Effects of chemical fertilizers on soil microbial communities, plant diseases and pesticide use

Long-term application of chemical fertilizers not only destroys soil microbial diversity, but also weakens plant immunity and encourages the reproduction of pathogens, further forcing farmers to rely on more pesticides, forming a vicious cycle that damages agricultural sustainability.

Soil health is the cornerstone of maintaining agricultural productivity and ecosystem services. Chemical fertilizers are widely used in modern agriculture to increase crop yields. Although chemical fertilizers have brought significant yield increases in the short term, there are growing concerns about their long-term sustainability and environmental impact. One issue worthy of concern is that long-term application of chemical fertilizers may disturb the balance of soil microbial communities, increase the proportion of harmful microorganisms, weaken the natural immunity of plants, and lead to the occurrence of plant diseases, thus forming a vicious cycle in which farmers rely on more pesticides to control diseases. This report explores how chemical fertilizers affect soil health and analyzes their complex relationship with plant diseases and pesticide use.

Long-term application of chemical fertilizers has significant effects on the balance and diversity of soil microbial communities1. Research shows that long-term application of nitrogen fertilizer will significantly change the pH value of the soil, thereby affecting the main bacterial species in the soil. Excessive application of nitrogen fertilizer can even lead to a significant reduction in the number of bacterial operational taxonomic units (OTUs)1. In addition, long-term use of chemical fertilizers will reduce soil organic matter, pH value, total nitrogen, nitrate nitrogen and total phosphorus content, and also lead to excessive accumulation of ammonium nitrogen and available phosphorus in the soil, thereby causing soil acidification, changing the bacterial community structure, and reducing fungal diversity.2. Long-term application of chemical fertilizers alone exerts deep selective pressure on soil microbial communities, leading to an increase in the proportion of obligate microorganisms and an enhancement of the characteristics of decisive processes, while reducing the richness and diversity of bacterial communities.3. Long-term fertilization will also lead to excessive residual ammonium nitrogen and available phosphorus in the soil. Ammonium nitrogen will lead to soil acidification and changes in bacterial community structure, while phosphorus will reduce the diversity of fungi.2. High-intensity mineral fertilizer applications can negatively impact soil organisms, reducing microbial species diversity and potentially creating niches for pathogenic organisms to colonize4. In contrast, organic farming increases the richness, reduces evenness, reduces dispersion, and changes the structure of soil microbial communities.5. Research also points out that chemical fertilizers may have harmful effects on soil microbial colonies, and microorganisms show sensitivity to the application of nitrogen, phosphorus, and potassium fertilizers.6. Overfertilization can lead to serious environmental problems, including toxicity to different beneficial microorganisms7. Although chemical fertilizers may alter the abundance of microbial populations and stimulate their growth by providing nutrients, they may not significantly affect bacterial and fungal richness and diversity. Changes in the abundance of individual bacterial or fungal species are mainly attributed to changes in soil chemistry caused by chemical or organic fertilization. Conventional fertilizers reduce the variety and amount of life in the soil, including microorganisms that are critical to soil structure and long-term productivity.

microbiota	Effects of long-term application of chemical fertilizers	Related literature
bacteria	Diversity decreases, composition changes, specific taxa (e.g.Pirellula、Bdellovibrio)Increase	1, 2, 3, 2, 4, 6
Fungi	Reduced diversity, altered composition, and fewer beneficial fungi (e.g., mycorrhizal fungi)	2, 3, 2, 4, 13, 14, 2
Nematodes	Increase in plant parasitic nematodes	70, 8
Arbuscular mycorrhizal fungi	Reduced colonization rate and diversity	13, 71, S_38, S_100, S_123, S_153, S_159
Azotobacter	Activity and abundance are suppressed	72, 72, S_122, S_125, S_131, S_142, S_166

