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Open Access Highly Accessed Research article

Genomic insights into an obligate epibiotic bacterial predator: Micavibrio aeruginosavorus ARL-13

Zhang Wang1, Daniel E Kadouri2 and Martin Wu1*

Author Affiliations

1 Department of Biology, University of Virginia, 485 McCormick Road, Charlottesville, Virginia 22903, USA

2 Department of Oral Biology, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07101, USA

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BMC Genomics 2011, 12:453  doi:10.1186/1471-2164-12-453

Published: 21 September 2011

Abstract

Background

Although bacterial predators play important roles in the dynamics of natural microbial communities, little is known about the molecular mechanism of bacterial predation and the evolution of diverse predatory lifestyles.

Results

We determined the complete genome sequence of Micavibrio aeruginosavorus ARL-13, an obligate bacterial predator that feeds by "leeching" externally to its prey. Despite being an obligate predator depending on prey for replication, M. aeruginosavorus encodes almost all major metabolic pathways. However, our genome analysis suggests that there are multiple amino acids that it can neither make nor import directly from the environment, thus providing a simple explanation for its strict dependence on prey. Remarkably, despite apparent genome reduction, there is a massive expansion of genomic islands of foreign origin. At least nine genomic islands encode many genes that are likely important for Micavibrio-prey interaction such as hemolysin-related proteins. RNA-Seq analysis shows substantial transcriptome differences between the attack phase, when M. aeruginosavorus seeks its prey, and the attachment phase, when it feeds and multiplies. Housekeeping genes as well as genes involved in protein secretion were all dramatically up-regulated in the attachment phase. In contrast, genes involved in chemotaxis and flagellum biosynthesis were highly expressed in the attack phase but were shut down in the attachment phase. Our transcriptomic analysis identified additional genes likely important in Micavibrio predation, including porins, pilins and many hypothetical genes.

Conclusions

The findings from our phylogenomic and transcriptomic analyses shed new light on the biology and evolution of the epibiotic predatory lifestyle of M. aeruginosavorus. The analysis reported here and the availability of the complete genome sequence should catalyze future studies of this organism.

Keywords:
Bacterial predation; Predator-prey interaction; Integrative and conjugative elements (ICEs); Hemolysin-related protein; Quorum sensing, RNA-Seq