Category Archives: Ecosystem knowledge

The microbiome and the medecine of the future, an analogy with Permaculture


Microbiome paradigm in science Ecosystems handling in Permaculture
The set of microbes inside our body is called the “microbiome”, it includes bacteria, archaea (primitive single-celled organisms), fungi, some protozoans and viruses.  Every ecosystems has developed a very specific biodiversity depending on its environment and include a multitude of biotic (plants, animals and microorganisms) and abiotic elements.
There are 10 times as many of these microorganisms as human cells inside us. Furthermore part of human cells cannot even be considered as living organisms (red blood cells). The volume of the microbiome put together is roughly equivalent to the volume of a human brain.  The complexity of physical, biological and chemical interactions in a humus substrate associated to a living soil ecosystem (fungi, bacteria, soil food web) providing nutrients to a plants is far from being known.
 The human microbiome is a source of genetic diversity and laboratories have reported a catalog of 3.3 million non-redundant genes in the human gut microbiome alone, as compared to the approximate 22,000 genes present in the entire human genome. The diversity among the microbiome of individuals is immense compared to human genomic
variation. If individuals are 99.9% identical genomically,  there hand or gut microbiome can be 80 to 90% different from one another. The microbiome is a signature that could replace fingerprints in human identification. A study done at the University of Cambridge, shows that 145 of the genes in the human genome are bacteria genes that have used a process known as horizontal gene transfer to fusion into human DNA over the course of evolution. Some microbiome between women and men have different specificity and babies born quasi exempt of microbiome inherit some of the microbiome of their mother during childbirth (raising concerns about the generalization of cesarean operations, preventing the beneficial propagation) and in the various steps of our life.
 The number of synergistic properties in the relationships between an ecosystem and a plant is innumerable and unknown, and the ecosystem metagenome at the genesis of these relationships is a scale factor up to the genome of a specific plant. This includes co-evolution symbiotic properties, generic exchanges based on plant categories and common ground biological mechanisms.
 The microbiome is a controller of disease, an essential component of immunity, and a functional entity, referred to as an “additional organ” by biologists, which influences our metabolism and modulates drug interactions. Researches, still in their infancy, show that the microbiome participate to digestion, immune system regulation, disease prevention, wound healing, obesity and appetite control, brain development, and emotions. The functional deficiency of our microbiome can play a role in depression, autism, allergies, neuron degenerative related diseases (e.g. Parkinson), asthma, obesity, and anxiety. For example a greater microbiome biodiversity is linked to lower allergies.  Biodiversity is the motor of the resilience of an ecosystem and key in the mechanisms of regeneration. By enhancing the number of interactions and the scope of nutrients available for plants and animals (like done in Permaculture) we ensure the stability of the ecosystem through all sort of mechanisms; weather control (carbon sequestration, humidity control), nutrient recycling and soil availability, disease control, plague control. A greater ecosystem biodiversity is linked to food production increase.
 The microbiome is not an independent organ, “magically” in charge of various functions, but instead is entirely integrated to our physiology and has evolved with humans for hundreds of thousands of years. A very illustrative example suggested by new studies shows that about 10% of every woman’s breast milk contains complex carbohydrates that cannot be digested by the infant but which fortify its microbiome, a prove of the intimate co-evolution we have had with these microorganisms.  An ecosystem is not an “alternative” context just in charge o environmental services (clean air and water, food, regulated weather, …), but instead a substrate where all forms of life find genesis and habitat and which has evolved concomitantly with the food we ingest and excrete. An illustrative example is the fact that industrial food, cut from most of ecosystems interactions has lost more than 60% of its nutrients, which would have been used for the energy they provide and the complex bio-chemistry they would have helped to produce in our body.
 The microbiome is a land still to be discovered and biologist have now the scanning and computer tools to decipher part of its complexity. The analysis of this new systemic set of data infers a limitless field of researches over the positive and negative impacts of the microbiome on the human body. Biologist think microbiome will be the key to the medicine of the future, considering its potential and its interaction with human physiology. Some stunning medical experiences have already taken place like the transplantation of microbiome extracts, with amazing results.  Permaculture is a domain of agroecology still in its infancy and rely on a non yet determined number of ecosystems properties and potentialities for food and habitat production.

