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Make Soil Organisms Work for You: Mythbusting practices that do and don’t work

By Molly Shaw and Charles Merfield

Soils are quite literally the foundation of the farm so ensuring they are well managed is a fundamental task for farmers and growers. For decades now we have been good at measuring and managing the chemical properties of the soil-pH, NPK levels etc.,-all the things that show up on a standard nutrient test, but soil biology has been largely ignored.

However, more recently, there has been increased interest in managing soil organisms and soil “health” in general. With all that interest also come some questionable theories and sales claims about products and methodologies that boost soil microbial activity, soil ‘health’ and/or plant productivity. To sort through the hard science and separate it from the myths and marketing hype, Natural England, part of the UK Government, commissioned a broad review of over 200 scientific studies related to the functioning of soil organisms in agricultural systems. Along with the literature review, they consulted with producers to work out which techniques were the most practical to implement in real-world farming [3]. The report can be downloaded from

Boiled down to the nitty gritty, here’s what they found:

Soil organisms give us these benefits:

  • Nutrient cycling and holding capacity (creating a fertile soil);
  • Good soil structure, with benefits such as reduce need for tillage, improved water infiltration and retention (well-aggregated, spongy, drought-resistant soil);
  • Promotion of crop growth/ health (e.g. rhizobacteria fixing N with legumes, mycorrhizal fungi).

You improve the work of soil organisms by:

  • Feeding the soil a diverse diet. This entails increasing the variety and overall amount of organic matter adding to the soil (e.g., having a range of crop residue types and using green manures); and / or
  • Reducing tillage, both the total amount and also intensity (e.g., surface working vs. ploughing); and / or
  • Diversifying cropping systems (having a wider range of crops and/or pasture).

In essence, bacteria, fungi, amoebas and all the other organisms in soil need food (organic matter) to live and reproduce, and they do best with a varied and abundant diet. Soil microbes also need a stable environment to set up house, and tillage disrupts this. Tillage also aerates the soil, and the influx of oxygen speeds the decomposition of organic matter, reducing the food source for the microbes in the long term

Farms that grow a wide range of crops and/or pasture types have the most success meeting the needs of the soil organisms. The biggest benefits are found when all three of these approaches are used together. “The sum is greater than the parts” in this case -- a system level effect. However, implementing at least one is much better than nothing.

Just as instructive as these tried and true principles of soil health were two types of claims that the review found to lack supporting evidence:

  • Point interventions to boost soil microbes (“magic pills”);
  • Withdrawal of insecticides and fungicides from the farming system.

Mythbusting: Not so magic pills

Some examples of “point interventions” that lacked scientific evidence to support their effectiveness in the field (as opposed to an isolated laboratory situation or a sterilized soil) were applications of ‘biological’ fertilisers (such as compost-teas) and microbial inoculations to promote plant growth (such as AM (arbuscular mycorrhizal) fungi). The review pointed out that where such practices have been adopted by producers, they are usually a small part of overall farming system changes that included changes in tillage and organic matter inputs, and in such circumstances it is impossible to ascribe positive soil changes just to the doses of inoculant.

As the reviewers state, “such system-oriented changes [decreased tillage, increased organic matter inputs] are likely to have broad-scale benefits for soil biota, with increases in both biomass and activity of all soil biota groups measured. Hence optimizing system management is also likely to increase the effectiveness of the indigenous soil microorganisms, including AM fungi, in plant growth promotion.”

In other words, if farmers and growers make the system changes, the soil organisms natively present will work better. If they don’t make the system changes, adding a few extra microorganisms is unlikely to bring much benefit. The exception, it is important to note, is that inoculating legumes with their specific rhizobacteria in new plantings does have good backing in science.

Call out: If farmers and growers make the system changes, the soil organisms natively present will work better. If they don’t make the system changes, adding a few extra microorganisms is unlikely to bring much benefit.

This is quite a salient conclusion. There are a growing number of ‘biological’ fertiliser and microbial inoculants being marketed to producers, often with an air of “scientificness” or based on some real research such as laboratory trials. However, the conclusion from this review of the literature is that there simply is no good evidence to show that these products actually do any good on real farms, and there are good theoretical reasons why they are unlikely to work.

For example, the ballpark microbial biomass of the top 30 cm of a hectare of soil is about 10 tonnes (3,000 m3 of soil in the plough layer, × 1.6 tonnes/m3 (bulk soil density) x 0.2% (percentage of soil that is microbial biomass (2 g/kg soil)). Many microbial inoculants are applied at rates of 1 kg / ha or less (dry weight of microbes), often much less if they are in solution, e.g., as little as 1 g / ha. Clearly 1 kg and especially 0.001 kg of microbes applied to the soil have a significant job to do to change the makeup of the 10,000 kg of microbes already present, especially when those microbes exist in a complex interacting ecosystem that is likely to be highly resistant to change from outside ‘invaders’.

