Garden & Greenhouse


Healthy Soil Has a Healthy Microbial Biomass

Posted February 7th, 2018 by Robin Nichols in

Microbial biomass (MB) is the best indicator of soil fertility because under normal conditions the MB correlates almost perfectly with soil organic matter (SOM) and the other critical nutrients that plants need.  Why does MB correlate with SOM?  Because in the normal course of events microbes convert dead plant material to soil organic matter, recycling it for next year’s crop.  Microbes feed on the SOM and other nutrients and pass them to the plant as they die.  Just as we humans feed our microbes and cannot thrive without them, plants and microbes are dependent on one another.

MB is high when the SOM and all other nutrients are in plentiful supply and there are no toxins or adverse conditions such as disease, drought or prolonged flooding – whatever kills plants, kills the microbes and vice versa.  In effect microbes are the canary in the mine. Compare the soil microbiome to a person, call him/her Pat, if adequate nutrition is available Pat is healthy and has a healthy body mass. If Pat’s diet is missing a critical amino acid, Pat cannot utilize her nutrition efficiently and loses weight, or if she is poisoned or diseased Pat will lose weight or die.

This graph taken from Ingham shows the effect of the microbes and the soil food web on plant health.

As you can see a plant in sterile soil weighs only 15% of one grown with all the microbes found in a healthy soil and this dramatically demonstrates that if the soil microbial biomass is suboptimal, the plant will fail to reach maximal growth. That is, unless the nutrients are supplied artificially which is the case for much of agriculture in the United States where high input use of chemical fertilizers (HIC) has killed off the microbial population making it dependent on chemicals. But feeding the plant with high input chemical fertilizers is inefficient so we must supply far more chemicals than can be utilized with the result that these chemicals are not retained in the soil the way nutrients in microbes are, but drain away.

High input chemical fertilizing is a cycle that results in loss of soil fertility (SOM) and the carbon stored in the soil, resulting in crops that are overly sensitive to drought and disease and erosion. The sensitivity to disease can lead to heavy use of pesticides another toxic addition to the food chain. HIC can be compared to drug addiction; the amount needed only increases as we kill even more of the soils MB and further degrade the soil: As a result, in the past 25 years the quantity of these chemicals used has increased three-fold in the U.S.

If high input chemical fertilizers are so damaging, why does agriculture continue to use them?  There are many reasons but the biggest is fear. American agricultural economy is dependent on high yields and dangerously low profit margins for farmers. Transition back to a healthy soil requires 1 to 3 years of remediation during which time there are lower yields. Most farmers cannot afford this investment and almost none of them would survive if the plan failed which is very possible. There is no one size fits all remediation solution and until recently no studies showing the profitability of healthy soil farming. At present it is a given fact that one cannot achieve the high yields seen with HIC with a healthy soil approach. Fortunately recent studies have shown that a farmer can achieve the same profit margin with a healthy soil approach, because the savings in fertilizer and pesticide costs compensate for the decrease in production:  this probably underestimates the cost savings because these farmers are increasing the fertility of their soil as they grow whereas HIC farming degrades the soil and eventually results in lower yields and finally unusable farm land.

So to examine in more detail the difference between soils that are healthy and soils that are high yielding: A healthy soil has a healthy microbial biomass which makes it resistant to disease, erosion, and drought and flooding. It also maintains or increases the fertility of the soil by replacing the carbon and nutrients that have been harvested and so reduces the need for fertilizer. One can compare a healthy soil to having money in the bank – because your microbes are storing the remains of last year’s crop to feed next year’s crop. Often a healthy soil is not as high yielding as a soil that has been extensively treated with high input chemical fertilizers, (HICs) but a large recent study of European farms showed that over a course of 10 years it was as profitable because of the lower input costs and the greater resistance of healthy soil crops to drought, wind, floods, disease and erosion.

Why do we need High Input Chemical Fertilizers? In a healthy soil, the carbon and nitrogen phosphorus etc. that result from the unharvested harvest or organic fertilizer is stored in microbes. The microbial population across the globe has been shown to contain these elements in the exact ratios that plants require, thus the microbes are the ultimate fertilizer. Until the plant needs these nutrients the microbes remain sleeping (dormant) and stuck tightly to the soil so they don’t wash away as HICs do. The plant farms the microbial population to release its contents to the plant when the plant needs them — this is on demand feeding. The plant grows the microbial population by releasing sugars and other nutrients that grow the bacterial population. This in turn feeds a growing protozoal population which feed the larger soil animals and this cycle releases the nitrogen and other nutrients that are stored in the soil.