Some systemic principles apply in the architecture of Permacultural “bio-landscape” and the amount of data available in order to optimize production is growing fast, but a mature science of Permaculture will need time to be able to finely monitor agroecological ecosystems toward optimal biodiversity, resilience and quality food and habitat production.

Permaculture and microbiome based science and medicine have that in common to push the frontier of our integrity; who we are, and enlarge our physical and ethical envelop to a coevolutive environment.

To substantiate and open the perspective here are some factors to consider;

  • An antibiotic is an “atomic bomb” for the microbiome, it kills bacteria without really discerning the good and bad guys.
  • Scientific research does not create new antibiotics, it tests the effect of natural molecules, therefore we are in a biomimicry approach more than a purely technological approach. Here there is a strong analogy with Permaculture where we do not give priority to new technology at first but prefer to integrate current know how from nature then in a second step add  technology to the natural cycles or let’s say integrate technology in a hybrid platform.
  • Antibiotics have been developed along history by the “West”, whereas a new segment of research ; the phages, or bacteriophages, which are viruses which have been studied by the “communist block”, creating an ideological split in medicine research. The phages have 2 particularities ; if antibiotics are mass destruction weapons phages are more like drones, having the capability to attack specific targets (bacteria.) This potential is now under focus in the west in the battle again resistant bacteria which are pointed as the main cause of mortality in the future by the OMS. The second particularity is that phages are not able to pass through biological membranes and need to be artificially transported to the cradle of disease in the body. Once again we may see here a relationship with Permaculture which uses human technology to enhance biological cycles by creating hybrid cycles.

Animal integration in a Permaculture farm

When you wish to integrate a new animal species in a Permaculture farm you need first to assess the particularities of the species you want to introduce (large , small, highly domesticated, compliant, independent, etc..) in relation with the available space, the animal social environment  including predators and the nutrients you can provide. e.g. a horse will need a lot of pasture (in which context ? tropical grass is less nutritive…) and need a herd to feel comfortable, a milk cow will need regular care, a goat will eat all young plants and even tree bark if in a confined environment, a pig is clever (more than a dog) and very adaptive but need biomass, a donkey is smart and sometime too independent to easily manage, guinea fowls will  form a very noisy orchestra if more than 1, a goose will challenge your children or any person insecure with farm animals, etc . If you made your choice over a specific animal, a difficult one to handle and integrate in your farm just be aware that it will take a lot of your energy that you could have spent in more productive activities, however Permaculture provides with a lot of spare time if you are smart enough so it is a feasible challenge …

Animals are very evolved forms of life, meaning that they are as well very sophisticated elements  of an ecosystem. It means that you are not introducing some kind of radish (my respect to radish)  but a highly context demanding organism in the ecosystem. If you do it wrong you’ll create suffering for you and the animal  you wish to introduce.

Rule 1 : start very very very small,

First create an habitat, observe day and year cycles, see how nutrients needs for this animal impact your farm (do you need to buy additional nutrients at the pet shop ?). Is your animal healthy ? How your animal impacts the design of the farm ?

You want to introduce ducks ? Ok, let’s start with that, some google search will prove you that ducks needs water bath…. A duck on the ground is like this Albatross from Charles Baudelaire, a clumsy clown looking desperately for a landing spot. It walks heavily and pitifully but when it come to swim and to fly then it is a change of paradigm and the chrysalis becomes butterfly you wish you could impersonate.

So you need a pond ?

That will become you first mistake ! … Of quantity not quality, meaning that you’ll focus so much in making such a big and fancy pond that in the end the pond will strain all your water resources.