Changes in microbial communities caused by chemical fertilizers may also lead to an increase in harmful microorganisms such as pathogenic fungi, bacteria and nematodes8. Excessive use of chemical fertilizers, especially nitrogen fertilizers, can lead to the accumulation of fewer beneficial bacteria and more pathogens in the rhizosphere9. Indiscriminate use of chemical fertilizers can adversely affect soil microbial communities, leading to increased numbers of pathogens and pests in soil-plant systems8. Intensive application of mineral fertilizers reduces the diversity of microbial species and creates niches for the emergence of pathogenic organisms4. Compared with chemical fertilizers, bioorganic fertilizers changed the composition of nematode communities and increased beneficial bacterivorous nematodes that feed on non-pathogenic antagonistic bacteria.10. Excessive use of chemical fertilizers can damage the soil environment, change the microbial community structure, and may facilitate the reproduction of pathogens11. Long-term fertilization may lead to the accumulation of pathogenic fungi12。

The use of chemical fertilizers can also lead to changes in soil microbial diversity and functional metabolic diversity. The arbuscular mycorrhizal fungal network on conventional farms had a simpler structure, weaker interactions, and a higher proportion of negative ties, which may indicate more intense competition among species. Organic farms have more complex networks13. Long-term application of nitrogen fertilizer can significantly affect most major soil bacterial species, while excessive application can lead to a significant reduction in the number of bacterial OTUs1. Long-term application of chemical fertilizers will reduce the richness and diversity of soil bacteria, while the combined application of organic and chemical fertilizers will increase the richness of bacteria and the diversity of fungi.14. Long-term fertilization significantly increases the structure of soil bacterial communities, which is further promoted by organic amendments15。

Certain chemical fertilizers, such as high-nitrogen fertilizers, can weaken a plant’s natural immunity, making it more susceptible to disease attack16. High concentrations of nitrogen affect the signaling pathways of peptide hormones involved in plant resistance to bacteria, thereby reducing this resistance16. High nitrogen supplies limit the availability of proteins (peptides) that make plants resistant to certain bacteria, making plants more susceptible to disease17. Nitrogen generally has a negative impact on physical defense and the production of antimicrobial phytoalexins, but has a positive impact on defense-related enzymes and proteins that influence local defense and systemic resistance.18. High nitrogen levels have been shown to increase a plant’s susceptibility to certain diseases, due to increased sap and rapid growth of the plant, making it more susceptible to pathogen attack19. Nitrate supply enhances hypersensitivity-mediated resistance, whereas ammonium supply impairs defenses20. In bananas infected with banana fusarium wilt, disease severity increases with nitrogen fertilizer use, and ammonium fertilizer is inversely correlated with disease progression-related protein 1, a key defense protein.21。

Chemical fertilizers affect plant metabolism and the production of defense-related compounds (e.g., phytoalexins, defense proteins)18. Nitrogen often has a negative impact on physical defenses and the production of antibacterial phytoalexins18. Accumulation of cadmium in plants disrupts nitrogen metabolism18. Nitrogen supply limits pathogen growth and affects the initiation and deployment of plant defenses18. High concentrations of nitrogen affect peptide hormone signaling pathways involved in plant immunity23. Nitrogen negatively affects phytoalexin production24. Ammonium-mediated plant immunity is related to amino acid metabolism18。

Increased plant susceptibility to disease under high chemical fertilizer application regimens16. Excessive nitrogen input may reduce yields and easily lead to the occurrence of pests and diseases18。

The use of chemical fertilizers can cause changes in soil pH and nutrient concentrations2. Long-term application of nitrogen fertilizer will reduce soil pH28. Long-term application of chemical fertilizers will cause soil acidification due to excess ammonium nitrogen.2. Ammonium-based fertilizers have the greatest potential to acidify soils. Nitrate-based fertilizers have no acidifying potential and can raise soil pH29. Application of ammoniacal nitrogen fertilizer significantly increases exchangeable acidity and decreases pH30. Ammonium-based fertilizers acidify the soil by producing hydrogen ions through nitrification.29. Ammonium-based fertilizers have the greatest potential to acidify soils. Nitrate-based fertilizers are non-acidifying and can raise pH31. Excess ammonium nitrogen can cause soil acidification2. Ammonium-based fertilizers are a major contributor to soil acidification through nitrification32. The use of ammonium-based nitrogen fertilizers at a rate that exceeds crop uptake is a major agronomic cause of soil acidification33. When ammonium in the soil is converted into nitrate, it produces acidity. The more ammonium nitrogen fertilizer is applied, the more acidic the soil becomes.34. Continued use of ammonium-based fertilizers can increase soil acidification because ammonium produces hydrogen ions when converted to nitrates35. Nitrate-based fertilizers can increase soil pH29. Long-term application of phosphate fertilizers has been shown to reduce soil pH[70。

