Understanding Soil


How to Grow Nutrient Dense Food

What is Soil?

And what makes some soils better than others?

Soil Structure

Soil starts out as rock.

  • Sedimentary: from seabed deposits of sand, silt & clay
  • Limestone: from chemicals in the seawater, leached into the land
  • Igneous: from liquid magma

Then what happens?

These rocks ultimately break down into simple elements (more on elements in the next section!)


​​oxygen, silicon, aluminum, iron, magnesium, calcium, sodium, potassium




Basic Composition of Soil

1. Elements (referred to as minerals)

  • Minerals are naturally occurring, with a fixed chemical formula
  • Minerals are a collection of one more elements
    • Elements: a collection of atoms





2. Organic Matter (also known as humus--wait until the next section!!)

3. Oxygen

4. Water



What's the deal with soil texture & composition?  PS.  What is loam?!

Let's get one thing clear:  

soil texture has nothing to do with composition!

Texture: the size of the particles IN the soil.

  • Sand: allows for lots of air and pore space 
  • Silt: smaller pore space
  • Clay: small & slippery! Clay particles, as you might have guessed, absorb A LOT of water.


LOAMthe best of all three textures:  the surface area of silt and clay to hold on to nutrients and water, and the pore space for drainage and air.

Loam is Ideal, sure.  So, what's going on in my compacted soil?

Here’s what happens:

--the soil gets wet, 

--water displaces soil air, 

--soil dries out and needs oxygen, 

--roots breathe in oxygen and exhale CO2 (soil biota do the same).  


If soil has reduced pore space, the soil air becomes too rich in CO2 and soil ecology starts falling.

That's soil texture.  

What's soil structure?


Soil structure accounts for texture, but also

  • for the food web
  • for the electrical charges on clay and organic matter that attract other chemicals (read: nutrients!)
  • An ideal soil contains a specific ratio of nutrients
    • 68% calcium​
    • 12% magnesium
    • 4% potassium
    • 2% sodium

Soil structure is held together by bacterial slime.  Yep, slime.  Not only that, but the slime allows earthworms the space to tunnel through and create air & water pathways.  And earthworms eat lots of things: bacteria, fungi, nematodes, protozoa, organic matter.

Which brings us to...

The soil food web, of course!

Soil is composed of more than just plants, their roots, and whatever nutrients that you put in or already exist.


Living among the plants, no matter perennial, annual, edible or ornamental, are a massively huge group of “creatures” that make up the soil food web.


These members include bacteria and fungi (think of them as tiny bags of fertilizer) and nematodes and protozoa (think of them as fertilizer spreaders), and earthworms, arthropods, slugs, snails (and on and on)




Huh? Bags of Fertilizer?

Bacteria have to eat, too!.  They eat plant and animal materials to ingest nitrogen, carbon compounds, and other nutrients. 

When any member of a soil food web dies, their bodies are eaten by other members and then redistributed in dung or decomposition by bacteria and fungi. 

When these bacteria and fungi die, they release those nutrients that were inside them into the soil.

As an added bonus, frequently the bacteria and fungi die close to the plant’s roots and the plants are able to quickly assimilate those nutrients.

What's the relationship between plants & this soil food web?

Plants work mostly in harmony with this web, using something called exudates to attract partners in their growth.


  • a mixture of carbs/sugars and proteins
  • secreted by the plants to attract specific bacteria and fungal partners to help them
    • access nutrients that they themselves can’t reach
    • to “fix” atmospheric nitrogen, something the plant is unable to do, but desperately needs to grow.   


A Fun Fact

Plants secrete different exudates depending on what kind of bacteria or fungi they want to attract and even the time of the season.


The area of exudate excretion is known as the rhizosphere.

Let's talk about two specific plant + microbe relationships that you might have heard about.

