeding and fungal-feeding nematodes.   Insect-patristic nematodes, living in a symbiotic relationship with certain bacteria that overwhelm the immune responses of certain pests, are reliably deployed as biological pest management.   


Enchytraeids, otherwise known as “potworms”, are larger than nematodes but smaller than earthworms.  They prey on nematodes, protozoa, and bacteria, and play an essential role in nutrient cycling and bioturbation—the mixing of mineral and organic matter.  Through burrowing, enchytraeids contribute to forming healthy soil structure or porosity, enhancing air and water flow, and enabling greater root penetration.


Arthropods have legs and shells, and include organisms such as mites, springtails, beetles, spiders, and ants.  In a personal correspondence, agricultural scientist Dr.  Charlie Clutterbuck has suggested springtails play a unique role in soil aggregation.   It is suggested that through the consumption of glomalin, springtails produce glomalin-related proteins hypothesized to provide the glues necessary for soil particles to stick together, although the phenomenon is poorly understood.

Arthropods specialize in the shredding and breaking down of larger pieces of organic matter. Unlike the other organisms we have discussed, with the exception of some earthworms which will be discussed in a separate post (there is so much to say about the earthworms!), arthropods tend to live on the surface of the soil in a layer known as the detritusphere.  There, they perform vital functions such as decomposition, nutrient cycling, microflora regulation, and bioturbation.  Their preference to dwell on the surface boils down to their anatomical design, which has contributed greatly to the evolutionary success for more than 500 million years.   Equipped with various appendages—antennae, claws, wings, and mouths—arthropods are able to occupy portions of the above world that other organisms cannot, and for this reason, are found amongst nearly every ecological niche on earth.  






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