These changes can contribute to the development of specific plant diseases in a variety of ways21. Soil pH affects diseases such as potato scab and cruciferous vegetable clubroot. Certain pathogens thrive more easily in specific soil types and pH levels36. Acidic soil conditions (low pH) can cause aluminum toxicity, damage plant roots, and may increase susceptibility to disease37. Soil pH determines nutrient availability to plants. A pH imbalance can weaken plants and make them more susceptible to pests and diseases. Raising soil pH can control clubroot, while alkaline soils are more susceptible to potato scab.38. Acidic soil reduces the availability of essential nutrients and increases the impact of toxic elements such as aluminum and manganese, affecting plant production and water use, and inhibiting beneficial soil bacteria39. Unfavorable soil pH can cause nutrient deficiencies or toxicity symptoms, making plants more susceptible to disease40. Banana Fusarium Wilt Exacerbated by Ammonium-Induced Soil Acidification21. Changes in soil pH can directly affect the survival and virulence of plant pathogens. Some pathogens thrive in acidic conditions, while others prefer alkaline soil. Altered pH can also affect the availability of essential nutrients, further stressing the plant and compromising its ability to fight disease. Increased solubility of toxic elements such as aluminum in acidic soils increases the risk of plant disease. Potato scab is inhibited at low pH, while clubroot of cruciferous vegetables is controlled by high pH. Fusarium wilt is more destructive in lighter and higher pH soils36. Banana Fusarium Wilt Exacerbated by Ammonium Fertilizer Acidifying Soil21。

Vicious cycle of increased plant diseases leading to increased pesticide use

There is a correlation between increased incidence of plant diseases caused by chemical fertilizers and subsequent increases in pesticide applications27. Regular application of chemical fertilizers can change soil pH, increase pest resistance, and increase pest attacks, resulting in reduced organic matter and stunted plant growth.41. Using more than optimal amounts of fertilizer can increase pest, disease, and weed infestations. Unbalanced fertilizer use can lead to nutritional imbalances that can lead to disease. Excess nitrogen can make plants succulent and more likely to attract insects and pathogens27. Pesticides play a key role in reducing disease and increasing crop yields worldwide42. The application of nitrogen fertilizers in long-term tea tree cultivation will change the bacterial composition and reduce soil pH, which may lead to an increase in diseases and require more pesticides and other interventions.43. Excessive application of nitrogen fertilizer will increase the incidence of crop diseases and insect pests27. High nitrogen input may lead to reduced yields and prone to the occurrence of pests and diseases42。

While pesticides provide protection in the short term, overuse can lead to soil contamination and may harm non-target organisms42. Over-reliance on chemical fertilizers can lead to soil depletion and create an environment for pests and diseases, requiring more chemical inputs27. High concentrations of nitrogen promote the growth of lush vegetation, but these vegetation are susceptible to pests and diseases and may require additional pesticide applications44。

Overuse of pesticides negatively affects soil health, biodiversity and the environment8. Pesticides and insecticides can significantly affect earthworms, reducing their numbers and negatively affecting soil fertility45. Pesticides, especially carbamate pesticides, are often toxic to earthworms. Certain fungicides and nematicides are also highly toxic to earthworms46. Earthworms are highly susceptible to pesticides and synthetic chemicals, leading to significant declines in their numbers and adverse effects on soil fertility45. Excessive use of chemical fertilizers and pesticides can lead to reduced soil fertility and increased numbers of pathogens and pests8. Pesticide contamination can spread beyond target plants, causing environmental contamination and affecting human health through food contamination42. Excessive use of chemical fertilizers and pesticides has negative impacts on the environment and human health47. Pesticide use has harmful effects on biodiversity, with short-term toxic effects on directly exposed organisms and long-term effects on habitats and food chains48. Pesticide pollution causes environmental pollution and affects human health42. Pesticides contaminate freshwater, marine ecosystems, air and soil and can remain in the environment for generations, disrupting the hormonal systems of humans and wildlife. Overreliance can lead to insecticide resistance in pests and damage soil health by disrupting beneficial microorganisms44. Pesticide pollution causes environmental pollution and affects human health42。

