![\"Copy](\"https:\/\/understandingag.com\/wp-content\/uploads\/2026\/07\/Copy-of-The-Nutrient-Cycle-Pt-4.png\" "\\"Copy")
\n\t\t\t\t\t<\/div>\n<\/figure>\nWhat We Learned in Part 4<\/b><\/h2>\n
In Part 4 of this series, we pulled back the curtain on how nutrients actually move through an ecosystem. We distinguished organic nutrients from inorganic ones and showed how they constantly shift between the two. We explored immobilization (nutrients getting locked up inside living tissue) and mineralization (nutrients being released back into available forms), and why healthy soils need a steady balance of both. Finally, we challenged two widely held assumptions: that plants can only absorb inorganic, water-soluble nutrients, and that synthetic fertilizers directly feed plants. The evidence says otherwise. Plants readily absorb amino acids, intact proteins, and even whole microbes. In fact, 40-60% of fertilizer nutrients never reach the plant in the year they’re applied, because the natural nutrient cycle, not the fertilizer bag, does most of the heavy lifting. The golden rule: <\/span>microbes eat first.<\/b><\/p>\n That brings us to the most important question in this whole series: who are the stars of this show? In Part 5, we introduce the biological players that make nutrient cycling actually work. From mycorrhizal fungi that extend a plant’s root system far beyond what it could reach alone, to the newly discovered rhizophagy cycle, where plants actively “farm” microbes for nutrients. The Soil Food Web is the engine behind everything we’ve covered so far. Understanding it is the key to unlocking the fertility that’s already sitting in your soil.<\/span><\/p>\n Missed part 4? Check it out <\/span>here<\/span><\/a>.<\/span><\/p>\n Nutrients become available to plants through two broad pathways: abiotic (non-living) and biotic (living) processes.<\/span><\/p>\n Abiotic pathways include the weathering of rocks by<\/span> carbonic acid<\/span><\/a> (formed when carbon dioxide mixes with water), along with glaciers, lightning, volcanic activity, and pressure. Some of these processes move quickly, but most take decades or centuries to make a meaningful contribution to the pool of plant-available nutrients.<\/span><\/p>\n Biotic activity is a different story entirely. Living organisms cycle nutrients on a timescale of minutes, days, and weeks. That speed isn’t luck or chance! It’s one of the defining features of life itself. Every organism needs a constant supply of energy and raw material to build and maintain its cells right here and right now. In other words: every living thing eats and excretes. No exceptions.<\/span><\/p>\n Life on Earth has been categorized into six large groups, called kingdoms. Each is defined by distinct cellular structures and modes of survival.\u00a0<\/span><\/p>\n Archaebacteria<\/b> Eubacteria<\/b> Protists<\/b> Fungi<\/b> Plants<\/b> Animals<\/b> This all might seem complex, but it\u2019s actually pretty simple when you zoom out. Every organism on Earth survives by taking in outside resources and converting them into usable energy and the building blocks for its own body. The authors of<\/span> Principles and Applications of Soil Microbiology<\/span><\/i><\/a> put it well: “The overall goal of all forms of metabolism (biological activities) is essentially the same – to obtain energy and carbon needed for the production of cellular constituents necessary for growth, survival, and reproduction… the metabolic diversity among microorganisms comes down to differences in strategies rather than the goals of these strategies.”<\/span><\/p>\n<\/div>\n Sometimes an organism gets ahead by competing with its neighbors for resources. Other times, it’s more profitable to team up and share. The late soil scientist Dr. Elaine Ingham calls the sum total of these relationships the “<\/span>Soil Food Web<\/span><\/a>“. \u201cFood web” is a far better phrase than “food chain,” because nutrient cycling isn’t linear. It’s circular. Organisms at the “top” are eventually broken down by decomposers at the “bottom,” closing the loop. The nutrients locked inside something eventually become food for something else, whether eaten directly or from something else consuming its nutrient-rich waste. This incessant consumption-waste-growth-waste cycle is one of the most important processes that move nutrients around a landscape and makes our planet habitable in the first place. And, it turns out, the smallest among us are the most important players in this great cycling of nutrients.