Fertilizer is more than just nutrients! Long-term use of chemical fertilizers is quietly destroying the soil ecosystem

Long-term reliance on chemical fertilizers not only changes the pH value of the soil, but also destroys the ecological balance of soil organisms such as microorganisms and earthworms, causing deterioration of soil structure and imbalance of nutrient cycles, further affecting plant health and food security. There is no time to delay in moving towards sustainable agriculture.

Soil is not only a supporting medium for plant growth, but also a vibrant ecosystem inhabited by extremely diverse microbial communities (including bacteria, fungi, archaea, protists, etc.) and soil animals (such as earthworms, nematodes, arthropods)1. This complex biological network plays a vital role in maintaining many fundamental ecosystem functions on Earth, including cycling of key nutrients (e.g., nitrogen, phosphorus, carbon), decomposition of organic matter, sequestration of carbon, regulation of water, and suppression of plant diseases.1. The health and productivity of terrestrial ecosystems, including agricultural systems, are closely linked to the biodiversity and functioning of their soils, highlighting the importance of understanding factors that may disrupt this delicate balance.

Industrial agriculture developed significantly during the 20th century in response to the demand for food from a growing global population, centered on the extensive use of synthetic or chemical fertilizers to maximize crop yields4. Typical chemical fertilizers are primarily composed of the three main macronutrients required by plants: nitrogen (N), phosphorus (P), and potassium (K), usually in the form of inorganic salts. They may also contain secondary nutrients such as calcium, magnesium, and sulfur, as well as certain micronutrients4. In the short term, chemical fertilizers have proven effective in promoting plant growth and increasing crop yields because they provide essential nutrients to plants immediately7。

However, there is growing concern about the potential long-term consequences of long-term reliance on chemical fertilizers on the soil itself and its wider environment4. A growing body of scientific research shows that long-term and often excessive use of chemical fertilizers can adversely affect the complex biological, chemical and physical properties of soil and may impair its ability to maintain high yields over the long term4。

This report aims to provide an in-depth look at the complex effects of long-term chemical fertilizer applications on soil ecosystems, focusing specifically on two key components: diverse beneficial soil microbial communities and ecologically important earthworm populations. We will examine how long-term exposure to chemical fertilizers affects the structure, diversity, and function of soil microbial communities, as well as earthworm abundance, biomass, and behavior. Additionally, this report will explore how these changes can lead to knock-on effects on basic soil functions, including nutrient cycling and soil structure, with subsequent impacts on plant health and overall ecosystem resilience. Finally, we discuss the long-term environmental implications of these impacts, such as soil degradation and biodiversity loss, and consider the implications of these findings for agricultural sustainability and environmental protection.