Long-term reliance on chemical fertilizers and pesticides can have cumulative negative impacts on soil health, biodiversity and agricultural sustainability[49, 50, 43, 41, 43, 51, 52, 3, 53, 54, 55, 41, 43, 44, 56, S_S152]. The co-application of earthworms and cow manure improves soil fertility, microbial diversity and community structure, promotes plant growth and provides a sustainable strategy while reducing the use of chemical fertilizers.49. Improper use of mineral fertilizers will damage the function of the soil, affect chemical, physical and biological indicators, reduce the content of soil organic carbon and beneficial organisms, hinder plant growth, and even lead to the emission of greenhouse gases.50. Long-term fertilization can lead to harmful environmental effects such as soil salinization, heavy metal accumulation, eutrophication, nitrate accumulation, greenhouse effect, and biomagnification. Overuse has caused soil, water and air pollution and reduced soil fertility, leading to severe soil degradation43. Long-term chemical fertilizer residues in soil can damage soil biodiversity41. Continued overuse of chemical fertilizers reduces soil organic matter content and degrades soil structure43. Continued use of chemical fertilizers reduces soil health and quality, causing soil pollution51. Excessive fertilization can cause serious environmental problems (loss of biodiversity, accumulation of heavy metals, eutrophication of water bodies, toxicity to beneficial microorganisms) and may contribute to the greenhouse effect52. Long-term application of chemical fertilizers alone will exert profound selective pressure on soil microbial communities, leading to degradation3. Long-term fertilization can lead to harmful environmental effects, such as soil salinization, heavy metal accumulation, eutrophication, nitrate accumulation, greenhouse effect, biomagnification, etc.53. Conventional fertilizers reduce the variety and amount of life in the soil, which is critical to long-term productivity54. Excessive use of chemical fertilizers can lead to deterioration of soil health, affecting soil quality, structure, pH and nitrogen cycling, reducing microbial diversity, and making soil and plants more susceptible to pests and diseases.55. Long-term chemical fertilizer residues in soil can damage soil biodiversity41. Long-term fertilization can have harmful effects on the environment, such as soil salinization, heavy metal accumulation, eutrophication, nitrate accumulation, greenhouse effect, and biomagnification. It also reduces soil organic matter content, activity of beneficial organisms, changes soil pH and increases pests43. Long-term use of pesticides can lead to shifts in the composition and dominance of species in ecosystems, causing ecological imbalances and undermining the sustainability of agricultural practices as pests develop resistance and soil health degrades44. Long-term use of chemical fertilizers will reduce soil organic matter content, reduce soil quality, harden the soil, reduce fertility, consume important soil mineral nutrients, and pollute the air, water and soil.56. The application of synthetic fertilizers and monocultures can degrade the soil over time, causing a host of problems and requiring more inputs. Long-term excessive use of chemical fertilizers can lead to soil salinization, heavy metal accumulation, eutrophication, nitrate accumulation, greenhouse effect and biomagnification.43. It also reduces soil organic matter content, changes soil pH, reduces the activity of beneficial organisms, and increases the occurrence of pests and diseases43. This continued dependence creates a vicious cycle that harms soil health and the environment.

