“Domestication and genetic improvement have reduced the ability of plants to interact with beneficial microorganisms…”
Rodrigo Mendes is a researcher at Embrapa’s Enviroment Unit and a graduate professor at the University of São Paulo.
Mendes is an agronomist with a Ph.D. from ESALQ/USP and postdoctoral experience at Wageningen University and the University of California.
AgriBrasilis – What is the importance of microorganisms for grain farming?
Rodrigo Mendes – Soil microorganisms play essential roles such as nutrient cycling, phosphorus solubilization, biological nitrogen fixation, and organic matter decomposition. They also directly promote plant growth through phytohormone production and protection against pathogens.
The interaction between plants and the soil microbiome is so deep that we now refer to them as a “superorganism,” which includes the host (the plant) and millions of associated microorganisms functioning as a single unit, also known as a “holobiont.” In grain farming, which often involves high nutrient demand and environmental stress, maintaining a healthy and balanced soil microbiome is key to resilience and productivity.
AgriBrasilis – Do agricultural inputs affect the soil microbiota? How?
Rodrigo Mendes – Yes, agricultural inputs — whether fertilizers, soil amendments, chemical or biological pesticides — directly or indirectly affect the composition and functionality of the soil microbiome. Nitrogen fertilizers, for example, can reduce the diversity of microorganisms involved in biological nitrogen fixation. Broad-spectrum fungicides can negatively affect beneficial fungi, such as mycorrhizae. On the other hand, biological inputs such as inoculants and biostimulants can enrich specific functional communities. The challenge is to understand these interactions systemically, as the microbiome responds not only to the type of input, but also to the method of application, the crop that is being cultivated, soil management practices, and the area’s usage history.
AgriBrasilis – How can the impact of biostimulants be evaluated?
Rodrigo Mendes – Evaluating the impact of biostimulants requires a multi-scale approach, from the laboratory to the farm, involving both agronomic and microbiological analyses. In our studies, we use microcosm experiments, microbial interaction network modeling, and DNA sequencing to detect changes in the structure and function of the microbiome.
Functional tests, such as enzymatic activity and metabolic profiling, also help in understanding microbial responses. It’s important that biostimulants are assessed for their ability to positively modulate the soil and rhizosphere microbial community and, consequently, their effect on crop yields.
AgriBrasilis – Why are rhizosphere bacteria considered the plant’s “first line of defense”?
Rodrigo Mendes – The first millimeters of soil surrounding plant roots harbor a highly specialized microbiota known as the “rhizosphere microbiome.” This microbiome is recruited by the plant itself through the exudation of organic compounds. Rhizosphere bacteria are the “first line of defense” because they form a biological barrier that competes with pathogens for space and nutrients, while also producing antimicrobial compounds and inducing systemic resistance in the plants. Their effectiveness depends on the diversity, density, and functionality of the microorganisms that are present in the rhizosphere.
“Domestication and genetic improvement have ultimately reduced the ability of modern plants to interact with beneficial microorganisms…”
AgriBrasilis – What other defenses do plants have against pathogens?
Rodrigo Mendes – In addition to interactions with beneficial microorganisms, plants possess innate defenses such as physical barriers (cuticle, cell wall) and chemical defenses (production of antimicrobial metabolites). They also have a sophisticated immune system that detects pathogen-associated molecular patterns and triggers local and systemic defense responses. In many cases, these responses are more effective when coordinated with the microbiome’s activity, demonstrating how biotic and abiotic plant defenses are interdependent.
AgriBrasilis – Why are some soils suppressive to plant pathogens?
Rodrigo Mendes – Suppressive soils are complex ecosystems where the microbiota plays a central role in disease control. In these soils, pathogens are naturally inhibited by competition, antibiosis, or parasitism from the native microbiome. This phenomenon is often the result of long-term sustainable management, with reduced use of chemical inputs, crop rotation, and high plant diversity. Understanding the mechanisms behind this property allows us to develop strategies to make conventionally managed soils more resilient.
However, new varieties are still being tested, and in the future, we will certainly see important changes in the apple market.
AgriBrasilis – What practices promote microbial diversity in crop fields?
Rodrigo Mendes – Practices that increase plant diversity and minimize physical and chemical disturbances to the soil tend to enhance microbiome diversity. These include crop rotation, no-till farming, organic matter addition, use of cover crops, and reduced agrochemical use. Agricultural system diversification creates ecological niches for different microbial groups and contributes to ecological balance in the soil, increasing its capacity to deliver ecosystem services.
AgriBrasilis – What are the latest advances in soil microbiology?
Rodrigo Mendes – Advances in soil microbiology, driven by “omics” technologies, show that the microbiome functions as an extension of the plant genome. Domestication and genetic improvement have reduced the ability of modern plants to interact with beneficial microorganisms. A promising alternative is to recover the ability of ancestral plants to interact with microorganisms and reintroduce it into modern cultivars. The current challenge is to transform this knowledge into simple, useful, and accessible solutions for farmers.
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