• Changes in overall microbial community structure and diversity:
  Long-term fertilization practices, including the use of chemical fertilizers, have been shown to induce significant changes in the chemical properties of soils and the microbial communities they inhabit in different agroecosystems 20 . Studies using advanced molecular techniques such as high-throughput sequencing have shown that long-term application of chemical fertilizers often results in reduced richness (number of different species) and diversity (evenness of species distribution) of soil bacterial communities 18 . However, it is worth noting that the effects of chemical fertilizers on overall microbial richness and diversity may not always be negative or statistically significant. Some studies suggest that chemical fertilizers primarily affect the abundance (population size) of specific bacterial and fungal species, rather than significantly reducing the total number of different microbial species present 4 . Observed changes in the abundance of individual microbial taxa are often related to changes in key soil chemical properties induced by long-term fertilization. These properties include soil pH, carbon to nitrogen ratio (C/N), and concentrations of various nutrients 4 . For example, a 10-year field experiment showed that continuous application of nitrogen (N) fertilizer significantly affected most major soil bacterial species mainly by causing changes in soil pH22. The study observed that the number of bacterial operational taxonomic units (OTUs) decreased to varying degrees with changes in nitrogen fertilizer application rates, and excessive application of nitrogen fertilizer led to a significant decrease in the number of OTUs. Increases in the rate of nitrification (the microbial oxidation of ammonia to nitrite and then nitrate), often promoted by chemical nitrogen fertilizer application, have been found to be associated with changes in microbial community richness and specific structure of ammonia-oxidizing bacteria 22 . Interestingly, although nitrogen fertilizer initially stimulates nitrification, excessive fertilization eventually adversely affects the abundance and activity of the nitrifying bacteria responsible for this process 22 . In contrast to single nutrient applications, mixed applications of organic and chemical fertilizers (CFM) have shown more positive effects on soil fertility and microbial communities in long-term studies. CFM treatment significantly increased bacterial species richness and fungal Shannon diversity index 20 compared to chemical fertilizer (CF) or nitrogen fertilizer (NF) alone. Furthermore, CFM treatment was observed to increase the relative abundance of beneficial soil bacteria while reducing the relative abundance of potentially pathogenic bacteria, suggesting that soil microbial communities are more balanced and potentially healthier 21 . Studies have also shown that long-term application of chemical fertilizers alone can exert strong selective pressure on soil microbial communities, leading to a higher proportion of obligate microorganisms adapted to the specific conditions caused by fertilizers, and to a stronger impact of deterministic ecological processes. This suggests that microbial communities in soils subject to long-term application of chemical fertilizers may be less resilient to environmental changes than soils under other management practices18. Finally, studies exploring reducing the amount of chemical fertilizers and adding organic fertilizers have found that this approach increases the richness and diversity of soil bacteria while conversely decreasing the richness and diversity of fungi10. This highlights the complex and often distinct responses of bacterial and fungal communities to changes in fertilization regimes.
• Impact on key beneficial microorganisms
• Azotobacteria: Disruption of the Natural Nitrogen Cycle:
  Nitrogen-fixing bacteria play a crucial role in converting atmospheric nitrogen into a form available to plants, but their health and activity can be negatively affected by conventional agricultural practices, including the use of chemical fertilizers and related pesticides25. Specifically, organochlorine pesticides (which have been widely used in the past and may remain in the soil) have been shown to inhibit nitrogen-fixing bacteria by interfering with important communication signals (flavonoid signaling) between leguminous plants (such as soybeans and alfalfa) and rhizobia. Rhizobium bacteria form symbiotic relationships in root nodules to fix nitrogen 25 . This suppression of natural nitrogen fixation may lead to lower crop yields and subsequent greater reliance on synthetic nitrogen fertilizers to compensate for reduced natural inputs, creating a detrimental feedback loop 25 . Additionally, the addition of excess nitrogen directly through chemical fertilizers may also reduce the need for plants to establish symbiotic relationships with nitrogen-fixing bacteria, resulting in inhibition of their activity and potentially leading to long-term declines in the numbers of these key microorganisms in the soil27. When nitrogen is plentiful, plants become essentially “lazy” and less reliant on natural processes. Studies have shown that nitrogen fertilizer may have a more significant impact on soil nitrogen-fixing bacterial community composition than increases in atmospheric carbon dioxide levels, potentially suppressing the diversity and overall abundance of these key microorganisms28. While some studies suggest that initial applications of conventional fertilizers may result in temporary increases in nitrogen-fixing activity compared to organic fertilizers (perhaps due to higher phosphorus content in certain chemical formulations), in the long term, organic amendments are often better at supporting the health and activity of nitrogen-fixing bacteria by focusing on building overall soil health and providing a more balanced nutrient environment 29 . High application rates of nitrogen fertilizer may also inhibit the process of soil nitrification and alter the rate of ammonification (the microbial conversion of organic nitrogen to ammonia), further disrupting the natural cycle of nitrogen in soil ecosystems 30 .

