4 Ecosystem Processes: Community Dynamics
(Part 1)

Succession (No, Not the HBO Series)

In 1687, mathematician Sir Isaac Newton published the Philosophiæ Naturalis Principia Mathematica (Mathematical Principles of Natural Philosophy) which described the laws of motion for objects and systems. Newton’s first law of motion states that an object in motion tends to stay in motion unless acted upon by outside forces. Similarly, an object at rest tends to stay at rest unless it is acted upon by an outside force. This is known as the Law of Inertia. Earth, along with the natural systems contained within it, are in constant motion so they obey the Law of Inertia. In fact, every second of every day on Earth can be thought of as an invisible battle between natural systems that are trying to keep the ball of life rolling and outside forces that are trying to bring them to a stable resting point. Stability and uniformity can be good qualities, but too much of a good thing is a bad thing in this case. When everything is the same and extremely stable, there are no gradients for energy to make anything happen. Many scientists believe this is the inevitable fate of the universe, thanks to entropy. Thankfully, that’s billions of years in the future. For now, we living organisms have a powerful weapon in our arsenal to fight against the forces seeking to create a uniform world where nothing happens anymore. That weapon is food. 


Food is simply a concentrated piece of energy and nutrients that living organisms internalize and use to their benefit. Our human digestive systems are designed to absorb nutrition from things like strawberries, sandwiches, salads and soups. Not everyone is like us, though. If you asked many types of microbes what they think food is, you’d look ridiculous because they can’t understand you. Despite this lack of communication, we know through observation that some microbes gain their nutrition from the energy and nutrients contained within rocks. Thank goodness for them because barren landscapes like rock faces or deserts are examples of systems largely “at rest”, biologically speaking. The compounds that make up the rocks and desert sands are chock full of energy and nutrients, but they are in very stable bonds with each other and are quite happy to remain in their current form. Therefore, it takes an outside force to break the compounds apart and get them moving into and out of the bodies of living organisms. In nature, this outside force is often the powerful chemical compounds produced by microbes.


The first organisms to extract energy and nutrients from an environment are called “pioneer species”. Examples include bacteria, fungi, lichens, mosses and others that multiply quickly after colonizing previously lifeless conditions. Given enough time, the pool of energy and nutrients that are bioavailable (available for living organisms to consume and use) will increase, which allows the system to support more complex forms of life. This process is called “ecological succession“. There are two categories of ecological succession. The first is “primary succession“, which describes the initial transformation of a lifeless habitat, such as the colonization of bare rock by microbes. “Secondary succession” refers to the transformation of a previously living habitat after a major disturbance, such as a forest recovering from a fire. In both cases, succession can be thought of as the invisible hand that moves a habitat’s composition toward intermediate species and a final “climax community“, such as grassland, savanna or forest communities. Annual rainfall is a key variable determining the composition of the climax community, with higher humidity and rainfall encouraging climax communities with trees and drier regions encouraging the formation of grasslands.

Primary succession refers to the initial transformation of a lifesless environment. Observe that soil depth increases over time.
Secondary succession refers to the transformation of a previously living environment after a major disturbance. Again, observe that soil is built as time passes and plant communities grow.

To better understand succession, let’s look at the youngest piece of land on planet Earth. On October 14, 1963, a volcanic eruption off the southern coast of Iceland became noticeable on the surface. The volcanic eruption began at 426 feet below sea level. It wasn’t until June 5, 1967 that the eruption ended, leaving Surtsey Island to cool and become the 0.50 square mile piece of real estate we see today. Volcanologists, botanists and ecologists have been studying it rigorously to understand how ecosystems develop from scratch. The images below show just how quickly succession proceeded on the once barren, steaming piece of exposed lava rocks. According to UNESCO, “Since they began studying the island in 1964, scientists have observed the arrival of seeds carried by ocean currents, the appearance of moulds, bacteria and fungi, followed in 1965 by the first vascular plant, of which there were 10 species by the end of the first decade. By 2004, they numbered 60 together with 75 bryophytes, 71 lichens and 24 fungi.”1

Surtsey Island on November 30, 1963, 16 days after the eruption reached the surface. Photo credit: Howell Williams.
Surtsey Island in 2018, 51 years after the eruption ended. Notice the successionary process taking place at different rates on different parts of the island.

Succession isn’t just a topic for biologists and ecologists. It’s a relevant agricultural point of emphasis. First and foremost, the soil that we all depend on is a product of succession. David Montgomery, geologist turned regenerative advocate, writes in The Hidden Half of Nature that, “Soil is curious stuff, part mineral and part organic, a weathered blanket of rotten rock and dead things. With a typical thickness of less than three feet, soils vary depending on the bedrock, climate, topographic position, and vegetation.” Rotten rock is a beautiful description of how biotic and abiotic forces wear down parent material into sand, silt and clay. Pioneer species speed up the process exponentially as they extract energy and nutrients contained within the parent material and bring them into the realm of the living. The carcasses of these heroes pile up over time and become nearly half of the organic matter in the soil.2 Available fertility, energy and water build up over time as soil minerals and organic matter accumulate, allowing land that was once barren or disturbed to become fertile soil able to support increasingly complex ecosystems teeming with life.


Understanding this process helps farmers, ranchers and advisors design management systems that mimic natural succession and reap the benefits it provides. One such benefit is a buildup of soil over time, rather than it eroding away. From a business standpoint, losing topsoil is costly because it is the most fertile, microbially-active and, consequently, productive portion of the soil profile. From a macro-geological standpoint, human civilization simply can’t afford to lose fertile soil year after year, decade after decade. To put into perspective just how thin the supply of soil is, three feet of soil depth (on average) out of the 4,025 miles to the center of the Earth represents 0.000014% of the planet’s radius. This means the layer that sustains all life and human civilization as we know it is equivalent to a sheet of paper on top of 3.32 Eiffel Towers. That’s all that separates us from starvation and extinction. It’s a sobering thought, but it’s one that should engender a desire to protect and build up this life-sustaining layer by mimicking the succession process that built it in the first place.


The fact is that all soils began as bare rock at one point in time. Succession driven by biology built soil upward from the rocky surface into what we see today. Many North American and European farmers are blessed with deep soils above the layer of parent material, so it’s not inherently obvious that the soil is 1) a thin layer and 2) was built up from rock over long stretches of time. However, this is the story of every soil on Earth, even the deepest and most fertile. No matter where you find yourself, the soil is like a thin layer of frosting on top of a thick, rocky cake. To visualize this concept, I’ve added pictures of soil on top of underlying rock from my travels to other countries. Each picture tells a unique story of how succession and the drift toward more complex communities happened in that location. Although the details are unique, it is the same basic process that built soil in each location, as well as everywhere else on the planet. The universal methods of succession that build soil up from bare rock are captured in the Six Principles of Soil Health and the Three Rules of Adaptive Stewardship, which is why they are applicable to every operation, no matter the location. What differs is the specific implementation of the methods to fit the individual operation’s context

The Cliffs of Moher in Ireland offer a unique cross-sectional view that shows how thin the layer of soil and plant life are compared to the rocky foundation underneath.
A similar illustration was observed in Helsinki, Finald. Notice the mosses and patches of white and red lichen growing on the rock, slowly bringing energy and nutrients to life.
Sheep grazing on grass growing in extremely thin soils on a cliffside in central England.
A thin layer of soil on top of rock is enough to support the growth of plants in Plitvice National Park in Croatia.