A key take-home message is that the relatively inexpensive techniques of (1) increasing the amount and diversity of organic matter inputs, (2) reducing the amount and intensity of tillage, and (3) diversifying the number of crops / pasture species, are going to do far more for soil biology than all the often expensive biological fertilisers and microbial inoculants you can buy. You can therefore consider these myths to have been pretty well busted.

Mythbusting: Insecticides and fungicides vs. herbicides

The claim that reducing insecticide and fungicide use will lead to few direct positive benefits for soil biota may come as a surprise. But the review found that “there is little evidence of long-term negative impacts of insecticides and fungicides [to soil organisms] used singly or in combination at field rates. Data on pesticide impacts has mostly been collected in laboratory microcosms which suggest that insecticides may have more direct toxic effects on non-target soil biota than other pesticides, but that the impacts of food resources and temperature often had larger effects.” In other words, soil organisms are more damaged by lack of food (organic matter) and high soil temperatures (exposure to sun) than by exposure to insecticides and fungicides used in an agricultural setting.

This contrasts with the conclusion that herbicides do reduce soil biological quality, due to their primary aim of killing weeds, i.e., reducing weed biomass, which reduces the amount and diversity of organic matter entering the soil, which is the exact opposite of what is required to improve soil quality. However, farming choices are complicated and full of trade-offs: if eliminating a herbicide means that extra cultivation is needed to control weeds, this change may lead to a net decrease in soil health.

Therefore the myth that pesticides as a whole are bad for soil biology is also considered busted. However, this is not to say that pesticides are without their problems, as they can have multiple other impacts on the wider ecosystem. A far more nuanced understanding of pesticide usage is required than a simple “bad versus good” mindset.

Pick and mix

Improving soil health by adding more and diverse organic matter, reducing tillage and increasing crop diversity may seem simple, but it should be encouraging that these basic principles were shown to be true by many groups in many parts of the world. And it should also be encouraging that with such broad recommendations for maintaining a healthy soil, there is quite a bit of room for creativity at the farm level. In other words, there are lots of paths that could lead to a healthy soil. One producer may opt to invest in a no-till planter while another producer may plough conventionally on the planting year but leave pasture in place for more months of the rotation. Both will have improved the health of their soil from where it was before. Each farm is unique: markets, available equipment, even producers’ personalities come into play when determining what soil-improving strategies will work on a given farm.

Quantifying soil biological quality

Of course, this “broad stroke” approach has practical limitations because it lacks any quantifiable measures to help producers know whether the net effect of all their management practices is the building of a healthier soil or degradation of the soil. As the saying goes, “if you can’t measure it, you can’t manage it.” This means there is an interest and growing demand from farmers and growers for biological soil tests, i.e., in a similar vein to chemical soil tests. However, the now routine and reliable nature of chemical soil testing belies the vast amount of research over many decades that underpins it. In comparison, biological soil testing is still very much in its infancy. Our knowledge of the diversity of soil species is still very poor. Our understanding of the interactions among these species (the ‘soil food web’) is even poorer, and making explicit linkages between a particular biological attribute such as a bacterial or a fungal ‘dominated’ soil and crop performance is simply not possible with our current level of scientific knowledge. Indeed, the best current knowledge indicates that some of these simple one-to-one linkages between a specific measurement (such as total active bacteria and crop yield) may not even exist, due to the huge complexity and the myriad interactions and feedback within the soil food web multiplied by the additional complexity and variation caused by the effects of different soils and climates. Considerable care therefore needs to be taken when deciding which biological soil testing approach and commercial provider to use.

For example, the Natural England report noted that there are a growing number of commercial biological soil testing labs, such as Laverstoke Park ( which provides the proprietary ‘Soil Foodweb’ testing approach. However, it said that there were few links to the soil biota indicators being developed at a national level in the UK and those in the Laverstock Park tests [2]. Mainstream soil biologists and ecologists are sceptical of some commercial / proprietary biological soils tests, including the fundamental ideas on which these soil tests are based, i.e., that there are direct links between measures such as the overall populations of fungi, bacteria, protozoa, nematodes, etc., and soil and crop health and performance. At the same time, there are an increasing range of scientifically and field validated tests, such as the Visual Soil Assessment (VSA) system in NZ, and Cornell University’s ‘Soil Health Test’ that are based on agreed scientific knowledge of soil biology and ecology.

Soil Health Testing

Visual Soil Assessment

The VSA system was developed in New Zealand in the late 1990s by Graham Shepherd and others at Landcare Research. It is a simple, in-field, means for land managers to visually score a range of key bio-physical indicators and using a weighted scorecard to create a combined overall score. The techniques it used have been validated against well-proven laboratory tests and refined over the past decade into an eminently practical and reliable tool. See for more information.

