Homologous Recombination in Core Genomes Facilitates Marine Bacterial Adaptation

Acquisition of ecologically relevant genes is common among ocean bacteria, but whether it has a major impact on genome evolution in marine environments remains unknown. Here, we analyzed the core genomes of 16 phylogenetically diverse and ecologically relevant bacterioplankton lineages, each consisting of up to five genomes varying at the strain level. Statistical approaches identified from each lineage up to ∼50 loci showing anomalously high divergence at synonymous sites, which is best explained by recombination with distantly related organisms. The enriched gene categories in these outlier loci match well with the characteristics previously identified as the key phenotypes of these lineages. Examples are antibiotic synthesis and detoxification in Phaeobacter inhibens, exopolysaccharide production in Alteromonas macleodii, hydrocarbon degradation in Marinobacter hydrocarbonoclasticus, and cold adaptation in Pseudoalteromonas haloplanktis Intriguingly, the outlier loci feature polysaccharide catabolism in Cellulophaga baltica but not in Cellulophaga lytica, consistent with their primary habitat preferences in macroalgae and beach sands, respectively. Likewise, analysis of Prochlorococcus showed that photosynthesis-related genes listed in the outlier loci are found only in the high-light-adapted ecotype and not in the low-light adapted ecotype. These observations strongly suggest that recombination with distant relatives is a key mechanism driving the ecological diversification among marine bacterial lineages.IMPORTANCE Acquisition of new metabolic genes has been known as an important mechanism driving bacterial evolution and adaptation in the ocean, but acquisition of novel alleles of existing genes and its potential ecological role have not been examined. Guided by population genetic theories, our genomic analysis showed that divergent allele acquisition is prevalent in phylogenetically diverse marine bacterial lineages and that the affected loci often encode metabolic functions that underlie the known ecological roles of the lineages under study.

and Diatoms during Cold-Water Phytoplankton Spring Blooms

Early spring phytoplankton blooms can occur at very low water temperatures but they are often decoupled from bacterial growth, which is assumed to be often temperature controlled. In a previous mesocosm study with Baltic Sea plankton communities, an early diatom bloom was associated with a high relative abundance of Glaciecola sequences (Gammaproteobacteria), at both low (2°C) and elevated (8°C) temperatures, suggesting an important role for this genus in phytoplankton-bacteria coupling. In this study, the temperature-dependent dynamics of free-living Glaciecola spp. during the bloom were analyzed by catalyzed reporter deposition fluorescence in situ hybridization using a newly developed probe. The analysis revealed the appearance of Glaciecola spp. in this and in previous spring mesocosm experiments as the dominating bacterial clade during diatom blooms, with a close coupling between the population dynamics of Glaciecola and phytoplankton development. Although elevated temperature resulted in a higher abundance and a higher net growth rate of Glaciecola spp. (Q10 ∼ 2.2), their growth was, in contrast to that of the bulk bacterial assemblages, not suppressed at 2°C and showed a similar pattern at 8°C. Independent of temperature, the highest abundance of Glaciecola spp. (24.0 ± 10.0% of total cell number) occurred during the peak of the phytoplankton bloom. Together with the slightly larger cell size of Glaciecola, this resulted in a ∼30% contribution of Glaciecola to total bacterial biomass. Overall, the results of this and previous studies suggest that Glaciecola has an ecological niche during early diatom blooms at low temperatures, when it becomes a dominant consumer of phytoplankton-derived dissolved organic matter.