To summarize, soil is largely a byproduct of biological activity. More biological activity means more soil is built. Just how quickly can soil actually be built? That question deserves a standalone article, which you can read by clicking here. In short, it does not take a hundred years or more to build an inch of topsoil IF there is active biology present. In an agricultural setting, the biggest influence on biological activity is our management, which can either speed biology up or slow it down. Taken to the extremes, long-term management practices are powerful enough to build soil, promote succession and regreen a desert or slow biological activity and desertify a fertile piece of land. This is why I believe it’s helpful to think about inertia. Our management practices are like the outside force that determine whether the biological system in motion speeds up or slows down. Recall that the odds are already stacked against us because there are always outside forces present that are constantly working to transform compounds and ecosystems into stabler, slower moving forms. Our job is to ensure that the ecosystems our farms and ranches are built upon have enough resources to overcome these forces and remain complex. After all, the living creatures that comprise ecosystems are made up of complex, unstable compounds formed by reactions that are extremely unlikely to happen on their own. We need to make sure that our management practices promote more of these unfavorable reactions, not fewer. (Unfavorable, in this case, refers to a reaction that does not happen spontaneously. Energy needs to be added to make them happen, like rolling a ball up a hill until it reaches the peak where it can roll down the other side on its own. Unfavorable reactions speak nothing of whether they are “good” or “bad”.)


One unfavorable reaction we want to encourage is the fixation of the dinitrogen (N2) gas that makes up 78% of the air.  Natural processes led to this incredibly stable compound which is happy to remain as N2 for decades. This is a huge problem for living organisms because Nitrogen is needed in large quantities, as it is a key constituent of proteins and genetic material. For this reason, Nitrogen is often the nutrient that limits biological activity in nature. So, how did living organisms solve this problem? Enzymes. Enzymes make chemical reactions happen millions of times faster than they would occur on their own, such as the breaking apart of N2. This reaction is facilitated by a microbial enzyme called nitrogenase. Chemists still don’t fully understand how nitrogenase is able to separate N2 so efficiently. This is why we still have to unlock Nitrogen by brute force in fertilizer factories. In those factories, N2 gas is heated up to 300 degrees Celsius and compressed 200-300 times normal atmospheric pressure. Only then will the two Nitrogen atoms release their grip from one another. The Haber-Bosch process, as it known, is so energy intensive that it makes up 1-2% of the world’s energy use.3 Miraculously, nitrogenase produced by single-celled microbes is able to fix Nitrogen into bioavailable ammonia (NH3) at moderate outdoor temperatures and normal atmospheric pressure. Plants that associate directly with Nitrogen-fixing microbes have a distinct advantage in nature, which is why species like clovers and red alder trees are are often among the first pioneer species on the succession timeline that reappear after a major disturbance. A common example you can see for yourself is an area that has heavy foot or vehicle traffic. Oftentimes clovers will be the first plant species to dominate if further disturbances are held to a minimum. The picture of clover below shows this exact situation.

Clover thriving on a previously bare patch of ground caused by heavy foot traffic in central England.
Red alder trees house Nitrogen-fixing bacteria in root nodules. Because of their ability to receive Nitrogen directly from bacteria, red alders are often the first tree species to grow in disturbed or heavily eroded land in the Pacific Northwest of North America.

Plants that associate with Nitrogen-fixing microbes increase the pool of available Nitrogen in the soil through their exudates and decomposing tissue. The soil is now able to support organisms that can’t fix their own Nitrogen, like grasses. Similar situations are observed with other nutrient deficiencies, not just Nitrogen. For instance, crabgrass and dandelions grow well in Calcium-deficient soils and release available Calcium throughout their life cycle.4 In addition to nutritional deficiencies, poor soil structure also gives certain plants a competitive advantage over others. Knotweed, plantain and quackgrass are examples of plants that outcompete others in compacted soils. This is why diversity is so important to soil health and succession. Every microbe, plant and animal has a unique nutritional composition that adds to the total pool of available nutrients which improves soil structure through increased biological activity. Better nutrient balance and soil structure creates healthier conditions for life to cycle energy, nutrients and water more efficiently. Talk about positive compounding and cascading effects!


As succession proceeds, height becomes a more important competitive advantage for plant species in crowded conditions, assuming no major disturbances that reset the succession clock. Regions with adequate rainfall support the growth of extremely tall plants like trees, while lower rainfall regions can only support shorter woody species, grasses and forbs. Factors like altitude, sunlight and temperature affect the composition of climax communities as well, but precipitation is the most important factor, as you can see from the maps below.
Climax plant communities of the U.S.
Lower 48 precipitation amount. Notice the stark contrast in precipitation between regions east and west of the Great Plains (Dakotas, Nebraska, Kansas, Oklahoma and Texas).

Just like a good friend after a bad breakup, succession tells us that everything happens for a reason. Species only survive and reproduce when the conditions are right for them in that time and place. There are thousands of variables that determine the livability of an ecosystem. A simple, yet important example is the level of oxygen in the air. Humans would not be able to survive if atmospheric oxygen levels suddenly disappeared. The same demise of all other oxygen-dependent organisms would be met if oxygen were no more. This singular change in conditions greatly affects who can survive and who can’t. As it turns out, less developed ecosystems, such as bare rock or a charred forest, share common conditions that make certain strategies work better than others. These are the strategies that pioneer species use at the beginning of succession. Pioneer species eventually change environmental conditions so much that other strategies become a competitive advantage. Intermediate species and climax community species tend to deploy these strategies as they strive to survive in a more developed ecosystem. Read on to learn about these strategies and how our management practices create the conditions that incentivize them.

Survival of the Strategies

The desire to reproduce is a ubiquitous trait among populations of organisms. This makes sense because a species that doesn’t care to reproduce would last approximately one generation. What’s interesting is that the universal desire within microbes, plants and animals to pass on their genes is driven by signals contained within the genes themselves. However, reproduction cannot happen out of thin air. The appropriate resources must be available and they must be utilized by an organism for offspring to be produced. The manner in which organisms deploy take advantage of available resources and local environmental conditions differs greatly. Similarities can be drawn from sports, war and business. The overarching goals are shared between groups (win the game, win the war or outlast business competitors), but the strategy to achieve each of these goals varies tremendously between groups. For example, some basketball teams prioritize hard-nosed defense, while others prioritize flashy offense to win the championship. Theoretically, the best strategies are preserved over time because they outlast other strategies. This is ecology in a nutshell. Ecologists study how populations and individuals compete and collaborate with one another as they work to pass on their genes to the next generation. Although reproductive strategies are unique, ecologists are able to place species onto a spectrum of strategies, based on certain shared traits. Organisms that fall on one side of the spectrum are called “r-strategists“, while organisms on the other half are called”k-strategists“.


