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The Story of Soil

by Rob Avis

What is the difference between soil and dirt?

Soil is alive. Dirt is dead. A single teaspoon of soil can contain billions of microscopic bacteria, fungi, protozoa and nematodes. A handful of the same soil will contain numerous earthworms, arthropods, and other visible crawling creatures. Healthy soil is a complex community of life and actually supports the most biodiverse ecosystem on the planet.

Modern soil science is demonstrating that these billions of living organisms are continuously at work, creating soil structure, producing nutrients and building defence systems against disease. In fact, it has been shown that the health of the soil community is key to the health of our plants, our food and our bodies.

Why is it then, that much of the food from the conventional agricultural system is grown in dirt? The plants grown in this lifeless soil are dependent on fertilizer and biocide inputs, chemicals which further destroy water quality, soil health and nutritional content.

How did we get here? How do we turn this around? This is the Story of Soil….

Turning and Ploughing Soil

It all started about 10,000 years ago when humans started ploughing the fields in the experiment called agriculture. The settlers noticed that when they ploughed the field their crops would grow faster. Based on this positive feedback it was concluded that ploughing must be constructive and more fields were turned. However, in actual fact the bacteria, fungi and arthropods in the soil are essentially nutrient locked up in biology. For example, bacteria is almost 90% nitrogen. Ploughing the soil was killing the life in the soil resulting in an unregulated jolt of nutrient available to the surrounding plants. Over time, with the death of all soil microbes, the soil is unable to naturally support life and the farmer had to move to more fertile ground. The agricultural pattern emerged: deforest, plough, irrigate, salinate, desertify, move on.

How the Synthesis of Acid Changed the World

About one hundred and fifty years ago humans discovered how to synthesize sulphuric acid. The synthesis of acid allowed for a major advance in industrial agriculture: the ability to dissolve rock minerals into a water-soluble form. This meant that macro-nutrients such as nitrogen (N), potassium (P) and phosphorus (K) could be added to the soil in a form that could be taken up by plants.

As acid was discovered at around the same time as petroleum, this meant the advent of harder, faster and larger-scale ploughing with the use of water soluble salt-based minerals. Again, what could be wrong with a system that produces so much?

Plants and Their Roots

Plants have two main types of roots: tap roots and hair roots. Tap roots are responsible for hydrating the plant, i.e. drinking water. Soil does not freely feed or give minerals (such as calcium, magnesium, etc) to plants and so in order to get minerals a plant must make a “trade” with the soil biota – this is the primary function of the hair roots. Therefore the hair roots are the mineral traders and create an environment around themselves called the rhizosphere – a habitat for soil biota.

Through the process of photosynthesis plants produce exudates (sugars) and commit up to fifty percent of these sugars to the action of feeding and trading with the biology in the soil. When the plant needs a certain mineral, say calcium, it offers exudates to the biota that can provide calcium. This is a symbiotic process in which the plants support the biota and the biota support the plant.

And so, if you plough soil and kill off the biota and soil microorganisms, how does a plant get minerals? The industrial solution is to feed the minerals to the tap roots, i.e. put water-soluble dissolved minerals in the drinking water, otherwise known as fertilizer. The advent of nitrogen, potassium and phosphorus fertilizer (NPK) meant that we did not need to rely on a bank of soil biology to make our plants grow. We could add macro-nutrients at whatever rate we desired and grow plants faster and quicker than ever before – in increasingly lifeless soil.

Have you ever salted a slug? What happens? The salt creates a large osmotic pressure on the creature’s cell wall and results in death. This analogy can be used to understand what happens to the soil biology when salt-based fertilizer is used (note that all fertilizer is based in mineral salts). So the salting of the land through broad-acre fertilization ensures that the biology is completely dead. As long as we keep applying fertilizer there is no chance for life to return.

Without life in the soil, no natural mineral exchange can occur. Also, with plants being forced to drink mineral soup through the tap root, less energy is devoted to developing an overall healthy root structure. Fertilizer has become an addictive drug. It has eliminated the soil biota, replaced that function in the ecosystem, and now must be continually applied. Whoever controls the fertilizer market secured their market share the same way as the cocaine dealer.