• Effects on earthworm abundance and biomass:
  Earthworms are widely regarded as the “ecosystem engineers” of the soil, playing a key role in soil aeration, drainage, nutrient cycling and organic matter decomposition. However, their populations and health can be significantly affected by agricultural practices, including the use of chemical fertilizers 42 . Interestingly, some studies suggest that inorganic nitrogen fertilizers may initially cause an increase in earthworm populations in agricultural fields. This is often attributed to increased crop residue production due to enhanced plant growth following fertilizer application, provided that soil pH is maintained at a near-neutral level that earthworms typically prefer 44 . However, certain types of nitrogen fertilizers, such as ammonium sulfate and anhydrous ammonia, have been found to have negative effects on earthworm populations. This is most likely because they tend to lower soil pH, creating a more acidic environment less suitable for earthworm survival and reproduction 44 . In particular, studies have shown that the minerals ammonium sulfate and thiourea significantly reduce the number and biomass (total weight) of earthworms in the soil, while also lowering soil pH 45. The overall effects of chemical fertilization on earthworm abundance and biomass are not uniform and can vary significantly depending on a variety of factors, including the specific type of fertilizer used, the rate of application, inherent properties of the soil (e.g., texture, organic matter content), and the specific earthworm species present in the ecosystem 45 . High application rates of fertilizers such as urea may lead to elevated ammonium concentrations in the soil, which may be toxic to bacteria and other soil microorganisms that serve as food sources for earthworms, thereby indirectly affecting their populations 48 . Additionally, phosphorus (P) and potassium (K) fertilizers have been shown to potentially reduce substrate-induced respiration of soil bacteria, which may also have indirect negative consequences on earthworm food availability 48 . Furthermore, excessive use of chemical fertilizers may disrupt the structure and diversity of soil microbial communities that are an important component of earthworm diets, which may reduce the quality or availability of their food 49 .
• Changes in Earthworm Behavior and Physiology:
  In addition to their effects on population numbers, chemical fertilizers may also produce significant changes in the behavior and physiological functions of earthworms 42 . Urea is a commonly used nitrogen fertilizer that has been shown to cause high mortality in earthworms, even at relatively low concentrations in the soil. It may also have a negative impact on its ability to reproduce, resulting in a 50 reduction in the number of offspring. Direct contact with inorganic mineral fertilizers, including urea, potassium chloride (MOP), and even superphosphate monohydrate (SSP) at high concentrations, can be toxic to earthworms, causing mortality and other adverse effects 33 . Ammonium sulfate fertilizers have been found to inhibit the growth of earthworms, causing them to lose weight and causing a range of morphological changes, including swelling of the annulus, shrinkage of the body, and even rupture. Histopathological examination revealed severe damage to the muscle tissue, digestive and circulatory systems52. Earthworms may exhibit avoidance behavior in response to high concentrations of certain chemical fertilizers in the soil. For example, they have been observed burrowing deeper into the soil to avoid contact with urea, suggesting that they actively strive to avoid adverse conditions 51 . Some studies suggest that “direct-acting” fertilizers (containing only one nutrient) may be more harmful to earthworms than “complex” fertilizers (containing multiple nutrients), possibly due to higher concentrations of individual potentially toxic compounds in direct-acting fertilizers 33 .

There are complex and often mutually beneficial interactions between earthworms and soil microorganisms that are critical to maintaining soil health and fertility2. Microorganisms play a key role in breaking down organic matter, which is the primary food source for many earthworm species. Earthworms, in turn, influence microbial communities through their feeding activities, digestive processes in the gut, and through the physical and chemical changes they cause in the soil through their burrowing and excrement (feces). Research shows the presence of earthworms in soil can boost crop growth by enhancing connections and interactions within a complex network of soil microbial communities, including bacteria, fungi and protists.55. This suggests a synergistic relationship in which earthworms promote microbial activity that benefits plant growth. However, the application of chemical fertilizers can significantly alter the structure and composition of these soil microbial communities (as discussed in Section 2), which in turn may disrupt their delicate balance with earthworms55. For example, changes in the abundance of certain bacterial or fungal taxa due to fertilization may affect earthworm food availability or quality. Studies comparing different fertilization methods have found that the application of organic fertilizers often leads to the development of more complex and interconnected soil microbial community networks than the use of chemical fertilizers55. This suggests that organic amendments may provide a more favorable environment for beneficial interactions between microorganisms and earthworms to flourish. Interestingly, studies have shown that the positive impact of earthworms on plant growth depends largely on the presence and activity of soil microorganisms, especially under different fertilization conditions56. This highlights the interconnectedness between the two groups and suggests that disruption of microbial communities caused by chemical fertilizers may indirectly diminish the benefits that earthworms provide to plants. Excessive application of nitrogen fertilizers has been shown to negatively affect soil physicochemical properties and disrupt microbial communities, which may affect earthworm populations by altering their habitat and food sources.49. In contrast, the application of earthworms mixed with organic matter (such as cow manure), while reducing the amount of chemical fertilizers, has been found to synergistically alter microbial community structure, thereby enhancing soil fertility and promoting plant growth.49. This suggests that integrating organic amendments can help mitigate some of the negative effects of chemical fertilizers on microbial-earthworm interactions. Furthermore, studies have shown that nitrogen fertilizer can directly alter the effects of earthworms on soil physicochemical properties and bacterial community structure, suggesting complex interactions between these factors.57。

