Soil looks simple. But a small clump contains an entire world teeming with life. Understanding microbial life in soil changes how people think about growing plants.
Microbial biomass carbon varies around a median of 206 micrograms per gram of soil.
The Invisible Workers Underground
Soil microorganisms, including bacteria, fungi, and archaea, drive essential soil functions such as nutrient cycling, organic matter decomposition, and disease suppression.
Bacteria often represent the most numerous group. They break down dead plant material and transform nutrients into forms plants can use. Some bacteria fix nitrogen from the air, turning it into fertilizer that plants need for growth.
Fungi contribute heavily to soil structure and the break down organic matter, significantly contributing to the conversion of carbon to stable organic matter. This makes fungi extremely efficient at building long-term soil health.
How Do Bacteria Help Plants Grow?
Bacteria do several important jobs in soil. As they decompose organic matter like leaf litter or dead roots, nutrients locked inside dead material are released and become available for plants to use.
Nitrogen-fixing bacteria work with plants in special partnerships. Bacteria like Rhizobium form symbiotic relationships that fix nitrogen, converting atmospheric nitrogen gas into usable ammonia that plants absorb through their roots. This free fertilizer helps plants grow strong without chemical additions.
Some bacteria dissolve minerals in soil. Bacteria such as Micrococcus, Enterobacter, and Pseudomonas play crucial roles in phosphorus solubilization, making phosphorus available for plant uptake. Plants need phosphorus for root development.
Understanding Fungi’s Critical Role
Fungi look different from bacteria; not only are they larger, but they have slightly different pigments. Fungal biomass is necessary for healthy soil—their size and structure give them special abilities.
Fungi break down tough plant materials like wood and tree bark. They produce special enzymes that dissolve lignin, the substance that makes wood hard. This decomposition creates rich, dark soil called humus that holds moisture and nutrients.
How Farming Practices Affect Soil Microbes
Fungi and bacteria keep each other in check through symbiotic relationships. Different plants prefer different ratios of fungi to bacteria. Annual crops may prefer lower fungal-to-bacteria ratios, while perennials prefer higher ratios. Forests have the highest ratios because trees depend heavily on fungal networks for nutrients.
According to a study by Lori et. al. in 2017, organic farming systems show 32 to 84 percent greater microbial biomass compared to conventional systems. Adding compost, manure, and cover crops feeds soil microbes and helps grow their populations.
Chemical fertilizers and pesticides harm soil microbial communities. Fungicides kill both harmful and helpful fungi. Without beneficial fungi, plants struggle to access nutrients and water. This forces farmers to add more chemicals, creating a cycle that damages soil health.
Understanding Soil as a Living System
Soil microbial biomass represents the foundation of productive agriculture and healthy gardens. When people protect and feed these microscopic workers, they foster plant-soil interactions and receive a stronger and healthier soil community.
Learning about soil microbes transforms how people garden and farm. Every decision—from whether to till, what to plant, and how to fertilize—affects billions of organisms working underground. Making choices that support microbial communities creates healthier soil, stronger plants, and better harvests that last for generations. Use the microBIOMETER® soil test to estimate your soil microbial biomass and ensure you have the healthiest soil possible.
Both microbial biomass and respiration are parameters used to assess soil health. Soil respiration is the measure of the carbon dioxide produced by the microbes in a given weight of soil while microbial biomass is the measure of the mass of microbes- both active and dormant.
Microbial biomass (MB) is an excellent predictor of soil health because the size of the microbial population correlates with the available nutrients in the soil. Interestingly, MB is low in soil treated with high levels of mineral fertilizers. Research has shown that the stimulus for the plant to grow a microbial population is its need for nitrogen and phosphorus. If these nutrients are artificially supplied, the plant is not being stimulated to feed the microbes that usually provide these nutrients to the plant. This can alter plant-microbe interactions and cause an increased need for pesticides in order to protect the plant, as microbes play a fundamental role in the function of the plant’s immune system.
Microbial respiration measures the amount of carbon dioxide (CO2) produced by the microbes in a given weight of soil. The soil is dried and then rewetted and put in an airtight jar that allows measurement of the amount of CO2 produced over 24 hours. The CO2 is produced by the activity of the microbes in the rewetted soil. Between 20% and 70% of the microbes die during drying, but their dead bodies often provide nutrition for the survivors to use and regrow the population to its original level. Respiration reflects the regrowing work that is being done. The respiration level is often mistakenly believed to predict microbial biomass, though it doesn’t.
People often assume a high respiration rate is good because it means there is a lot of microbial activity occurring. However, it doesn’t necessarily mean the soil is healthy. Microbes in a low pH or toxic soil have to work harder, and therefore their respiration rate is higher, just as your respiration rate in the gym is higher than when you are watching TV. High respiration rates can indicate an unstable microbial population, which, for example, can be seen after excessive tillage occurs. Tillage aerates the soil, so right after there is often a boost of microbial respiration. That increased activity however does not always last, as the other damage done by tillage – disruption of microbial life and destruction of existing plants- can lead to a decreased soil microbial population over time.