The Downward Spiral

By the late fifties farmers were using NPK at record levels, tractors were highly advanced and the soils in the world were on a fast track to doom. The use of mono-culture crops, heavy tilling, irrigation and fertilizer was killing the soil and making our plants weak and addicted to chemicals. Monocrops of these obese and sick plants became an all-you-can-eat buffet for pests and the degraded and depleted soils a great opportunity for pioneer species (i.e. weeds).

“No worries!” proclaimed the Chemical Companies, “we’ve got the solution for that too”. Let’s kill these pests and nasty weeds that are causing all the problems – and thus pesticides and herbicides were born.

Without healthy soils to support beneficial fungal population the next problem to emerge for farmers was fungal issues. The “next solution” – apply fungicide!

We are now left with dead, acidic and salted soils that are only good for holding up plants.

Weeds and What they Tell Us

Carbon is the building block of life. Any soil scientist, gardener or farmer will tell you that a soil with no carbon is a dead soil. Carbon and nitrogen like to bond together at a rate of 30:1 and most gardeners know that mixing too much carbon in (like mulch or straw) will decrease available nitrogen. The reverse is true as well and adding nitrogen (in the form of fertilizer) actually reduces carbon levels in the soil. Without carbon, fungus has no food source and dies. The soil collapses, leading to hard packed dirt and anaerobic conditions (no oxygen). What comes next are nature’s signs of a sick system trying to heal itself: weeds, pests and erosion.

It has been proven that the weeds that grow on the surface of the soil are a response to a condition in the soil. For example, pig weed and thistle grow in soils high in nitrates (i.e. fields that have had a history of fertilizer use), and bracken ferns and blady grass grow in soils deficient in potassium (i.e. soils that have burned). Therefore, most of the agricultural weeds that we spray with herbicides actually have an ecological function. Club root, dandelion, knapweed, chickweed and amaranth all indicate too much nitrogen and anaerobic conditions – they are trying to build the topsoil carbon levels.

Weeds such as these do not divert a lot of the photosynthesis energy into soil biology relationships and instead they produce thousands of seeds and lots of carbon – they are fast carbon pathways. As the carbon in the soil increases, the soil is able to support fungal associates and bacterial populations encouraging the next stage of succession and return to soil health. Fast growing weeds and pest attacks are mechanisms in nature to eliminate monospeciation and increase biodiversity. If we truly wanted to stop the weeds and pests, the only real solution is to first understand why they are there. Weeds give us clues as to how to repair the soil and how to prescribe techniques to speed up the repair process. For example, if thistles are trying to build soil so that biodiverse life can return to it, we can speed up the soil-building process by adding the right plants and life back into the soil.

Patterns Repeat Themselves

Instead of seeing the pattern that got us here in the first place we tend to trust in the system that misunderstood it from the beginning. The countermeasures in industrial agricultural have all been based on too narrow a definition of what is wrong. When a decision is made to cope with the symptoms of the problem, second generation problems are created. It has now come to the point where we’ve invented and hybridized plants to grow in degraded soil/dirt and genetically modified our food to be tolerant of pesticides, herbicides and fertilizer. However, the use of chemicals is not just stopping the natural succession of the ecosystem, it is turning the clock backward toward death or desert.

I find it particularly interesting that the soil & chemical Ag industry is the same pattern as the human & pharmaceutical industry. Treat the symptoms, patent the “cures” and profit from the lack of health. I also suspect that the slow death of the healthy soil ecology over the last hundred years of intensive agriculture could be directly correlated to the increase in disease, illness and mineral deficiency in the human species.

There is an old saying from a farmer that I am particularly fond of: “I am sick of growing things that die and killing things that want to live”. It is amazing to me how much energy and money we spend in our quest to kill when all nature wants to do is live. Imagine what the world would look like if we invested the billions of dollars that currently go into killing weeds, pests, and fungi on processes that encourage life, and work with rather than against nature. The more you look at the current system the more you realize that our quest for domination over the soil is perpetuating a system of scarcity. What we need more than ever is a new paradigm to support a system of abundance and life.

