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Researchers Team Up to Investigate Microbes and Their Effect on Plant Growth

Researchers team up to investigate microbes and their effect on plant growth

Michigan State University (MSU) microbiologist Cecilia Martinez-Gomez is co-principal investigator (PI) on a four-year, $1.77 million National Science Foundation (NSF) Dimensions in Biodiversity grant comprised of five research teams, each under a different PI with expertise in evolutionary biology, ecology, microbial physiology or methylotrophy (that is, the capacity of a microorganism to use one carbon compound as a sole source of energy and mass). The grant runs through 2022.

“This award allows us to synergize our expertise and strengthen our efforts to dissect numerous dimensions of biological nature to overcome the difficulties of distinguishing the diverse metabolic roles of closely related natural isolates and their effect in higher organisms,” said Martinez-Gomez, an assistant professor in the Department of Microbiology and Molecular Genetics.

Martinez-Gomez’s work involves using a new and efficient method to further differentiate closely related microbial strains to define, in a dynamic manner, the bacterial community structure on the surface of plants’ leaves. She will also integrate analysis of the metabolomic and transriptomic profiles of the microbial community to better characterize bacteria-plant interactions. In doing this, she aims to describe the mechanisms by which methylotrophic bacteria enhance the growth of plants, particularly soybean.

The need for an improved sequencing technique arose when she and her colleague, Chris Marx, an evolutionary biologist at the University of Idaho, lead PI on the grant, noticed that the DNA sequencing of standard markers, such as 16s rRNA, which should distinguish between different microbial species, seemed inadequate to the task. Specifically, they observed that seemingly identical bacterial strains were responding very differently to ecological factors and substrate availability. These inconsistencies were hindering their analysis of ecological differentiation, necessitating refinement of the standard markers used to differentiate close species. Sequencing whole genomes can bypass this problem, but it can be cost prohibitive and analysis of the data labor intensive.

This award allows Martinez-Gomez and Marx to develop and to test a new methodology: a simple barcoding system for natural isolates using deep sequencing to efficiently study experimental ecology. A library with identical DNA sequencing except for one nucleotide in each case is inserted into a plasmid, that is, a foreign piece of circular DNA carrying these unique sequences that can integrate in the chromosome of each methylotrophic strain but doesn’t modify their metabolism; it just acts as an identifier, a barcode of sorts, integrated in the genome of each microbe.

“The clever barcoding approach developed by this team will enable them to define key genetic traits within diverse communities of these rare-earth users that contribute to broader function of the ecosystem,” said Victor DiRita, MMG department chair, and Rudolph Hugh Endowed Chair in Microbial Pathogenesis.

Martinez-Gomez will use 97 methylotrophic strains isolated from Michigan soybean fields, and Marx will integrate the barcode into each strain. Martinez -Gomez will inoculate the labeled community either on the surfaces of the leaf of the plants, in their soil, or in both, and follow the community composition over time in each compartment. She will also follow profiles to determine their metabolic potential by integrating transcriptomic and metabolomics studies and will sort those strains that are predominant or fail to survive and correlate the community structure and function with the effect on plant growth. Martinez-Gomez is particularly interested in defining what differences are observed when she adds metals known to affect metabolism of methylotrophs (that is, microorganisms able to do methylotrophy), known as lanthanides.

Additional members of the team are also interested in addressing the experimental evolution of the microbial community, to look into conservation of traits within the community and how much these traits influence genetic exchange across the microbial population.

Findings from this project can be applied to developing technologies that will further the agricultural industry; microbes that are predominant and with beneficial characteristics can be marketed as probiotics for improving harvests and, potentially, food security in areas where agricultural conditions are challenging.

“Dr. Martinez-Gomez does fundamental work in how rare-earth elements contribute to the physiology of microbes,” DiRita said. “She is a pioneer in understanding how bacteria use rare-earth elements and is now translating that knowledge toward research to increase crop yields through the activities of such bacteria.”

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