• Disruption of nutrient cycling:
  Long-term application of chemical fertilizers can lead to significant imbalances in the availability of essential nutrients in soil ecosystems 8 . While these fertilizers provide plants with a concentrated source of specific nutrients, their continued use may disrupt natural processes that regulate the recycling of other important elements. For example, excessive application of nitrogen fertilizers can cause an imbalance in the ratio of nitrogen, phosphorus, and potassium in the soil, which can lead to deficiencies in other essential nutrients required for optimal plant growth and development 14 . Chemical fertilizers can also directly affect soil nutrient cycling and the microbial breakdown of organic matter, a key source of slow-release nutrients for plants1. These fertilizers alter the activity and abundance of microorganisms involved in nutrient conversion, potentially causing inefficiencies in the overall recycling process. Additionally, chemical fertilizers can disrupt the natural nitrogen cycle by reducing the number of ammonia-oxidizing bacteria that are essential for the nitrification process (converting ammonia into a form of nitrate that is easily absorbed by plants), and by affecting denitrification (converting nitrates back to atmospheric nitrogen). The availability of phosphorus to plants after chemical fertilization may be limited by a number of factors, including precipitation reactions that convert soluble phosphorus into an insoluble form or immobilization by binding to soil particles, especially in soils with high calcium, magnesium, iron, or aluminum contents 4 . This means that even if a high-phosphorus fertilizer is applied, plants may not receive adequate amounts of this critical nutrient in the long term. Research has also shown that potassium chloride (KCl), a common potash fertilizer, may not always lead to increased crop yields and may even have adverse effects on the overall soil ecosystem 4 . In contrast, organic fertilizers tend to release nutrients into the soil more slowly, mimicking the natural decomposition process and helping to maintain a more balanced and consistent supply of nutrients that plants need for long-term growth4.
• Deterioration of soil structure:
  Long-term excessive use of chemical fertilizers can negatively affect the physical structure of the soil, which is critical for supporting plant growth by affecting water infiltration, aeration, and root penetration 58 . These fertilizers are composed of mineral salts that disrupt the natural agglomeration of soil particles, which is essential for the formation of a stable and porous soil structure 58 . Over time, accumulation of these salts, especially when applied in excess, can lead to soil compaction, increased surface crusting, and reduced water infiltration and retention capabilities within the soil profile 14 . This ultimately increases the risk of soil erosion and nutrient loss. In addition, long-term application of chemical fertilizers can change soil pH, making it too acidic or too alkaline, which can adversely affect soil structure by affecting the activity of soil microorganisms and the stability of soil aggregates 14 . For example, some nitrogen fertilizers can cause soil acidification. Soil acidification and crusting problems caused by long-term use of chemical fertilizers can also lead to a reduction in soil organic matter content, an important component in maintaining good soil structure and overall soil health 9 . Earthworms are natural “tillers” of the soil and play an important role in improving soil structure and tillability through their burrowing and excretion activities, but they can be negatively affected by chemical fertilizers (as discussed in Section 3), further exacerbating the deterioration of soil structure 3 . In contrast, organic fertilizers help improve soil structure, increase water-holding capacity and improve overall soil tillability by adding organic matter to the soil.4.
• Effects on plant health and stress resistance:
  While chemical fertilizers initially promote rapid plant growth and increase crop yields, their long-term use may negatively impact the overall health and stress resistance of plants 9 . Soil nutrient imbalances caused by long-term chemical fertilization can make plants more susceptible to attack by pests and diseases and may require increased pesticide use9. Excessive application of nitrogen fertilizer can cause rapid, overly lush vegetative growth of plants, but this may come at the expense of proper root development, flowering, and fruiting, ultimately reducing the overall health of the plant and yield quality7. Disruption of beneficial soil microorganisms (such as mycorrhizal fungi) impairs nutrient uptake (especially phosphorus and trace elements) and weakens plant tolerance to various stresses (drought, salinity, pathogens), significantly compromising plant health and stress resistance when these symbiotic relationships are compromised by long-term use of chemical fertilizers 37 . Additionally, the accumulation of potentially toxic substances in plant tissues, such as heavy metal impurities that may be present in some chemical fertilizers, may pose risks to plant health as well as to the health of animals and humans who consume these plants 7 . In contrast, organic fertilizers help grow plants that are generally healthier, more resistant to environmental stresses, and less susceptible to pests and diseases by providing more balanced and slow-release nutrients and supporting a diverse and healthy soil microbial community.4