Lucky for us that new paradigm exists! It is a branch of soil science that is called the Soil Foodweb. Paul Taylor of “Trust Nature” has been an organic farmer for over 30 years and is one of many to show that the use of aerobic compost and compost tea can turn dead degraded dirt into life-giving soil in as little as three years. The cycle of biocides is being replaced with a cycle of life. When we design properties to harvest water which fix the water cycle, and apply biology through compost, the results are nothing short of miraculous. Nature wants to come back, we just have to help her out a bit. Best of all, permaculture gives us all of the design tools to make this a reality.


If you are interested in more information on soil health, I highly recommend the book: “Teaming with Microbes, A Gardener’s Guide to the Soil Food Web”, Lowenfels & Lewis. The Soil Foodweb organization is another great resource.

Further Reading:



  1. Very inspirational read Rob. While filming supporting material for Geoff Lawton’s Soil DVD we shot a segment on the diversity of living life found in a Permaculture garden in just one square foot of topsoil! One square foot! No more. Once the straw mulch was removed, it was like lifting a roof of a city and looking into another world. The number of small creatures from a predator lizard down to inch worms, spiders, ants, tiny mites and microbes was extraordinary. But you needed a high powered macro lens and patience to see it all.
    Read about it here:
    “Teaming with Microbes” is an excellent book too. Highly Recommended.

  2. It’s been a few years since I looked into compost tea. I left then with the conclusion that its efficacy was unproven and I haven’t used it. Anybody have any links to newer studies on this?

  3. Thanks Rob: This is a terrific summation of the of the state of the soil at present. The good news is that we now have a cost effective and realistic way of ‘turning this all around’, and we can move into successful soil regeneration very quickly. What we have destroyed in the past 50-100 years can begin to regenerate within just a 2-3 year period. This is now being termed ‘regenerative agriculture’ (see where we have the technology, the science and the experience to ‘turn things around’. We can now use agriculture as a way of regenerating soils whilst maintaining production, we can now ‘turn the problem into the solution’ and use agriculture as the path to soil regeneration and environmental health.
    I see soil as the living skin of the earths, it is what produces life and what keeps CO2 in balance, vital soils hold more than 100 tonnes of living organisms per hectare…just think, living organisms are plant available nutrients, living organisms feed plants, living organisms are responsible for the soils ability to accept and hold water, living organisms protect productive plants (and much much more).
    How is this done?? ‘Simple’, we make vital ‘aerobic thermal compost’ that is at least 50% living organisms, if we have enough compost we can spread 5 tonnes or more per hectare over our soils to reinvigorate soil life and replace lost organisms that preform all these functions. If we don’t have enough compost, we make a vital soil inoculant (commonly know as AACT (actively aerated compost tea) and apply this solution to the soils.
    How we do this is to take a few kgs of vital compost and wash the microbes off the compost and into the solution using a ‘compost tea brewer’, we then add ‘microbe foods’ and over a 24 hr period we grow ‘hundreds of thousands’ into ‘thousands of millions’ of a great diversity of microbes and apply the solution to our soils to revitalize our soils and replace the lost diversity of beneficial organisms. for more information, see and
    we can turn this around…if not now, then when? and if not us, then who?


  4. I found this article very helpful too, thanks.

    “So the salting of the land through broad-acre fertilization ensures that the biology is completely dead.”

    How absolute is that? Surely it vary from land to land and over time?

  5. J Bob

    I think that it is important to scrutinize those studies before you draw any conclusions from them. A silver bullet like aerated compost tea without changing the practice of farming will have little to no effect on the system. It is important that any application of these sorts of technologies are driven with design.


  6. I just don’t see why some get so excited about compost tea. I would tend to think that most soil already has hundreds or thousands of species present and that by improving physical (e.g., aeration, temperature moderation)and chemical (e.g., no more fungicides, more OM, more needed nutrients) parameters the micro-herd will adjust species ratios and populations all on their own.

