Tracing Genomic Divergence of Vibrio Bacteria in the Harveyi Clade

Abstract

The mechanism of bacterial speciation remains a topic of tremendous interest. To understand the ecological and evolutionary mechanisms of speciation in Vibrio bacteria, we analyzed the genomic dissimilarities between three closely related species in the so-called Harveyi clade of the genus Vibrio, V. campbellii, V. jasicida, and V. hyugaensis. The analysis focused on strains isolated from diverse geographic locations over a long period of time. The results of phylogenetic analyses and calculations of average nucleotide identity (ANI) supported the classification of V. jasicida and V. hyugaensis into two species. These analyses also identified two well-supported clades in V. campbellii; however, strains from both clades were classified as members of the same species. Comparative analyses of the complete genome sequences of representative strains from the three species identified higher syntenic coverage between genomes of V. jasicida and V. hyugaensis than that between the genomes from the two V. campbellii clades. The results from comparative analyses of gene content between bacteria from the three species did not support the hypothesis that gene gain and/or loss contributed to their speciation. We also did not find support for the hypothesis that ecological diversification toward associations with marine animals contributed to the speciation of V. jasicida and V. hyugaensis. Overall, based on the results obtained in this study, we propose that speciation in Harveyi clade species is a result of stochastic diversification of local populations, which was influenced by multiple evolutionary processes, followed by extinction events. IMPORTANCE To investigate the mechanisms underlying speciation in the genus Vibrio, we provided a well-assembled reference of genomes and performed systematic genomic comparisons among three evolutionarily closely related species. We resolved taxonomic ambiguities and identified genomic features separating the three species. Based on the study results, we propose a hypothesis explaining how species in the Harveyi clade of Vibrio bacteria diversified.

The Acquisition of the scr Gene Cluster Encoding Sucrose Metabolization Enzymes Enables Strains of Vibrio parahaemolyticus and Vibrio vulnificus to Utilize Sucrose as Carbon Source

“…We compared the scrAKB region of strain V. parahaemolyticus 16-VB00198 to the genome of the V. alginolyticus reference strain ATCC 33787 (accession CP013485 ). In general, these two Vibrio species are related belonging to the Vibrio harveyi clade ( Ke et al, 2018 ) and sucrose utilization has been used as an important phenotypic feature for biochemical differentiation of these bacteria. The comparison of the scr region of the two Vibrio strain genomes is depicted in Figure 4A .…”

“…Sequence identity is shown in light gray (approximately 70%) and in dark gray (>95%). (Ke et al, 2018) and sucrose utilization has been used as an important phenotypic feature for biochemical differentiation of these bacteria. The comparison of the scr region of the two Vibrio strain genomes is depicted in Figure 4A.…”

Biological and Genomic Characterization of a Novel Jumbo Bacteriophage, vB_VhaM_pir03 with Broad Host Lytic Activity against Vibrio harveyi

“…vB_VhaM_pir03 was shown to have a broad host lytic activity against different Vibrio species within the Harveyi clade [ 69 , 70 ]. To our knowledge, only one other Vibrio phage, KVP40 was reported to infect multiple Vibrio species [ 71 ].…”

Primer reporte de bacterias y dinoflagelados marinos luminiscentes del Parque Nacional Isla del Coco, Costa Rica

“…Las aislados de V. alginolyticus y V. parahaemolyticus, no pertenecen al clado Harveyi, el cual es un complejo de bacterias que hasta el momento comprende 12 especies (V. rotiferianus, V. azureus, V. sagamiensis, V. jasicida, V. natriegens, V. mytili, V. harveyi, V. campbellii, V. owensii, V. rotiferianus, V. jasicida y V. hyugaensis). La complejidad de este grupo se debe a que los fenotipos y genotipos de esas especies son muy similares entre sí, por lo que su identificación por métodos bioquímicos y moleculares es compleja (Ke et al, 2018). Lo anterior evidencia que es necesaria una caracterización bioquímica y molecular de los aislamientos obtenidos en este estudio para confirmar la identidad de los aislados luminiscentes recuperados de la Isla del Coco.…”