Modularity and function of symbiotic genetic systems

Plant-microbe symbioses, such as the legume-rhizobium mutualism and phylosphere endophytes, are critical to nutrient cycling, crop productivity, and ecological interactions. These mutualisms rely on intergenomic interactions, metabolic coordination, and regulatory mechanisms that affect the phenotype and fitness of the partners involved in the relationship. Here, we investigate genetic, genomic, metabolic and ecological aspects of symbiotic partner interactions using systems and quantitative genetics, transcriptomics and pangenomics approaches across microbe and plant interactions. In Sinorhizobium meliloti, we analyzed a superset of 191 natural isolated strains and a subset of 20 strains that significantly vary in partner quality using dual-RNAseq, weighted gene co-expression network analysis, and pangenomics. Key genes and pathways on the symbiosis plasmid (pSymA) were identified as significant contributors to plant biomass, with presence-absence variations in gene clusters on pSymA being strongly associated with high and low-quality symbiotic relationships on a single plant genomic background. Genomic and transcriptomic variations are the theoretical basis of differences in a variety of metabolites like amino acid, sugar, and polyamines.To test this hypothesis, we did untargeted metabolomics in developed nodules, which revealed different balances of several pathways and metabolites depending on the presence and absence variation on pSymA across strains. Using the legume-rhizobia model, we found novel genetic and molecular mechanisms on the accessory genome that have strong influence on determining symbiotic partner quality, based on plasmid content variation across bacterial strains. In a different experimental model, we asked about the effects of phyllosphere microbial communities on soybean, we aimed to understand how different leaf-endophytic microbes influence plant health and transcriptomic responses on a tri-partner system. For this purpose, we performed inoculation experiments with field-collected Methylobacterium and Colletotrichum isolates in soybean across different environmental conditions. Our studies revealed that co-inoculation of foliar endophytes enhances plant growth under sterile, nutrient-deprived conditions only in the absence of soil microbes. Transcriptomic analyses of this sterile soil inoculated phyllosphere indicated that co-inoculation with both Methylobacterium and Colletotrichum modulates plant stress and defense responses and benefits plant growth. These experiments revealed the importance of phyllosphere endophytes in soybean health and remarked on the importance of non-legume-rhizobia mutualistic interactions on an ecosystem level.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Microbiology

Grantor

University of Illinois Urbana-Champaign

Year dc:date

2025

Author dc:creator

• Sosa Marquez, Ivan

Contributors dc:contributor

• Heath, Katy D.
• Heath, Katy D
• Whitaker, Rachel J
• Bell, Alison
• Vanderpool, Carin

• Symbiosis
• Genomics
• Genetics
• Evolution
• Bacteria
• Nitrogen

Statement dc:rights

• Copyright 2025 Ivan Sosa Marquez

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/130103

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F130103