Phylogenetic Revision of the Genus Aliivibrio: Intra- and Inter-Species Variance Among Clusters Suggest a Wider Diversity of Species

Abstract

Genus <i>Aliivibrio</i> is known to harbor species exhibiting bioluminescence as well as pathogenic behavior affecting the fish farming industry. Current phylogenetic understanding of <i>Aliivibrio</i> has largely remained dormant after reclassification disentangled it from the <i>Vibrio</i> genus in 2007. There is growing evidence of wider diversity, but until now the lack of genomes and selective use of type strains have limited the ability to compare and classify strains firmly. In this study, a total of 143 bacterial strains, including 51 novel sequenced strains, were used to strengthen phylogenetic relationships in <i>Aliivibrio</i> by exploring intra-species and inter-species relations. Multilocus sequence analysis (MLSA), applying the six housekeeping genes <i>16S ribosomal RNA</i> (<i>rRNA</i>), <i>gapA</i>, <i>gyrB</i>, <i>pyrH</i>, <i>recA</i>, and <i>rpoA</i>, inferred 12 clades and a singular branch in <i>Aliivibrio</i>. Along with four new phylogenetic clades, the MLSA resolved prior inconsistencies circumscribing <i>Aliivibrio wodanis</i> and formed a unique clade we propose as the novel species <i>Aliivibrio</i> sp. "friggae." Furthermore, phylogenetic assessment of individual marker genes showed <i>gyrB</i>, <i>pyrH</i>, and <i>recA</i> superior to the 16S rRNA gene, resolving accurately for most species clades in <i>Aliivibrio</i>. In this study, we provide a robust phylogenetic groundwork for <i>Aliivibrio</i> as a reference point to classification of species.