Mycorrihizal Fungi


The Nitrogen Cycle aka "fixing" nitrogen

Mycorrihizal Fungi

A MAJOR advantage fungi have over bacteria is that they can grow in length (as well as eat tougher to digest foods)

One such symbiotic partnership between plants and fungi is Mycorrhizal Fungi.


90% of ALL plants have such a partnership.


What do they do?!

Phosphorus is relatively immobile in soil (it binds tightly to soil particles).  Mycorrhizal fungi provide plants with phosphorus in return for carbon exudates.  MF also deliver other immobile nutrients like zinc, copper, iron and manganese.


Mycorrhizal Fungi, Continued

Along with nutrient delivery, the MF partnership aids plants in several other ways:

  1. They provide plants with physical protection: the fungus is a barrier to invasion of pathogenic bacteria, both physically (forming a protective sheath) & chemically (producing antibiotics that inhibit disease organisms)
  2. They help increase production of growth hormones
  3. They help with the establishment of nitrogen fixing nodules in legumes (How?: the increased uptake of phosphorus increases the colonization of the Rhizobium bacteria within the plant roots).

More on that next!



Certain vegetable families don’t form partnerships with mycorrhizae, including brassicas (kale, cauliflower, broccoli) and chenopods (swiss chard, beets, spinach, quinoa).  


Why? Their roots release a natural anti-fungal defense which stops them thriving.  They do best on bacterially dominated soil.

You might have heard about "fixing" nitrogen and that beans do a good job.  Let's explore why.

The Nitrogen Cycle

Atmospheric nitrogen--78% of the earth's atmosphere--is off limits to plants.  The plants are unable to break the triple covalent bonds that hold it together.  Luckily, they have friends who can.  Bacteria friends.


Friends with names like Rhizobia (best friends with legumes) and Frankia.  Their enzymes break apart the triple bonded nitrogen atoms, in exchange for housing & carbon based exudates.


The atmospheric nitrogen is transformed into ammonium (NH4+) or nitrate (NO3-)



Plant Useable Nitrogen

Plants are then able to use nitrogen as ammonium or nitrate.

  • NH4+: ammonium: fungi release ammonium and the resulting soil conditions favor plants that like fungally dominated soils:  perennials, trees

  • NO-3: nitrate: bacteria convert ammonium into this—these bacteria require a soil pH of 7, but unfortunately fungi enzymes are very acidic, so it’s a balancing act of fungi vs bacteria

This means: The more fungi, the more acidic the soil, the fewer nitrogen fixing bacteria.  More ammonium is available to plants, which is a pro/con depending on the plant.

One more thing--

As you might recall, as part of the soil food web, protozoa eat bacteria and fungi. Bacteria and fungi waste products contain carbon and ammonium. 


SO: 80% of the nitrogen a plant needs comes from the wastes of protozoa.  These wastes are delivered to the root because so many bacteria and fungi hang around the root area and this where they get eaten.

What role does compost and humus play in this soil web and soil structure?

First, a few definitions:

  • Soil Organic Matter (OM)composed of plant & animal residues in different stages of decomposition, cells of soil microorganisms, and substances that are so well-decomposed it’s impossible to tell what they were to begin with.  
    • ​classified as Active or Passive (or Slow--which is in between active and passive)

Organic Matter, Cont.


Active soil organic matter is breakfast/lunch/dinner for microbes. It is the readily digestible and easily decomposed portion of fresh organic (meaning carbon-containing) residues.

As these plant/animal materials are decomposed by soil organisms, the process helps:

  • stabilize soil aggregates (a group of soil particles)
  • releases nutrients by mineralization
  • provides food for microbial activity ( which can lead to suppression of plant diseases and enhanced plant growth)

Organic Matter, Cont.


Also known as HUMUS.  

Passive OM is not biologically active.  This means that it provides very little food for soil organisms.

Humus can take hundreds or even thousands of years to fully decompose!

Once completed, it's resistant to decomposition.

Humus helps with:

water retention, erosion reduction, nutrient retention, and disease suppression.