Let’s say we are in the tropics … when the sun is high and the duck will have eaten all the aquatic plants (they will need about 2 hours to devastate this) what will remain ? a Turkish bath in the open air, getting warmer and warmer in the tropics and boiling with duck feces and anaerobic bacteria …

Ok, I think you got the picture, your ducks will evolve in a s… swamp by the end of the day. Over three days they’ll get sick because their pond is as well a soup which help them to process food. So what is the solution ?

If you start small you’ll observe, when it is raining, that a duck likes clean water, a puddle will become then the happy scenery of “I’m singing under the rain “. It means that if you want to build a sustainable environment for your ducks, either you have a lake with the capacity to handle water regeneration at a large scale or you have a backyard and you want to provide with a puddle large enough to make your duck happy and small enough that your source of water (constant and clean) will renew it and remove anaerobic bacteria in it.  So maybe the solution is not a huge pond but a small one which water you can renew easily, for example connected with a buffer tank harvesting rain water from a roof nearby,  and the capability to use the polluted water out of the pond as a fertilizer for your vegetable garden down the hill…

Did I say; “how to integrate and handle ducks in your farm” ? No , I said “start small and observe”, a systemic approach to integrating animals depending on your context. I guess you may find hundreds of specific information about ducks on the internet; that they lay eggs in the morning so that you release them after 9 am if they usually go errand during the day, that you may let them fly away if they know that they will find a source of food in their native yard and come back, having as a result very healthy duck finding all they need for their  diet elsewhere if missing in your farm, meaning that you would have to specifically care about their comfort and protection; you’ll observe that their claws will cut the higher part of a plastic sheet, if you use this material for your pond, when they jump out of the pond, requiring you to protect it with stone, logs, used tires,etc., making sure as well that the water level does not go beneath this protection; that they love slugs and snails but as well tender vegetation like young trees, banana leaves, vegetables and they will remove all vegetation if in a confined area. etc.  All this will impact the design of your operational processes and functions and change your development choices; what will be the kind of food they like and how and where can I grow them; can I let them go errand in specific areas assuming that their impact will be controlled, can they help controlling snails in the veggie garden, so how should I design the beds so to protect them from their voracious hunger ? etc.

Every context a different approach, every animal a different discovery.

If things go wrong, animals will take all your available time preventing you even to care about regular operations, which can be very impacting.

Rule 2: Search for information and challenge opinions

As everyone knows, Internet is part information and part opinions and many articles are  generous on duplicating knowledge that the authors never tested.
So search and search and search and even check with your experienced neighbors and if you find discordance then it is time to try to understand what is the problem between mainstream “expectation” and reality.

An example; the “Caramujo Africano”. It is a African snail introduced in Brazil long time ago with the hope that people would become adept to the french or portuguese way which consists in forgetting that this animal was slimy before to be cooked, did not worked and the snails were thrown away in nature, without predators to contain their development. It is now a plague which devours vegetable gardens, hidden in the mulch layer and continuing its nocturne progression all over Brazil.

If you Google “Caramujo Africano” in Brazil you’ll see that this animal is the devil. In its intestine and slobber it hides virus, pathogens and some amoeba with an obscure Latin nickname that will kills you in the next  minutes if you are unlucky enough just to look at it without gloves. However if you look further you see that they are 5 percent of information streams which tells you that Caramujo Africano is not a vector of this famous killing amoeba in Brazil. Indeed this sickness exist in Africa but no case of sickness ever happened in Brazil. This erroneous information has been duplicated so many time with the help of a consensual Google that it has become a Brazilian official statement making difficult to find the truth.

The same happens for raised bed. In this case if you look for a success story about Hugel Kultur you’ll find no balance, either a total success or a total failure in the tropics. The issue is that the hot temperatures dries everything so quickly that a raised bed become a dry bed in 2 days if you do not add an irrigation feature to it, even if made with a lot of organic matter.

Only if you really look for information and not “opinions” you’ll find the truth about it. One way to discern information from opinion is when article substantiate the reasons of such method they describe, not giving you a recipe but the underlying reasons of the solutions they propose.

