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You probably already know this – but it is still mind-blowing – that there are more living organisms in a teaspoon of decent soil than number of people on the planet! Such a teaspoon of soil could well contain more than 75,000 species of bacteria, 25,000 species of fungi, 1,000 species of protozoa and 100 species of nematodes. It is also amazing that microbes consume 95% of what is produced by green plants, whereas animals only consume 5%!

The creatures living in our soil are, after all, responsible for making nutrients accessible to plants, for determining the structure of the soil, for water and air movement, for disease control and for plant growth.

Clearly, life in the soil is a critical component of life on and in the earth! Until now most of us haven’t given them much thought but we now need to!

The life in our soils, (microbes or microorganisms) has been depleted through tillage, compaction, artificial fertilisers and all manner of chemicals.

This creates an environment where there is a serious imbalance between the numerous forms of soil life, so inhibiting their vital contribution to the cycle of life and nutrition.

You see, naturally our soils will absorb nutrients and release some too, including carbon through the breakdown of organic materials, such as leaves, twigs, microbes and animals. We should be adding and better protecting more organic materials with more microbes to assist the retention of carbon, thus protecting the environment from increasing carbon dioxide levels.  At the moment we have the balance wrong and we are emitting too much carbon dioxide in this way and not trapping enough, because the microbes in the soil are not being allowed to do their thing!

It is also vital to manage our water cycle better, helping to build soil to act as a sponge that can absorb water.  Farmers can also benefit from good management of the water cycle as climate change facilitates more frequent severe weather events, including droughts or floods.

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When soil is turned over, initially, plants will grow better because the microorganisms die and release their nutrients into the soil, but if tillage is repeated too soon the soil will become barren! Without the microorganisms feeding the plants, aerating the soil, making both water and nutrients accessible, plants become weakened and prone to pests and disease. As a result, farmers have tended to opt for the short-term solution which has catastrophic longer-term results.  They have added artificial fertilisers and killed off any remaining microorganisms. Tillage also exposes the soil organic matter (SOM) – the main mass of soil which acts as a sponge for both water and carbon.  When SOM is exposed to light and heat it releases carbon dioxide through a chemical process called oxidisation, a chemical reaction, a bit like burning. The light burns it and ultraviolet rays sterilize it, releasing carbon dioxide which we don’t need!


Created by ever larger and heavier farm vehicles, plus livestock, not only allows water run-off, soil loss and nutrient loss, but it also means there is not enough space for oxygen to flow through the soil. When soil, or indeed compost, lacks oxygen, anaerobic bacteria grow.  These bacteria prevent nutrient cycling, so plants don’t get the nutrients or the oxygen they need.


Much like tillage, this exposes the life and organic matter in the soil to oxidation and ultraviolet light and releases our precious, trapped carbon.  Moreover, as with compaction, bare, exposed soil allows organic matter to be flushed away by rain and blown away in the wind. Unfortunately, when this happens, it can take the nitrogen from fertilisers with it, over-stimulating algae in our rivers and oceans, suffocating and destroying life in the water.


are now known to confuse the dynamics of soil life. Ordinarily, nitrogen and phosphorus are cycled through various life forms before being taken up by a plant. If, for example, a plant is given nitrogen directly, it doesn’t have to work hard enough for it by photosynthesis, pushing sugars down the roots to feed the life processes there. Consequently, it misses out on trace elements and other minerals which get fed along with the nitrogen by the microbes.  So, artificial fertilisers may give a short-term impression of being good for our plants and soils, but they are building disaster for the near future.  It is vital that complex additives such as good compost are used instead of artificial chemical concoctions so that a full balance of nutrients really does give nutrition and life to our soils and sustains them for the long-term (see compost section). 

Life in the soil has suffered with a lack of food sources ordinarily given by a healthy mix of decomposing plants as well as from the sugar food from their roots. A diverse mixture of plants will be able to feed and support different concentrations of different microbes at different depths of the soil. These microbes can then feed nutrients to the plants and make healthy plants for us to eat. If a mono-crop is repeatedly grown, far fewer microbes will be fed and they will only exist within a far smaller depth of the soil.

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It is interesting to note that – despite previous understanding – plants have a significant part to play in determining the ph of soil. Here’s how: Bacteria and fungi in the Soil Food Web consume sugars from the roots of plants. Bacteria converts them into nitrates and fungi converts them (humic acids, to be specific- see below) and synthesises ammonium. It just so happens that nitrates make soils more alkaline and ammonium makes soils more acidic. So plants put out specific foods to attract the microbes they need to create these specific nutrients that adjust pH. Amazing!