The study compared the effects of different fertilization methods, such as chemical fertilizers and organic fertilizers, on the incidence of plant diseases and the amount of pesticides used.5. Arbuscular mycorrhizal fungal networks are more complex in organic farming than in conventional farming13. The co-application of earthworms and cow manure creates a synergistic effect, improving soil fertility and microbial diversity while reducing the amount of chemical fertilizers.49. The combined application of organic and chemical fertilizers significantly improves soil fertility and increases beneficial bacteria while reducing pathogenic bacteria14. Organic fertilizer treatment significantly reduced the content of heavy metals and increased beneficial bacteria in rhizosphere soil and tea leaves57. Earthworms and cow manure promote the growth of beneficial bacteria such as Bacillus and reduce pathogenic fungi49. Phosphate-soluble biofertilizers are considered a greener and often cheaper alternative to chemical phosphate fertilizers, offering benefits such as enhanced nutrient uptake, plant hormone production and biological control58. Inoculation of arbuscular mycorrhizal fungi can effectively reduce overuse of chemical fertilizers in corn production59. Organic fertilizers enhance microbial diversity and support beneficial microorganisms compared to chemical fertilizers60. Bioorganic fertilizers change the composition of nematode communities and increase beneficial bacterivorous nematodes that feed on pathogen-antagonizing bacteria, thereby suppressing pathogens10. The application of microbial fertilizers significantly increases the richness of soil microorganisms, maintains soil microecological balance, effectively improves the soil environment, and enhances plant disease resistance.11. Organic farming increases the richness, reduces evenness, reduces dispersion, and changes the structure of soil microbial communities compared to conventionally managed soils where mineral fertilizers are applied alone5. Animal fertilizers increase the diversity of the soil microbiome, while plant fertilizers maintain its stability. Plant fertilizers also have lower risk factors such as antibiotic resistance genes and viruses61. Bio-organic fertilizers applied together with nitrogen, phosphorus and potassium fertilizers will increase the number of bacteria6. Animal fertilizers increase soil microbiome diversity, while plant fertilizers maintain stability62. Organic fertilizers help shape microbial composition and recruit beneficial bacteria, thereby improving tea quality and reducing heavy metal levels in rhizosphere soil and tea leaves.12. Organic fertilizers improve soil health and plant growth by improving soil organic matter, structure, nutrient uptake, water-holding capacity and microbial activity, and can increase tolerance to abiotic stresses63. Nitrogen-fixing bacteria perform better on organic farms than on conventional farms, and they are particularly sensitive to the toxic effects of chemical pesticides. Organic amendments help build soil health and fertility in the long run51. Research shows organic farming can reduce pesticide use64。

In summary, long-term application of chemical fertilizers will have many negative impacts on soil microbial communities, leading to a reduction in microbial diversity and an increase in the proportion of harmful microorganisms. These changes weaken the plant’s natural immunity, making it more susceptible to disease attack. In addition, changes in the soil environment caused by chemical fertilizers, such as reductions in pH and changes in nutrient concentrations, create favorable conditions for the development of specific plant diseases. Increases in plant diseases in turn prompt farmers to use more pesticides to control diseases, creating a vicious cycle with long-term negative consequences for soil health, biodiversity and agricultural sustainability.

To break this vicious cycle, we recommend the following measures:

1. Promote integrated fertilization strategies: Use a combination of organic fertilizers, bio-fertilizers and appropriate amounts of chemical fertilizers to maintain the balance and diversity of soil microbial communities, enhance plants’ natural immunity, and reduce dependence on chemical pesticides14。
2. Reduce the use of high-nitrogen fertilizers: Research shows that excessive use of nitrogen fertilizer can weaken plant immunity. Nitrogen fertilizer should be applied accurately based on the actual needs of the crop and soil testing results16。
3. Improve soil pH: Monitor soil pH and use lime or other amendments to adjust soil pH as needed to create an environment that is less conducive to pathogen growth and more conducive to plant health and nutrient uptake.29。
4. Implement permaculture practices: Employ a variety of agricultural practices such as no-till or reduced-till, cover crops, and crop rotation to improve soil structure, increase organic matter content, and promote the growth of beneficial microorganisms to improve soil health and plant disease resistance.46。
5. Strengthen research and education: More research is needed to gain insight into the long-term effects of different fertilization methods on soil microbial communities and plant health, as well as to educate farmers on permaculture knowledge and techniques and encourage them to adopt more environmentally friendly farming practices.
6. Develop relevant policies: The government and relevant departments should formulate policies that are conducive to the development of sustainable agriculture, encourage the reduction of the use of chemical fertilizers and pesticides, and promote organic and green agriculture, thereby protecting soil health and the environment.

Through these comprehensive measures, we can gradually reduce our dependence on chemical fertilizers and pesticides, build a healthier and more resilient agricultural ecosystem, and ultimately achieve sustainable development of agriculture and food security.

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