Conclusion; search for contextual information (Variant of Principle no 2 of David Holgrem : catch local resource), e.g. adaptation of an animal to a specific climate, country, forest vs pasture, etc… and search for marginal information (Variant of Principle no 11 of David Holgrem: “Use edges & value the marginal”, adapted here to research and observation.)

Rule 3: Be aware that things change

A pet becomes adult, has a salvage dimension you should respect and could invade your domesticated space with maybe some confrontation.

As well; you’ll change… it is famous that animal farmers are more rude than vegetable or crop farmers. Vegetables growing makes you tender and patient, in some Asian culture you even “listen vegetables growing”… . Animals growing makes you hierarchical and authoritarian. When you need to check an animal for disease you’ll have no time to wait and many time you need to go against the will of the sick animal to cure him. I have seen many situations where animals were put on the ground and immobilized rudely to be able to access the wounds and heal the animal. If you have time to gain the trust of an animal and apply a soft approach that’s fine, then once again ; start small it will give you the time you need for this kind of method, otherwise you may face an ethical problem.

Rule 4: Be aware of your duties

A plant can be let alone for an extended period of time, an animal, if highly domesticated will need your constant presence. Chicken needs to be put in the coop every night for predator protection, a milk cow needs to be cared frequently, a dog needs food everyday, etc. Having an animal in the farm will change your routine as it creates sophisticated dependency with the farm functioning. You may ask friend to help when you are away but they will need some experience in that matter.

Slash and burn

Slash and burn technique is typically a misconduct in agriculture based on the belief that removal of existing vegetation will re- mineralize the soil and benefit to the next succession of plants, having as well the capacity to remove weed and unwanted vegetation and bugs.

Recent studies show that ;

  • the edible nutrients provided by burning the vegetation is coming mainly from the destruction of the living ecosystem of the top soil (bacteria, fungus, …) which release minerals and nitrogen then available for plants. In tropical climate most of these nutrients will be washed away or inside the subsoil and only a small percentage will benefit the newly planted vegetation, resulting in a impoverishment of the soil. Only high plants (trees with deep tap roots) will be able to recover these minerals.
  • the production of charcoal  coming from the burning of the vegetation will not be activated (to be transformed in Biochar) with nutrients since gravity will push these nutrients down or away.
  • The belief that ashes are a concentrated material of potassium needs to be put in perspective since most of potassium will be either evaporated with heavy smokes or washed away by rain. Only charcoal represent a stable and persistent material but needs activation.

These believes come mainly from the mimic of the process used by native Indian in the amazon. The difference is that in the latter case the slash and burn process is part of the rotation of a forest succession with a long period of recovery. Intensive agriculture does not benefits from the slash and burn technique, it only accelerates the death of soil ecosystem then lost of fertility and soil compaction. It is a short term technique creating desertification.

Other drives in this popular belief are that fire can renew life, that slash and burn of an existing forest indeed create an important reserve of nutrients and that fire can remove bugs, undesirable for the newly planted vegetation.

Micro-biology and soil analysis

In these 3 videos Dr Elaine Ingham gives a basic and easy to follow protocol for microbiology analysis of a soil sample, using a microscope of 400x optical resolution. This methodology can be used by growers and do not need expensive equipment. It represents a good alternative to lab sample analysis which can become expensive on the long term and is of limited value.

Microbiology is essential in assessing soil health and fertility. Soil ecosystem analysis is a pretty new domain of study in science and we realize that giving back life to soil is the only solution for sustainable agriculture. The geological and chemical analysis of a soil provides with very limited information and farmers facing soil depletion begin to search for solutions based on organic management and biodiversity increase. Microbiology analysis provides with the necessary feedback to understand soil quality and find adequate solutions for improvement.

Plants – Bacteria – Fungi



It is important to understand that symbiosis is an ancient form of collaboration between various forms of life and key in an ecosystem construction. Only by imagining the long genesis of two interrelated organisms and the tools of interconnection they have developed to collaborate we may start to consider the importance of such mechanisms in a complex ecosystem. Scientists think that plants / mycorrhizae symbiosis started 450 million years ago, when plants migrated to land. Legumes / rhizobia (nitrogen fixing bacteria) symbiosis is more recent; 60 million years old and may have evolved from plant fungi symbiosis mechanism.