  7. Hi JBob

    Full disclosure: First off I have studied with Dr. Elaine Ingham and became a Certified Soil Foodweb Advisor. I have clients that I do Soil Foodweb Lab testing with, and I either make (or teach them to make) Actively Aerated Compost Teas and highly biological custom composts for their specific soil and plant groupings. I found out about Dr. Ingham and the Soil Foodweb from some Biologists while attending one of Geoff Lawton’s PDCs. I was intrigued by what I heard, and so went to Oregon to learn directly from Dr. Ingham. But it wasn’t until I returned to Mexico and ran my own compost tea control trials over the course of a year (see that I began to think that biological teas (when made correctly) could be a very valuable wrench in my regenerative ag toolbox. From a commercial practical perspective, my experience and that of the Soil Foodweb Labs around world show some dramatic results. There are many variables when making and using compost teas (I think more than compost) and showing repeatability and extract-ability between/among fields and growing systems can be difficult. Not an excuse on the lack of peer reviewed journaled scientific testing, but I think the lack of quantitative published data on a number of permaculture techniques could also be used to ignore the qualitative results people are having “in the field.”

    So yes, there’s isn’t a lot of peer-reviewed published control studies on the disease suppression of aerobic compost teas. But, there are more studies than Chalker-Scott’s selection. She doesn’t seem to dig too much or go beyond her own field testing before she comes to a conclusion that AACT doesn’t have disease suppressive capacities and/or other benefits. I do think it is a problem that there isn’t adequate research into AACT. The research on compost is quite clear: compost does have disease suppressive capacities. Some recent research coming from an Israel scientist I’ve communicated with clearly shows that the most disease suppressive compost is made from the plants you want to treat (in his work, compost made from olive tree waste showed more disease suppressing microbes for olive pathogens than compost NOT made with olive tree waste). So, with compost, the published research is relatively strong. Teas, not a lot. And, that is a problem. If you’re interested in learning more than Chalker-Scott’s perspective, I encourage you (depending where you are in the world) to call a Soil Foodweb Lab and see if some growers who use the method are in your area. Visit them and ask the growers themselves what their results are. In the meantime, here are a few published studies that Chalker-Scott seems to have missed:

    Scheuerell, S.J. and W. F. Mahaffee. 2004. Compost tea as a container medium drench for suppressing seedling damp-off caused by Pythium ultimum. Pytopathology. 94(11): 1156-63.

    Diánez, F., M. Santos, A. Boix, M. de Cara, I. Trilla, M. Avilés, and J.C. Tello. 2006. Grape marc compost tea suppressiveness to plant pathogenic fungi: role of siderophores. Compost Science and Utilization. 14(1): 48-53.

    Conforti, C., B. Marney, K. Hutchins, and J. Koch. 2003. The effects of compost tea on golf course greens: Presidio Golf Course, San Francisco CA. November 24, 2008.

    Larkin, R.P. 2007. Relative effects of biological amendments and crop rotations on soil microbial communities and soilborne diseases of potatoes (abstract). Soil Biology and Biochemistry. 10:1016. 40:1341-1351.

    Scheuerell, S.J. and W.F. Mahaffee. 2002. Compost tea: Principles and prospects for plant disease control. Compost Science Utilization. 10(4): 313-338.

    Reiten, J. and C. Salter. “Compost tea for suppression of Xanthomonas in carrot production.” Growing Solutions Incorporated. April 2002.

  8. Hi JBob

    Just noticed I didn’t address your point about if we stop abusing the soil that “micro-herd will adjust species ratios and populations all on their own.” Yes, they will do this but the speed at which they bounce back could be considerable and beyond our lifetimes. I think I’ve heard Geoff say once that as we humans are the only species that has been able to unleash such massive global environmental damage, we are also perhaps the only species that can also repair the damage quickly enough (for us): “we are the weeds that can repair the earth” Geoff said (or something like this).

    When I teach about biological agriculture and the soil food web one of the most important things I stress is to get people to stop doing a bunch of things (some that you mention) that kill certain soil microbes. A lot of what we do in both conventional chemical agriculture and organic agriculture (including dare I say some permaculture techniques) degrades soil from a microbiological standpoint. There is an ecological succession pattern that exists in the soil where microbes in partnership with plants will “heal” on there own the land by evolving or succeeding into more complex and healthier ecosystems. I mentioned the microbial succession pattern in a comments sections of another PRI post here:

    So, the question is how bad is our particular soil and how much time do we have to bring things back?

