Soil Biology

Soil is made up of a multitude of physical, chemical, and biological entities, with many interactions occurring among them. Soil is a variable mixture of broken and weathered minerals and decaying organic matter. Together with the proper amounts of air and water, it supplies, in part, sustenance for plants as well as mechanical support.

The diversity and abundance of soil life exceeds that of any other ecosystem. Plant establishment, competitiveness, and growth is governed largely by the ecology below-ground, so understanding this system is an essential component of plant sciences and terrestrial ecology.


Soil Food Web


Dr. Elaine Ingham is an American microbiologist and soil biology researcher and founder of Soil Foodweb Inc. and is considered by many to be the pioneer of understanding these relationships. Please visit her website to learn more about the soil food web: soilfoodweb

"An incredible diversity of organisms make up the soil food web. They range in size from the tiniest one-celled bacteria, algae, fungi, and protozoa, to the more complex nematodes and micro-arthropods, to the visible earthworms, insects, small vertebrates, and plants.

As these organisms eat, grow, and move through the soil, they make it possible to have clean water, clean air, healthy plants, and moderated water flow.

There are many ways that the soil food web is an integral part of landscape processes. Soil organisms decompose organic compounds, including manure, plant residue, and pesticides, preventing them from entering water and becoming pollutants. They sequester nitrogen and other nutrients that might otherwise enter groundwater, and they fix nitrogen from the atmosphere, making it available to plants. Many organisms enhance soil aggregation and porosity, thus increasing infiltration and reducing runoff. Soil organisms prey on crop pests and are food for above-ground animals." By: Elaine Ingham



Although invisible to the naked eye, soil microorganisms are an important part of the below- ground community in farm soils, and they are a potentially valuable asset to the grower. Their value lies in the roles they play in the decomposition of organic matter, improvement of soil structure, cycling of nutrients, and as a living reservoir of nutrients. the microbial community is most beneficial to the grower when it is diverse, abundant, and active. Microbial populations play active and passive roles in soil fertility. (

EARTHFORT is another highly regarded resource for understanding soil biology. They point out several important relationships between the soil biome and plant health.

  • There is a direct correlation between the pH of the soil, the biological balance of the soil and how well the nutrient cycle is going to be working based on the plants grown in that soil. (EARTHFORT)
  • The pH around the roots systems of the plants can be modulated by the biological processes of the rhizosphere can actually adjust the soil pH up to 2 pH points. So a soil with a pH of 5, with the correct microbiology, can actually adjust the soil around the roots to 7! An Alkaline soil at a pH of 8 can be brought down to 6. So understanding your soil biology is very important. (EARTHFORT)
  • Managing soil biology can lead to a 30%-50% reduction in fertilizer use.


Rhizobacteria are root-colonizing bacteria that form symbiotic relationships with many plants. The name comes from the Greek rhiza, meaning root. Though parasitic varieties of rhizobacteria exist, the term usually refers to bacteria that form a relationship beneficial for both parties (mutualism).

Rhizobacteria are root-colonizing bacteria that form symbiotic relationships with many plants. The name comes from the Greek rhiza, meaning root. Though parasitic varieties of rhizobacteria exist, the term usually refers to bacteria that form a relationship beneficial for both parties (mutualism).

Bacteria are a major class of microorganisms that keep soils healthy and productive. They are directly tied to nutrient recycling especially carbon, nitrogen, phosphorus and sulfur.

Lowenfels (2006, pg. 44) states that bacteria are among the earth's primary decomposers of organic matter, second only to fungi. Bacteria decompose plant and animal material in order to ingest nitrogen, carbon compounds and other nutrients. These nutrients are then held immobilized inside the bacteria; they are released only when the bacteria are consumed or otherwise die or are themselves decayed.

There are many different kinds of bacteria and they all occupy different roles

Bacteria perform many important ecosystem services in the soil including improved soil structure and soil aggregation, recycling of soil nutrients, and water recycling. Soil bacteria form microaggregates in the soil by binding soil particles together with their secretions. These microaggregates are like the building blocks for improving soil structure. Improved soil structure increases water infiltration and increases water holding capacity of the soil (Ingham, 2009).

Bacteria perform important functions in the soil, decomposing organic residues from enzymes released into the soil. Ingham (2009) describes the four major soil bacteria functional groups as decomposers, mutualists, pathogens and lithotrophs. Each functional bacteria group plays a role in recycling soil nutrients.    

The decomposers consume the easy-to-digest carbon compounds and simple sugars and tie up soluble nutrients like nitrogen in their cell membranes. Bacteria dominate in tilled soils but they are only 20-30 percent efficient at recycling carbon (C). Bacteria are higher in nitrogen (N) content (10-30 percent nitrogen, 3 to 10 C:N ratio) than most microbes (Islam, 2008).  