<\/span><\/p>\n<\/div>\n To understand how something as small as a microbe can be so important to life on Earth, you have to think about life from a microscopic point of view, not from ours. It\u2019s a microbial world and we\u2019re just livin\u2019 in it.<\/span><\/p>\n Microbes are everywhere. They are hardy, they are highly adaptable and they reproduce astonishingly fast. Some bacteria can double in population size roughly once every 20 minutes, viruses even faster<\/span>21<\/span>. Compare that to humans, who might reproduce once or twice by age 30. That reproductive speed doesn’t just grow microbial populations quickly. It also raises the odds of beneficial mutations appearing and spreading. On top of that,<\/span> epigenetic<\/span><\/a> and<\/span> quorum sensing<\/span><\/a> regulation lets individual microbes switch genes on and off to adapt to changing conditions, while<\/span> horizontal gene transfer<\/span><\/a> lets microbes share useful genetic information from organism to organism with no reproduction required. Genius! If something works, it can spread and it can spread very quickly.\u00a0<\/span><\/p>\n It’s no surprise, then, that microbes have figured out how to make a living in nearly every environment on Earth with their various levels of available nutrients.<\/span><\/p>\n<\/div>\n If microbes can conquer landscapes from chilly mountaintops to underwater steaming-hot thermal vents, imagine what they do in a temperate, moist environment loaded with resources, constant moisture, and an ideal temperature. In many ways, healthy soil is exactly that: an optimum environment chock-full of resources and moisture in a moderate temperature range. For this reason, among others, some estimates suggest nearly 60% of all life on Earth lives in the soil, and microbes make up the overwhelming majority of that diversity.<\/span>22\u00a0<\/span><\/p>\n This diversity is crucial to nutrient cycling because every species carves out its own niche by extracting energy from a specific resource.<\/span> Diazotrophic<\/span><\/a> microbes, for example, pull nitrogen gas out of the air and convert it into ammonia or ammonium, which are forms life can actually use. That newly available nitrogen then supports other microbes that have carved out a niche in pulling phosphorus out of rock, and still others that do the same for potassium<\/span>23<\/span>, sulfur<\/span>24<\/span>, calcium<\/span>25<\/span>, silicon<\/span>26<\/span>, on and on. As these microbes die or get eaten, the nutrients they built into their bodies re-enter circulation within the food web.\u00a0<\/span><\/p>\n And here’s the encouraging part: most nutrients, including phosphorus and potassium, are already abundant in soil. They’re just locked in inaccessible forms. As researchers studying phosphorus availability note, phosphorus is “abundant in soils,”<\/span>27<\/span> and potassium is described as “an abundant element present in the soil but in an inaccessible form.”<\/span>28<\/span> The fertility is already there. The job is unlocking it and cycling it.\u00a0<\/span><\/p>\n If you want this system of nutrient cycling to run efficiently, you have to keep feeding it. Without a steady food supply, hungry microbes will burn through soil organic matter faster than it gets replenished. Kentucky farmer Jesse Frost of <\/span>The No-Till Growers<\/span><\/i><\/a> pithily puts it, \u201cIf the soil is not being fed, the soil will feed on itself.\u201d<\/span><\/p>\n And how do we feed the underground herd? Amendments like compost and manure certainly help when applied thoughtfully, but the single most effective way to feed soil biology is by growing a plant. It sounds too simple, but it is true. More photosynthesis occurring on the landscape means more organic matter to feed the underground herd, as the fixation of CO<\/span>2<\/span> into glucose is the origin of all organic matter\/humus.\u00a0<\/span><\/p>\n This is a very important reason why “keeping a living root in the soil for as long as possible throughout the year” is one of the <\/span>six principles of soil health<\/span><\/a>. Living plants are the bottleneck that transforms solar energy into a form that all other life forms can use. That energy, then, is what powers the furious pace of biological nutrient cycling, a process which benefits every organism in the system, plants most of all.