283-A Soil Chemistry Primer: How Protons and Electrons Influence Soil Moisture and Fertility

| Grow, Podcast

Gardeners know that adding organic material to soil improves its fertility, but to understand the reasons why organic matter is such an effective soil amendment, it’s necessary to get down to the molecular level. My guest this week, retired horticulture professor Debbie Flower, is here to offer a soil chemistry primer on cation-exchange capacity and how positive and negative charges in soil affect fertility.

Debbie currently lives in California in the Sacramento area and has worked in wholesale and retail nurseries and for university cooperative extensions and experiment stations around the country. Before moving to California, she lived and gardened in New York, New Jersey, Arizona, Oregon and Nevada — so she has experience growing in all sorts of climates and soil conditions. She hold a bachelor’s in plant science from Rutgers University in New Jersey and a master’s in urban horticulture from UC Davis in California, and she’s twice been the president of the California Association of Nurseries and Garden Center.


Debbie Flower

Debbie Flower, a retired horticulture professor, knows the nitty-gritty of soil chemistry and how it influences fertility and the ability of plants to take up nutrients.


Debbie has a vast breadth of gardening and horticultural knowledge, but what brings her to the podcast this week is her expertise in soil chemistry. She explains how positively charged and negatively charged ions make all the difference in how water, soil particles, organic matter and nutrients behave in soil.

Before proceeding with my conversation with Debbie about soil chemistry and cation-exchange capacity, I want to take a second to remind you that I have a new book out that was released last month. It’s titled The Vegetable Gardening Book: Your complete guide to growing an edible organic garden from seed to harvest” and can be found both online and at local bookstores. It’s chock full of insider tips and new-to-you information that will help you step up your gardening game and tackle challenges. 

And on tap for 2023 is my new Online Gardening Academy™ premium course, Organic Vegetable Gardening. Sign up for the waitlist here.

Meet Debbie Flower

Debbie grew up gardening with her grandparents and loves the outdoors, two factors that contributed to her decision to get into horticulture. Despite a number of setbacks during her academic and professional careers that were out of her hands, she persevered.

She met her husband during a student exchange program when she was based at an agriculture experiment station in Puerto Rico. “I worked there on sugar cane and pigeon peas and mangoes,” she says.

Next, she moved to Tucson, Arizona, where she worked on pistachios and pecans, and then moved again, this time to Portland, Oregon, where she worked at another ag experiment station, where they worked on using composted sewer sludge as an amendment in container media for growing plants. She also became a certified Master Gardener while living there.

Debbie found that she excelled with computers so worked on databases for corporations conducting mine reclamation in Wyoming and Montana. Then her family’s next move brought her to Reno, Nevada, where she started her graduate degree in horticulture.

“These environments were all very different,” she says. “I always gardened everywhere I went, but I had to learn about them and figure them out. And that was frustrating. I felt like I was back in kindergarten every time I started. But the result of that is that the more general terms of horticulture have become more apparent to me than the specifics. If I can understand generally what I’m looking for, then get the specifics, I can sort of figure it out from there.”

Unfortunately, when she was 19 credits into a 30-credit graduate program in Nevada, the university shut down the program. Her academic adviser said to go to the University of California, Davis, which precipitated her family’s move to California. However, UC Davis would only accept five of her 19 credits when she transferred, which set her back a bit. In 1992, she finally earned her master’s degree in urban horticulture and went to work for Sacramento County Cooperative Extension — then the state ran out of money, so she lost her job. 

Debbie next taught horticulture at a vocational school for adults. “We had a greenhouse, we maintained the landscape. So it was very hands-on: fixing lawnmowers, starting seedlings in the greenhouse, planting them, having plant sales, composting the waste from the cafeteria, which was another vocational program. And I did that until my kids needed me home more.”

She switched to part-time work, but she had three part-time jobs at once: working for a whole nursery and a retail nursery, and teaching computer applications. She went on to be a professor at several community colleges, doing hands-on work.

In retirement, she continues to stay busy including frequent appearances on “Garden Basics with Farmer Fred,” a Sacramento-based podcast for beginner gardeners. “We try to discuss topics that any gardener anywhere would be faced with,” she says, noting that she uses her experience of having gardened all around the country. 

Sand, Silt & Clay

Good soil is made up of 45% minerals, 5% organic matter and 50% air and moisture. The mineral component of soil falls into three categories: sand, silt and clay.

Debbie explains that in a soil lab, sand, silt and clay are designated strictly by particle size. Sand has the largest particle size, and clay has the smallest. 

