Abstract
Burkholderia gladioli has high versatility and adaptability to various ecological niches. Here, we constructed a pan-genome using 14 genome sequences of B. gladioli, which originate from different niches, including gladiolus, rice, humans, and nature. Functional roles of core and niche-associated genomes were investigated by pathway enrichment analyses. Consequently, we inferred the uniquely important role of niche-associated genomes in (1) selenium availability during competition with gladiolus host; (2) aromatic compound degradation in seed-borne and crude oil-accumulated environments, and (3) stress-induced DNA repair system/recombination in the cystic fibrosis-niche. We also identified the conservation of the rhizomide biosynthetic gene cluster in all the B. gladioli strains and the concentrated distribution of this cluster in human isolates. It was confirmed the absence of complete CRISPR/Cas system in both plant and human pathogenic B. gladioli and the presence of the system in B. gladioli living in nature, possibly reflecting the inverse relationship between CRISPR/Cas system and virulence.
Highlights
The impact of environmental variability is an important issue in the evolution of microbial genomes, contributing to phylogenetic position, as well as the diversity of metabolic capabilities to which it is adapted [1,2]
Recent comparative genomic studies have demonstrated that bacterial adaptation to the environment in the host is closely related to biological capabilities, which are changed by the result of gene gain/loss or genome reduction/expansion [1,5]
Of fourteen B. gladioli, ten pathogenic B. gladioli isolates were classified by niches, and the others were integrated into the nature group
Summary
The impact of environmental variability is an important issue in the evolution of microbial genomes, contributing to phylogenetic position, as well as the diversity of metabolic capabilities to which it is adapted [1,2]. Environmental pressure for genomic evolution can include pH, temperature, oxygen, nutrient availability, competition with other bacteria, and stress-inducing defense mechanisms, from habitats and hosts [2,3,4]. The genomic architecture of microbes shows signatures of a long journey of adaptive evolution for different specialized lifestyles. Even in the taxonomically distant lineage, microbes within similar lifestyles exhibit similar genomic inventory to acclimatize to common environmental conditions in each niche [3,6]. Information on bacterial genomic diversity regarding dynamic interactions between the microbe and habitat or host conditions is currently limited
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