In recent studies we learn that fungi and bacteria use a mechanical and chemical stimulation to start a symbiotic connection with a plant.

After reception of the signal by a fungus the plant builds a canal. Once the path is completed inside the plant the fungus is informed, penetrates the plant at canal level and starts to grow inside the plant to form an anchor for resources exchanges.

Such a “civic” processes presuppose an essential and productive collaboration between the 2 organisms and the importance of promoting this type of interconnection in modern agriculture for better yield.

In the case of symbiosis with nitrogen fixing bacteria the plant goes even further and the root hair of the plant when receiving the bacteria signal will trap the colony of bacteria curling the hair root around it.

Plant / Bacteria association

Plants attract bacteria to their root zones by producing “exudates” (sugar = soluble carbohydrates). Bacteria feed on these exudates.

Bacteria are the most protein dense organisms and the main nutrient material of the soil food web. They attract predators; protozoa and nematodes mainly, which feed on them and reject nitrogen and other minerals in surplus.

The minerals are then used by the plant as nutrients. The loop is closed.

In addition to this process 2 important mechanisms play a role in plants and bacteria association;
– Plant symbiosis with nitrogen fixing bacteria (it is the case for leguminous trees and mycorrhizae). In a depleted system (poor in nitrogen) an important ratio of leguminous species is necessary to help plants growing.
– Competition between plants and bacteria to access nitrogen. Here biodiversity is important so that bacteria predators can control this competition.

nutrient-transporters-plant-fungus-soilPlant / Fungi association

The symbiosis with fungi (mycorrhizal), another building block of soil food web, uses as well exudates, this time to trade fungi capacity to extend the plant root system and route minerals, water and phytochemicals over long distances. Fungi have much smaller diameter than plants root which allow them to penetrate the soil more effectively and reach nutrients and water over long distances.

Not tilling allows to respect the fragile network of fungi and increase plant nutrients uptake.

Organic nitrogen, phosphorus, sulfur, potassium, calcium, magnesium, iron and essential trace elements such as zinc, manganese and copper are returned to plant hosts in exchange for carbohydrates.

Fungi plays as well a direct role in Carbon storage and Nitrogen uptake;

There are 2 types of mycorrhizal fungi; ecto and ericoid mycorrhizal fungi, abbreviated as EEMF or EEM, and arbuscular mycorrhizal fungi, abbreviated as AMF or AM.

– Plants absorb carbon dioxide from the atmosphere and release part of the carbon into the soil; this carbon is taken up principally by the AMF, which processes it rapidly and act as a buffer, releasing the carbon gradually to other microorganisms in the soil over time.

– EEMF produces nitrogen-degrading enzymes, which allows them to extract more nitrogen from the soil than the AMF type and gives a competitive advantage to the plants against microorganisms for nitrogen availability. The resulting effect of a better nitrogen uptake is the reduction of carbohydrate decomposition and a higher ratio of carbon per unit of nitrogen.

Fungus and bacteria symbiosis with plant have been identified but many other symbiosis take place in the soil food web, for example nitrogen-fixing bacteria have been found inside ectomycorrhizae mantle.

Flow exchanges in the food web

Plants play 4 essential roles: harvest energy from the sun, fix carbon from the atmosphere, store the energy in the form of carbohydrates and feed the soil ecosystem.
Bacteria play 3 essential roles; store plant energy into a stable organic form (themselves) inside the soil, fix nitrogen from the air and provide food for the ecosystem (themselves).
Fungus play 3 essential roles: store carbon from the plant into the soil, extend plant root system access to nutrients, water and other resources and help nitrogen uptake by the plant

These 3 organisms have as well another important role; degrade matter for nutrients uptake (rocks, carbohydrate, lignin, …)

Bigger the plants (mostly trees and perennials) more energy is harvested from the sun and more influential is the orchestration of the soil life and the resulting fertility of the soil.