Sand, silt and clay are all pieces of broken rock. “The rock has weathered over time and released these pieces,” she says. “Now, certain minerals will only break down to certain sizes.”

The size of particles can clue you in to what minerals may be included in them, and the sizes also give the particles different chemical qualities. “One is their ability to hold water in the soil,” Debbie says. The bigger the particles, the less water they can hold — so sand drains faster than silt and clay. 

When Debbie taught classes, she used a big jar full of balls for a demonstration. When water is poured into the jar — like rain from the sky or irrigation from a hose — it quickly finds a place to go in the spaces between the balls. In contrast, in a jar stuffed with pennies, the water has less space to travel into, so it moves very slowly around the pennies. 

We think of water moving through soil in one direction: down. But water really moves along the edges of each particle.

Each molecule of water, or H20, is made up is two hydrogen atoms and one oxygen atom.

“The hydrogens are positively charged, and the oxygen is negatively charged,” Debbie says. If you make a 105° angle with your thumb and pointer finger, you can imagine one hydrogen atom at the tip of each finger, and the oxygen is right at the base between the two fingers.

The positively charged hydrogen is attracted to the negative charge of oxygen on another water molecule — and that’s how water sticks to water. This is why if you drip water on a flat surface, it beads together.

“Water can also stick to other things that are charged, and all soil particles are negatively charged to different amounts,” Debbie explains. “The amount is dependent on how much surface area each particle has. Sand, because it’s big, has the lowest surface area per area it occupies. Clay has the most surface area.”


different types of soil

Soil can be loaded with organic matter but it can also have too much clay or be too sandy for growing vegetables and other crops. (Photo Courtesy of Debbie Flower)


Why Adding Rocks to a Container Doesn’t Improve Drainage

It’s common to add rocks to the bottom of a pot before adding soil in an effort to improve drainage — but it just doesn’t work.

“Let’s say we have a container full of media, whichever type — sand, silt, clay, or it could even be organic matter, which is a soilless mix typically used in container production,” Debbie says. “It is all one homogenous texture, and you add the water at the top. And that string of water attaches to the sides of the particles, and it moves through the particles.”

Once the water gets down to the gravel in the root zone, it stops. “The amount of charges in that gravel — negative charges that would hook to those positive charges on the water column — is drastically different,” she says. “And so the water stops, and it builds up in the container until the container is completely full. 

“So not only is the water around the outside of the particles, it’s filling the spaces between the particles. There is no room for oxygen, and roots have to have oxygen.”

If the roots go too long without oxygen, which means they can’t perform respiration, the plant will experience root rot.

If you add more water to the pot from the top, the new water will displace the existing moisture in the container and push out water from the bottom. Though some water came out of the container, the soil is still full to capacity, so the roots remain water-logged. 

“It pushes it into that gravel, and then it ultimately pushes it out the holes, but the soil above the gravel will remain saturated until the roots can absorb it or some can evaporate off the top of the surface,” Debbie says.

Water moves down in saturated soil due to gravitational pull, but in unsaturated soil, water can move in any direction — up, down, sideways — due to capillary action caused by the charge on soil particles.

I made a video demonstrating why adding gravel to containers is a bad idea, for just this reason that Debbie just explained, and I have never gotten more negative comments on a video.  Some people just won’t believe it, even when they see with their own eyes how gravel does not improve drainage. 


Drainage demonstration

Watch my demonstration and, then, try it for yourself. Water will drain through a cup filled with all soil, but that water will remain where gravel and soil meet.


The Importance of Organic Matter in Soil

“Organic matter solves all soil problems,” Debbie says. 

Let’s look at heavy clay soil. Clay is great at holding nutrients but too good at holding water. Because it is slow to drain, plants can essentially drown in clay soil and get root rot. However, adding organic matter adds more space for oxygen and allows water to drain more readily.

“But over time, that organic matter breaks down,” Debbie points out. “The rate of breakdown of organic matter is dependent on many things, often temperature. Warmer areas have more activity in the soil, and so you tend to have faster breakdown of organic matter.”

Conversely, in cooler climates, organic matter is slower to decompose. “Thus we get things like peat bogs up in the north, in Canada and above, which is an accumulation of organic matter,” Debbie adds.

The organic matter breaks down due to microorganisms that live in the soil.

“Soil is very much alive, and that’s how we want it to be,” Debbie says. “We want it to have macro-organisms like worms and other composting organisms, things that will eat that organic matter, get what they can out of it, break it down — and they poop.”

