Evolution of a Vegetarian Vibrio: Metabolic Specialization of Vibrio breoganii to Macroalgal Substrates

Abstract

While most Vibrionaceae are considered generalists that thrive on diverse substrates, including animal-derived material, we show that Vibrio breoganii has specialized for the consumption of marine macroalga-derived substrates. Genomic and physiological comparisons of V. breoganii with other Vibrionaceae isolates revealed the ability to degrade alginate, laminarin, and additional glycans present in algal cell walls. Moreover, the widely conserved ability to hydrolyze animal-derived polymers, including chitin and glycogen, was lost, along with the ability to efficiently grow on a variety of amino acids. Ecological data showing associations with particulate algal material but not zooplankton further support this shift in niche preference, and the loss of motility appears to reflect a sessile macroalga-associated lifestyle. Together, these findings indicate that algal polysaccharides have become a major source of carbon and energy in V. breoganii, and these ecophysiological adaptations may facilitate transient commensal associations with marine invertebrates that feed on algae.IMPORTANCE Vibrios are often considered animal specialists or generalists. Here, we show that Vibrio breoganii has undergone massive genomic changes to become specialized on algal carbohydrates. Accompanying genomic changes include massive gene import and loss. These vibrios may help us better understand how algal biomass is degraded in the environment and may serve as a blueprint on how to optimize the conversion of algae to biofuels.

Keywords: Vibrio; Vibrionaceae; adaptation; algae; degradation; ecology; horizontal gene transfer; macroalgae; macroalgal carbohydrates; metabolic specialization; polysaccharide; seaweed.

FIG 1

Substrate utilization and CAZyme content of diverse Vibrio populations. (A) Differential growth of representative Vibrio populations on diverse carbohydrates. Each square of the heatmap reflects a growth score. Differences between initial and maximum OD₆₀₀ values for each replicate were scored for growth according to threshold criteria, with average scores shown (<0.05, 0; 0.05 to 0.15, 1; 0.15 to 0.25, 2; >0.25, 3). Rows are ordered according to the phylogenetic species tree of the genomes based on concatenated ribosomal genes. Columns are arranged using hierarchical clustering, such that carbohydrate utilization scores with similar phylogenetic distribution are placed closer together. Only carbohydrates that displayed differential growth among strains are included here. The growth scores for all carbohydrates are shown in Fig. S1. (B) Hierarchical cluster analysis of all CAZymes in representative Vibrio genomes reveals the mosaic presence and absence of GH families as well as cohesive CAZyme repertoires indicating similar glycan catabolism and scavenging strategies within populations. All results are consolidated in a matrix, where rows represent species and columns represent CAZymes. Each cell depicts the absolute abundance of a CAZyme family in a strain. The CAZyme abundance matrix is presented as a heatmap, where rows are ordered according to the phylogenetic species tree of the genomes based on concatenated ribosomal genes. Columns are arranged using hierarchical clustering, such that CAZymes with similar phylogenetic distributions are placed closer together. Thus, absent or present blocks indicate loss or gain of a set of related genes in related species, respectively, e.g., the loss of chitin metabolism (GH18 and GH19) or the acquisition of laminarinases (i.e., GH16) in all Vibrio breoganii strains. The CAZyme contents shown here reflect differences between V. breoganii and other populations. Comprehensive CAZyme content is provided in Fig. S2. (C) Differential growth of representative Vibrio populations on amino acids. Each square of the heatmap reflects a growth score. Differences between initial and maximum OD₆₀₀ values for each replicate were scored for growth according to threshold criteria, with average scores shown (<0.05, score 0; 0.05 to 0.15, score 1; 0.15 to 0.25, score 2; >0.25, score 3). Rows are ordered according to the phylogenetic species tree of the genomes based on concatenated ribosomal genes. Columns are arranged using hierarchical clustering, such that amino acid utilization scores with similar phylogenetic distribution are placed closer together. The amino acid substrates shown here reflect differences between V. breoganii and other populations. All amino acid substrate results are shown in Fig. S3.

FIG 2

Features differentiating V. breoganii from other marine Vibrio species. Ecological associations and physiological traits distinguish V. breoganii from most other marine Vibrio species. Here, we illustrate properties common among other marine vibrios but absent in V. breoganii (A), and traits specific to V. breoganii (B). Superscript letters denote the type of supporting evidence for each feature: E, experimental evidence; C, CAZyme database analysis; G, gene cluster analysis.