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Compost /compost tea or extract when done well, is a fantastic way of inoculating soil with life. It should preferably be made from a diverse mixture of inputs, but generally consisting of around 30% green waste to feed bacteria, 60% woody waste to feed fungi, 10% high nitrogen waste. It can benefit from having a little biologically-rich, previously-made compost, or a tiny bit of soil from a forest, woodland or hedgerow, thus already containing plenty of microorganisms to inoculate the new compost. Compost isn’t only about adding suitable organic matter to feed nutrients into the soil. It’s about adding lots of different microbes and fungal spores, so these can then cycle nutrients and give them to plants.  Farming is about managing microbes.  If you can produce a good, healthy compost, a little will go a long way because microbes are tiny, yet in such large numbers!  A small amount of compost can be used to mix in water and then be spread easily on the fields. Obviously, do not put this liquid in a container with chemical residues that are designed to kill some of the microbes.  This will produce an imbalance in microbial populations, which could cause problems. It takes research, experimentation and time to mature, but is less extractive than humates and fits in with the circular economy far better. Nature has amazing ability to heal, but when our fields are inoculated with beneficial microbes and fungal spores we reboot the most precious resource we have, similar to giving the soil medicine.  One application should work for many years, but soil may need rebooting more frequently after repeated crop extraction or flooding etc. Worm counting and bird numbers and diversity can be a good indicator as to how healthy soil is. (See compost section).


Adding animals into an arable rotation brings additional microbial life from their dung, urine and saliva. Again, this is not necessarily easy, but it can be well worth the trouble and could help bring farmers together in cooperation for other benefits. British farming does not have a great record in this area, but there are many successful examples abroad and now, more than ever before, we need to work together better. Such animals need to eat from multi species, herbal leys with a diversity of root types which reach different depths of the soil, providing for the needs of a wide variety of microbes.


Replace rye grass and clover pasture with a mix of at least 7 different species. Gabe Brown’s and the Jena Experiments in Germany (see further reading section below) demonstrated that this reboots fungal and microbial populations. Ensuring that around 30% of this mix of species are legumes ensures enough nitrogen production and therefore good plant growth. It is, however, important not to use tillage as a means of establishing a mixed, herbal ley.  Advice is available on this from farmers on the conservation and direct drill sections of The Farming Forum and on the Facebook page, ‘Regenerative Farming UK’. In order to maintain such mixed pasture, mob grazing methods need to be introduced, otherwise animals will just pick off the species they prefer to eat and quite quickly reduce the mix.


Cover crops give microorganisms food for the winter and protection from the elements. If possible, use a mixture of crops providing microbes with different varieties of roots in different parts of the soil. As mentioned, seven or more varieties reboots fungal network growth. Keeping living roots in the soil is vital as roots feed the microbes with sugars / exudates and help with soil structure /aggregate development and carbon capture, thus building soil.  If the land is not covered, the precious microbes and organic matter are lost through oxidisation, UV light and weathering.


Diversity is the key both to compost making and building healthy, profit making, growing soil. Diverse soil foods from compost, manure and different plant root sugars feed different, healthier populations of microorganisms. High numbers of all the different types of microbes increase nutrient cycling, increasing aggregate growth, humus/ SOM production and carbon sequestration. All of which are needed right now. The bonus is that this also increases profitability over time and ELMS is there to support this transition.

Once the soil is healthy, it will absorb water better, helping control not only flooding and drought, but also contributing positively to the whole global water vapour/ water cycle system.  Water vapour is the largest greenhouse “gas” and therefore it is important that the balance is right! (See presentations by Walter Jehne on Youtube or https://www.ecofarmingdaily.com/supporting-the-soil-carbon-sponge/

There is still much to learn about the amazing web of life sustained in our soil. The production of glomalin or stable carbon by fungi was only discovered in the early 1990’s.  It is still not clear why mycorrhizal fungi doesn’t grow under certain plants including brassicas, such as cabbages, or ericoidal plants, such as rhododendrons.

Soil organic matter (SOM) is composed of the “living” (microorganisms), the “dead” (fresh residues), and the “very dead” (humus- see below). Active SOM is composed of the fresh plant or animal material which is food for microbes and is composed of easily digested sugars and proteins. Active SOM improves soil structure and holds nutrients available for plants. The passive SOM is resistant to decomposition by microbes (higher in lignin).

It is significant that, if they not nurtured and supplemented, up to 60% of the organic matter in bacterially dominant soils can be lost, whereas only 20% of the organic matter in fungally dominant soil may be lost. Therefore, it is evident that fungally dominant soils make for better carbon sequestration, although bacteria is still vital, with plant roots and all the other natural contributors to support them.

Soil organic matter serves several functions.  From a practical agricultural standpoint, it is important for two main reasons:

1) as a “revolving nutrient fund”

by which organic matter serves two main functions:

  • Plant residues are the basis of soil organic matter, thus they contain all of the essential plant nutrients. Hence, accumulated organic matter is a storehouse of plant nutrients.
  • The stable organic fraction (humus) absorbs and holds nutrients in a plant-available form

2) as an agent to improve soil structure, preparation of the soil surface and minimize erosion

It is clear that we need to put more life back into the soil than we take out, both above and below the surface of the ground.  Healthy soils, with leaf matter, microorganisms, plant roots and mycorrhizal fungi, capture carbon in organic form, whether alive or dead.  Yet most organic carbon, like most microbial life, is in the top layer of the soil.  It must be kept there and not be washed away, dug over or killed with an imbalance of chemicals.  In fact, we lose ten times as much carbon dioxide from such loss as we do currently from fossil fuel usage, so good management of our soils will reap massive rewards.