Worm poop, called worm castings, is further broken down by fungi and bacteria, and what the fungi and bacteria excrete is broken down even more by even smaller fungi and bacteria.

“This process goes on until the organic matter has kind of nothing left to give, and it is what we call humus,” Debbie says. “Humus particles are very small, and they’re very stable, meaning they won’t break down anymore. If you have 2 to 5% humus in your soil, you would have huge, what we call, cation-exchange capacity, meaning a great ability of your soil to hold onto plant nutrients that plants need and to give them up to the plant as needed.”


Joe Lamp'l applying compost

Amending soil with compost and other organic materials will help clay soil drain better and will help sandy soil retain water better. (photo: Tobi McDaniel)


Understanding Anions & Cation-Exchange Capacity

Cations are positively charged ions, while negatively charged ions are known as anions.

Plants require 16 or 17 different nutrients, in various amounts, in order to complete their lifecycles. But they can only take up nutrients that are in water.

“Everything comes to the plant in water and travels through the plant in water, and so in order to get these nutrients to the plant, they have to be in anionic form,” Debbie says.

Nutrients in anionic form move through soil particles and organic matter easily because they are negative ions traveling through particles and matter that are covered in negative charges. Dissolved in water, the nutrients travel freely.

“If you ever played with two magnets, you put the two negative ends together and they repel,” Debbie says. “You put a negative and a positive together, and they attach. So the anions stay in the water, and they travel all through the media, and they travel to the roots.”

If the roots pick up the nutrients, those nutrients go into the plant. If not, the nutrients keep moving, right out of the root zone, and eventually end up in a waterway, which explains nitrate pollution and phosphorus pollution.

Meanwhile, cations travel in water as well. They are in a salt form and are attracted to negative charges. 

“The more negative charges you have in your soil — the more organic matter, the more clay you have — the more of those nutrients you’re going to hold onto. And that’s great, but somehow they have to get to the plant too,” Debbie says.

One way this happens is when fresh water with no cations comes through. It knocks off the cations from the soil particle or organic matter, and hydrogen atoms take the cations’ place. “So the nutrient goes back into solution and travels to the plant,” Debbie says.

The other way plants can free the cations from the soil is to release exudates from their roots into the root zone. Positively charged exudates feed microorganisms and knock the nutrients off soil particles and organic matter. 

“This positive particle that came out of the plant attaches to the soil particle and lets the nutrition go back to the plant, so that’s the ‘exchange’ part,” Debbie explains. 

It gets more complicated than just positive charges and negative charges. Some particles have double-positive charges and some have triple-positive charges, and there is a hierarchy of which one is more powerful than the other, she says. 


Plant roots

Plants influence the soil and microorganisms in their root zone with their root exudates. (Photo Courtesy of Debbie Flower)


A Healthy Mix

Plants “know” which nutrients they need most, so they will release the exudates that will help them obtain the correct nutrients found in cations in the soil — assuming that nutrients are present in the soil. That’s why having a healthy soil mix with lots of organic matter leads to healthier, more vigorous plants. In healthy, organic soil, the nutrients are made available to the plant when the plant needs them. 

“It makes gardening so much easier,” Debbie says. “You don’t have to go out there and fertilize all the time. The plant and the soil are taking care of that. The organic matter is breaking down. And the other side of that is if you apply synthetic fertilizers, you can throw that whole balance off. You can cause nutrients that are attached to the soil particles — that the plant ultimately needs — to be displaced by the nutrients you decided to throw in the soil that aren’t necessarily what the plant needs.”

When the Organic Matter Level in Soil Is Too Much

If 5% organic matter content in soil is good, is 10 or 15% better? Well, no. Adding too much organic matter in soil can lead to more problems than it solves. 

The organic matter that holds onto nutrients the best is the very tiniest particles, the humus. But it takes a long time for humus to form. 

Too much organic matter can attract an abundance of unwanted insects. Earwigs, for example, eat organic matter and help it decompose, but if there are too many earwigs around, they may also devour your seedlings. 

Excess organic matter can also lead to waterlogging because of drastic differences in the texture of soil between the rootzone media and the texture of the soil below it. 

Debbie recalls attending a presentation by renowned gardener Rosalind Creasy, who wrote several books on edible landscaping. Rosalind explained that since she changed out her garden plants twice a year and added organic matter each time, it got to the point that her garden had too much organic matter, leading to fungal disease problems. 