Source: Colin Averill, College of Natural Sciences at University of Texas in Austin.
Source: Proceedings of the National Academy of Sciences (PNAS)
Source: Jean-Michel Ané – University of Wisconsin-Madison

NPK management in Organic farming

N=Nitrogen , P=Phosphorus , K=Potassium (from medieval latin Kalium = Pot of Ashes)

In agro-industrial farming these 3 macro nutrients are obtained by chemical synthesis and mineral extraction. It is now acknowledged that mineral fertilizers impact negatively soil life and provoke its death in fine, making the soil not suitable anymore for plant growth (compact and not adapted to nutrients uptake). External resource : Read this amazing article to understand why

Organic and sustainable management of the soil requires additional understanding, knowledge and some ecosystem monitoring. This mindmap gives a synthesis of NPK nutrients role, the consequences if not available and the different means to provide plants with them in the process of organic farming. (click on the mindmap to enlarge it)



Nitrogen is available from the air in a stable chemical form. Bacteria are the main organisms responsible for the capture (fixation) and the transformation of nitrogen into a plant edible form.

Mycorrhizal fungi play an important role by transporting biologically fixed nitrogen to plants in organic form, for example as amino acids.

The predominant form of Nitrogen found in the soil is protein (in organic matter and organisms).

The next predominant form is inorganic; (NO3, NO2-Nitrite, NH4)

Annuals plants need the Nitrate (NO3) form of nitrogen
Perennials need the Ammonium (NH4) form of nitrogen (feeding trees with nitrate can provoke disease)


Potassium is found in the soil in 4 different forms;

– Potassium as a component of soil minerals
– Fixed potassium
– Exchangeable potassium
– Water soluble potassium

The first 2 forms exist in high quantity in the soil (for example clays of type vermiculite, illite and smectite have a lot of fixed potassium). These 2 forms are not directly edible by plants. Fixed potassium is released in low exchangeable potassium conditions, and mineral potassium is released by weathering, which is a slow process. Recent studies show that silt may represent as well an important reservoir of potassium.

Water soluble potassium which is present in compost is edible by plants but subject to leaching when heavy rains.

Organic matter in the soil favors bacterial, fungal and root activity which accelerate the transformation of non edible potassium into edible one. Macro-organisms (e.g. worms) plays as well an important role by preparing the soil for further bacterial and fungus processing.

To summarize Potassium is an abundant resource which need adequate management (living and active soil ecosystem, good monitoring of compost storage and distribution). Culture rotation may not be needed if the soil ecosystem is very alive and active although guilds will increase biodiversity of the soil ecosystem and concur to its fertility.


Phosphorus is the Achilles’ heel of industrial agriculture and the world food supply (read more at Reserves of phosphate in the world are now handled by a reduced number of countries (Morocco and China) and Phosphate peak could happen in the next decades. Although fossil fuel replacement and water recycling are predominant concerns and see a larger spectrum of solution every day phosphorus world depletion is ignored by most of the population and represents the real challenge when it comes to aggro-toxic farming.

The challenge is simple; plants cannot grow without phosphorus and this mineral become a limited resource. The only solution is therefore reducing, recycling and increase phosphorous availability in the soil. At the moment industrial agriculture is posing a threat to humanity by wasting enormous quantities of phosphorus which end-up in the rivers and the sea.


– A vegetarian diet represent 0.6kg of phosphorus per year, a meat-based diet requires 1.6kg phosphorus a year
– reducing the usage of phosphate fertilizers to the exact required proportions


– Recycling farm waste
– Recycling human wastes (sewage) Since crops leave the farm to feed the population it is necessary to get the phosphorus back to the location of production. The most advanced countries in recycling organic matter or sewage already perform such a recycling.

Increase availability.

Phosphorus concentration varies a lot depending on the soils. As for potassium only a small percentage of it is edible (in solution) by plants. Various techniques allows to increase this availability.