<\/span><\/p>\n Plants have developed close relationships with the microbial communities that surround them on their leaves, stems, roots, and even inside their tissue. The zone of interaction between plants and microbes above ground is called the “<\/span>phyllosphere<\/span><\/a>“; below ground, it’s the “<\/span>rhizosphere<\/span><\/a>.” Microbes that live inside plant tissue are called “<\/span>endophytes<\/span><\/a>.”<\/span><\/p>\n<\/div>\n The vast majority of <\/span>archaea<\/span><\/a>, bacteria, protists, fungi<\/span>,<\/span> and small animals associated with plants are neutral or beneficial for nutrient acquisition, even in the phyllosphere, where some leaf-dwelling microbes fix nitrogen from the air, much like the bacteria that partner with legumes.<\/span>29 <\/span>Unfortunately, the phyllosphere remains the least-studied of these relationships, so there’s still a lot of room for research, especially as foliar feeding grows in popularity. For now, we’ll focus on what’s best understood: the rhizosphere and endophytic relationships.<\/span><\/p>\n The rhizosphere is technically just the 2-3 mm zone surrounding a root, but don’t let the small size fool you. It may be the most complex ecosystem on the planet.<\/span>30<\/span> Life, death, consumption, competition, cooperation, and constant information-sharing all happen here, every day, right beneath a farmer’s boots. Many regenerative producers describe a genuine sense of awe the first time they understand what’s happening underground and that awe tends to translate into a real sense of responsibility to protect it, which is both an ecologically sound and economically smart long-term strategy.<\/span><\/p>\n We all know that roots have the ability to absorb, which can drain an area of its easily available nutrients and water. What many people don\u2019t know is that roots can also exude compounds from inside out. Plants exude organic acids and other compounds to release additional nutrients from nearby minerals and organic matter that are physically and chemically more protected. While this increases access to what they need, roots still need outside help to acquire everything they need to nourish themselves. Enter, microbes.<\/span><\/p>\n Microbes, namely viruses (sort of! Viruses, by definition, are not living creatures), archaea, bacteria, fungi<\/span>,<\/span> and protists, are like any good employee. In order to bring nutrients and water to the plant, they expect to get paid for their labors, and plants do pay generously. Plants feed microbes both passively (sloughed-off root cells and the mucus-like substance that eases root growth through soil) and actively (targeted exudates that recruit specific microbial species depending on the plant’s needs at that point in its life cycle). As a result, the rhizosphere hosts 10-50 times more bacteria and 5-10 times more fungi than soil away from the roots.<\/span>31<\/span><\/p>\n<\/div>\n In exchange, plants receive nutrients they couldn’t easily mine themselves. As mentioned earlier, all kinds of microbes have carved out niches making different minerals plant-available. Nitrogen-fixing partnerships legumes and rhizobia, as well as free-living diazotrophs like<\/span> Azotobacter<\/span><\/i><\/a>,<\/span> Clostridium<\/span><\/i><\/a>, and<\/span> Azospirillum<\/span><\/i><\/a>, are another well-known example. Certain strains of <\/span>Bacillus<\/span><\/i>, <\/span>Pseudomonas<\/span><\/i>, <\/span>Burkholderia<\/span><\/i>, and <\/span>Acinetobacter<\/span><\/i> can increase zinc and iron availability for crops like mung bean, rice, and corn.<\/span>32<\/span>\u00a0 The same is true for every nutrient.\u00a0<\/span><\/p>\n So, suffice it to say, more life means more nutrients become available to plants in the immediate rhizosphere.<\/span><\/p>\n The Rhizophagy Cycle: How Plants Farm Their Own Microbes<\/b><\/p>\n In one of the more exciting discoveries in soil biology, research now shows plants actively consume microbes from the rhizosphere for nutrition. Dr. James White and his team at Rutgers University were the first to detail this process. They called it the “rhizophagy cycle” (“rhizo” = root, “phagy” = eat) in 2018, and it has reshaped how scientists think about soil biology and plant nutrition.<\/span>33<\/span><\/p>\n Root hairs, then, aren’t just specialized cells for absorption. Water and nutrient absorption through root hairs may actually be a secondary benefit of this process, not its original purpose. Arguably the main purpose of them is to eject colonies of microbes back into the soil. The image below from Dr. James White shows the abundance of root hairs with and without bacteria present.