Compounds and function of humus

Humus – or humified organic matter – is the remaining part of organic matter that has been used and transformed by many different soil organisms. It is a relatively stable component formed by humic substances and is probably the most widely distributed organic carbon-containing material in both terrestrial and aquatic environments. Humus cannot be decomposed readily because of its intimate interactions with soil mineral phases and is chemically too complex to be used by most organisms. It has many functions.

One of the most striking characteristics of humic substances is their ability to interact with metal ions, oxides, hydroxides, mineral and organic compounds, including toxic pollutants, to form water-soluble and water-insoluble complexes. Through the formation of these complexes, humic substances can dissolve, mobilize and transport metals and organics in soils and waters, or accumulate in certain soil horizons. This influences nutrient availability, especially those nutrients present at micro concentrations only.

Humic and fulvic substances enhance plant growth directly through physiological and nutritional effects. Some of these substances function as natural plant hormones and are capable of improving seed germination, root initiation, uptake of plant nutrients and can serve as sources of N, P and S, Indirectly, they may affect plant growth through modifications of physical, chemical and biological properties of the soil, for example, enhanced soil water holding capacity and improved tilth and aeration through good soil structure.

About 35-55 percent of the non-living part of organic matter is humus. It is an important buffer, reducing fluctuations in soil acidity and nutrient availability. Compared with simple organic molecules, humic substances are very complex and large, with high molecular weights. The characteristics of the well-decomposed part of the organic matter, the humus, are very different from those of simple organic molecules. While much is known about their general chemical composition, the relative significance of the various types of humic materials to plant growth is yet to be established.

Humus consists of different humic substances:

  • Fulvic acids: the fraction of humus that is soluble in water under all pH conditions. Their colour is commonly light yellow to yellow-brown.
  • Humic acids: the fraction of humus that is soluble in water, except for conditions more acid than pH 2. Common colours are dark brown to black.
  • Humin: the fraction of humus that is not soluble in water at any pH and that cannot be extracted with a strong base, such as sodium hydroxide (NaOH). Commonly black in colour.

The term acid is used to describe humic materials because humus behaves like weak acids.

Fulvic and humic acids are complex mixtures of large molecules. Humic acids are larger than fulvic acids. Research suggests that the different substances are differentiated from each other on the basis of their water solubility.

Fulvic acids are produced in the earlier stages of humus formation. The relative amounts of humic and fulvic acids in soils vary with soil type and management practices. The humus of forest soils is characterised by a high content of fulvic acids, while the humus of agricultural and grassland areas contains more humic acids.

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Carbon sequestration is measured in terms of total organic carbon stored in the soil. Total organic carbon is mainly comprised of two carbon pools: the active pool and the passive pool. The active pool consists of very labile carbon [labile means “unstable, tending to slip or change”] labile carbon and the passive pool consists of less labile carbon and non-labile carbon.   Active pool carbon is an indicator of the small portion of soil organic matter that can serve as a readily available food and energy source for the soil microbial community, thus helping to maintain a healthy soil food webPassive pool carbon is mainly responsible for soil carbon sequestration.

Further reading & research:

For details of research into how we can further increase plant’s ability to store more carbon: https://ensia.com/articles/plants-co2/

Liquid Carbon Pathway – Dr Christine Jones – https://www.youtube.com/watch?v=C3_w_Gp1mLM

Here you can see how humus is made – https://vimeo.com/122856716?ref=fb-share&fbclid=IwAR28gzigkm5hQJyQusNAYrTaxIglAchGnrngH8MQt6BlzAkB6D6wJ-jyI9w

Read about how tillage at different times using different methods effects SOM / SOC and CO2 release- https://cropwatch.unl.edu/2018/long-term-tillage-and-soil-co2-fluxes

More about microbiology in soil – https://microbenotes.com/microorganisms-in-soil/#positive-effects-of-viruses-in-soil

Soil carbon saturation- myth or reality – https://lachefnet.wordpress.com/2019/08/03/soil-carbon-saturation-myth-or-reality/

The Jena Experiment – http://the-jena-experiment.de/

Gabe Brown – Gabe Brown – How to build healthy soil – http://brownsranch.us/category/videos/

Gabe Brown – do we need fertilisers – https://www.youtube.com/watch?v=UEOVLpZrvvU

Guide for farmers from the Soil Ass – https://www.soilassociation.org/media/4672/7-ways-to-save-our-soils-2016.pdf