HICs kill microbes by increasing the salt level. We routinely see well below 100ug/g microbial carbon in such soils. Since it is the microbes that are supposed to provide the plant with N, P, K etc. we now have to provide these nutrients in chemical form. But this creates problems: the microbes provide nutrients on an as needed basis, HICs must be added to bare or nearly bare soil and in order for there to be sufficient left in the soil for when the plant needs them, far too much must be used – the excess washes into streams and rivers.

Healthy soil farming increases the fertility of the soil because it increases the soil’s organic matter. Ninety percent of soil organic matter is microbial remains but the original source of the carbon was the plant material that microbes digested. SOM is carbon rich; in fact there is 3-4 times more carbon in the soil than in the atmosphere. Estimates are that modern farming methods have decreased soil carbon by almost half. We have been discussing that microbes supply the plant with N, P, K and other minerals so what is the importance of the carbon rich SOM to the system? Microbes need a carbon source to grow and their carbon source is the SOM, the exudates of plants or carbon supplying fertilizers.

Today there is a lot of discussion about the need for soil microbial diversity. The term diversity is used differently by academics and practitioners. Practitioners tend to mean that diversity means, bacteria, fungi, protozoa etc. whereas academics tend to use the term to indicate riches of species, e.g. how many different kinds of bacteria. No matter how you use the term, we know that diversity is good and that research has shown is that a microbe rich system is rich in diversity. Research has shown that the microbial populations of soil are predominately dictated by climate and soil composition factors. Plants may control the microbial population composition of the rhizosphere, but beyond the rhizosphere climate and soil composition rule.

Further, we know that the microbial population together with the soil plants form an extremely complex and interdependent society, so complex and interdependent that at this stage of knowledge it is almost impossible to remediate soil with various species. A cubic centimeter of good soil contains > 400 ug/MBC, that means that the top 1 cc x 10 cm of soil contains over 4000 ugMBC; a cubic meter contains 1.6x 10 -7ugMBC;  An acre 6.4 x 10 -11 .ug MBC.  The best amendments and compost teas provide only 400ug MBC/10ml and if sprayed at 100 gals/acre provide only 1.6 x 10-5. This translates to the tea/amendment providing 1 microbe to every 4 million endogenous soil microbes making it hardly likely that the added microbe would have any effect, especially if it is not native to that soil– one of the characteristics of microbial populations is that they fiercely defend their area from intruders, this is why they are so good at protecting their areas from pests. So why is compost tea such a potent organic fertilizer:  because it contains soluble organic matter and the quality of that SOM is predicted by the fact that it supports a healthy microbial population. Compost tea fertilizes mainly because of the SOM it contains: the microbes that it contains probably die or are eaten by the soil microbes. Foliar tea sprays on the other hand can contain microbes that appear to be effective.

The above discussion of microbial additions to soil does not apply to seed and root amendments.   Fortunately, we are beginning to know enough about many of the microbes that live attached to or within the plant or in the rhizosphere to be able to supplement seeds and roots with beneficial organisms.

Via exudates including chemical messengers, the plant tightly controls the size and even the composition of the microbial population in the root area (rhizosphere which extends only 1 mm around the root) and this in turn effects the non-rhizosphere population, as well as. But it is important not to make too big a distinction between the microbes in the rhizosphere and the population we generally refer to as the microbial biomass of the soil in discussions of how MB reflects fertility. These 2 populations are neighbors that are highly dependent on one another, similar to the way that the population of a suburb is to a city — no city means no suburb and no suburb means no workers for the city.

The critical information that MB provides about soil health has not been available to practitioners because the laboratory tests that provide this information cost between $100 and $500 making them impractical. The on-site Microbiometer® test allows healthy soil seekers to decrease risk as they strategize the building or the maintenance of healthy soils.

Judith Fitzpatrick, Ph.D. is the president Prolific Earth Sciences. You can visit here website at

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