Adaptation of Surface-Associated Bacteria to the Open Ocean: A Genomically Distinct Subpopulation of Phaeobacter gallaeciensis Colonizes Pacific Mesozooplankton

Abstract

The marine Roseobacter group encompasses numerous species which occupy a large variety of ecological niches. However, members of the genus Phaeobacter are specifically adapted to a surface-associated lifestyle and have so far been found nearly exclusively in disjunct, man-made environments including shellfish and fish aquacultures, as well as harbors. Therefore, the possible natural habitats, dispersal and evolution of Phaeobacter spp. have largely remained obscure. Applying a high-throughput cultivation strategy along a longitudinal Pacific transect, the present study revealed for the first time a widespread natural occurrence of Phaeobacter in the marine pelagial. These bacteria were found to be specifically associated to mesoplankton where they constitute a small but detectable proportion of the bacterial community. The 16S rRNA gene sequences of 18 isolated strains were identical to that of Phaeobacter gallaeciensis DSM26640^T but sequences of internal transcribed spacer and selected genomes revealed that the strains form a distinct clade within P. gallaeciensis. The genomes of the Pacific and the aquaculture strains were highly conserved and had a fraction of the core genome of 89.6%, 80 synteny breakpoints, and differed 2.2% in their nucleotide sequences. Diversification likely occurred through neutral mutations. However, the Pacific strains exclusively contained two active Type I restriction modification systems which is commensurate with a reduced acquisition of mobile elements in the Pacific clade. The Pacific clade of P. gallaeciensis also acquired a second, homolog phosphonate transport system compared to all other P. gallaeciensis. Our data indicate that a previously unknown, distinct clade of P. gallaeciensis acquired a limited number of clade-specific genes that were relevant for its association with mesozooplankton and for colonization of the marine pelagial. The divergence of the Pacific clade most likely was driven by the adaptation to this novel ecological niche rather than by geographic isolation.

Keywords: Phaeobacter gallaeciensis; attached bacteria; bacterial adaptation; genome evolution; high-throughput cultivation; zooplankton.

FIGURE 1

Number of positive enrichments of Phaeobacter and phylogenetically related genera obtained from zooplankton > 300 μm collected along a longitudinal transect in the Pacific (respective Latitudes of sampling sites are given) in defined medium AM or complex medium HD.

FIGURE 2

Maximum likelihood phylogenetic tree of Phaeobacter strains based on ITS sequences. For comparison, Phaeobacter strains representing different ITS lineages identified previously (Breider et al., 2017; Freese et al., submitted) were chosen. The tree based on 767 aligned nucleotide positions. Numbers adjacent to branches give percentage of support from 1000 bootstrap replicates. Strains chosen for genome sequencing are marked.

FIGURE 3

Synteny and sequence similarity of the 7 Phaeobacter gallaeciensis strains. The Mauve alignment depicts large collinear, and presumably homologous blocks as colored rectangles. Collinear blocks cover 87.2–92.4% of the whole genomes. Gray scale of wedges between the genomes indicates the level of sequence identity (%) between genomic blocks. The genome phylogeny on the left was inferred from pairwise genome to genome nucleotide sequence distances (GGDC) using BIONJ and the scale gives the genomic distance. Prophages (labeled p), and plasmids (labeled according to their names, for instance “a” corresponding to pP11_a or pP128_a) are also depicted.

FIGURE 4

Phylogenetic network of 35 Phaeobacter strains inferred by NeighborNet analysis from 68858 core-genome SNPs estimated by Parsnp. Scale bar, 0.1 changes per polymorphic site. The long branch to P. porticola is depicted incompletely and Pacific strains are highlighted in bold.

FIGURE 5

Differences in the summed sequences of mobile elements (plasmids, phages, genomic islands) between P. gallaeciensis clades. Horizontal lines show median and ^∗∗ denotes t-test with p < 0.002.