Mineralizing Soil

A soil test can reveal if your soil is short of certain minerals or if the pH is not ideal for what you’re growing. Mineralizing the soil with soil amendments can resolve these issues.

You can add calcium to your soil, in the form of garden lime, to raise the pH, or add sulfur to make it more acidic. Greensand is another popular product to add minerals. But know that lime takes weeks to have an effect on plants, sulfur takes months and greensand takes years. 

Why Adding Sand to Clay Soil Is a Bad Idea

Because clay drains too slowly for a garden, it seems like adding fast-draining sand would resolve this issue. The problem with that idea is that clay plus sand equals concrete.

“The thing that you want to add to change your texture in your growing soil is organic matter,” Debbie says. “Organic matter opens up the clay, gives it better drainage.”

The organic matter can be turned in to add it to the soil, or, if you’re patient, it can be laid on the surface of the soil. Nature will take its course, integrating organic matter on top of the soil with the soil itself, but it will be years before the soil becomes noticeably different. 

At the other end of the spectrum is sandy soil. Water goes right through sand, and sand has fewer sites for holding cations, so it doesn’t hold nutrients well either. Rather than constantly adding fertilizer to keep your plants fed and watering frequently to keep the soil moist, amend the soil with organic matter to slow down drainage while also adding nutrients and improving nutrient retention.

How pH Influences a Plant’s Ability to Take Up Nutrients

Even when nutrients are present in the soil, they may not be readily available to plants if the soil pH is out of whack — meaning the soil is either too acidic or too alkaline. When the pH (“power of hydrogen”) is outside of the ideal range, certain nutrients become bound in soil.

Debbie explains that pH is a measure of the concentration of hydrogen ions in something. To test soil pH, the soil is added to pure water, and then the pH of that water is measured.

The pH scale ranges from 1 to 14, which each step denoting a 10-factor change. So the difference between a pH of 5 and a pH of 6 is a 10x difference, and the difference between a pH of 5 and a pH of 7 is a 100x difference.

The lower the number on the scale, the more acidic, and the higher, the more alkaline, or basic. A pH of 7 is considered neutral.

“You’re aiming for right around 7 because most of the nutrients that plants need are readily available to plants at that pH,” Debbie says.

There are acid-loving plants, such as blueberries, but generally speaking, the more that pH strays from neutral, the more plants struggle to get the nutrients they need. For example, when soil is too alkaline, iron becomes unavailable to plants. Debbie explains this is due to the presence of calcium, magnesium and sulfur in the soil that raise the pH. “The iron has gotten tied up in a molecule that the plant can’t absorb,” she says. 

Where Debbie lives in the West, it’s common for soil pH to be too high.  In areas where there is more frequent rain — like 40 inches of rain a year — the soil is more acidic because the rain brings acids from organic matter decomposition into the soil. “When you don’t have regular rain, you don’t have that regular acidification of your soil,” she says. 

Another interesting fact is that roots, through their exudates, can influence the pH in their root zone to make it more favorable for absorbing the nutrients they need. This ability is limited, and will not turn a pH of 9 into a 7, but it does highlight the importance of taking soil samples from the root zone for testing. 


soil tests

Soil tests will reveal your soil’s pH, which you can then change by adding soil amendments to ensure roots can readily take up nutrients in the soil.


How Phosphorus Builds Up in Soil

Phosphorus is an exception to the anion rule. It doesn’t move readily with water to the root zone. Debbie says this is because of the form of phosphorous. 

To overcome this, phosphorous in fertilizer is often chelated, meaning it’s wrapped in something else so it will travel more readily to the plant. But naturally occurring phosphorous just doesn’t travel that easily.

Phosphorus is used for energy in the plant and exists in every plant cell, Debbie points out. “If you’re adding compost, you’re adding plant cells, and those plant cells have phosphorus in them,” she says. And if the plants you are growing are not taking that added phosphorus out of the soil, the phosphorous can build up to an excessive level.

“There was a worldwide phosphorus shortage I can’t tell you how many years ago, and all of a sudden, because of that shortage, we learned we don’t need to apply as much phosphorus as we thought we did for plant production,” Debbie says. “And we’ve also realized that excess phosphorus in plant production can become a pollutant.”

The good news is when phosphorus is off-the-charts high on a soil test, the plants growing in that soil are not necessarily adversely affected.  

Establishment Irrigation

When plants are raised commercially in containers, the media that they grow in is usually 100% organic material — it’s not sand, silt and clay. In some cases, there may be a mineral component of perlite, vermiculite or sand, but container media is still worlds apart from the soil in the ground.

