The impact of spontaneously produced lysogenic phages on the ecology and biology of soybean bradyrhizobia
Date
2021
Authors
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Publisher
University of Delaware
Abstract
Currently, soybeans are among the select few crops that can potentially solve our massive humanitarian challenge of global protein nutrition in an environmentally sustainable manner. In addition, soybeans are one of the largest crops in the United States supporting an approximately 20 billion dollar soybean industry that is projected to grow 7.5% annually for the next few years. Soybean Bradyrhizobium spp., both figuratively and literally, are in the root of this burgeoning soybean industry. Bradyrhizobia nodulate the root of soybean plants and convert atmospheric nitrogen to plant-usable ammonia in a process known as biological nitrogen fixation (BNF), providing for almost all of this proteinaceous plant’s nitrogen requirements. BNF therefore reduces our reliance on commercial nitrogen fertilizers obtained from an environmentally harmful and energy intensive Haber-Bosch process, one of the largest contributors of greenhouse gases. ☐ While many commercially available bradyrhizobia inoculants, applied in the soybean fields, are highly efficient in BNF, they compete with less efficient indigenous strains for soybean root nodulation, which can reduce soybean yields. The University of Delaware Bradyrhizobia Culture Collection (UDBCC) was established to study the diversity of soybean root-nodulating bradyrhizobia in the state of Delaware, United States. Assessment of this culture collection revealed that several members show spontaneous or chemical phage induction. While a lot of research has been done on soybean-bradyrhizobia interactions, little or no data is available on the phages produced by this bacteria. Phages are known to impact bacterial fitness, alter community dynamics, and drive microbial evolution, all of which may be significant for soybean-bradyrhizobia interactions. ☐ In this dissertation research, UDBCC was assessed using the most widely used phenotypic and genotypic methods which revealed a high correlation between these two methods. Four UDBCC bradyrhizobia accessions, selected based on genotypic and phenotypic data, were sequenced and assembled to understand the genomic context of nodulation, nitrogen fixation and rhizobitoxine production. This analysis also highlighted the presence of an expansive mobilome consisting of 1) various families of insertion sequences capable of functioning as composite transposons, and 2) megaplasmids containing a genetic framework required to undertake conjugation events, both of which may mobilize bradyrhizobia host DNA in the population. Finally, phage DNA sequencing and delineation of accurate phage boundaries using a unique read mapping approach revealed the diversity of spontaneously produced phages in soybean bradyrhizobia that are also capable of mobilizing bacterial DNA via horizontal gene transfer. The research in this dissertation hints towards a troika of genetic elements (insertion sequences, plasmids, and phages) that mobilize DNA in the host populations and can significantly impact the symbiosis gene pool of bradyrhizobia and consequently, the billion dollar soybean industry.
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Keywords
Bradyrhizobia, Horizontal gene transfer, Mobilome, Soybean, Spontaneous phage induction