    If you want to dive more deeply into this and you’re not doing too much on a Saturday night you could read Eldor Paul’s contemporary classic soil microbiology text “Soil Microbiology, Ecology and Biochemistry.”

  9. the reason we get excited about properly made ‘vital soil inoculant’ (actively aerated compost tea) is because ‘we can’t grow what we don’t have’. When we lose important species by overuse of chemicals or by outdated soil management practices, we need to restore species diversity. If we do not restore species diversity, then natural functions that support productive plants just don’t happen and we have to rely on additional inputs. I agree that nature can adjust species ratios on her own, but we need the species to be there in the first place. This is the key to reducing plant stress, ensuring soil health, making non plant available nutrients plant available and much much more. What we focus on at is to deliver a practical understanding that works in the field rather than getting lost in the complex sciences of soil microbiology and plant nutrients. The science is extremely important but how to apply the science in the field is what matters to those working on the ground.

    In response to “pebble” yes, the effect of chemicals does depend on soils, practices, and time. What we do know is that some important species are lost when we apply chemicals and when we lose species, we become increasingly more dependent on chemical inputs to the point where we are totoally reliant on chemicals for production (and not necessarily profitable even then).

    When we deal with lack of soil moisture and compacted soils, we can be pretty sure that we have lost important species. When we have increasing reports about how we are losing production while we are increasing chemical inputs, we are pretty sure that we have lost important species that plants depend on for productive health.

    From my point of view, we need to remember that term ‘Bio-Logical Farming’, ‘Bio’ means ‘full of life’ and ‘logical’ means that ‘it makes sense to you’. One important thing to remember is that chemical farming relys on the ability to kill things, where bio-logical farming depends on the ability to give additional life to systems in order to aid production.

  10. Great post Rob! Very nice summary indeed.
    A big hello to you and Michelle from Taranaki Farm!

    On the subject, Paul Taylor will be presenting along side Eugenio Gras (visiting from Mexico) on an Australia tour for the upcoming RegenAG BioFertile Farms workshops.

    A first ever, double bill intensive 3-day soil biology workshop covering the soil food web, compost teas and then exploring the exciting field of ‘bio-fertilisers’. Eugenio through the dynamic COAS group in Mexico, have developed a sophisticated array of biological soil stimulant ‘brews’ made from common farm materials using simple, but specially constructed fermenter bins.

    These workshops are intended as the ultimate primer in soil biology for those looking for practical, immediately useable information and it’ll be great to see these complimentary approaches over the three days. Visiting Tas, Vic, Nsw Qld & Nz.

    Ben Falloon

  11. Thanks Doug and Paul. The reason I asked my question is because I know that a lot of smart people DO get excited by compost teas. Their enthusiasm got me interested, but I’ve just never seen enough field trials or demonstration plots to get me to go through all the effort of brewing up a big batch of tea. I know that things don’t have to be peer-reviewed to be true, and that soil microbiology is an extremely complicated subject of study. But I don’t think more examples like the Mexican corn at your link (with replication?) are too much to ask for.

  12. Hey, thanks for the mention of our book, “Teaming With Microbes” now in second edition, and re subtitled “The Organic Gardener’s Guide to The Soil Food Web.” I love your site. It is fantastic. Would love to come down to the other side of the earth, I am in Alaska, to talk soil food web!

    Keep up the fantastic work!

    Teaming with Microbes,

    jeff Lowenfels
    Anchorage, Alaska

  13. (Also posted on the PRI Forum)


    The efficacy of compost teas or rather extracts has come under some question more recently in this forum and on the home website following Rob Avis’ article, and now that we are offering these RegenAG ‘BioFertile Farms’ workshops across eastern Australia and NZ. I have seen both great and nil results from using this technique, just as I have seen good and horrible results from using a whole range of other ‘therapies’… we see the evidence of campesino farmers in Mexico who are getting great results actually raising a crop of corn when their neighbours have not….They and others are the proof of success where others perhaps are not taking the care that they should.