  • Breakdown Organic Matter
  • Consume Mineral Content of the Soil
  • Gather Nutrients and Store Nutrients in their Bodies
  • Produce Alkaline Substances

Plant–bacterial interactions in the rhizosphere are the determinants of plant health and soil fertility. Hayat et. al. 2010 explain that: "Free-living soil bacteria beneficial to plant growth, usually referred to as plant growth promoting rhizobacteria (PGPR), are capable of promoting plant growth by colonizing the plant root. PGPR are also termed plant health promoting rhizobacteria (PHPR) or nodule promoting rhizobacteria (NPR). These are associated with the rhizosphere, which is an important soil ecological environment for plant–microbe interactions.

PGPR have the potential to contribute to sustainable plant growth promotion. Generally, PGPR function in three different ways: synthesizing particular compounds for the plants, facilitating the uptake of certain nutrients from the soil, and lessening or preventing the plants from diseases. Plant growth promotion and development can be facilitated both directly and indirectly. Indirect plant growth promotion includes the prevention of the deleterious effects of phytopathogenic organisms. This can be achieved by the production of siderophores, i.e. small metal-binding molecules. Biological control of soil-borne plant pathogens and the synthesis of antibiotics have also been reported in several bacterial species. Another mechanism by which PGPR can inhibit phytopathogens is the production of hydrogen cyanide (HCN) and/or fungal cell wall degrading enzymes, e.g., chitinase and ß-1,3-glucanase. Direct plant growth promotion includes symbiotic and non-symbiotic PGPR which function through production of plant hormones such as auxins, cytokinins, gibberellins, ethylene and abscisic acid." Soil beneficial bacteria and their role in plant growth promotion: Annals of Microbiology. December 2010, Volume 60, Issue 4, pp 579–598



Fungi are another type of soil microorganism. Yeast is a fungus used in baking and in the production of alcohol. Other fungi produce a number of antibiotics. We have all probably let a loaf of bread sit around too long only to find fungus growing on it. We have seen or eaten mushrooms, the fruiting structures of some fungi. Farmers know that fungi cause many plant diseases, such as downy mildew, damping-off, various types of root rot, and apple scab. Fungi also initiate the decomposition of fresh organic residues. They help get things going by softening organic debris and making it easier for other organisms to join in the decomposition process. Fungi are also the main decomposers of lignin and are less sensitive to acid soil conditions than bacteria. None are able to function without oxygen. Low soil disturbance resulting from reduced tillage systems tends to promote organic residue accumulation at and near the surface. This tends to promote fungal growth, as happens in many natural undisturbed ecosystems.

Many plants develop a beneficial relationship with fungi that increases the contact of roots with the soil. Fungi infect the roots and send out root-like structures called hyphae. The hyphae of these mycorrhizal fungi take up water and nutrients that can then feed the plant. The hyphae are very thin, about 1/60 the diameter of a plant root, and are able to exploit the water and nutrients in small spaces in the soil that might be inaccessible to roots. This is especially important for phosphorus nutrition of plants in low-phosphorus soils. The hyphae help the plant absorb water and nutrients, and in return the fungi receive energy in the form of sugars, which the plant produces in its leaves and sends down to the roots. This symbiotic interdependency between fungi and roots is called a mycorrhizal relationship. All things considered, it’s a pretty good deal for both the plant and the fungus. The hyphae of these fungi help develop and stabilize larger soil aggregates by secreting a sticky gel that glues mineral and organic particles together. Sustainable Agriculture Research & Education

Plants with mycorrizhal fungi have been shown to grow up to 20 times faster than those without.(EARTHFORT)

  • Breakdown Organic Matter
  • Consume Mineral Content of the Soil
  • Gather Nutrients and Store Nutrients in their Bodies
  • Filaments bind together to create soil structure
  • Produce Organic Acids (Acidic Substances)
  • Certain Types of Fungi Sensitive to Tilling
Fungal hyphae growing on root. Photo by TeaLab

Fungal hyphae growing on root. Photo by TeaLab

Fungal innoculation of compost. Photo by: TeaLab

Fungal innoculation of compost. Photo by: TeaLab



Figure 1: Close up view of a ciliate (protozoa) with various bacteria in the background. Photographed by Tim Wilson. Ohio State Univeristy

Figure 1: Close up view of a ciliate (protozoa) with various bacteria in the background. Photographed by Tim Wilson. Ohio State Univeristy

Protozoa are single-celled animals that feed primarily on bacteria, but also eat other protozoa, soluble organic matter, and sometimes fungi. They are several times larger than bacteria - ranging from 1/5000 to 1/50 of an inch (5 to 500 µm) in diameter.Then they release their waste product into the root system of the plant as soluble nutrient that gets converted to bioavailable forms the plants roots can uptake through osmosis. Protozoa tend to be the biggest predators of bacteria in tilled soils (Islam, 2008).