The “r” in r-strategist stands for reproduction. These organisms think that having one kid at a time seems like a risky plan, which makes sense because their genes die out if that child doesn’t survive to reproduction. So, r-strategists spend their reproductive energy on the production of huge numbers of offspring. It’s nature’s version of not putting your eggs in one basket. The drawback is that energy and nutrients are spread between many individuals, making each individual relatively weak. Because of this, a good portion of offspring die before they themselves reproduce. R-strategists don’t mind because it’s all part of the plan. Only a small percentage of their babies need to survive and reproduce to cause the population to rise quickly.


What kind of situation could possibly warrant this irresponsible parental behavior? It turns out that this strategy is particularly well-suited in conditions that are resource-poor, low competition and/or out-of-balance, such as bare rock or a charred forest after a major fire. Not many organisms can reliably reproduce in these harsh environments, so r-strategists’ shotgun approach gives them a huge competitive advantage. The more offspring for them, the more likely a few will survive to sexual maturity. If you’re thinking that this sound suspiciously similar to the description of pioneer species, your hunch is correct. Pioneer species are most often r-strategists because they deploy these reproductive strategies.


Other traits that help r-strategists pass on their genes include the tendencies to mature quickly, to reproduce at a young age and to have very short gestation periods. All of these factors result in the defining characteristic of r-strategist populations: quick exponential growth, meaning it takes them a very short amount of time to take their population size to tremendous heights. This flash-in-the-pan growth is unsustainable as the population outpaces available resources. The population of these species will subsequently crash and yo-yo up and down wildly throughout time. The capricious nature of r-strategist populations is a crazy ride, but it’s an important first step toward improving energy, nutrient and water cycling in the local environment. They essentially set the table for more diverse forms of life to survive as long as there are no further disturbances that reset the succession clock. Examples of r-strategists include bacteria, mosses, insects, oysters, salmon and rodents.5

Seeds production per plant of various r-strategist species. Courtesy of Robert Norris, PhD.
Corn rootworm eggs. A female may lay an average of 500 eggs over several weeks in clutches of about 80 eggs.

The important takeaway from an agricultural point of view is that the organisms we consider pests, namely disease-causing microbes, crop-munching insects and yield-robbing weeds, tend to be r-strategists/pioneer species. Their job isn’t to make the lives of farmers and ranchers miserable. It’s actually to colonize a system that’s out-of-whack, create some semblance of order and set the table for other species to move in and join them. This is the real first step on the road to minimizing pest outbreaks permanently without tillage and pesticides. As Sun Tzu, author of the 5th century B.C. classic The Art of War, said, “If you know the enemy and know yourself, you need not fear the result of a hundred battles.”6 Let’s take a couple of examples. We know that pigweed is well adapted to grow and produce up to 117,000 seeds per plant7 in compacted soils with low competition. Similarly, thistles prefer “overused and otherwise disturbed land.”8 As for insects and microbes, their bread and butter is targeting unhealthy plants and animals.9,10 With this knowledge in hand, farmers and ranchers can deter and even prevent detrimental pest outbreaks by promoting the opposite conditions that naturally lead to their domination. In the landscape, opposite looks like a well-aggregated soil with minimal compaction that supports a rich, diverse biological community who keep the pest in check and continue to positively influence the cycling of energy, water and nutrients. Therefore, it’s critically important that farmers and ranchers find ways to minimize disturbances like tillage and pesticide applications that leave the soil bare, create compaction, reduce diversity and hinder energy, nutrient and water cycling. Disturbances like these have their use in the short-term, but the long-term effect is that they continually reset the succession clock back to the point where r-strategists, like pigweed, thistles, aphids and grasshoppers, thrive.11 In living organisms, opposite looks like healthy individuals with strong innate and adaptive immune defense systems and a rich, diverse microbiome.


Now, let’s assume a farmer or rancher heeded this advice and did not reset the succession clock of their field or pasture. They implemented practices like adaptive multi-paddock (AMP) grazing, minimized tillage passes and planted cover crops between their cash crops. As r-strategists reproduce and improve the natural system, k-strategists eventually show up and join the party. “K”, in this case, is the abbreviation for a term called “carrying capacity“. Carrying capacity refers to “the average population density or population size of a species below which its numbers tend to increase and above which its numbers tend to decrease because of shortages of resources. The carrying capacity is different for each species in a habitat because of that species’ particular food, shelter, and social requirements.”12 As you can see in the chart below, K-strategist populations rise much more slowly and do not yo-yo near as wildly as r-strategist populations. K-strategist populations hover around the carrying capacity of the land as time advances, assuming conditions are not disturbed by a natural or agricultural event. Another difference is that k-strategist species produce lower numbers of offspring per reproduction event. While this does run the risk of putting more eggs in fewer baskets, each individual offspring tends to be larger and stronger in comparison to r-strategist individuals which increases the odds that each individual will survive to reproduction. This strategy works well when conditions provide sufficient available energy, nutrients and water.


Other strategies that k-strategists exhibit are that they tend to have long gestation periods lasting several months, mature slowly (thus extended parental care), and have long life spans. Lastly, and most importantly for agricultural purposes, they tend to inhabit relatively stable biological communities, such as late-successional or climax forests.13 Examples of k-strategists include elephants, eagles, whales and, of course, humans.

On the left, growth curves show population swings in r- and k-strategists relative to the land's carrying capacity. On the right, survivorship curves show how k-strategist individuals (Type 1) live much longer than r-strategist individuals (type 3).
Schematic of the general changes occurruing when fresh plant residues are added to a soil. The top graph shows r-strategists rapidly consume easily digestible, water-soluble compounds, leaving resistant compounds for K-strategists. The bottom graph shows a phenonmenon known as the "priming effect": Intense microbial activity initially lowers total soil humus, but the level is higher by the end of the process. Courtesy of Brady & Weil (2017)

Annuals, Perennials and Microbes (Oh my!)

To summarize what we’ve learned so far, environmental conditions affect species composition and species composition affects environmental conditions. As one changes, so does the other. This two-way relationship is particularly true with plants and their surroundings. Harsh conditions tend to favor plants that can muster up enough energy to live for one growing season. We call these plants “annuals”. As you may have guessed, annual plants tend to be r-strategists and pioneer species. The three terms are not exactly interchangeable, but their definitions do heavily overlap. The main objective of annual plants is to grow their population size rapidly with quickly maturing individuals that produce thousands of seeds in their first and only year of life. Only after years of living roots amending the soil and its biological community will conditions be able to support more “perennial” plants that live for many years. Perennial plants tend to exhibit characteristics more like k-strategists and make up a significant portion of intermediate and climax communities. Check out the image below and pay attention to the timeline. Short, annual plants show up and set the table for taller, perennial plants to survive later on.

