Pan-genome Analysis of Pantoea agglomerans Strains to Investigate their Ecological and Functional Diversity

Abstract

Pantoea agglomerans is a Gram-negative, facultatively anaerobic, rod-shaped bacterial species in the genus Pantoea and the family Erwiniaceae. Strains of this species have been isolated from a broad range of ecological niches globally and are often found in association with both plant and animal hosts. Individual strains demonstrate potential for the use in a range of biotechnological applications, including bioremediation, biological control and the production of biopharmaceuticals and biofertilizers. However, the commercial use of this species has been hampered by its implication in opportunistic human infections and plant pathogenicity. In this study, a comprehensive comparative genomic analysis was undertaken to elucidate the ecological and functional diversification of P. agglomerans, with the aim to dissociate between pathogenic strains and strains of biotechnological value. Chapter one encompasses a comprehensive review of literature on the biology of P. agglomerans. This covers the taxonomic history of P. agglomerans, isolationist ecological diversity as well as what is known about its pathogenesis to both plant and animal hosts and its biotechnological potential. Chapter two outlines the comparative genomic methodologies employed in this study. This involved the analysis of P. agglomerans from the pan-genome perspective of the species, through to the genomes of individual strains and finally to the minutiae of its pathogenesis, environmental resistance and secondary metabolite production. The results of this study, and their interpretations, are documented in chapter three. This revealed that P. agglomerans delineates into two subspecies (P. agglomerans subsp. 1 and subsp. 2) and has an open pan-genome. This open pan-genome can be attributed to the expansive and variable mobilome of P. agglomerans, comprised of plasmid elements, bacteriophages, integrative and conjugative elements (ICEs) and transposable elements that confer various phenotypes underpinning the ecological success of this species. P. agglomerans harbours multiple secretion systems, which facilitates interactions with varying hosts and environmental niches. The secretome of P. agglomerans displayed resistance to a wide range of antimicrobials, antibiotics and environmental pollutants. P. agglomerans produces an array of secondary metabolites furthering its biotechnological potential. Chapter four provides a succinct summary of the key findings in this study and future perspectives. The comprehensive comparative genomic study of this fascinating species adds towards the body of knowledge of its ecological and lifestyle diversification, contributing towards the end goals of a deeper understanding of its pathogenesis towards a broad range of hosts and driving its biotechnological application.