ORCID Identifier(s)

ORCID 0000-0002-5362-498X

Graduation Semester and Year

Summer 2024

Language

English

Document Type

Dissertation

Degree Name

Doctor of Philosophy in Quantitative Biology

Department

Biology

First Advisor

Woo Suk Chang

Abstract

Rhizobia are soil bacteria that facilitate biological nitrogen fixation (BNF) through a symbiotic relationship with legumes such as soybeans. As an eco-friendly alternative to chemical nitrogen fertilizers, rhizobial inoculants can enhance plant growth and yield. However, they face various stresses, including drought (i.e., desiccation). Rhizobia can manage desiccation stress by accumulating trehalose, a disaccharide produced by genes such as otsA, otsB, and treS. Extracytoplasmic function (ECF) sigma factors sense external signals and regulate these desiccation-related genes during the stress. Previous studies have highlighted the importance of EcfG in response to desiccation stress and symbiosis. Based on the protein sequence similarity, it is hypothesized that the ECF sigma factors Bll2628/PrtI and Bll3014 function similarly to EcfG, potentially playing a role in drought and symbiosis. The deletion of these genes in Bradyrhizobium japonicum USDA110 resulted in impaired symbiosis, reduced desiccation survival, and diminished BNF. We also investigated the interaction between ECFs and a periplasmic signal peptide, Blr5636. Deletion of the blr5636 gene slightly decreased rhizobial survival under desiccation, but did not affect intracellular trehalose levels. However, this deletion significantly impacted BNF and symbiosis, likely due to the loss of an iron transport regulator in the mutant strain. In a differential gene expression study, the absence of the Blr5636 protein led to downregulation of bll2628 and bll3014. The comparative genome analysis of drought-tolerant B. japonicum TXVA and TXEA strains with other rhizobia revealed core differences, gene orthologs, strain-specific gene clusters, and distinct molecular markers associated with desiccation tolerance in TXVA and TXEA. The study elucidates the molecular mechanism by which TXVA and TXEA strains perform superior stress tolerance and symbiosis compared to conventional inoculants. In the context of a changing climate, our research aims to enhance the understanding of how rhizobial inoculants function at a molecular level to support sustainable soybean production.

Keywords

ECF sigma factor, desiccation, symbiosis, biological nitrogen fixation, signal peptides, drought-tolerant Rhizobia, orthologs, pangenome, unique genes

Disciplines

Bacteriology | Bioinformatics | Biotechnology | Environmental Microbiology and Microbial Ecology

License

Creative Commons Attribution 4.0 International License
This work is licensed under a Creative Commons Attribution 4.0 International License.

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Available for download on Wednesday, August 13, 2025

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