Why Test Soil Biology

Below are examples of how you can identify the root cause of a problem based on the soil biology test results.

Bacteria make enzymes to decompose and pull nutrients from organic matter & sands, silts and clays. Aerobic bacteria release about 80% carbon as CO2 while decomposing materials and retain all other nutrients (e.g. N, P, S, K) in their bodies preventing them from leaching and volatilizing. They also glue mineral particles and organic matter together into micro-aggregates thus creating smallest blocks of soil structure. Anaerobic bacteria, on the other hand, release about 50% of carbon as CO2, but also release methane (CH4) and other important plant nutrients as gases (e.g. N as NH3, S as H2S, P as PH3) basically blowing off soil fertility into the atmosphere. These bacteria also produce strong organic acids and ethanol that harm plants and some of them are plant or human pathogens. Some facultative anaerobes like actinobacteria or nitrogen-fixing bacteria perform important functions in soil when in normal ranges. So we want diverse mostly aerobic bacteria to extract and retain a diverse set of nutrients and start building structure to prevent anaerobic conditions.

• Low/no bacterial biomass. Bacteria are usually present in any soil unless there was some serious contamination or disturbance. Low bacterial biomass can be, again, a result of some kind of disturbance (e.g. a drought), contaminants (e.g. herbicides, pesticides, salts, heavy metals) or low soil organic matter, low/no vegetation.
• High bacterial biomass is not a problem if there are enough fungi and microorganisms from other trophic levels for the plant’s stage of succession* (read about F:B ratio below). High imbalanced bacterial levels are typical for tilled soils (fluffed layer). Tillage slices, dices and crushes all organisms larger than bacteria, and destroys soil macro-aggregates built by fungi as well as passageways and structures built by protozoa, nematodes and larger critters. Bacteria then bloom due to increased oxygen levels, limited competition, and greater access to previously unavailable surfaces of organic matter. In this scenario the soil no longer can grow plants without external inputs like fertilizers that only aggravate the problem with biology further. Composts that have been turned and mixed too much / made with too much nitrogen materials are also mostly bacterial dominated.
• Anaerobic bacteria are common for compacted soils, waterlogged or where an excessive amount of nitrogen or manure has been applied. The main causes of compaction are leaving soil bare (compaction from the rainfall), tillage (compaction layers below fluffy layers where a plow share presses down the soil), heavy equipment and lack of beneficial biology for some reason (e.g. contamination, disturbance) which leads to lack of structure. In water, the oxygen diffusion rate is very low, that’s why waterlogged soils are anaerobic. Excessive high nitrogen materials promote growth of anaerobic bacteria because initially aerobic bacteria start growing rapidly on those food sources and use up oxygen faster than it diffuses into soil/compost so that anaerobic conditions occur.

Fungi, Yeasts and Oomycetes. Fungi that are beneficial for plants are mostly aerobic. Along with bacteria, fungi decompose organic matter and can obtain nutrients from the mineral soil particles. However, while bacteria prefer simple foods, fungi are able to decompose hard-to-digest organic materials like lignins in woody plants. Fungi are also good in storing carbon in their cell walls and things like calcium oxalate crystals on the surfaces of their hyphae which helps in balancing Ca:Mg ratio and floculation of clay. Like bacteria, fungi produce glues and don’t get washed away retaining nutrients in soil. Another important function of fungal hyphae is physically binding micro-aggregates and soil particles into stable macro-aggregates that are necessary for a good soil structure. Well-structured soil has high water infiltration and water holding capacity and is full of oxygen which prevents anaerobic pathogenic organisms from growing. Some fungi can also protect plants from pathogens directly such as nematode-trapping fungi that parasitize disease-causing nematodes and fungi that feed on insects. Among fungi there is a type of mutualistic fungi called Mycorrhizal fungi. In exchange for carbon, mycorrhizal fungi solubilize phosphorus and deliver nutrients and water from far away directly to the plant. Yeasts are single-celled anaerobic fungi that preferentially metabolize sugars converting them into alcohol (harmful for roots) and CO2. They also produce strong organic acids such as succinic acid, acetic acid that can help reduce pathogens, but in large amounts make soil too acidic. Some beneficial filamentous fungi have a yeast phase to survive anaerobic conditions. Pathogenic fungi and Oomycetes (that resemble fungi morphologically but are not fungi phylogenetically) are mostly anaerobic. 60-70% of Oomycetes species can cause decreased production or plant death if conditions are right. So we want to see diverse, mostly aerobic fungi to provide all the benefits for plants and soil. Beneficial fungi should be more than double the oomycetes’ and disease-causing fungi’ biomass to out-compete them and hold in check.

• Low/no fungal biomass is common for agricultural soils where tillage and fungicides as well as any other -icides have been used. Other disturbances (e.g. flooding) and contaminants kill fungi and other beneficial microbes as well. For instance, high concentrations of salts are detrimental for soil life including fungi. Examples of salts: synthetic fertilizers, lime, gypsum (salt and a fungicide!), salty manure, salts in irrigation water. Basically, the same factors are harmful to bacteria, fungi and the rest of the Soil Food Web except for tillage that promotes bacterial growth.
• High fungal biomass is not a problem if there are enough bacteria and microorganisms from other trophic levels for the plant’s stage of succession* (read about F:B ratio below).
• Disease-causing fungi, yeasts, oomycetes. Lack of oxygen in compacted or waterlogged soils naturally selects against aerobic (beneficial) fungi and promotes growth of anaerobic pathogenic organisms. Read about the root causes of low oxygen in soils in the section above.

F:B ratio is the ratio between fungal and bacterial biomass in soil/compost. It is important because it defines the pH and the ratio between nitrate NO3- and ammonium NH4+ which correlates with plant succession. This means that plants from different stages of succession (weeds, veggies, grasses, shrubs, trees etc) require different nitrate-ammonium ratio and therefore different F:B ratio to thrive.