One thing for later!

Humus behaves as if it has an anion exchange capactiy.


So, Humus is Stable.  

Where does Compost fall in all of this?


  •  artificially accelerates the decomposition of crude organic matter and its recombination into humus. Basically it speeds up, significantly, a natural process.  Years are cut to months.  


  • BUT— compost that seems ready to work into soil may not have become humus yet. Though brown and well decomposed, it may only have partially rotted. If this is the case, compost doesn't act at once like powerful fertilizer and won't immediately contribute to plant growth until it has decomposed further. 



How does Composting Work?


Compost is the result of soil microbes, heat, water, air, and organic materials acting in a complicated dance to break down the organic materials into a humus like texture and material.  


The organic materials included need to be a mixture of materials that are high in carbon (“brown”: leaves, bark, woodchips, branches) and materials that are high in nitrogen (“green”: grass, weeds, kitchen scraps).  



Composting ,Cont


Bacteria and other microbes use the carbon to fuel their metabolism.  They use nitrogen to make proteins and enzymes. 

A common rule of thumb for a compost bin is 25 C : 1 N


If composting is allowed to proceed until virtually all of the organic matter has changed into humus, a great deal of biomass will be reduced to a relatively tiny remainder of a very valuable substance far more useful than chemical fertilizer.

We've talked about soil, the soil food web, and compost first.  But now it's time to understand how plants eat, what they eat, and how that translates into healthy foods and soils.

Let's start by understanding more about nutrients...

Nutrient Basics

A refresher chemistry lesson:

  • Atoms:  the smallest unit of an element that retains the properties of that element


  • Elements: a collection of atoms.  Each nutrient is an element.  
    • There are 118 elements.  ALL plants need 17 of the 90 naturally occurring elements.

Electrons & Protons

Each atom has a central nucleus.  Inside the nucleus are protons (+ charge) and neutrons (no charge)

The nucleus is surrounded by electrons (- charge).  


An element’s atomic number is the number of protons in an element. 


Electrons love to pair up.  Each atom can have more than one charge—these charges repel or attract each other, allowing atoms to hook together and become molecules.  Na + Cl= NaCL (salt)

Nutrients that Plants Need

Let's Break Down those Necessary Elements!

  • Carbon
  • Oxygen
  • Hydrogen


Supplied by air and water.  H, O, and C account for 96% of the mass of a plant!

The Other Nutrients...

The other essential nutrients are supplied by soil or added as fertilizers.  They enter through the roots.  These nutrients are classified as macro or micro.


Nutrients required in large amounts by plants

  • nitrogen
  • phosphorus
  • potassium
  • calcium
  • magnesium
  • sulfur
  • silicon


Still just as essential as macronutrients, but required in smaller amounts: 

  • iron
  • aluminum
  • chlorine
  • zinc
  • molybdenum
  • boron
  • manganese
  • copper
  • sodium
  • cobalt

How do Nutrients Enter Plants?

Most atoms are electrically neutral—they have the same number of orbiting electrons as they have protons in the nucleus. 


BUT, when atoms gain or lose electrons and develop a charge, they’re called ionsthis is how nutrients enter plants.


Nutrients are either “cations” (positively charged ions) or “anions” (negatively charged ions).


These are held on negatively charged sites on clay and humus.

  • potassium (base)
  • sodium (base)
  • aluminum (acidic)
  • calcium (base)
  • hydrogen (acidic)
  • magnesium  (base)


Let's get back to humus, quickly.  Only humus can attract anions, so if there isn't enough humus in the soil, certain anions are more likely to leach out because there's nothing for them to hold on to.

  • Sulfate
  • Phosphate
  • Nitrate
  • Borate

And now, a Non-Exhaustive Look at a Few Nutrients

Calcium and Magnesium

Crops don't grow without calcium being present in greater quantity than all other elements combined.