When we put that container-grown plant in a hole in the ground, we expect the roots to grow from that container mix into the field soil, but it doesn’t happen instantly. 

Because the container media is one texture and the field soil is a different texture, water will not move easily from one to the other. “So we need to irrigate that newly planted plant in a way that’s going to help it stay alive while it forces its roots into the field soil,” Debbie says.

For an experiment in Davis, California, Debbie planted hundreds of drought-tolerant shrubs that had been in 1-gallon containers, making sure that an inch of the container media stuck out of the ground because it is organic matter that will break down in time. (Planting high prevents the shrub from sinking and becoming the low spot in the field where water accumulates.)

When it was time to water the shrubs, Debbie followed the principle of establishment irrigation: She watered the container media (now in the ground) as needed and watered the field soil much less frequently. By practicing this method, all of the shrubs took to their new home successfully.

The reason this method worked is that the container media dried out faster than the field soil. Had she watered the container media and the field soil the same amount, the field soil would never dry down. And because the field soil would be wet all the time, the roots would not enter it. On the other hand, if she only watered the container media when the field soil was dry, it would not be enough to keep the container media adequately moist. 


In establishment irrigation, water the container media frequently and the field soil surrounding it sparingly.

In establishment irrigation, water the container media frequently and the field soil surrounding it sparingly. (Photo Courtesy of Debbie Flower)


I hope you enjoyed my conversation with Debbie Flower. If you haven’t listened yet, you can do so now by scrolling to the top of the page and clicking the Play icon in the green bar under the page title. 

Have you studied soil chemistry to become a better gardener? Let us know in the comments below.

Links & Resources

Some product links in this guide are affiliate links. See full disclosure below.

Episode 028: The Role of Minerals in Making Great Soil

Episode 116: Understanding the Soil Food Web, with Dr. Elaine Ingham

Episode 153: The Science Behind Great Soil

Episode 223: How Soil Microbes Make Good Soil Great

Episode 282:The Vital Role of Soil Bacteria in the Garden, with Jeff Lowenfels

joegardener TV YouTube: How to Get the Best Drainage for Your Container – And Why What You’ve Been Taught Is All Wrong

joegardener Online Gardening Academy™: Popular courses on gardening fundamentals; managing pests, diseases & weeds; seed starting and more.

joegardener Online Gardening Academy Organic Vegetable Gardening: My new premium online course membership opens in 2023. Sign up for the waitlist here.

joegardener Online Gardening Academy Beginning Gardener Fundamentals: Essential principles to know to create a thriving garden.

joegardener Online Gardening Academy Growing Epic Tomatoes: Learn how to grow epic tomatoes with Joe Lamp’l and Craig LeHoullier. 

joegardener Online Gardening Academy Master Pests, Diseases & Weeds: Learn the proactive steps to take to manage pests, diseases and weeds for a more successful garden with a lot less frustration. Just $47 for lifetime access!

joegardener Online Gardening Academy Perfect Soil Recipe Master Class: Learn how to create the perfect soil environment for thriving plants.

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Disclosure: Some product links in this guide are affiliate links, which means we get a commission if you purchase. However, none of the prices of these resources have been increased to compensate us, and compensation is not an influencing factor on their inclusion here. The selection of all items featured in this post and podcast were based solely on merit and in no way influenced by any affiliate or financial incentive, or contractual relationship. At the time of this writing, Joe Lamp’l has professional relationships with the following companies who may have products included in this post and podcast: Rain Bird, Corona Tools, AeroGarden, Milorganite, Soil3, Greenhouse Megastore, PittMoss, Territorial Seed Company, Earth’s Ally, National Wildlife Federation and TerraThrive. These companies are either Brand Partners of and/or advertise on our website. However, we receive no additional compensation from the sales or promotion of their product through this guide. The inclusion of any products mentioned within this post is entirely independent and exclusive of any relationship.

About Joe Lamp'l

Joe Lamp’l is the creator and “joe” behind joe gardener®. His lifetime passion and devotion to all things horticulture has led him to a long-time career as one of the country’s most recognized and trusted personalities in organic gardening and sustainability. That is most evident in his role as host and creator of Emmy Award-winning Growing a Greener World®, a national green-living lifestyle series on PBS currently broadcasting in its tenth season. When he’s not working in his large, raised bed vegetable garden, he’s likely planting or digging something up, or spending time with his family on their organic farm just north of Atlanta, GA.

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