Primary succession from a rocky environment to a forest climax community. Notice how annual plant species appear prior to perennial species. In addition, the depth of fertile soil gradually increases as time passes.

One of the biggest changes over time that allows perennial plants to survive at a higher rate is a shift in soil microbial species. Many annual plants can survive to reproduction when microbial activity is scarce, but most perennial plants require a healthy soil with diverse, rich populations of soil microbes to thrive. Fungal activity is a particularly important microbial indicator of whether a soil system is better suited for annuals or perennials. One study found that early-successional plants (which tend to be annuals) grew 40% smaller with an inoculation of beneficial soil fungi relative to non-inoculated controls. Late-successional plants (which tend to be perennials) grew 383% larger with the inoculation relative to the non-inoculated controls.14 Another study found that perennial warm-season C4 grasses and forbs generally benefited significantly from symbiotic relationships with soil fungi, whereas biomass production of the cool-season C3 grasses was not affected. In addition, fourteen of the fifteen perennial legumes were highly responsive to mycorrhizal fungal inoculation.15 The reason why fungal activity influences plant composition so drastically is due to the numerous services they provide to the soil and plants. Certain plants have developed strategies to withstand the absence of these services, while others have developed strategies that require them. This makes sense in light of the fact that r-strategists/annual plants are individually endowed with lower inputs of energy and nutrients from their parents (what was called “weaker” earlier), meaning they can survive when the going gets tough and resources are scarce. On the other hand, k-strategists/perennial plants require more energy and nutrients per individual, so it makes sense that they struggle without the myriad services handed to them by soil fungi and other microbes. One could say perennials are the Millennials of the plant world because they only tend to show up when conditions are comfortable and their demands have been met by others. Just for the record, I’m not saying that… but one could.


Back to fungi. The services that they provide include residue breakdown, nutrient scavenging and defense against root fungal pathogens.16 Arguably the most important function that soil fungi provide is their ability to reinforce soil macroaggregate tensile strength.17 Macroaggregation refers to the binding of tiny microaggregates made of sand, silt, clay and organic debris. This process is of utmost importance for farmers and ranchers thinking about succession because macroaggregation reduces compaction and increases soil function, thereby creating an environment conducive to greater diversity. A soil that is not well-macroaggregated resembles a jar full of flour because the microaggregates are fine and fill most of the pore space. Think about what happens to water as it is poured onto the flour. Not ideal. A well-aggregated soil resembles a jar full of marbles with adequate pore space that allows water to infiltrate and be held for later use. Water is held because the marble-like macroaggregates are more like round sponges. They are porous and are full of electrically charged, carbon-rich organic matter that holds onto water and nutrients exceptionally well. Gas exchange is also positively influenced as air containing oxygen and nitrogen is able to flow into the soil profile, while CO2-heavy air rises upward, hopefully to be captured by a growing leaf and used once again as plant food. Lastly, soil organisms larger than bacteria require proper macroaggregation to survive and provide ecosystem functions that benefit farmers and ranchers. For example, one study found that “changes in soil nematode assemblages corresponded largely to those in soil porosity of the macroaggregates.”18 The authors also note that macroaggregate porosity likely supported the observed high density of nematodes that consume bacteria and make nutrients plant-available. All of these benefits are impossible without the work of soil fungi. I recommend reading The Biology of Soil Compaction by the Ohio State University for a very informative explanation of the process of macroaggregation.


Farmers and ranchers need to know this information because management practices affect soil fungi and, consequently, succession. The practices that harm fungi include glyphosate application19, fungicide application20,21, tillage22 and even the removal of animals from the landscape23. This is likely why research investigating over 2,100 soil samples from mainland France found that the highest values of fungal density came from natural or semi-natural environments (forests and grasslands), and the lowest values came from agricultural soils (crops and vineyards & orchards).24 Similarly, a study out of the UK observed lower fungal populations and lower fungal-to-bacterial ratios (F:B) in agricultural plots, prompting the authors to write that “the diversity of arbuscular mycorrhizal fungi is strikingly low in arable sites compared with a woodland.”25 Given all of the benefits that soil fungi bring, these are not encouraging findings. Even more unfortunate is that a soil with a low F:B ratio is commonly found in early succession landscapes, which we know gives a competitive advantage to weeds (and pest insects and pathogenic microbes).

Preferential fungal-to-bacteria ratios of various plants.

Although tillage and other disturbances can have their purposes in the short-term, the net result is negative in the long-term. Over time, high disturbance regimes dramatically slow down an ecosystem, limiting the efficiency of the Energy, Water and Nutrient cycles to the point where it resembles the conditions of an early succession landscape. This is the origin of the never-ending cycle of disturbances and worsening conditions that many farmers and ranchers find themselves spinning inside. Whether producers decide to get out of the cycle or continue to run on it depends on which of the two approaches they take to address their issues.

Fight the Power

When it comes down to it, there are really only two strategies for creating an ecosystem that won’t be dominated by pests, disease and weeds. The first is to eliminate everything and everyone. Nobody can dominate if nobody exists, right? This idea of sterilization is the approach utilized in hospital operating rooms, for example. Sterilization makes sense in a surgical setting because the human body’s natural barriers are broken open and foreign objects come into contact with a patient’s internal tissue. In addition, the surgery and/or medication often leaves the patient’s immune system weaker, making them more vulnerable to an infection by microbes. Therefore, the safest management practice during surgery is for medical professionals to ensure that their instruments and hands do not expose the patient to an opportunistic microbe. This strategy of sterilization is great for avoiding infection in the hospital during acute treatments, but it isn’t advised if we are trying to achieve long-term health and balance in a biological system.


For one, disturbances that are designed to kill (i.e. pesticides, antibiotics, antifungals, etc.) run the risk of eliminating not just the target group, but large swaths of beneficial organisms. Let’s use our own guts as an example. The density of bacterial cells in the colon alone has been estimated at 1011 to 1012 (10 with 11 to 12 zeroes!) per milliliter, making the colon one of the most densely populated microbial habitats known on earth.26 Do you think we would be able to survive if all bacteria in our colon were “bad guys”? Of course not! The vast majority of them are either neutral or beneficial to human health.27 Only a select few, such as Clostridioides difficile, or C. diff  (a highly contagious bacterium that causes diarrhea and colitis) cause harm under the right circumstances. The right circumstances, according to the prestigious Cleveland Clinic, involve a wiping out of the microbial population. They write that, “C. diff often infects people who’ve recently taken antibiotics. A course of antibiotics is the most common cause of C. diff infection. Most antibiotics, including broad-spectrum antibiotics meant to target a wide range of microorganisms, are ineffective against C. difficile. But they’re effective against the other bacteria living in your gut, both the bad and the good kind. Using them upsets the balance in your gut microbiome, allowing C. diff to dominate while diminishing other bacteria.”28 This is why people are 7 to 10 times more likely to get C. diff  infection while taking an antibiotic and during the month after.29 Despite everyone’s best intentions, broad spectrum antibiotics unintentionally create an early succession landscape with few natural enemies which gives a competitive advantage to the opportunistic C. diff bacteria.