The long-term and often excessive use of chemical fertilizers has been linked to widespread harmful environmental impacts that are not limited to farmland itself7. These impacts include soil salinization, accumulation of heavy metals in soil, eutrophication of water bodies, accumulation of nitrates in groundwater, increased emissions of greenhouse gases, and potential biomagnification of harmful substances through the food chain. As discussed in previous sections, long-term use of chemical fertilizers can lead to a significant decrease in overall soil fertility and create serious soil degradation problems, affecting its ability to support plant growth and other essential ecosystem functions5. Loss of soil microbial diversity, particularly due to long-term application of chemical fertilizers alone, is a major concern because these diverse microbial communities play a critical role in supporting a variety of essential ecosystem services, including organic matter decomposition, nutrient cycling, and plant primary production. This reduction in biodiversity can negatively impact the ability of soils to perform these functions efficiently and may make ecosystems less resilient to environmental changes18. Excess nutrients from chemical fertilizers, especially nitrogen and phosphorus, can leach into groundwater or run off from farmland into nearby water bodies, causing severe water pollution. This excess of nutrients can trigger eutrophication, a process of excessive algae growth that consumes oxygen in the water and creates “dead zones” that are harmful to aquatic life.4. Nitrogen fertilizers, in particular, release nitrous oxide (N₂O) during the nitrification and denitrification processes in soil, a potent greenhouse gas with much higher global warming potential than carbon dioxide4. The use of chemical fertilizers may also lead to the accumulation of heavy metals that may be present as contaminants in the raw materials used to produce these fertilizers and accumulate in soil and plant systems. These heavy metals may then enter the food chain, posing potential risks to human and animal health1. Soil degradation caused by long-term use of chemical fertilizers, including loss of organic matter and deterioration of structure, will increase soil sensitivity to drought, wind and water erosion, further exacerbating environmental problems12. Finally, the destruction and reduction of soil biodiversity, including beneficial microorganisms and earthworm populations, due to the effects of long-term chemical fertilizers, can weaken the overall resilience and functional capacity of soil ecosystems, making it more difficult to adapt to environmental stresses and provide essential ecosystem services5。

As detailed in previous sections, long-term application of chemical fertilizers has complex and often negative effects on soil microbial communities and earthworm populations. Chemical fertilizers can directly change soil chemistry, favoring the growth of certain microbial groups while inhibiting the growth of others, and may be directly toxic to earthworms at certain concentrations or under long-term exposure. Indirectly, changes in plant biomass due to fertilization may initially benefit earthworms, but subsequent soil degradation and disruption of microbial communities (the main food source) may have negative consequences. The interconnection of these effects is critical. Altered microbial communities will affect nutrient availability to plants and earthworms, while reductions in earthworm populations will reduce soil aeration, water permeability, and organic matter decomposition, further affecting microbial activity and diversity. Long-term application of chemical fertilizers often disrupts these delicate balances, resulting in reduced functionality and resilience of soil ecosystems.

Soil pH is a key factor in regulating the effects of chemical fertilizers on soil organisms. Nitrogen fertilizers, in particular, will acidify the soil when used over a long period of time. This decrease in pH can directly harm earthworms, as earthworms generally prefer neutral to slightly alkaline conditions. Furthermore, soil pH significantly affects nutrient availability and the composition and activity of microbial communities. Acidic conditions may favor certain types of fungi while inhibiting many beneficial bacteria, including nitrogen-fixing bacteria.