The use of soil primers stimulates an increase in soil organic matter (SOM) decomposition, which temporarily increases microbial respiration. Excessive decomposition of SOM can cause a loss of stored soil carbon and other mineral nutrients, allowing for the increased production of CO2. Basically, when you stimulate the soil using a fertilizer or biostimulant, it’s an all-you-can-eat buffet for the microbes. It wakes them up and they start growing and reproducing. But whether they can continue to grow depends on the continual supply of existing nutrients and plant life in the soil. It’s very important that there be sufficient food for the microbes after stimulation. For most soils, this requires that the fertilizer have the correct C:N ratio for the soil and crop. A fertilizer with too high a C:N ratio will cause the microbes to harvest some of the stored carbon, nitrogen and other nutrients in the soil, boosting respiration. This means the stored carbon is being depleted and released into the atmosphere as CO2, the microbes won’t be able to nourish the plant and build soil structure as needed. Adoption of less invasive management practices, such as select-till and reduced chemical fertilizers can reduce CO2 emissions from agricultural soils by retaining soil organic matter.
Priming can be a good way to understand the difference between and uses of respiration data and microbial biomass data. Testing for both initial respiration and long term microbial biomass population can tell you if the priming worked and if the increase in microbial activity led to increased soil microbial biomass and therefore increased soil health and fertility.
IngenuityWorx has been working to prove that the application of nanobubble oxygen as an irrigation/fertigation tool can provide low cost, easily applied plant benefits both indoors and outdoors.
It has been known for over 40 years that increased oxygen to plant roots in soil improves nutrient absorption, reduces effects of saline water or sodic soils, and increases plant growth and yields. However, traditional aeration technology prevented its use. Aerated water was limited to very short application duration and limited travel time in an irrigation line with low oxygen transfer efficiency.
The new science of nanobubbles allows us to add high dissolved oxygen concentrations, reaching 30-50 ppm, and the oxygen transfer will continue to take place for weeks. The nanobubbles don’t coalesce and break like macro bubbles, they move within the water using Brownian motion, and upon giving up all their oxygen produce small amounts of reactive oxygen species including hydrogen peroxide. This feature provides a built-in cleaning process that removes biofilm.
The microBIOMETER® analysis here shows that high dissolved oxygen in the irrigation water stimulated the microbial biomass and fungi to increase in number indicating a healthy microbiome in the soil for plant growth.
Additional work is ongoing to measure and understand the effects of the oxygenated water and microbial increases as it relates to soil carbon utilization, and its impact on carbon reserves and available nutrients. For more information, please contact bo*@***********rx.com.
Increasing your soil microbes increases carbon sequestration. Carbon is stored in the soil as “humic materials” i.e. C,N,P,K etc.; rich organic matter which is the soil organic carbon or sequestered carbon in the soil.
The formation of humus, the final stable carbon, is a stepwise process. All organic carbon in soil comes from plants, either directly or via digested plant material. It starts with plant material being digested by soil microbes, or in the case of brown manure, being predigested by animals and further digested by microbes. The breakdown process begins with soil fungi and bacteria. As these microbes are fed carbon, they multiply. If fresh carbon stores are not utilized, they become attached to soil particles and become stored, therefore, less available as food sources. As microbes die, if they are not immediately cannibalized, their remains also become part of the more recalcitrant humic material.
Slowly, this humic material, which is as much as 80% the bodies of dead microbes, builds up. We measure it as soil organic carbon (SOC) and it reflects the carbon sequestered in the soil, but it also contains all the minerals and other plant nutrients. To increase SOC, the fresh organic matter required to feed the microbes and in turn the plant via the microbes, there needs to be an excess of the minimum required for a low microbial population. If there is an excess, the microbial population increases, and their dead bodies will increase the humic matter, in return increasing carbon sequestration. If it is not adequate, the soil microbes will be stimulated by the plant to mine the stored organic matter, which will decrease the stored carbon. It is not surprising that scientists have compared the plant/microbe/soil fertility index to economic models. A rich soil, like a rich man, has money in his pocket and money in the bank, for soil the currency is carbon.
This system is very much like our agricultural complex. There is fresh food, which we utilize within days, food we freeze or can, which requires freezers and can openers to access, and food stores (our sequestered carbon) that we maintain in silos as protection against disaster.
Source: How Plants ‘Farm’ Soil Microbes and Endophytes in Roots
UPDATE: Dr. White sat down with Dr. Fitzpatrick and Jeff Lowenfels to discuss rhizophagy. Click here to view the webinar. (Jan. 15, 2021)
A summary of James F. White’s presentation at BioFarm, 2020 (Nov. 12, 2020).
The rhizophagy cycle is an amazing process recently discovered by James White’s laboratory at the University of New Jersey, by which root tips “ingest” bacteria and absorb nitrogen and phosphorus and other nutrients from them.
The microbes pictured here in roots are called endophytes because they can live inside plants. The bacteria are attracted to the root tip by root exudates. They then enter the root where the cell walls are dissolved using superoxide, allowing nutrients to leak out to the plant. But the plant does not kill the microbes instead the microbes stimulate the formation of root hairs, which are escape routes for the microbes.
After ejection from root hair tips, bacterial cell walls re-form. The bacteria fatten up and are soon ready to acquire soil nutrients and become another meal for the plant.
Source: How Plants ‘Farm’ Soil Microbes and Endophytes in Roots
Not only does rhizophagy provide mineral nutrients, it is also the stimulus for formation of root hairs, which are critical to the establishment of a healthy root as can be seen in this photo of a plant root with and without endophytes.