So, if antibiotic use can have the unintended consequence of providing a competitive advantage to a deadly bacteria, is it possible that fungicides, herbicides, nematocides and other agricultural killing agents also inadvertently promote certain pests and disease? Recent research indicates the answer is yes. Take insects, for example. Similar to gut microbes, the abundance of insects in nature is mind boggling. One estimate in North Carolina calculated that there were approximately 124 million invertebrates per acre, of which 90 million were mites, 28 million were springtails, and 4.5 million were other insects.30 Thank goodness the majority of these insects aren’t harmful in agricultural production.31 There’s no way we would ever produce a crop if all insects were “bad guys”! In fact, we rely on the millions of beneficial insects to provide us services, so it’s imperative that we investigate whether or not the chemicals intended to take out pests are harming the rest of the population as well. Unfortunately, studies are showing that beneficials are in fact harmed, just like antibiotics hurt a large range of gut microbes. One such study found that insecticide seed coatings on soybean significantly reduced natural enemy communities32, while a study from Sweden observed that insecticides killed natural enemies and increased insect damage in a cabbage crop.33 It shouldn’t come as a surprise, then, that a recent study found pest insects to be 10-fold more abundant in insecticide-treated corn fields than on insecticide-free regenerative farms.34 


Echoing the Cleveland Clinic’s description of why C. diff can run amok after taking broad-spectrum antibiotics, Michigan State University writes, “When broad-spectrum insecticides are applied, pest and non-pest species are killed and the balance of the community is disrupted. For example, pesticide use in pear orchards to control codling moth can also destroy the natural enemies of pear psylla. In the absence of its natural enemies, pear psylla can reach high densities and cause significant damage to the fruit.” 35 Imagine the time and money spent by the farmers that think they’re doing the right thing for their crop only to make the situation worse. It’s an unfortunate unintended consequence of conventional farming methods.


For more information on the subject, check out the research that Dr. Jonathan Lundgren has complied at the Ecdysis foundation website, as well as this database compiled by the UK’s Agriculture and Horticulture Development Board to learn more about specific insecticides and their effect on natural enemies.

Secondary outbreaks of pest insects often shows up after insecticides kill natural enemies. Courtesy of the University of California.

How about the fungi that we encounter in agriculture? These microbes represent the largest group of plant pathogens and account for around 14% of global crop yield losses annually36, so just the mention of rhizoctonia, phytophthora, tar spot, powdery mildew or any others can make a farmer want to reach for the fungicide. Is this always the right response, though? Let’s review the facts.  First off, fungi exist in large numbers nearly everywhere on the planet, especially in the soil. Globally, the total length of mycorrhizal fungal (fungi living symbiotically with plant roots) mycelium in the top 10 cm of soil is more than 450 quadrillion km, or half the width of the Milky Way galaxy.37 In addition to their sheer quantity, it appears that species diversity is also enormous as scientists have only discovered and named roughly 3-8% of all fungal species on the planet.38 Once again, many, if not most, of them are not harmful to human health or agricultural production. We’d all be in big trouble if most of them were the pathogenic, zombie-creating monsters depicted on TV and the movies! To the contrary, beneficial fungi are prevalent in nature and society relies on the numerous indispensable services they provide.39


It’s true, though, fungi don’t always behave in a manner that humans find helpful. Sometimes they cause illness and crop yield loss. In those cases, fungicides or antifungal medication may be prescribed to solve the issue. Sometimes this is the right course of action, but sometimes it isn’t. We need to think about the consequences of annually applying these chemicals and decide whether the short-term relief outweighs any long-term unintended consequences. One such consequence appears to be the killing of beneficial fungi40,41 just like we saw with bacteria in the gut and insects in the field. One fascinating study found that the use of fungicides and subsequent decline in arbuscular mycorrhizal fungi richness in croplands was enough to reduce Phosphorus uptake by 43%.42 Interestingly, another study found that the attempt to curb a fungus involved in worldwide amphibian declines with agricultural disinfectants and fungicides actually led to increased fungal disease in the amphibian community.43 At the end of the day, managing fungal pathogens is a tricky issue because the extent of damage is never quite so straightforward, just like everything else in agriculture and ecology. A lot depends on the species of fungi, the active substance, the mode of action, the mode of application and the dosage.44,45 With that said, fungicides aren’t the only disturbance that is potentially harmful to beneficial fungi. Many agricultural operations complete the one-two punch by tilling the soil and disrupting soil fungal communities further.46,47  Among the negative consequences of tillage are the tendency to homogenize the soil’s physicochemical properties and fungal species contained with it48, as well as the tendency of conventional tillage regimes to create an environment where “fungi can utilize mature plant residues that are turned into the soil with tillage as pioneer colonizers, and then produce large numbers of conidia (reproductive spores).”49 Sound familiar? This is the description of an early succession landscape and the r-strategists that thrive in those conditions. Instead of setting ourselves up for a future of resilience and health, the long-term unintended consequences of fungicides and tillage appear to be a reduction in beneficial services and an increase in disease risk.


It’s important to emphasize at this point that antibiotics, insecticides, fungicides and other chemicals are simply tools in our toolbox. Just because their irresponsible use can lead to some bad outcomes doesn’t mean we should never use them. We just need to be much more judicious with how and when we use them as we collectively reduce the need for them. A little bit of humility will also go a long way because the organisms we’re targeting have been using chemical warfare for much, much longer than we have. They’ve got centuries of experience under their tiny belts that help them survive, evade, resist and escape from our best efforts, and it’s a growing concern in both public health and agriculture.

Developing arbuscule of Glomus mosseae in a root cell with fine branch hyphae. Research has shown that this beneficial fungi is negatively affected by certain fungicide applications. Courtesy of Xiangshi.

Our attempt to sterilize away the “bad guys” is not only killing beneficial species, it’s creating chemical resistance in the very organisms we’re attempting to get rid of. Ever since 1928 when Andrew Fleming accidentally discovered a fungal compound that killed bacteria, the scientific world has embraced the concept of using chemistry to wipe out our adversaries, both big and small. Many public health victories followed and antimicrobial drugs were thought to be an integral part of a future that would phase out infectious disease once and for all. In fact, U.S. Secretary of State George Marshall stated in 1948 that “The war against diseases has been won”.50 Most of us were taught Fleming’s serendipitous discovery of penicillin and the subsequent public health victories that followed, but how many people know of his prediction just 8 years later in 1936 that bacteria would become resistant to them? Fleming said his discovery would cause, “a revolution, but doctors will overuse it, and because bacteria have to survive – they are very very clever – they will become resistant to it.”51 Unfortunately, Fleming’s observations of the shifty nature of microbes have proven prescient and mankind has not won the war against diseases. We’ve scored many victories along the way and we should all be thankful for medical breakthroughs of the past 150 years, but all-out victory against disease has not been achieved. Further, treating microbes as the enemies in a war is a mistake for a bevy of reason, not least of which is the tendency to create more resilient pathogenic microbes. The same goes for pest insects and weeds.