    I would also add that I am a synergist and encourage the practice of understanding the whole rather than looking for single silver bullets, bullets that often work like ‘Russian Roulette’! That is the essence of the RegenAG series…that we look at the wholes and work accordingly. By understanding this and looking at the palette of techniques and approaches accordingly a producer can make his or her mind up about which of these they will apply and do so without risking the farm. Holistic Management helps us to determine what we actually need and provides a list of ‘Testing Decisions’ to refine more effective decisions. That is why HM is at the top of the RegenAG program of modules.

    The other element of this particular course is that of farm-based ‘BioFertiliser’ manufacturing. This is Bayer (the Chemical Giant) technology that has been refined (in Latin America: particularly in Columbia, Mexico and Brasil by the COAS group – such that farmers can do it themselves using locally available materials. I would have to say that this has been a more effective and pervasive technology than Compost Tea (in those countries), in the main because it is so much less technical and requires a lot less training etc.

    Agriculture, whether its organic, biodynamic or otherwise is in the business of mining minerals and so these need to be dealt with somehow where mineral cycles aren’t more closed (such as in a more ideal Permaculture). Therefore BioFertiliser’s are a key to doing this whilst not creating a strong dependency on off farm products. The resistance to adopting the more scientific ‘Soil Food Web’ array of approaches in developing countries (and to an extent here in Australia) is because it requires so much more in terms of understanding and ultimately technology, as opposed to the BioFertilisers which are basically anaerobic ferments, requiring simple available vessels & materials. Plus its less difficult than the primary fermentation in beer making!

    We are encouraging producers to make their own minds up by being informed as to the possibilities as experienced by other producers rather than it all coming from someone with something to sell. Of course this will to an extent be difficult (to stop people greasing their own wheels) but its better than the alternative: rolling on with whole industrial ag approach be it conventional or organic.

    All the best,


  14. Hello All:

    I believe that this is great dialogue and gets us all thinking, what I am very much looking forward to is using a combination of bio-fertilizers with compost tea. If we can ‘get off the drip’ altogether and make our own compost, our own compost tea, and our own bio-fertilizer, then we can ‘go to the shed’ rather than ‘go to the shop’, become extremely self reliant and have valuable tools to teach, use and share.

    In the 70’s we made ‘manure teas’, ‘comfrey teas’, and compost, and we got mixed results, now, because work of Dr. Elaine Ingham, Dr. Christine Jones and others, I have a new perspective of what we were actually doing scientifically and that makes me look again and change some of my practices.

    We now have the science, the technology and the experience to use agriculture as the path for regenerating degraded soils, let’s ‘connect the dots’ and join methodologies so that this can be achieved. It is the sharing of knowledge that makes the difference in the long term and this is why I am so pleased with the regenerative agriculture initiative.

    Many thanks: Paul Taylor

  15. Brilliant article Rob! You & others might also be interested in David R Montgomery’s book Dirt: The Erosion of Civilizations. Basically from the Ice Age to the present, how agriculture got into such a mess; from absentee owners to non-owning managers – & slave labour – to today’s corporate loonies. Gives a big stick to biotech solutions, economists & politicians of all persuasions, & takes us all to task for our insane overuse of oil “eighty million barrels a day – enough to stack to the moon and back two thousand times,” and the constant rise in food costs, “If the poor can’t afford to buy food, increased harvests won’t feed them.” He covers the history of organic farming from the 1920s on &applauds the work of all organic movements and natural systems farmers for providing polycultures that reduce pests, provide their own nitrogen, and use species appropriate to the local environment. I recommend it to all.

  16. It Takes a Community of Soil Microbes to Protect Plants from Disease:

    “ScienceDaily (May 7, 2011) — Those vegetables you had for dinner may have once been protected by an immune system akin to the one that helps you fight disease. Scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and the Netherland’s Wageningen University found that plants rely on a complex community of soil microbes to defend themselves against pathogens, much the way mammals harbor a raft of microbes to avoid infections.” See:

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