Calcium=very abundant, very forceful at attaching itself to exchange sites.


The ration of Ca to Mg has a huge effect on soils' air supply:  when Ca:Mg is in balance, the soil requires less compost.  



“A regulating chemical”—it’s not a constituent of any organ, organelle, or structural part of plants. 

  • The ions play a key role in the movement of water into and out of cells. 
  • It regulates more than 60 key enzymatic reactions and is crucial in the formation of starch.


Determines speed at which plants grow.  A component of DNA and RNA and the base for the ATP molecule (the bonds contain energy).


Unfortunately phosphorus is really expensive and planet is experiencing peak phosphorus. 

Q:  So how do you not break the bank?

A: Increase anion exchange capacity of soil.  Phosphorus will stay in soil longer if it hooks up with humus.  And, if it hooks up with calcium or iron, it will be insoluble.


two chemical forms:

NO3: an anion (nitrate)

NH4: a cation (ammonium)


Nitrogen comes from decomposition of soil organic matter (ie: when members of the soil food web die) & from the atmosphere. Most natural nitrogen production appears during the warmest two months, so it's recommended to add nitrate fertilizer to gardens in the spring.

You NEED nitrogen to form proteins.

Nitrogen is mobile inside a plant.  It will go where it’s needed.


Iron is critical to nitrogen fixation—the conversion of atmospheric nitrogen and nitrate relies on iron.  Iron is so important to a plant that plants release ions into the soil to lower the pH to prevent iron from becoming unavailable.

A brief overview of pH and CEC*

*Cation Exchange Capacity

Cation Exchange Capacity

Clay and humus hold cations (positively charged nutrient ions). This prevents them from being leached out of range of plant roots. 


The soil solution and humus hold anions (negatively charged nutrient ions) .  Because they mostly reside in the soil solution, they are very susceptible to leaching.  This is how nitrates (anions) readily leach out of topsoil and into our water supply.  Think: DEAD ZONES


Cation Exchange Capacity (CEC): The soil's ability to hold onto cations. 

A Deeper Dive into CEC and a glimpse into pH

The cation nutrients that are added to the soil or already exist in the soil are “purchased” by plant roots.  And this is where pH comes into play. 


A plant’s root hairs use a specific currency to exchange their cations for nutrient cations.  The exchange currency is H+ hydrogen cations.  The plant gives away H+ for cations like potassium that are attached to clay and humus particles.


Every time a hydrogen cation is exchanged for a nutrient cation, the concentration of H+ increases and the pH lowers—becoming more acidic. 


Luckily, this acidity usually balances out because root surfaces also take up anions, using hydroxy,l OH- anions, as an exchange.

Acidity vs Alkalinity

(and why it matters)

Acidity and alkalinity are measured as pH (parts/potential Hydrogen), expressed in a logarithmic scale from 0 to 14. 


Acidity is associated with an increase in hydrogen ions

Alkalinity is associated with an increase of hydroxyl ions 


The differences in pH affect how molecules (ie: potential plant nutrients) will interact in the soil.


Ideal Soil pH & Other Factors

Most vegetables and landscape plants grow best in soil with a pH of 6.0 to 7.5.

When soil pH falls below 6.0, nitrogen, phosphorus, and potassium are less available to plants.

When the pH rises above 7.5, iron, manganese, and phosphorus are less available.


If the environment is too acidic, the plant will not attract enough hydrogen.

If the environment is too alkaline, the plant will attract too much hydrogen.


A numerical pH decrease just means that the number of hydrogen ions has increased. 

pH is the negative log of H+. 

One more time:

The lower the pH, the more H+ ions there are.  The more H+ there are, the more acidic it is. 

Soil becomes acidic when basic elements (calcium, magnesium, sodium, potassium) are replaced by hydrogen ions.