To understand why organisms gain resistance to chemical treatments, it’s important for us to step outside of the bounds of our human experience and think about life from the perspective of microbes, plants and insects. Humans take a very long time to reproduce and typically pass on their genes to fewer than three offspring, roughly speaking. We are k-strategists through and through. Other organisms, especially microbes, reproduce much more quickly and have many more offspring per individual. This is important because one of the most common ways an organism becomes resistant to a medicine or pesticide is through random genetic mutation. Genes are the instructions contained in every cell that an organism uses to produce what it needs to survive. Cells, and the genes contained inside each cell, are constantly replicating themselves to stay healthy and functional. Sometimes the sequence of genes doesn’t get copied perfectly, the proofreading system doesn’t catch it and the change gets passed on to the new cell. This is a random genetic mutation, and sometimes it provides an organism with a brand new ability that others around it don’t have. Increasing the number of individuals replicating and the speed at which they are replicating are two ways of increasing the odds that a random mutation will occur in the population. Many times the mutation has no effect, but sometimes the changed sequence of genetic material has a positive or negative effect on the organism. Take E. coli bacteria. Given the right conditions, a single E. coli bacteria can become a million in only 8 hours because they are able to replicate themselves in under 20 minutes.52 With every replication, there is a tiny chance that an individual will randomly mutate. Now, consider what happens when a change is made to the environment so that one mutation could confer a massive competitive advantage to an E. coli individual. Scientists say that this “pressure” is a big driver of change over time. For E. coli, the presence of an antibiotic drug is a cataclysmic change to the environment and most of the bacteria are killed during the treatment. The antibiotic puts enormous pressure on individuals to discover a way to defend themselves against its mode of action. Given the speed and volume of E. coli’s reproduction, there is a decent chance that one bacteria’s genes will randomly mutate in such a way that an individual can now sidestep the antibiotic. This mutant will now replicate like gangbusters and pass on its resistant genes because the vast majority of its neighbors have died from the antibiotic and it has increased access to available space and resources. There is a decent chance that the mutant E. coli strain with the resistant genetics will quickly grow in population size and dominate the new landscape. This short video by Harvard University shows a real experiment showing this process that resulted in a strain of bacteria that survived 1000x the dose that would kill a normal strain. Such is the advantage of reproducing at high speeds and high numbers.


Another way in which organisms overcome pressure relates to a relatively new branch of genetics is called epigenetics. Until recently, conventional science taught that genetic changes can only happen by a physical change in the sequence of genetic material. This is a key teaching point in classical genetics. We now know that this is not always the case. The products of an organism’s genes can also change by physically switching the genes on and off, or by making them produce more or less, like a dimmer switch for a lightbulb.  Researchers are just beginning to investigate the role of epigenetics in resistance. One group of scientists write that, “Since well-documented biochemical or genetic changes fail to fully explain mechanisms underlying antibiotic resistance, it is becoming increasingly evident that we need to shift our focus to newer, nonclassical mechanisms such as epigenetic regulation.”53  Although the mechanism of change is different than classical genetics, the same concept of competitive advantages applies. Individuals are more likely to pass on their genes when they are able to change in such a way that helps them overcome pressure from their environment. They then have a better chance to pass on these advantages conferred by the on/off/dimmer switches to their offspring or replicates.


Finally, microbes are particularly quick to respond to changing conditions because of their unique ability to share genetic information non-sexually with their neighbors in a process called “horizontal gene transfer“. Horizontal gene transfer is in contrast to “vertical gene transfer” which is the passing down of genes from parent to offspring. During a special form of horizontal gene transfer called “conjugation”, bacteria and archaea transfer genes to each other in the form of a structure called a plasmid. These genes are separate from the main string of genetic material, a.k.a. the “chromosomal DNA”, that codes for many day-to-day tasks. The genes inside of plasmids are important because some of them provide unique competitive advantages against pressures, such as antibiotic resistance.54,55 As you can see from the image below, the F plasmid is copied and transferred to its neighbor through a structure called a pilus. Although this may sound and look like sexual reproduction, it is considered non-sexual because the transfer can happen with non-sexually compatible neighbors. After the transfer has been made, there are now two bacteria that have the genetic ability contained inside the F plasmid. Horizontal gene transfer is an absolute game-changer for microbes because genes that are able to mix, match and transfer to one another build resilience against disturbances and/or changing conditions. I like to think the human equivalent is our ability to verbally share ideas and information with other humans. We can drastically reduce the learning curve on all kinds of processes with our ability to share what works and what doesn’t work, just like in horizontal gene transfer. Genes are, after all, pieces of coded information.


There are two other common methods of non-sexual gene mixing and transferring called transformation and transduction. In transformation, a bacterium can absorb a free-floating piece of DNA like someone picking up a five dollar bill on the ground. Sometimes it’s more like finding a winning lottery ticket when the genes provide the bacterium with a huge competitive advantage, proving just the high degree of randomness that genes can be shared with one another on the microscopic level. Transduction refers to the DNA that is transferred and shuffled from one bacterium to another by a virus. Although they are not technically living organisms, viruses play a huge role in facilitating genetic diversity on the planet. In fact, scientists estimate that remnants of viral genes make up a relatively large part of modern human DNA. And, not only that, these pieces of DNA likely boost our immune system by helping us to fight off infections.56 Imagine how much more influential they are in the fast-paced world of microbes!


Lastly, it’s worth mentioning that fungi are able to share genetic information horizontally with non-sexually compatible neighbors, just in a different manner. This amazing video from UCLA and UC Berkley shows how fungal communities pass around whole nuclei (the main structure containing genetic material) to one another, further blurring the lines between the genetics of one individual organism to its neighbor.57

Conjugation allows bacteria to share genetic material with individuals that are not necessarily sexually compatible.

To quote the great Ferris Beuller, life moves pretty fast, especially in the microbial world. The only difference is they don’t have time to stop while they’re looking around and gathering information on a rapidly changing environment. Microbes, and higher order creatures, that have survived to this point have done so largely because of their built-in methods of sensing changes to external conditions and having the ability to react to these pressures. Add sheer random mutation to the mix and you get a resilient population of organisms that can handle many challenges and come out the other side stronger. These are very handy sets of behaviors to have, especially since humans have created enormous change to the planet through the introduction of agriculture thousands of years ago and the mass use of antibiotics and pesticides in the last 100 years or so. Microbes, insects and weeds are simply reacting to these changes in the best way they know how: survive, advance and pass on the advantage. No one is more aware of this fact than the medical community. The Center for Disease Control (CDC) writes that, “Antimicrobial resistance is an urgent global public health threat, killing at least 1.27 million people worldwide and associated with nearly 5 million deaths in 2019, according to a report released in The Lancet.”58 Examples of antimicrobial resistance in bacteria includes cephalosporin-resistant E. coli,  methicillin-resistant Staphylococcus aureus (MRSA) and Klebsiella pneumoniae that is resistant to critical antibiotics. Fungi like Candida auris and parasites that cause malaria are also exhibiting resistance to drugs that worked effectively in the past. One of the biggest dangers of resistance from these microbes is that patients are increasingly administered last-resort drugs like carbapenems, of which resistance is already being observed across multiple regions.59,60 This is especially dangerous because the discovery and development of new antibiotics have slowed dramatically since the 1990’s. Since then, only three new antibiotics have received FDA approval in the last 30 years.61 Protecting the efficacy of antimicrobial drugs is of utmost importance if we are to avoid a reversion to the days of fearing that a small cut will turn into a life-altering infection.


