Microbes in Agriculture: Roles, Limitations and Risks

Microbes are all around us. They are present in our air, water, and foods. These have both beneficial and harmful effects. Microbes in agriculture have significant roles and benefits. 

Microbes influence soil health, disease suppression, nutrient cycling, and plant growth in agriculture. These positive impacts increase the production of crops. Besides increasing crop productivity, microbes also benefit agricultural ecosystems’ soil fertility and functioning. 

However, the microbes in agriculture may be ineffective in some areas, sometimes increase disease transmission between plants, and negatively impact human health. Besides the limitations, microbes are considered the sustainable approach to improving agricultural productivity. 

Role of Microbes in Agriculture

Microbes in agriculture have many unique and essential roles. From impacting various aspects of plant growth to improving soil health. 

Harnessing the potential of microbes in agriculture can lead to more sustainable farming practices and reduces chemical inputs. 

Some of the critical functions of microbes in agriculture are nitrogen fixing, supporting plant growth, nutrient cycling, bioremediation, waste management, nutrient upcycling, and the production of foods by fermentation.  

Nitrogen fixation 

Nitrogen-fixing bacteria can convert atmospheric nitrogen into a form that plants can utilize. A symbiosis relationship exists between bacteria and leguminous plants like peas, clover, and soybeans. These bacteria reside inside the specialized structure known as nodules in plants’ roots. Using these bacteria provides plants with nitrogen, reducing the need for synthetic fertilizers. 

Nutrient cycling

Microbes have a role in the decomposition of organic matter in the soil. The complex organic materials from plant and animal manure are broken down by microbes into simple forms, thus releasing nutrients like phosphorus, nitrogen, and potassium. The process is called mineralization, where nutrients are available for plant uptake, promoting healthy plant growth. This process not only helps in the recycling of nutrient but also help in waste management because animal manure and crop residues are decomposed for nutrient recycling. 

Diseases suppression

The microorganisms can act like natural biocontrol agents that help to suppress plant diseases caused by pathogens. The beneficial microbes colonize plant surfaces like the rhizosphere (the soil around the plant root), compete with harmful organisms for resources, and produce antimicrobial compounds or induce systemic resistance in plants. It is an environmentally friendly alternative for biocontrol hence reducing the use of chemical pesticides. 

Plant growth promotion

Beneficial microbes help plant growth directly by producing growth-promoting substances or helping in nutrient uptake. For example, a symbiotic relationship between mycorrhizal fungi and plant roots helps extend their reach in the soil to improve nutrient (especially phosphorus) absorption. Likewise, some bacteria produce hormones that enhance plant growth and increase a plant’s tolerance capability to environmental stress like drought and disease.  

Fermentation and food production

Microbes play a crucial role in fermentation, where yeasts or bacteria ferment sugars into alcohol, gases, or organic acids. The process is helpful in the production of foods like beer, bread, cheese, yogurt, wine, sauerkraut, and other fermented foods. 


Microbes can degrade various soil contaminants, which makes them valuable in bioremediation efforts. These microbes can break down pollutants from pesticides, petroleum hydrocarbons, and herbicides in soil and water, which helps clean polluted agricultural sites. 

Soil structure and aggregation

Soil aggregate formation and stabilization are crucial to improving soil structure, which prevents erosion. Filamentous fungi and bacterial species produce stick substances called extracellular polymeric substances that bind soil particles together to create stable soil aggregates. The aggregates improve soil porosity, root penetration, water infiltration, and facilitation of plant growth.   

Limitations and Risks of Microbes in Agriculture 

Although microbes are highly beneficial to agriculture, it has some limitations and challenges associated with their use. Some limitations and risks of microbes in agriculture are the need for knowledge and understanding, limited range of action, effectiveness variability, competition and survival challenges, risk to human health and ecological impacts, and cost of application and logistics differences. 

Need for understanding and knowledge

Although many types of research on microbial use in agriculture have advanced, there are much more areas to learn. The complex interactions between microbes, plants, and the environment are yet to be studied. There are yet to be in-depth studies on the mechanisms applied by microbes to suppress plant disease and enhance plant growth and nutrient cycling. The lack of in-depth research can limit microbial interventions’ precise and targeted application in agriculture.    

Specificity and limited action range 

Some microbial strains are effective against specific pathogens or pests only. This limitation restrict their use in diverse agricultural systems. Adding to that, some beneficial microbes can be effective only on certain crops under specific environmental conditions. So, the action range of beneficial microbes is narrow and specific, which limits their use in broad agricultural areas.   

Variability in effectiveness

All microbes do not provide consistent and reliable results in all the fields of the environment. Environmental conditions, specific microbial strains, crop productivity, and soil type shows that the microbes’ effectiveness varies in agricultural areas. The efficacy of microbial applications hence requires careful selection for desired outcomes. 

Application cost and logistics

Different logistics, like addition infrastructures, equipment, and management considerations, are required for adding microbes and microbial products in agricultural practices. Applying microbial products requires appropriate timing, dosage, and application methods. Likewise, the cost of using and acquiring microbial products can be high. The expense of adding microbes and microbial products becomes a limiting factor for farmers with resource-constrained agricultural systems.  

Regulatory considerations

Different countries or regions have additional regulatory considerations due to human health concerns. The use of microbes can lead to toxicity, allergies, and spreading of antibiotic resistance among bacteria that are pathogenic to humans. The regulatory concerns help ensure microbial products’ safety, quality, and efficacy. The regulatory considerations generate complex approval processes. The complexity arising due to the regulatory considerations can add to these products’ adaptation time and availability in the agricultural fields. 

Competition and survival challenges

Beneficial microbes face competition from native microorganisms already in the soil or plant when first introduced to the environment. Microbial competition, adverse soil consciousness, predation, and interactions with existing microbial communities can influence the survival and establishment of introduced microbes. The successful colonization and persistence of introduced beneficial microbes can be challenging.

Disease transmission

Instead of suppressing plant diseases, beneficial microbes can sometimes act as pathogens. If these are not managed, the addition of pathogenic microbes can spread diseases among crops. The spread of infection can lead to economic losses and environmental damage. So, quality control, rigorous testing, and following biosecurity protocols are crucial for minimizing the risk of disease transmission.  

Ecological impacts

Adding non-native or genetically modified microbes to the environment may disrupt natural microbial communities, which alters the ecosystem processes. So, evaluating the potential environmental impacts is crucial before introducing the microbes to agricultural settings.

Development of resistance

Pests and pathogens can develop resistance to microbial products like biopesticides and bio fungicides after extensive use. Proper stewardship practices like the rotation of different control measures and integrated pest management strategies should be used to mitigate this risk.  


  • Sundh, I., Del Giudice, T., & Cembalo, L. (2021). Reaping the Benefits of Microorganisms in Cropping Systems: Is the Regulatory Policy Adequate?. Microorganisms, 9(7), 1437. https://doi.org/10.3390/microorganisms9071437 
  • Ray P, Lakshmanan V, Labbé JL and Craven KD (2020) Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture. Front. Microbiol. 11:622926. doi: 10.3389/fmicb.2020.622926
  • Beneficial microorganisms in Agriculture. Retrieved from http://eagri.org/eagri50/AMBE101/pdf/lec25.pdf 

Ashma Shrestha

Hello, I am Ashma Shrestha. I had recently completed my Masters degree in Medical Microbiology. Passionate about writing and blogging. Key interest in virology and molecular biology.

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