Development of synthetic bacterial communities with the ability to combat fungal diseases in soybean

• Grant number: 24/23306-2
• Support Opportunities: Scholarships in Brazil - Master
• Start date: June 01, 2025
• End date: July 31, 2026
• Field of knowledge: Biological Sciences - Microbiology - Biology and Physiology of Microorganisms
• Principal Investigator: Paulo José Pereira Lima Teixeira
• Grantee: Jose David Correa Oviedo
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil

Abstract

All plants are colonized by a vast diversity of microorganisms that form highly complex and dynamic communities, known as microbiomes. These communities inhabit both the interior and surface of plant tissues, directly influencing host development and its interaction with the environment. Recently, plant-associated microbiomes have been recognized as an extension of the plant immune system, providing an additional layer of protection against pathogens. Thus, the strategic manipulation of these microbiomes, aiming to introduce or promote the enrichment of beneficial microorganisms, emerges as a promising approach for controlling plant diseases in agriculture. In this context, our research group established the Soybiome collection, composed of approximately 3,000 bacteria isolated from soil, leaves, and roots of soybean cultivated in field conditions in Brazil's main producing regions. This collection has been explored to identify members with traits of interest, such as the ability to inhibit pathogens. In an initial evaluation of 637 members of the collection, we identified 81 bacteria capable of inhibiting the in vitro growth of some of the main soybean pathogenic fungi, including Phakopsora pachyrhizi, Fusarium tucumaniae, Colletotrichum truncatum, Sclerotinia sclerotiorum, Macrophomina phaseolina, and Corynespora cassiicola. This master's project aims to build on these efforts by evaluating the capacity of the Soybiome collection to protect soybean against diseases in in planta assays. To this end, bacteria that demonstrated strong antifungal activity in vitro will be tested for their ability to prevent diseases in two systems: (I) Monoassociations, where plants will be treated with a single bacterium at a time to evaluate the individual protective capacity of each strain; and (II) Synthetic Communities (SynComs), where combinations of distinct bacteria, based on their antifungal effects and taxonomy, will be used to identify communities that provide superior protection compared to individual members. With this strategy, we aim to determine principles for assembling robust SynComs that can invade natural communities, persist under cultivation conditions, and express phenotypes of interest. Thus, this project may contribute to the identification and molecular characterization of protective microorganisms, which is essential for the future development of efficient plant disease control strategies based on the rational manipulation of the plant microbiome.