We need to realize that there are patterns exhibited in ecological systems of all shapes and sizes, whether it be a microbe, the rhizosphere, the human body, a forest or the planet as a whole. This is why it’s important for us in the agricultural world to study the issues that the medical community are facing. The successes and failures of both fields translate to the other because many of their issues stem from the collective attempt to sterilize our way to health. The trouble is that we simply don’t have enough knowledge to predict all of the negative unintended consequences that result from man’s attempt to strong-arm nature into submission. So, if the medical community accepts that their management of disease has caused negative downstream effects, why has the agricultural community been so slow to recognize that our management practices might be resetting the succession clock and leading to many of the same unintended consequences? It’s time we learn from each other and realize our issues are intimately related. Case in point is the rise in resistance against pesticides.


Starting with insects, scientists estimate that up to 30–40% of crops are lost because of pests62, so it is is imperative for global food, fiber and fuel security that these six-legged creatures don’t wreak havoc on our fields and pastures. The primary strategy to keep insects at bay for the past century has been to develop and use industrial chemical products and, as of recently, genetic modification. These products and technologies have their purpose, but scientists have known about the ability of insects to gain resistance to chemical products for over 100 years when it was discovered in 1914 that sulfur lime was becoming less effective at controlling the San Jose scale (a.k.a orchard aphid).63 Since then, the agricultural community has put itself further and further into a chemical arms race with insects. Who’s winning the race is up for debate. The USDA reports that  11 additional cases of resistance to inorganic insecticides were observed from 1914 to 1946.64 A major breakthrough in insecticide technology came with the development of organic insecticides, such as DDT. (Side note- DDT, banned in 1972 for its adverse effects, proves that organic/natural products do not automatically translate to “healthy”!)  These new organic insecticides initially gave hope to scientists that insecticide resistance would not be achieved, due to their natural origin. Unfortunately, housefly resistance to DDT was already documented by 1947. It turns out that insects don’t really care where a compound comes from. If something is trying to hurt them, they’ll do their best to fight back, and fight back they did. No matter the insecticide class introduced throughout the 20th century, whether it be cyclodienes, carbamates, formamidines, organophosphates, pyrethroids, or even Bacillus thuringiensis (bt), insects figured out ways of sidestepping them, usually within two to 20 years.64 Just like antimicrobial drugs, the increased use of insecticides appears to have been a double-edged sword. At the same time as they were killing scores of target insects, they were also placing enormous pressure on our six-legged compatriots that forced them to quickly figure out ways around the chemicals. To do this, insects used a “variety of behavioral, biochemical, physiological, genetic, and metabolic methods to deal with toxic chemicals, which can lead to resistance through continuous overexpression of detoxifying enzymes.”65 Individuals that produce these enzymes rapidly became a greater percentage of the population and rendered the insecticide less and less effective against pests. It’s simply another case of survive, advance and pass on the advantage.


So, what’s the extent of insecticide resistance? The University of Clemson reports that as of 2015, “550 insect species have been reported as resistant to 325 insecticides and five insecticidal traits in genetically engineered plants.”66 Graphical representation of this data can be viewed below. Another group of scientists estimated in 2023 that “As many as 1000 species of insect pests have developed resistance to different class of insecticides,67 and the list keeps growing, including a recent study from November 2023 showing novel resistance by bluegreen aphid to organophosphates, omethoate and chlorpyrifos.68 If you believe what the Insecticide Resistance Action Committee (IRAC) has to say then you shouldn’t expect this list to stop growing because they report that cases of insecticide resistance far exceed the cases of other agricultural pesticides.69 These findings should cause us in agriculture to think long and hard about whether we will continue to rely on insecticides as our first line of defense against pest insects.


For anyone interested in digging deeper into insect species and insecticide resistance, Michigan State University has a great arthropod pesticide resistance database that is open to the public.

Cumulative increase in (a) the number of species resistant to one or more insecticides, (b) number of insecticides for which one or more species has shown resistance, and (c) number of GMO traits for which resistance has been reported. Image courtesy of Sparks and Nauen (2015).

And the fungus among us? As was mentioned earlier, fungi represent the largest group of plant pathogens and pose possibly the greatest biotic challenge to global food security70, so it’s crucial that we figure out whether or not they’ve developed resistance to the chemicals we’ve been spraying on them for decades. Unsurprisingly, the answer is a resounding yes. Resistance to fungicides first reared its ugly head in the 1960’s and has become a growing issue ever since.71  Oklahoma State University reports that, “Fungicide resistance problems in the field have been documented for nearly 200 diseases (crop – pathogen combinations), and within about half of the known fungicide groups. Many more cases of resistance are suspected but have not been  documented.”72 They go on to describe the process of how this happens. Stop me if you’ve heard this one before. “The build-up of resistant strains is caused by repeated use of the fungicide which exerts selection pressure on the population. The fungicide selectively inhibits sensitive strains, but allows the increase of resistant strains.”72 Same story, different organism. This process can happen astonishingly quick in fungi, as exhibited by Cercospora sojina, a fungus that causes frogeye leaf spot on soybean. Nebraska University has found that over 1.5 trillion Cercospora sojina conidia (reproductive spores) are produced from a 40-acre soybean field heavily infested with frogeye leaf spot, assuming there are 5 million or more soybean plants in the average 40-acre field. This results in 15,000 mutant isolates in a heavily infested 40-acre field.73 Imagine how many mutant isolates are created during a county-wide outbreak spanning thousands of acres! My educated guess would be millions of mutants in one growing season, each with varying rates of resistance. The actual method of defense that fungi utilize to protect themselves against fungicides also varies. Recognized modes of defense include increased activity of efflux pumps, metabolic circumvention, detoxification, standing genetic variations and regulation of stress response pathways.74 In other words, fungi are quick, they’re shifty and continuing our chemical arms race with them might not be the wisest strategy moving forward, especially with the decline in introduction rate of new fungicides.75


One unintended consequence of encouraging fungal retaliation is that resistance appears to spill over into the world of human health. Matthew Fisher of the MRC Centre for Global Infectious Disease Outbreak Analysis at Imperial College London and a team of experts write that, “The intimate relationship between environmental populations of fungi and ensuing exposures to antifungals means that emerging environmental resistance is likely to affect the clinical management of fungal infections… [A]s with licensed medical antifungals, agricultural fungicides used in agriculture have broad-spectrum activity across the fungal kingdom. As such, resistance arises not only in the crop pathogens per se but also in other environmental fungi that include potential human fungal pathogens.”76 One such example is the link between azole fungicide application and the rising rates of azole-resistant Aspergillus fumigatus infections in humans.77 Part of the issue is their lipophilic (fat-loving) nature, which makes the chemical structure of azoles highly stable in a soil. This means that they can maintain their antifungal properties in the environment and in food for months.78,79 All of this should serve as a stark reminder that our attempt to sterilize fungi with industrial chemicals impacts more than just agriculture.


