Nineteen Vibrio anguillarum-specific temperate bacteriophages isolated across Europe and Chile from aquaculture and environmental sites were genome sequenced and analyzed for host range, morphology and life cycle characteristics. The phages were classified as Siphoviridae with genome sizes between 46,006 and 54,201 bp. All 19 phages showed high genetic similarity, and 13 phages were genetically identical. Apart from sporadically distributed single nucleotide polymorphisms (SNPs), genetic diversifications were located in three variable regions (VR1, VR2 and VR3) in six of the phage genomes. Identification of specific genes, such as N6-adenine methyltransferase and lambda like repressor, as well as the presence of a tRNA^Arg, suggested a both mutualistic and parasitic interaction between phages and hosts. During short term phage exposure experiments, 28% of a V. anguillarum host population was lysogenized by the temperate phages and a genomic analysis of a collection of 31 virulent V. anguillarum showed that the isolated phages were present as prophages in >50% of the strains covering large geographical distances. Further, phage sequences were widely distributed among CRISPR-Cas arrays of publicly available sequenced Vibrios. The observed distribution of these specific temperate Vibriophages across large geographical scales may be explained by efficient dispersal of phages and bacteria in the marine environment combined with a mutualistic interaction between temperate phages and their hosts which selects for co-existence rather than arms race dynamics.

Zonula occludens toxin (Zot) is a conserved protein in filamentous vibriophages and has been reported as a putative toxin in Vibrio cholerae. Recently, widespread distribution of zot-encoding prophages was found among marine Vibrio species, including environmental isolates. However, little is known about the dynamics of these prophages beyond V. cholerae. In this study, we characterized and quantified the zot-encoding filamentous phage VAIϕ, spontaneously induced from the fish pathogen V. anguillarum. VAIϕ contained 6117 bp encoding 11 ORFs, including ORF8^pVAI, exhibiting 27%–73% amino acid identity to Inovirus Zot-like proteins. A qPCR method revealed an average of four VAIϕ genomes per host genome during host exponential growth phase, and PCR demonstrated dissemination of induced VAIϕ to other V. anguillarum strains through re-integration in non-lysogens. VAIϕ integrated into both chromosomes of V. anguillarum by recombination, causing changes in a putative ORF in the phage genome. Phylogenetic analysis of the V. anguillarum Inoviridae elements revealed mosaic genome structures related to mainly V. cholerae. Altogether, this study contributes to the understanding of Inovirus infection dynamics and mobilization of zot-like genes beyond human pathogenic vibrios, and discusses their potential role in the evolution of the fish pathogen V. anguillarum.

Bacteriophages are the most abundant biological entities in the oceans and play key roles in bacterial activity, diversity and evolution. While extensive research has been conducted on the role of tailed viruses (Class: Caudoviricetes), very little is known about the distribution and functions of the non-tailed viruses (Class: Tectiliviricetes). The recent discovery of the lytic Autolykiviridae family demonstrated the potential importance of this structural lineage, emphasizing the need for further exploration of the role of this group of marine viruses. Here, we report the novel family of temperate phages under the class of Tectiliviricetes, which we propose to name “Asemoviridae” with phage NO16 as a main representative. These phages are widely distributed across geographical regions and isolation sources and found inside the genomes of at least 30 species of Vibrio, in addition to the original V. anguillarum isolation host. Genomic analysis identified dif-like sites, suggesting that NO16 prophages recombine with the bacterial genome based on the XerCD site-specific recombination mechanism. The interactions between the NO16 phage and its V. anguillarum host were linked to cell density and phage–host ratio. High cell density and low phage predation levels were shown to favor the temperate over the lytic lifestyle for NO16 viruses, and their spontaneous induction rate was highly variable between different V. anguillarum lysogenic strains. NO16 prophages coexist with the V. anguillarum host in a mutualistic interaction by rendering fitness properties to the host, such as increased virulence and biofilm formation through lysogenic conversion, likely contributing to their global distribution.