One major difference between chemical and organic fertilizers is their effect on soil organic matter. Chemical fertilizers mainly provide inorganic nutrients and do not increase the organic matter content of the soil. In fact, some studies suggest that long-term use of chemical fertilizers may even lead to a decrease in soil organic matter. Organic matter, on the other hand, is essential for supporting diverse and abundant soil life. It provides a source of energy and nutrients for microorganisms, improves soil structure, enhances water-holding capacity, and aids in nutrient cycling. The depletion of organic matter due to reliance on chemical fertilizers may exacerbate many of the negative impacts discussed in this report.

Various effects of long-term application of chemical fertilizers—including shifts in microbial communities, reductions in earthworm populations, imbalances in nutrient cycling, deterioration in soil structure, and reduced plant health—can be classified as a deterioration in overall soil health. While chemical fertilizers can increase crop yields in the short term, they often come at the expense of the soil’s long-term sustainable function and ability to support healthy plant growth without ongoing large inputs of synthetic fertilizers. This degradation can lead to a vicious cycle, as more and more fertilizer is required to maintain yields as the soil’s natural fertility declines.

Long-term application of chemical fertilizers has been shown to have significant and often negative effects on soil microbial communities, leading to shifts in structure, diversity and function, particularly affecting beneficial taxa such as nitrogen-fixing bacteria and mycorrhizal fungi. Earthworm populations, biomass, and behavior are also adversely affected by long-term exposure to certain chemical fertilizers, especially those that acidify soils or are directly toxic. These impacts on soil organisms can disrupt the delicate balance of interactions between microorganisms and earthworms that are critical to maintaining soil health. The knock-on effects of these changes include disruption of essential nutrient recycling processes, deterioration of soil structure, and negative effects on plant health and stress resistance, often resulting in plants being more susceptible to attack by pests and diseases. Ultimately, widespread long-term use of chemical fertilizers can lead to serious environmental problems, including soil degradation, water and air pollution, and loss of biodiversity, threatening the sustainability of agricultural systems and the health of the planet.

Deterioration of soil health caused by the long-term use of chemical fertilizers poses a serious threat to the long-term productivity and resilience of agricultural systems worldwide. As soil loses its natural fertility and ability to support healthy plant growth, farmers increasingly rely on higher doses of synthetic fertilizers, creating a potentially unsustainable cycle. To mitigate these negative impacts and promote agricultural sustainability, a shift toward integrated nutrient management strategies is necessary. This includes reducing and making more judicious use of chemical fertilizers, combined with the use of organic amendments such as manure, compost and cover crops, which help improve soil structure, increase organic matter content and support a more diverse and functional soil biome. Practices that enhance soil organic matter, such as no-till or reduced-till farming practices, legume crop rotation and the use of green manures, should be encouraged to improve overall soil health and reduce the need for high levels of synthetic fertilizer inputs. The exploration and adoption of biofertilizers, which utilize beneficial soil microorganisms such as nitrogen-fixing bacteria, phosphorus-solubilizing microorganisms and mycorrhizal fungi, can provide a more environmentally friendly approach to plant nutrition and reduce reliance on chemical fertilizers. Responsible and targeted use of pesticides is critical to minimizing harm to beneficial soil organisms such as earthworms and non-target microorganisms. Regular monitoring of key soil health indicators such as microbial diversity, earthworm populations, organic matter content and soil structure is critical to assess the long-term impact of agricultural practices and guide the adoption of more sustainable management strategies. The wider environmental consequences of long-term chemical fertilizer use, including water and air pollution and loss of biodiversity, require concerted efforts to adopt more sustainable agricultural practices that minimize these negative impacts and promote environmental stewardship for current and future generations.

In summary, moving to agricultural systems that prioritize soil health, rely less on chemical fertilizers, and adopt more ecological principles is critical to ensuring long-term food security and environmental health. By cultivating healthy and resilient soil ecosystems, we can create more sustainable and environmentally responsible agricultural practices that benefit people and the planet.

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