Last but not least, many plant species are now resistant to the herbicides that producers apply to wipe them out. This should come as no surprise because plants are arguably Earth’s greatest organic chemists, producing thousands of complex compounds that help them communicate with their neighbors, defend themselves and entice animals to spread their seed.80 What they lack in movement, they make up for in chemical wizardry, so attempting to cut them off at the knees with industrial chemicals is only playing to their strength. The numbers back this up. In 2021, the University of Minnesota wrote that, “By 1991, 120 weed biotypes were resistant to triazine herbicides and 15 other herbicide families were documented throughout the world.  Since then, nearly 500 unique cases of herbicide resistance have been reported.”81 2024 data from the International Herbicide-Resistant Weed Database reports that there are currently “530 unique cases (species x site of action) of herbicide resistant weeds globally, with 272 species (155 dicots and 117 monocots). Weeds have evolved resistance to 21 of the 31 known herbicide sites of action and to 168 different herbicides. Herbicide resistant weeds have been reported in 100 crops in 72 countries.”82 Among them, many of the most economically damaging weeds have developed resistance to glyphosate, the most sprayed active ingredient on the planet. These include Palmer amaranth, tall waterhemp (Amaranthus rudis), common ragweed (Ambrosia artemisiifolia), giant ragweed (Ambrosia trifida), hairy fleabane (Conyza bonariensis), horseweed (Conyza canadensis), burningbush, Italian ryegrass (Lolium multiflorum), annual bluegrass (Poa annua), and johnsongrass (Sorghum halepense).


The process of herbicide resistance is similar to all the other processes of resistance we’ve encountered so far. Herbicide resistance occurs because, “Each time the herbicide is applied, susceptible plants die and those with resistance survive.”83 As Robert Battel of Michigan State University writes, “It’s “survival of the fittest” in fast forward.”84 Even worse is that herbicide-resistant genes don’t disappear from the genome (total gene pool) of weeds even after a herbicide is taken off the market. Plants, as well as microbes and animals, carry resistant genes with them for generations like a scar from a battle wound. This is an important fact for two reasons. First, plants have been using chemical warfare for millennia, so some of them may have a resistant gene tucked away in their genome that helps them evade a “novel” herbicide. Continued application of a herbicide creates the pressure that causes this ancient gene to express itself, save the plant from death and grow in the population, making the herbicide less effective over time. Second, the ability to hold onto genetic traits for generations means an ineffective herbicide is potentially taken out of our arsenal forever.”85


Losing herbicides is a threat to global food supplies, especially as chemical companies are struggling to bring new herbicides to the market. In a 2024 article titled, ” Crop-killing weeds advance across US farmland as chemicals lose effectiveness“, journalists Rod Nickel and Tom Polansek of Reuters interviewed two dozen farmers, scientists, weed specialists and company executives and reviewed eight academic papers published since 2021 to learn more about the threat of herbicide resistance. Bob Reiter, head of research and development for Bayer’s crop science division, told Nickel and Polansek that, “We’re really desperate for (new modes of action) if we’re going to sustain uses for farmers.  Two decades ago, companies commercialized a product for every 50,000 candidates, but it now takes 100,000 to 150,000 attempts.” Part of the issue appears to be increasingly stringent environmental testing required for each new product, increasing the amount of time and money required to bring a product to the market. As a result,  “Over the last two decades, chemical companies have reduced the share of revenue devoted to research and development spending and are introducing fewer products, according to AgbioInvestor, a UK-based firm that analyzes the crop protection sector.” The amount of time and money to develop a new herbicide is simply becoming too much for company executives to justify the efforts. Despite this, there are some encouraging signs for the industry as “FMC plans the 2026 launch of an herbicide to kill grassy weeds in rice crops based on the industry’s first new mode of action, a term for the way a chemical kills a weed, in three decades. The herbicide was in development for 11 years.” Even so, the challenges detailed in Nickel and Polansek’s article should question whether playing chemical catch-up with herbicides is the right direction weed management should take in the first place. 


The closing of the article is a fitting end to this section on sterilization in agriculture and its negative effects on succession: “Bill Freese, scientific director of the Center for Food Safety in Washington, said farmers should shift away from crops genetically engineered to tolerate herbicides, which lead to plants becoming resistant to multiple chemicals through repeated sprayings. “It’s like this toxic spiral,” Freese said. “There’s no end in sight.””86

The process of herbicide resistance. Courtesy of the Univeresity of Minnesota.
Cumulative increase in the number of individual cases of resistance for insecticides, herbicides and fungicides. Courtesy of Sparks and Nauen (2015).

Hopefully this discussion on the consequences of a sterilizing approach to health in both both healthcare and agriculture gives you a better perspective of why many proponents of regenerative agriculture view pesticides as tools to be used toward the end of the treatment process, not the beginning. In an ideal world, we’d never use these products, but farming and ranching is extremely difficult and nature can be a cruel mistress sometimes. Therefore, these products have their time and place, just like life-saving antimicrobial drugs have their time and place. The issue is that agricultural production methods have so diminished ecosystem functioning that farmers and ranchers are now reliant on them to produce a reliable harvest year after year. Like a human on a life-support system or someone reliant on a chemical compound such as caffeine or alcohol, quitting cold turkey is likely to be the wrong approach. Most production sites need to go through a weaning period before alternative methods of protection can be utilized. We will have a worldwide disaster if everyone decides to stop using pesticides cold turkey or even too quickly, just like cold turkey abstainers of coffee or beer get caffeine headaches and experience alcohol withdrawal symptoms while their bodies readjust.


Resistance to chemical products is a spectrum and there are many great people working to inform us on how to use antimicrobial drugs and pesticides efficiently so their effectiveness is extended into the future. However, the fact remains that the current system’s reliance and overapplication of them does not regenerate life and ecosystem functioning. In many cases, the opposite effect is observed and the succession clock is reset to a place where r-strategy opportunists thrive. Chemical products have a place, but that place is fixed within a system that prioritizes a richness and diversity of life because that is where truly sustainable health and balance are found. Microbes, insects and weeds are simply too vast and too adaptable to ever fully control in our bodies and on the land.

To Be Continued

Are there techniques farmers and ranchers can implement to work with succession in the ecosystems they manage? Is there reason to be optimistic about the future of pathogen, weed and insect management? Click here to read Part 2 and find out!