Abstract
BackgroundMembers of the bacterial family Flavobacteriaceae are widely distributed in the marine environment and often found associated with algae, fish, detritus or marine invertebrates. Yet, little is known about the characteristics that drive their ubiquity in diverse ecological niches. Here, we provide an overview of functional traits common to taxonomically diverse members of the family Flavobacteriaceae from different environmental sources, with a focus on the Marine clade. We include seven newly sequenced marine sponge-derived strains that were also tested for gliding motility and antimicrobial activity.ResultsComparative genomics revealed that genome similarities appeared to be correlated to 16S rRNA gene- and genome-based phylogeny, while differences were mostly associated with nutrient acquisition, such as carbohydrate metabolism and gliding motility. The high frequency and diversity of genes encoding polymer-degrading enzymes, often arranged in polysaccharide utilization loci (PULs), support the capacity of marine Flavobacteriaceae to utilize diverse carbon sources. Homologs of gliding proteins were widespread among all studied Flavobacteriaceae in contrast to members of other phyla, highlighting the particular presence of this feature within the Bacteroidetes. Notably, not all bacteria predicted to glide formed spreading colonies. Genome mining uncovered a diverse secondary metabolite biosynthesis arsenal of Flavobacteriaceae with high prevalence of gene clusters encoding pathways for the production of antimicrobial, antioxidant and cytotoxic compounds. Antimicrobial activity tests showed, however, that the phenotype differed from the genome-derived predictions for the seven tested strains.ConclusionsOur study elucidates the functional repertoire of marine Flavobacteriaceae and highlights the need to combine genomic and experimental data while using the appropriate stimuli to unlock their uncharted metabolic potential.
Highlights
Members of the bacterial family Flavobacteriaceae are widely distributed in the marine environment and often found associated with algae, fish, detritus or marine invertebrates
The comparative genomics analysis performed in this study demonstrated that 16S ribosomal RNA (rRNA) gene- and singlecopy marker gene-based phylogeny, rather than life strategy of the organisms is the main factor correlated to the functional profile of Flavobacteriaceae
Phenotypic assays showed the formation of spreading colonies for some of the tested flavobacteria that had the complete set of type 9 secretion system (T9SS)-gliding homologs, confirming that not all potentially gliding bacteria form spreading colonies on agar
Summary
Members of the bacterial family Flavobacteriaceae are widely distributed in the marine environment and often found associated with algae, fish, detritus or marine invertebrates. There has been a vast increase in the number of described genera within the Flavobacteriaceae from ten [5] to 158 [6] in the past 20 years Due to this large number of members, the family has been divided into the following clades: Marine, Capnocytophaga, Flavobacterium, Tenacibaculum-Polaribacter and Chryseobacterium, based on 16S ribosomal RNA (rRNA) gene-based phylogenetic analysis [1]. Marine flavobacteria have been found either free-living or attached to detritus in the water column [9, 10] Their lifestyle includes colonization of the surface of algae [11], and close association with invertebrate animals such as sponges [12], corals [13] and echinoderms [14]
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