Soil Biology 101

Identifying Key Microorganisms

We use Dr. Elaine Ingham’s research and methods of assessing microorganisms to interpret the conditions in your soil based on the levels and diversity of microorganisms present.

By quantifying the biomass and populations of the various microorganism groups in soil, we can identify which groups are lacking and develop strategies for reintroducing a fully functioning soil food web.

The fertilizer bags.

Under aerobic conditions, these single-celled organisms are responsible for a significant portion of nutrient cycling in living soil. Decomposer bacteria mine and absorb nutrients from minerals and organic matter. They are then consumed by one of their respective micrograzers (protozoa or bacterial-feeding nematodes) who excrete the nutrients for root absorption. For this reason, we often refer to soil bacteria as the ‘fertilizer bags’ in the soil.

Learn more about bacteria →

Breaking it down since the beginning of time.

Decomposer fungi is beneficial to plant life and manufactures all of the necessary enzymes and organic acids to mine and pull plant-essential nutrients out of the sand, silt, clay, mineral and organic matter fractions of soil. They also create soil structure that allows efficient water and oxygen infiltration. In turn, plants also release foods for beneficial fungi. 

Learn more about beneficial fungi →

Eat, excrete, repeat.

Protozoa are single-celled organisms consisting of three groups: flagellates, amoebae and ciliates. Their role in the soil food web is to consume bacteria and excrete plant-available forms of nutrients. Without proper numbers of protozoa in soil or compost, soluble nutrients are never released from decomposer bacteria and nutrient cycling does not occur.

Learn more about protozoa →

Worming their way into your heart and soil.

Also known as roundworms, nematodes are microscopic snake-like organisms that are quite large in comparison to bacteria. Bacterial-feeding nematodes and fungal-feeding nematodes are key micrograzers for nutrient cycling in living soil. They are responsible for a significant portion of soluble nutrient release from bacteria and fungi and indicate healthy aerobic conditions.

Learn more about nematodes →

Lean, mean, disease fighting machines.

Actinobacteria are very thin filamentous bacteria that were once believed to be fungi. They can exist in both aerobic and anaerobic conditions, and they are capable of secreting antibiotics around their bodies, which is why they are utilized as a biocontrol to fight certain plant diseases. 

Learn more about actinobacteria →

We’re not all bad!

Oomycetes are also known as water molds and they are filamentous organisms that resemble fungi, however they are not true fungi. Although they can take on roles as either saprophytes or pathogens, they have a cell wall composed of cellulose instead of chitin, as with fungi, and include some of the most notorious plant pathogens such as downy mildew, blights, phytophthora, and pythium. 

Learn more about oomycetes →

Aerobic vs. Anaerobic Soil Conditions

What's so bad about anaerobic soil conditions?

Anaerobic bacteria and fungi do not store and cycle nutrients in soil. Instead, they cause disease and off-gas nutrients into the atmosphere in forms such as ammonia gas, phosphine gas and hydrogen sulfide gas, rendering the soil of its fertility. Under anaerobic conditions, plant pest and disease organisms harm roots and aerobic organisms which leads to crop loss.

How can we change the soil to aerobic conditions?

When conditions are aerobic, anaerobic organisms cannot manufacture the enzymes necessary to exist, therefore they cannot compete in a healthy living soil. Identifying key anaerobic-indicator organisms with the microscope (i.e. ciliates, actinobacteria, oomycetes and excessive bacteria) before they take over is important so we know to fix conditions and get aerobes back into the system. In addition, the smell of the soil can often indicate that soil conditions are becoming completely anaerobic.

Why is the fungi to bacteria ratio important?

The Bacteria to Fungi Relationship

The fungi to bacteria ratio (F:B) increases through succession from weeds to brassicas to grasses and grains to tubers through shrubs, then deciduous trees to conifer forests and finally, to old growth forest. That means we see more bacteria in the earlier stages and more fungi in the later succession ecosystems.

Tillage is a Killer

Unfortunately, our agricultural soils are in bad shape from generations of tillage and abuse. Soil biology has been overlooked for too long and the majority of agricultural soils have very little fungi. When there are no fungi in the system and bacterial biomass is in the extreme, this caters to early succession plants, such as weeds, and may lead to the occurrence of pest and disease in later succession plants and trees.

By the Numbers

For weeds, we see an F:B ratio of < 0.1 – 0.3:1; for grasses, we get closer to 1:1; orchards are typically 10:1; and forests are 100:1 all the way up to 1,000:1 in really healthy old-growth forest.