Genome of the R-body producing marine alphaproteobacterium Labrenzia alexandrii type strain (DFL-11(T))

Abstract

Labrenzia alexandrii Biebl et al. 2007 is a marine member of the family Rhodobacteraceae in the order Rhodobacterales, which has thus far only partially been characterized at the genome level. The bacterium is of interest because it lives in close association with the toxic dinoflagellate Alexandrium lusitanicum. Ultrastructural analysis reveals R-bodies within the bacterial cells, which are primarily known from obligate endosymbionts that trigger "killing traits" in ciliates (Paramecium spp.). Genomic traits of L. alexandrii DFL-11(T) are in accordance with these findings, as they include the reb genes putatively involved in R-body synthesis. Analysis of the two extrachromosomal elements suggests a role in heavy-metal resistance and exopolysaccharide formation, respectively. The 5,461,856 bp long genome with its 5,071 protein-coding and 73 RNA genes consists of one chromosome and two plasmids, and has been sequenced in the context of the Marine Microbial Initiative.

Keywords: Alexandrium lusitanicum; Alphaproteobacteria; aerobe; dinoflagellates; high-quality draft; motile; photoheterotroph; symbiosis.

Figure 1

Phylogenetic tree highlighting the position of L. alexandrii relative to the type strains of the species of selected genera (see [1,3] and the results of the Greengenes database search described above) within the family Rhodobacteraceae. These genera form a clade [1,3], but it might be better not to place them in this family [3]. The tree was inferred from 1,366 aligned characters [8,9] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [10] and rooted with Pseudovibrio. The branches are scaled in terms of the expected number of substitutions per site (see size bar). Numbers adjacent to the branches are support values from 1,000 ML bootstrap replicates [11] (left) and from 1,000 maximum-parsimony bootstrap replicates [12] (right) if larger than 60%. Lineages with type-strain genome sequencing projects registered in GOLD [13] are labeled with one asterisk.

Figure 2

Ultrastructure of L. alexandrii DFL-11^T and its R-bodies. (A) Survey view of the cells from the near-surface position of a colony. Many bacterial remnants are visible, one of which contains an R-body; such bodies are shown enlarged in (B) and (C). (B) A pair of R-bodies, oriented at right angle towards each other, one as a cross-section and the other one cut oblique-longitudinally. The bipartite, black-white organization of the spiral layers is shown, and the averaged intensity profile (C, inset) of the boxed area shows a regular spacing of 10 nm.

Figure 3a

Graphical map of the chromosome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 3b

The larger of the two plasmids (LADFL_5, not drawn to scale with the chromosome). From outside to the center: Genes on forward strand (color by COG categories), genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 3c

The smaller of the two plasmids (LADFL_6, not drawn to scale with the chromosome). From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.