Plasmid Transfer in the Ocean - A Case Study from the Roseobacter Group

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 NS6^T, 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 DFL12^T. 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.

Keywords: conjugation; evolution; horizontal gene transfer; plasmid synteny; type IV secretion systems.

FIGURE 1

Synteny plot of the 185-kb RepABC-2 type plasmid from Confluentimicrobium naphthalenivorans NS6^T (pNS6001) and the two sister plasmids from Dinoroseobacter shibae DFL12^T (pDSHI01, pDSHI03). Long-range homologies with conserved genes are shown with fading gray bars and syntenic regions including the type IV secretion systems (T4SS) for plasmid conjugation are shown in green. Plasmid replication systems of the RepABC-2 and RepABC-9 type are highlighted in yellow and blue, respectively. Adjacent toxin/antitoxin systems are shown in orange. A D. shibae specific insertion is highlighted in turquoise. Homologous genes were determined by comparative TBLASTN analyses (see Supplementary Table S1).

FIGURE 2

(A) Phylogenetic RpoB analysis from roseobacters based on 69 sequences and 1374 amino acid positions. Strains harboring natural syntenic RepABC-2 type plasmids such as Dinoroseobacter shibae and Confluentimicrobium naphthalenivorans or served as a recipient for plasmid conjugation (Phaeobacter inhibens) are highlighted in red. The color code of the seven subtrees (clades) corresponds to a phylogenomic analysis presented by Michael et al. (2016); the complete tree is shown in Supplementary Figure S1. (B) Principal component analysis of the relative synonymous codon usage of replicons from D. shibae and C. naphthalenivorans. Chromosomes, chromids and plasmids are shown by squares, triangles and circles, respectively. The positioning of the syntenic RepABC-2 type plasmids is indicated by red arrows.