Protozoa play an important role in mineralizing nutrients, making them available for use by plants and other soil organisms. Protozoa (and nematodes) have a lower concentration of nitrogen in their cells than the bacteria they eat. (The ratio of carbon to nitrogen for protozoa is 10:1 or much more and 3:1 to 10:1 for bacteria.)  Bacteria eaten by protozoa contain too much nitrogen for the amount of carbon protozoa need. They release the excess nitrogen in the form of ammonium (NH4+). This usually occurs near the root system of a plant. Bacteria and other organisms rapidly take up most of the ammonium, but some is used by the plant. (See figure below for explanation of mineralization and immobilzation.)

Another role that protozoa play is in regulating bacteria populations. When they graze on bacteria, protozoa stimulate growth of the bacterial population (and, in turn, decomposition rates and soil aggregation.)  Exactly why this happens is under some debate, but grazing can be thought of like pruning a tree - a small amount enhances growth, too much reduces growth or will modify the mix of species in the bacterial community.

Protozoa are also an important food source for other soil organisms and help to suppress disease by competing with or feeding on pathogens.



Nematodes are tiny filiform roundworms that are common in soils everywhere. They may be free-living in soil water films; beneficial for agriculture or phytoparasitic, and live at the surface or within the living roots (parasites). Free-living nematodes graze on bacteria and fungi, thus they control the populations of harmful micro-organisms. These nematodes are 0.15-5 mm long and 2-100 mm wide. Nematodes can only move through the soil where a film of moisture surrounds the soil particles. They live in the water (they are hydrobionts) that fills spaces between soil particles and covers roots. In hot and dry conditions, they enter into a dormant stage, and as soon as water becomes available, they spring back to activity.

Nematodes are recognized as a major consumer group in soils, generally grouped into four to five trophic categories based on the nature of their food, the structure of the stoma (mouth) and oesophagus, and the method of feeding (Yeates and Coleman, 1982): bacterial feeders, fungal feeders, predatory feeders, omnivores, and plant feeders. The bacterial feeders prey on bacteria (bacterivores) and may ingest up to 5 000 cells/minute, or 6.5 times their own weight daily. This helps disperse both the organic matter and the decomposers in the soil. Bacterial- and fungal-feeding nematodes release a large percent of N when feeding on their prey groups and are thus responsible for much of the plant available N in the majority of soils (Ingham et al., 1985). The annual overall consumption may be as much as 800 kg of bacteria per hectare and the amount of N turned over in the range of 20-130 kg (Coleman et al., 1984).

Beneficial nematodes (Steinernema feltiae, Steinernema carpocapsae and Heterorhabditis bacteriophora) are used for the control and management of various soil pests. Photo courtesy of Green Methods

Beneficial nematodes (Steinernema feltiae, Steinernema carpocapsae and Heterorhabditis bacteriophora) are used for the control and management of various soil pests. Photo courtesy of Green Methods

Phytoparasitic Root Knot Nematode

Phytoparasitic Root Knot Nematode


Improving the biological properties of soil

Soil Management: National Organic Program Regulations | ATTRA

Improving soil physical and chemical properties is important for both conventional and organic production, but improving biological properties is particularly important for organic production. Producers describe soil biological health in terms of "earthy smell," "soil crumbliness," and "greasy feel." Soil scientists measure soil biological health in terms of microbial biomass, microbial communities, and rate of organic matter decomposition.

Organic production relies on nutrients released through the decomposition of plant and animal residues. Decomposition is a biological process involving a variety of soil organisms, including beetles and other insects, worms, nematodes, fungi, bacteria, and algae. You can evaluate your soils for healthy biological properties by monitoring the following characteristics.

  • Plant and animal residues added to the soil are readily broken down and decomposed so that plant nutrients become available.
  • A good soil structure, provided by stable organic compounds, remains following the decomposition of plant and animal materials.
  • Soil is well-aggregated; that is, it is composed of soft clumps held together with fungal threads and bacterial gel.
  • Plants have a relatively high resistance to soil-borne diseases.

(Fun Video) How soil biology leads to nutrient density.


While this video is about food, it can be clearly inferred that biological farming takes precedence with providing increased nutrition.

When you have the full availability of minerals and nutrients cannabis needs, it will achieve a broader range of terpenes, bioflavinoids and polyphenols.