Abstract
Plasmid mediated horizontal gene transfer (HGT) has been speculated to be one of the prime mechanisms for the adaptation of roseobacters (Rhodobacteraceae) to their ecological niches in the marine habitat. Their plasmids contain ecologically crucial functional modules of up to ∼40-kb in size, e.g., for aerobic anoxygenic photosynthesis, flagellar formation and the biosynthesis of the antibiotic tropodithietic acid. Furthermore, the widely present type four secretion system (T4SS) of roseobacters has been shown to mediate conjugation across genus barriers, albeit in the laboratory. Here we discovered that Confluentimicrobium naphthalenivorans NS6T, a tidal flat bacterium isolated in Korea, carries a 185-kb plasmid, which exhibits a long-range synteny with the conjugative 126-kb plasmid of Dinoroseobacter shibae DFL12T. Both replicons are stably maintained by RepABC operons of the same compatibility group (-2) and they harbor a homologous T4SS. Principal component analysis of the codon usage shows a large similarity between the two plasmids, while the chromosomes are very distinct, showing that neither of the two bacterial species represents the original host of those RepABC-2 type plasmids. The two species do not share a common habitat today and they are phylogenetically only distantly related. Our finding demonstrates the first clear-cut evidence for conjugational plasmid transfer across biogeographical and phylogenetic barriers in Rhodobacteraceae and documents the importance of conjugative HGT in the ocean.
Highlights
Horizontal gene transfer (HGT) dominates prokaryotic evolution (Koonin, 2016)
We show that a syntenic plasmid is naturally present in two phylogenetically distant species of the Roseobacter group, i.e., Confluentimicrobium naphthalenivorans and Roseovarius indicus
The improvement of sequencing technologies in the last decade resulted in an exponential increase of completely deciphered bacterial genomes with more than 400 Rhodobacteraceae currently deposited in public data bases
Summary
Horizontal gene transfer (HGT) dominates prokaryotic evolution (Koonin, 2016). In addition to plasmid transfer by conjugation, two other mechanisms of HGT are known in the ocean, namely, transformation via direct uptake of DNA and transduction by phages or gene transfer agents (GTAs). It could be demonstrated that two syntenic sister plasmids of Dinoroseobacter shibae DFL12T, which originate from a plasmid duplication and the recruitment of a novel RepABC-type replication module (Wagner-Döbler et al, 2010), can be transferred to Phaeobacter inhibens DSM 17395 by conjugation in vitro (Patzelt et al, 2016).
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