Phage-bacterial interaction studies routinely apply phage lysates at final concentrations of up to 10% of the culture. Consequently, bacterial metabolites such as quorum sensing (QS) signaling molecules are transferred along with the phage lysate to recipient bacterial cells. Here, we show that the Pseudomonas aeruginosa QS molecules 3OC12-HSL and C4-HSL are rapidly degraded in phage lysates. In contrast, the hydrophobic QS molecule PQS is remarkably stable, for at least one year, due to its binding within outer membrane vesicles. Strikingly, we find that PQS exceeds concentrations of 10 µM in standard phage lysate preparations. We show that PQS carried over from phage lysates induces QS-controlled production of the virulence factor pyocyanin in P. aeruginosa . This PQS carryover does not oppose previous conclusions of phage infection-induced PQS production, as we show here, that this response is also triggered by PQS-free phage lysates. Since other bacterial species, including Paracoccus and Vibrio harveyi , also produce hydrophobic QS molecules that are bound within outer membrane vesicles, it is likely that phage lysates from these bacteria may similarly contain stable QS molecules. Collectively, we demonstrate that membrane-bound QS molecules may significantly confound QS-related physiological outcomes of phage-host interaction studies. This can be avoided by using QS synthase mutants for phage propagation or by purifying phage particles from lysates to eliminate QS molecule carryover.

In the evolutionary battle between bacteria and mobile genetic elements, such as bacteriophage viruses and plasmids, bacteria have developed intricate defense systems. Among these, the CRISPR-Cas system has been extensively studied and harnessed as a revolutionary gene editing tool. However, while the biochemical process by which this microbial immune system acquires genetic CRISPR memory and immunity against invaders has been comprehensively examined, fundamental questions about the bacterial physiological state underlying how and when CRISPR memory is formed have only been partially explored. Naïve CRISPR adaptation is generally rare, but occurs more frequently when bacteria are challenged with replication-deficient phages. In such scenarios, bacteria are not under immediate threat and have ample time to adapt to the phage DNA, without risking cell death. Accordingly, slow growth caused by low temperatures, low aeration, or bacteriostatic antibiotics promotes CRISPR adaptation, possibly by allowing the Cas complexes more time to adapt before being outpaced. Persister cells are dormant antibiotic-tolerant subpopulations of cells with limited metabolic activity. When a mobile genetic element invades a persister cell, its replication is halted until the host cell resumes growth, providing an ideal opportunity for CRISPR adaptation. Here, we show that transiently dormant Escherichia coli persister cells acquire CRISPR immunity 10-fold more frequently than the general bacterial population. Thus, persister cells, in addition to being notoriously antibiotic tolerant, are primed for CRISPR-Cas adaptation and may be in a state of heightened immune capacity and evolution, securing the survival of the population.

CRISPR-Cas is an adaptive immune system of bacteria and archaea that protects against foreign genetic elements. In Escherichia coli and Salmonella , CRISPR-Cas is inhibited by the conserved global repressor the histone-like nucleoid structuring protein (H-NS), which blocks the expression of AT-rich horizontally acquired genes. While the opportunistic pathogen Pseudomonas aeruginosa harbours two partially redundant H-NS homologues, MvaT and MvaU, their role in CRISPR-Cas regulation in this bacterium remains unexplored. Here, we demonstrate that in the absence of both MvaT and MvaU, CRISPR-Cas activity increases more than tenfold, as measured by a reduction in the transformation efficiency of a CRISPR-targeted plasmid. Importantly, we find that in the absence of MvaT and MvaU, Cas proteins are already produced at low cell density prior to the onset of quorum sensing-mediated activation of CRISPR-Cas, which occurs at high cell density. Moreover, the ∆ mvaT ∆ mvaU mutant has a significantly reduced growth rate, known to independently increase CRISPR-Cas activity. In addition to regulating CRISPR-Cas, the absence of MvaT and MvaU affects phage–host interactions, including enhancing the adsorption of the LPS-binding phage JBD44, highlighting their broader role in coordinating bacterial defence mechanisms. This article is part of the discussion meeting issue ‘The ecology and evolution of bacterial immune systems’.