Prey range and genome evolution of Halobacteriovorax marinus predatory bacteria from an estuary

Abstract

BackgroundHalobacteriovorax are saltwater-adapted predatory bacteria that attack Gram-negative bacteria and therefore may play an important role in shaping microbial communities. To understand the impact of Halobacteriovorax on ecosystems and develop them as biocontrol agents, it is important to characterize variation in predation phenotypes such as prey range and investigate the forces impacting Halobacteriovorax genome evolution across different phylogenetic distances.\n\nResultsWe isolated H. marinus BE01 from an estuary in Rhode Island using Vibrio from the same site as prey. Small, fast-moving attack phase BE01 cells attach to and invade prey cells, consistent with the intraperiplasmic predation strategy of H. marinus type strain SJ. BE01 is a prey generalist, forming plaques on Vibrio strains from the estuary as well as Pseudomonas from soil and E. coli. Genome analysis revealed that BE01 is very closely related to SJ, with extremely high conservation of gene order and amino acid sequences. Despite this similarity, we identified two regions of gene content difference that likely resulted from horizontal gene transfer. Analysis of modal codon usage frequencies supports the hypothesis that these regions were acquired from bacteria with different codon usage biases compared to Halobacteriovorax. In BE01, one of these regions includes genes associated with mobile genetic elements, such as a transposase not found in SJ and degraded remnants of an integrase occurring as a full-length gene in SJ. The corresponding region in SJ included unique mobile genetic element genes, such as a site-specific recombinase and bacteriophage-related genes not found in BE01. Acquired functions in BE01 include the dnd operon, which encodes a pathway for DNA modification that may protect DNA from nucleases, and a suite of genes involved in membrane synthesis and regulation of gene expression that was likely acquired from another Halobacteriovorax lineage.\n\nConclusionsOur results support previous observations that Halobacteriovorax prey on a broad range of Gram-negative bacteria. Genome analysis suggests strong selective pressure to maintain the genome in the H. marinus lineage represented by BE01 and SJ, although our results also provide further evidence that horizontal gene transfer plays an important role in genome evolution in predatory bacteria.