Cornell Soil Health Test

Researchers at Cornell University in New York State have also developed a “Soil Health Test”. It puts numbers to those illusive properties like “friability” and “biological health.” Soil samples are collected and sent to the lab just like normal soil samples, with the addition of a “penetrometer test” in field—a probe used to find the severity and strength of hard pans under the soil surface. The lab provides the producer with a breakdown of the various measures of soil health. After a decade of testing and tweaking on vegetable and field crop farms, the test has been well vetted by producers, who are using it to pinpoint strategies that improve the soils on their individual farms.

The Cornell soil health test measures three criteria of a healthy soil:

  • soil structure—things like water holding capacity, aggregate stability (how well the soil crumbles hold up to pounding rain) and water infiltration;
  • activity of soil organisms—things like potential nitrogen release and carbon cycling, as well as a disease assay;
  • chemical soil properties we have measured and managed for decades, including pH, P, and K.

Results are calibrated by soil texture (sand, silt, clay), then given a score. Green means good, yellow means border-line, and red means the soil has lost significant functionality in that area. Tests are most useful when taken in pairs comparing fields with different histories (low-till versus conventional till, just out of pasture versus just out of grain, vegetable field versus hedgerow, etc). Farmers and growers can see how different management has affected the health of their soils and plan for the future accordingly.

If the soil health test shows that the soils could use improvement, it also prescribes ways to improve the low-score indicators, usually by adding organic matter and/or decreasing tillage frequency or intensity. For example, low aggregate stability can be improved fairly quickly by growing a fine-rooted sod crop like ryegrass. Other recommendations specific to the field conditions come up from time to time, such as deep ripping to break up a hardpan found in the field, but usually the test results suggest the broad “systems changes” that were highlighted by the Natural England report discussed above—reduced tillage and increased organic matter inputs. Consequently, you might wonder what the benefit of the soil test is, if it just tells you what you already know.

If you’ve ever noted the soil organic matter levels reported over the years on a basic soil test, you know how slowly they change. To be able to determine if a particular practice (reducing tillage, for instance) was boosting the overall soil health by looking just at soil organic matter, it would take years to see that number budge. The great thing about the new soil health test is that the finer measurements of structure and biological function can show change in just a single season, a much easier time frame to use when experimenting on the farm. For instance, if a soil test shows low “aggregate stability” (soil surface melts and crusts after a rain), just a year or two in a sod crop with tiny fibrous roots can boost that number, improving the germination and stand of small-seeded crops.

For more information on the Cornell Soil Health Test see


Why all this fuss about Healthy Soil?

Researchers are continually harping on about Soil Organic Matter, about how important it is for soil health and therefore plant health. Soil organic matter is the food for soil organisms, whose daily living activities and excretions lead to a healthier more productive soil that requires fewer fertilizers and pesticides to produce a high quality crop than a worn-out soil low in organic matter. The list of benefits enjoyed by a high-organic-matter soil include:

Better water infiltration when it rains—water soaks in faster and soil erodes less

Higher water holding capacity—plants can access more water in times of drought

Less soil crusting—seedlings emerge better after a rain, so plant stands are stronger

Better nutrient holding capacity—less fertilizer leaching and loss

What grower wouldn’t want that list of benefits working on his side?



There is a lot of confusion out there among farmers and growers about soil biology, soil health, biological fertilisers and related topics, so if you feel a bit bewildered by it all, you are not alone. While there are many companies selling a range of merchandise and analysis services, truly independent soil biologists and ecologists are mostly sceptical of these offerings, and the international research shows that they are not necessary. That does not mean that soil biology and ecology, the soil food web, etc., are also inaccurate or that they are unimportant. Nothing could be further from the truth: the health of your soil is the primary determinant for the health of your crops and stock, the health of the environment and the health of your bottom line. With the current change from the yield maximisation paradigm of the last sixty years to the multiple demands now expected of the farming system, (continuing to produce sufficient food while at the same time reducing nutrient pollution of waterways and green house gas emissions), improving soil health is now a key management objective for farmers and growers. Fortunately it does not require lots of expensive proprietary soil testing services or fertilisers. The most effective means to increase soil health: increasing organic matter inputs; reducing tillage and increasing crop diversity; are among the least expensive to implement, and some can even save you money!


1. Black, H.I.J., Ritz, K., Campbell, C.D., Harris, J.A., Wood, C., Chamberlain, P.M., Parekh, N., Towers, W., and Scott, A., SQID: Prioritising biological indicators of soil quality for deployment in a national-scale soil monitoring scheme. Summary report 2008, Natural Environment Research Council, Centre for Ecology & Hydrology.

2. Ritz, K., Black, H.I.J., Campbell, C.D., Harris, J.A., and Wood, C., Selecting biological indicators for monitoring soils: a framework for balancing scientific opinion to assist policy development. Ecological Indicators, 2009. 9(6): p. 1212-1221.

3. Stockdale, E.A. and Watson, C.A., Managing soil biota to deliver ecosystem services. Natural England commissioned reports, number 100. 2012.