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Agriculture Made Sustainable, Episode 4: Plant Microbiome

“Agriculture Made Sustainable” is a Food Circle project designed to create an awareness-raising process about sustainable agriculture, especially organic farming. It discusses the barriers, problems, challenges, advantages, and disadvantages of sustainable development in organic agriculture. Since various sectors such as plant nutrition, pest control, plant protection, soil, seeds, agricultural tools, and machinery are parts of the process, awareness can promote and develop sustainable agriculture to reduce the adverse effects of climate change global warming.

What are we talking about?

The plant microbiome is one of the most influential determinants of vegetation survival, especially concerning strategic plants used by humans. The microbiome is an essential issue if we can create robust vegetation by identifying beneficial microbes and microorganisms. Healthy plant microbiomes are also stable in the desired agricultural ecosystem. The connection between plant microbiome and microbiology science has led to new resistant plants. Therefore, the plants would strengthen against adverse environmental factors, pests, diseases, etc.

"Indeed, plants harbor a wide diversity of microorganisms both inside and outside their tissues, in the endosphere and ectosphere, respectively. These microorganisms, which mostly belong to Bacteria and Fungi, are involved in major functions such as plant nutrition and plant resistance to biotic and abiotic stresses. Hence, the microbiota impact plant growth and survival, two key components of fitness. (Philippe Vandenkoornhuyse et al., 2015)" [1]

In recent years, examples of these resistance phenomena concerning resistant seeds have created outstanding experiences in agriculture. With the genetic development of these plants and strong breeds, many plant diseases that cause significant damage in the early stages of plant growth will be eradicated. On the other hand, the consumption of specialized pesticides is reduced in these stages. "One proposed approach is the use of the driven factors that influence the microbiota community composition to stimulate its beneficial members. Some examples of these influential factors are the use of bio inoculants, proper agricultural practices, and certain environmental conditions. On the other hand, micro-organisms with critical roles in the microbiome can be isolated, formulated, and become a new biological product. Regardless of the approach to be used, innovations with the use of microbiomes represent the future of sustainable agriculture. (Lidiane Figueiredo Santos and Fabio Lopes Olivares, 2021)" [2]

The process of microbiome strengthening is a progressive practice in sustainable agriculture and can be considered a critical factor in achieving the goals of integrated sustainable agriculture management. The procedure has a positive effect on increasing the yield of agricultural products and increasing productivity.

Plants are involved with a wide range of microbes in nature, which can cause damage or positive changes in soil and vegetation. The process of amplifying beneficial microbiomes can help strengthen the desired vegetation. Healthy microbiomes have a broad range of activities and, if enhanced, will produce positive changes in vegetation. Beneficial microbes are directly related to the ecology and physiology of plants. Can say that plants' key and superior traits and the characteristics of plant genes naturally identify these beneficial microorganisms. If we strengthen these functional traits, we will support vegetation and microbes with manipulations in this field by genetic knowledge.

"The role of the microbiome and its relationship to plant health, productivity, and biogeochemical cycles should be considered as much as the plant itself. An extension of this notion is that molecular breeding or genetic modification of plants could be used to modulate the microbiome intentionally, recruiting disease antagonists and plant-growth promoters to improve agricultural production. (Thomas R. Turner et al., 2013)" [3]

Soil health is one of the main issues pursued concerning sustainability goals. There are many microbiomes in the soil that play a crucial role in the roots' absorption of water and salts. If occupied by beneficial microbes, interactions between the ground and the environment around the roots can provide very favorable conditions for plant uptake. On the other hand, this absorption is not limited to water and minerals. Physicochemical reactions around the plant root will also be most effective for plant growth if carried out by beneficial microbes. In this case, the plant microbiome will be at its highest available yield.

"Soil is living and dynamic and the resultant of a million years of evolution. The rhizosphere is the area around the root zone that is very important for a plant to fulfill its water and nutrient requirement. Different microbes form microbial communities vis-àvis plant roots and perform the exchange of chemicals and nutrient cycling in the zone of the rhizosphere (Jacoby et al. 2017). Together they plant exudates and microbial communities in the rhizosphere called ‘microbiome’ are the result of millions of years of co-evolution. (Leila Bensidhoum and Elhafid Nabti, 2020)" [4]

The plant microbiomes influence plant nutrition also nutrient deficiencies in plant organs. Significantly when water and minerals are spread through these organs to different parts of the plant, the plant microbiome ability can affect the capability of plant uptake and excretion. They will have more effects when plants experience stomatal obstruction or when harmful pathogens have invaded the plant. Strengthening microbiomes can also reduce the detrimental impact of plant stomata. Will highlight the problem concerning environmental stresses and a variety of physiological deficiencies if the plant microbiome is inefficient. Although various factors are involved in this situation, strengthening microbiomes can reduce the negative effects.

Integrated management in sustainable agriculture as a strategy to reduce chemical methods and develop a healthy product requires creating tools. Organic farming and contributing factors of this method as the most prominent tool in integrated management have a decisive role. On the other hand, some requirements such as physical and mechanical methods are also of great importance. The role of plant microbiomes in this method can act as an invisible and efficient tool for the development of sustainable agriculture through integrated management.

In Conclusion:

A holistic view of plants as part of life on Earth allows us to examine them in more detail. This view is not a suggestion or hypothesis; it is a necessity. Much of the planet's life is threatened by climate change. Unfortunately, it will not quickly repair irreparable parts of these threats. Exploring plant physiology and its relationships with other microorganisms can help restore vegetation. On the other hand, by considering the plant microbiomes and strengthening their parts, the earth territories constantly exposed to erosion can be primarily repaired. These methods will help achieve the overall goals of sustainable agriculture.

Author: Majid Zamanshoar


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  1. Philippe Vandenkoornhuyse et al., The importance of the microbiome of the plant holobiont, [online] Available at:

  2. Lidiane Figueiredo Santos and Fabio Lopes Olivares, Plant microbiome structure and benefits for sustainable agriculture, [online] Available at:

  3. Thomas R. Turner et al., The plant microbiome, [online] Available at:

  4. Leila Bensidhoum and Elhafid Nabti, Biofertilizers and Biopesticides: Microbes for Sustainable Agriculture, [online] Available at: