Genotypic to phenotypic attributes of spontaneously-produced lysogenic phages of soybean Bradyrhizobium
Date
2023
Authors
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Publisher
University of Delaware
Abstract
Soybean (Glycine max) is a popular widely-grown legume rich in protein and oil used for human consumption, animal feed, and industrial purposes. As a cost effective and environmentally sustainable alternative to synthetic nitrogen fertilizers, soybean bradyrhizobia (Bradyrhizobium spp.) can meet the nitrogen requirements for high crop yields. Soybean bradyrhizobia in soil form a symbiotic relationship with soybean, fixing nitrogen (N2) into bioavailable ammonia (NH3) in root nodules. However, bradyrhizobia differ in their symbiotic effectiveness and saprophytic ecology, both of which may be altered by phage-mediated horizontal gene transfer (HGT). ☐ The University of Delaware Bradyrhizobium Culture Collection (UDBCC) contains root nodule soybean bradyrhizobia isolates collected from 31 Delaware farms plus reference USDA strains. The collection (n=352) consists of species common to North America: Bradyrhizobium japonicum, B. diazoefficiens, B. elkanii, B. ottawaense. Many UDBCC strains spontaneously produce high numbers of phage in culture (without chemical induction). Characterization of these lysogenic phages and their potential for horizontal gene transfer is critical to understanding possible viral impact on the bradyrhizobia-soybean symbiosis. ☐ In this dissertation research, a representative subset of 98 phenotypically and phylogenetically diverse strains from UDBCC was chosen for phage morphology screening. The majority of strains (69%) spontaneously produced virus-like particles when examined by epifluorescence microscopy. Transmission electron microscopy revealed variety among tail types, capsid shapes and collar or baseplate presence. Twenty-one UDBCC bradyrhizobia accessions, selected based on genotypic and phenotypic data, were sequenced and assembled to understand the genomic context between the four species. This analysis also highlighted differences of nodulation, nitrogen fixation and rhizobitoxine islands among genomes. Whole genome sequencing helped identify 39 putative prophages, representing the diversity of spontaneously produced phages in soybean bradyrhizobia which have the potential to mobilize bacterial DNA through HGT. Finally, a large-scale greenhouse experiment showed soybean plant growth phenotypes when inoculated with each of the genomically-characterized bacterial strains. The research in this dissertation connects bacteriophage genotypes, bacterial genotypes, and bacterial phenotypic characteristics to better understand how viral-host interactions impact the bradyrhizobial-soybean symbiosis.
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Keywords
Bacteriophages, Bradyrhizobium, Lysogeny, Soybean bradyrhizobia, Glycine max