University of Kentucky
: Exogenous alteration of plant DNA methylation affects their ability to assemble soil microbiomes
Grade Level at Time of Presentation
Junior
Major
Agricultural and Medical Biotechnology
Minor
Microbiology
KY House District #
6
KY Senate District #
23
Faculty Advisor/ Mentor
Carlos Rodriguez Lopez
Department
Horticulture
Abstract
Soils are a crucial component for sustaining healthy plants and are essential to a wide range of ecosystems. Microbial communities provide multiple benefits to their hosts, including better access to nutrients, enhanced growth, and improved tolerance to biotic and abiotic insult. Plants can modify the composition of such communities via the exudation of metabolites that enhance or prevent the abundance of certain microbial species. Epigenetic mechanisms, such as DNA methylation, have been proposed as one of the interphases that regulate the interaction between microbes and their hosts. Here, we used non-targeted soil metabolome analysis, metabarcoding sequencing, and labelled immunoassays to characterize and epimutant population of soybean generated using the demethylating agent 5-Azacytidine. We hypothesized that demethylated plants (epimutants) will present a unique set of mutant epialleles which will alter the plant’s metabolic machinery, resulting in an altered ability to synthesize root exudates, and therefore a unique soil microbiome. In addition to the expected modification of the plant’s morphological and developmental characteristics, non-targeted metabolomic analysis showed the metabolite profiles of soils containing epimutant plants are significantly different from those containing a wild-type plant. Importantly, next generation sequencing results indicate that exogenous plant DNA demethylation results in 1. Partial loss of the plant’s ability to alter the soil microbial communities (P=0.45; T-stat= 2.73; P-val= 0.005); 2. Increased variability in the epimutants capacity to alter the bulk soil microbiomes compared to the wild-types; and 3. A significantly lower ability of epimutants to prevent the growth of pathogenic bacterial species and promote the growth of beneficial taxa. Taken collectively, our results support the hypothesis that DNA methylation is involved in the ability of plants to direct the assembly of its microbiota. These findings signify the importance of epimutant plant populations as a resource for the identification of plant genes regulating soil microbiota assembly.
: Exogenous alteration of plant DNA methylation affects their ability to assemble soil microbiomes
Soils are a crucial component for sustaining healthy plants and are essential to a wide range of ecosystems. Microbial communities provide multiple benefits to their hosts, including better access to nutrients, enhanced growth, and improved tolerance to biotic and abiotic insult. Plants can modify the composition of such communities via the exudation of metabolites that enhance or prevent the abundance of certain microbial species. Epigenetic mechanisms, such as DNA methylation, have been proposed as one of the interphases that regulate the interaction between microbes and their hosts. Here, we used non-targeted soil metabolome analysis, metabarcoding sequencing, and labelled immunoassays to characterize and epimutant population of soybean generated using the demethylating agent 5-Azacytidine. We hypothesized that demethylated plants (epimutants) will present a unique set of mutant epialleles which will alter the plant’s metabolic machinery, resulting in an altered ability to synthesize root exudates, and therefore a unique soil microbiome. In addition to the expected modification of the plant’s morphological and developmental characteristics, non-targeted metabolomic analysis showed the metabolite profiles of soils containing epimutant plants are significantly different from those containing a wild-type plant. Importantly, next generation sequencing results indicate that exogenous plant DNA demethylation results in 1. Partial loss of the plant’s ability to alter the soil microbial communities (P=0.45; T-stat= 2.73; P-val= 0.005); 2. Increased variability in the epimutants capacity to alter the bulk soil microbiomes compared to the wild-types; and 3. A significantly lower ability of epimutants to prevent the growth of pathogenic bacterial species and promote the growth of beneficial taxa. Taken collectively, our results support the hypothesis that DNA methylation is involved in the ability of plants to direct the assembly of its microbiota. These findings signify the importance of epimutant plant populations as a resource for the identification of plant genes regulating soil microbiota assembly.