How Plants Eat & Drink

All life, including ours, is comprised of four groups of molecules: 



proteins (nitrogen based molecules composed of amino acids)

 nucleic acids

Pathways with Weird Names

Water moves through plant cells in several simultaneous ways:


  1. Apoplastic pathway:  located in cell walls—water travels from wall to wall
  2. Symplastic pathway: located in interior parts of cells—water travels through cell membranes
  3. Direct pathway: water moves through regardless of walls/membranes

Plants obtain nutrients from several sources:

  1. The Soil solution (those dissolved in soil moisture)
  2. via Cation Exchange
    • Remember: humus can hold and release cations and anions; clay can hold and release anions. 
    • These cations and anions stand ready to immediately replace whatever plants remove from the soil solution. 
    • “CEC is like the food in the pantry”

Knock, Knock

Certain nutrient molecules enter the cell’s wall easily.

Oxygen, nitrous oxide, and water all enter through diffusion: the movement of ions/atoms/molecules from areas of high concentration to areas of low concentration (this is known as osmosis when it's water). 


All other nutrient molecules need the help of special proteins and carbs to get into the plant cell.

They're in. Now What?

Once these nutrients and water enter the plant cells, they’re carried throughout the plant through 2 kinds of vascular tissue (tissue=a group of plant cells)


  1. xylem: carries water and nutrient ions
  2. phloem: transports sugars and organic molecules synthesized inside the plant


Aka: What's the deal with those numbers on the box?

What do Synthetic Fertilizers Do?


Many synthetic fertilizers are anions--farmers prefer fertilizers that are instantly soluble in water.  These anions (like nitrate and phosphate) are also easily leached. 



Chemical fertilizers completely ignore the complicated microbial assisted method of how plants obtain nutrients.  This means that there’s less need for these vital microbial populations and they dwindle in size. 


Plants get fed but soil structure doesn’t get built:  bacteria and fungi are killed and repelled. 


Lost is the bacterial slime and fungal hyphae that normally stick and weave soil particles together which creates pore space, air/water reservoirs, places for smaller organisms to hide from predators.

Factors that Affect Nutrient Availability 

And What to Feed Plants


In early spring you need to be aware of nitrogen and phosphorus.


Cold temperatures mean less nitrogen cycling and mycorrhizal phosphorus.  Useable nitrogen production occurs between 75 and 95 degrees.


Compost can buffer soil ph by absorbing hydrogen ions and increasing the number of cation exchange sites.


Plants also control the soil ph by releasing exudates of various components.  Additionally, nitrifying bacteria don’t do well in acidic conditions.

Soil Aeration

In poorly aerated soils, carbon dioxide can build up and react with water to form an acid.  


If carbon dioxide reacts with organic matter, that organic matter can begin to ferment.


Also, microbes that require oxygen begin using other nutrients instead.


Soils with a low CEC don't hold nutrients well, so the gardener needs to mete out nutrients over an extended period of time so they won’t all leach away. 


If your soil has a good CEC, then expect nutrients to be held.  CEC has a lot to do with mobility of nutrients in soil.  Assuming an adequate CEC, the anions chlorine, nitrate, molybdenum, and sulfur are mobile in soil.  Cations ammonium, calcium, copper, iron, magnesium, and manganese are much less mobile.  Nickel, phosphorus, potassium, and zinc are relatively immobile. 


Mobile elements have to be replaced more frequently than immobile b/c they are readily taken up by plants and they leach.

Periods of Initial Growth

You need:


Nitrogen, phosphorus, potassium, zinc, iron, magnesium, manganese, copper, sulfur, molybdenum 


In the greatest quantities.

Flowers and Fruiting


You need:


Ample amounts of boron and calcium

(boron for pollen formation and calcium to produce the flowers)

Understanding Soil & Growing Nutrient Dense Food

By meaghin0103

Understanding Soil & Growing Nutrient Dense Food

A brief overview of the soil food web, where soil comes from, ph and the Cation Exchange Capacity of soil, and different nutrient requirements of foods and seasons.

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