Abstract
BackgroundHerbaspirillum seropedicae is an environmental β-proteobacterium that is capable of promoting the growth of economically relevant plants through biological nitrogen fixation and phytohormone production. However, strains of H. seropedicae have been isolated from immunocompromised patients and associated with human infections and deaths. In this work, we sequenced the genomes of two clinical strains of H. seropedicae, AU14040 and AU13965, and compared them with the genomes of strains described as having an environmental origin.ResultsBoth genomes were closed, indicating a single circular chromosome; however, strain AU13965 also carried a plasmid of 42,977 bp, the first described in the genus Herbaspirillum. Genome comparison revealed that the clinical strains lost the gene sets related to biological nitrogen fixation (nif) and the type 3 secretion system (T3SS), which has been described to be essential for interactions with plants. Comparison of the pan-genomes of clinical and environmental strains revealed different sets of accessorial genes. However, antimicrobial resistance genes were found in the same proportion in all analyzed genomes. The clinical strains also acquired new genes and genomic islands that may be related to host interactions. Among the acquired islands was a cluster of genes related to lipopolysaccharide (LPS) biosynthesis. Although highly conserved in environmental strains, the LPS biosynthesis genes in the two clinical strains presented unique and non-orthologous genes within the genus Herbaspirillum. Furthermore, the AU14040 strain cluster contained the neuABC genes, which are responsible for sialic acid (Neu5Ac) biosynthesis, indicating that this bacterium could add it to its lipopolysaccharide. The Neu5Ac-linked LPS could increase the bacterial resilience in the host aiding in the evasion of the immune system.ConclusionsOur findings suggest that the lifestyle transition from environment to opportunist led to the loss and acquisition of specific genes allowing adaptations to colonize and survive in new hosts. It is possible that these substitutions may be the starting point for interactions with new hosts.
Highlights
Herbaspirillum seropedicae is an environmental β-proteobacterium that is capable of promoting the growth of economically relevant plants through biological nitrogen fixation and phytohormone production
Sequencing and analysis of the H. seropedicae SmR1 genome allowed identification of the genes involved in nitrogen fixation, genes related to nitrate metabolism, plant ethylene stress-relieving 1-aminocyclopropane-1-carboxylate deaminase and the plant-bacteria interaction type three secretion system (T3SS) [6]
After the second round of gap closure, 4 gaps remained in the genome that corresponded to repeat regions and ribosomal RNA (rRNA) operons and were resolved individually using blastn and FGAP
Summary
Herbaspirillum seropedicae is an environmental β-proteobacterium that is capable of promoting the growth of economically relevant plants through biological nitrogen fixation and phytohormone production. The first described species of the genus Herbaspirillum was the bacterium Herbaspirillum seropedicae, which was found colonizing the roots and aerial parts of important crops such as rice, sugarcane, maize and tropical species such as pineapple and banana [1,2,3]. Since its isolation, this species has been verified as an endophytic non-pathogenic bacterium. Sequencing and analysis of the H. seropedicae SmR1 genome allowed identification of the genes involved in nitrogen fixation (nif ), genes related to nitrate metabolism (nar, nas, nir), plant ethylene stress-relieving 1-aminocyclopropane-1-carboxylate deaminase (accD) and the plant-bacteria interaction type three secretion system (T3SS) [6]
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