– Increase of microorganisms activity (living and active soil, rich in organic matter). They will mineralize organic matter to make phosphorus available and degrade non edible forms of phosphorus compound to transform them in an edible form.
– Phosphate moves very slowly in soils, deep roots and symbiosis with fungus helps in reaching phosphorus in lower layers of the soil. This can be facilitated by a good soil structure and the mix with perennial plants having in average deeper root system.

To go further and generalize; recycling (mainly avoiding leaching) and soil microbiology are the answers to NPK uptake

Dr Elaine Ingham (microbiology world famous expert) goes further;

– NPK is in enough quantity in the soil for millions of years of agriculture. Just is needed a living soil and its food-web to make it available to plant
– Taking care of NPK fertilizing only is a simplistic vision and more we go more we realize the importance of other chemical elements.
– Classical soil analysis inform only on the ratios of directly available minerals not taking into account the reserve of non directly available minerals that the food web can convert into nutrients. As well soils analysis by giving a PH value does not highlight the fact that PH varies in high proportion at different locations of the plant roots; the plant being able to bio-chemically orchestrate the soil ecosystem (including PH) to feed itself and optimize nutrients exchange at root level.
– Compost, which is an inoculum and not a direct nutrient is key in giving back life to the soil.

Here is Dr Ingham at a conference – a dense and extremely interesting talk

Clay – Sand – Silt – Loam and Humus


Clay, sand and silt are definitions of textures. The following picture show respective sizes of these 3 different particles;



Sand, by its comparative large size does not have a chemical valence (capability to interact with charge particles) therefore does not hold minerals in the soil. Water molecules find as well easily their way through sand and get away by the action of gravity. The advantage of sand is its permeability to plants roots which can develop without obstacles. The inconvenient of sand is its poor water and plants nutrients retention. When cultivating with a sandy soil a lot of organic matter needs to be present in the soil to store moisture and nutrients. Biochar helps as well by its structure to mechanically increase water retention in sandy soils.


Clay in agriculture

Clay, on the opposite, is very closed in size to elementary charged particles and react with ionized minerals. Different types of clay have different capabilities to exchanges cations (read more about CEC and measures of fertility) in the soil, playing a role in plant nutrients storage and availability. Usually clays in soils which have been weathered intensely and seen high bacterial activity for long geological periods (e.g. in the tropics) have structures less prone to interacts with minerals. It is one of the reason soils have a lack of minerals in the tropics. These minerals not being held by clay have been washed away by intense rains. In this case organic matter or more precisely humus play the role of nutrients storage with a higher electrostatic capability to interact with minerals than clay. The density of organic matter although is located in the top soil and reduce quickly in lower layers. The greater volume of clay compensate with the reduced capacity to hold nutrients. Plants with deep roots and symbiosis with fungus allow to access this reserve of nutrients in the subsoil.

Clay in building and waterproofing

Clay expand when in contact with water and shrink when getting dry. This particularity impact the different techniques of clay building. Mixing sand and clay using water create a solid aggregate when drying. Sand can be compared to stone and clay to mortar in this mixture.

The flexible expanding and self sealing properties of bentonite make this clay suitable for pond waterproofing. Other techniques using gley (organic material transformed by anaerobic reaction) are a less expensive alternative to bentonite.


Silt is a sediment material with an intermediate size between sand and clay. Carried by water during flood it forms a fertile deposit on valleys floor. Silt is easily compacted.


Loam is a mixture of clay, sand and silt and benefits from the qualities of these 3 different textures, favoring water retention, air circulation, drainage and fertility.


Humus is a highly complex substance still not fully understood. It is a stable and uniformly dark, spongy and amorphous material which come from the mechanical degradation of organic matter. Humus is fertile and gather all properties suitable for optimal plant growth. It is formed by complex chemical compounds, of plant, animal and microbial origin. Humus cannot form in the presence of high levels of inorganic nitrogen, due to the inhibition of the microbes essential to sequestration.