\u00a0<\/span><\/p>\n<\/div>\n Not so long ago, almost no one would have guessed that plants “farm” their own microbes for nutrients, but the evidence is mounting that this is certainly the case.<\/span><\/p>\n The million dollar question that producers need answered is whether or not the rhizophagy cycle supplies a good amount of nutrients to plants. If it doesn\u2019t supply a significant amount, then it\u2019s a fun story that doesn\u2019t help much (from a production standpoint). It\u2019s still early days, but initial research by Dr. White and his lab suggest that grass plants acquire 30% of their nitrogen from the rhizophagy cycle.<\/span>34<\/span> His research also suggests that absorption of metal elements like zinc, copper, iron<\/span>,<\/span> and magnesium from microbes is an important benefit of the rhizophagy cycle. Stay tuned, because future results might surpass our wildest expectations.<\/span><\/p>\n For further information on the rhizophagy cycle, check out <\/span>this great talk by John Kempf<\/span><\/a> at the National No-Till Conference. John explains how he regularly sees producers cut their nitrogen bill by 30-70%, and in some cases 100%, by maximizing biological nutrient cycling. Of course, this is anecdotal, but there\u2019s no reason it couldn\u2019t be true given everything we\u2019ve learned so far. <\/span>Teaming<\/span> with Bacteria<\/span><\/i><\/a>Meet the Underground Herd<\/b><\/h2>\n
Abiotic vs. Biotic Nutrient Cycling<\/b><\/h3>\n
The Six Kingdoms of Life<\/b><\/h3>\n
\n<\/span>These are single-celled organisms lacking a nucleus that thrive in extreme environments like hot springs, deep-sea vents, and salt lakes, often using unusual metabolic pathways to survive. Even so, many are found in the soil and play a role in nutrient cycling!\u00a0<\/span><\/p>\n
\n<\/span>Closely related to Archaebacteria, but distinct enough are the Eubacteria, or true bacteria, which are also single-celled.\u00a0<\/span><\/p>\n
\n<\/span>Next, we move to organisms with a nucleus and other membrane-bound organelles. These organisms are termed the \u201ceukaryotes\u201d, while archaebacteria and true bacteria are termed \u201cprokaryotes.\u201d The Protists form a highly diverse group of mostly single-celled organisms, such as amoebas and algae, that don’t fit neatly into the other kingdoms.\u00a0<\/span><\/p>\n
\n<\/span>The Fungi, which include single-celled yeasts, molds, mushrooming species, and non-mushrooming species like the oft-discussed mycorrhizal fungi we will discuss later at length.\u00a0<\/span><\/p>\n
\n<\/span>These are multicellular organisms that produce their own food through photosynthesis, forming the foundation of most terrestrial ecosystems.\u00a0<\/span><\/p>\n
\n<\/span>Finally, the Animals are multicellular eukaryotic organisms that obtain energy by consuming other organisms and are typically capable of movement at some stage of their lives. <\/span><\/p>\n<\/div>\n![\"6](\"https:\/\/understandingag.com\/wp-content\/uploads\/2026\/07\/6-kingdoms-of-life.png\" "\\"6")
\n\t\t\t\t\t<\/div>The Soil Food Web<\/b><\/h3>\n
![\"The](\"https:\/\/understandingag.com\/wp-content\/uploads\/2026\/07\/The-soil-food-web.png\" "\\"The")
\n\t\t\t\t\t<\/div>![\"Soil](\"https:\/\/understandingag.com\/wp-content\/uploads\/2026\/07\/Soil-Food-Web-2.png\" "\\"Soil")
\n\t\t\t\t\t<\/div>Why Microbes Are Built for This Job<\/b><\/h2>\n
![\"Gene](\"https:\/\/understandingag.com\/wp-content\/uploads\/2026\/07\/Gene-Transfer.png\" "\\"Gene")
\n\t\t\t\t\t<\/div>The Rhizosphere: Where Plants and Microbes Strike a Deal<\/b><\/h2>\n
Feeding the Underground Herd<\/b><\/h3>\n
Teaming Up<\/b><\/h3>\n
![\"Rhizosphere](\"https:\/\/understandingag.com\/wp-content\/uploads\/2026\/07\/Rhizosphere-Phyllosphere.png\" "\\"Rhizosphere")
\n\t\t\t\t\t<\/div>How Plants Feed Microbes And Get Paid Back in Nutrients<\/b><\/h3>\n
![\"Rhizosphere\"](\"https:\/\/understandingag.com\/wp-content\/uploads\/2026\/07\/Rhizosphere.png\" "\\"Rhizosphere\\"")
\n\t\t\t\t\t<\/div>How the Rhizophagy Cycle Works, Step by Step<\/b><\/h3>\n
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![\"Rhizosphagy](\"https:\/\/understandingag.com\/wp-content\/uploads\/2026\/07\/Rhizosphagy-Cycle.png\" "\\"Rhizosphagy")
\n\t\t\t\t\t<\/div>![\"root](\"https:\/\/understandingag.com\/wp-content\/uploads\/2026\/07\/root-hair.png\" "\\"root")
\n\t\t\t\t\t<\/div>Nutrient Acquisition by the Rhizophagy Cycle<\/b><\/h3>\n