A genomic comparison of 13 symbiotic Vibrio fischeri isolates from the perspective of their host source and colonization behavior

Abstract

Newly hatched Euprymna scolopes squid obtain their specific light-organ symbionts from an array of Vibrio (Allivibrio) fischeri strains present in their environment. Two genetically distinct populations of this squid species have been identified, one in Kaneohe Bay (KB), and another in Maunaloa Bay (MB), Oahu. We asked whether symbionts isolated from squid in each of these populations outcompete isolates from the other population in mixed-infection experiments. No relationship was found between a strain's host source (KB or MB) and its ability to competitively colonize KB or MB juveniles in a mixed inoculum. Instead, two colonization behaviors were identified among the 11 KB and MB strains tested: a 'dominant' outcome, in which one strain outcompetes the other for colonization, and a 'sharing' outcome, in which two strains co-colonize the squid. A genome-level comparison of these and other V. fischeri strains suggested that the core genomic structure of this species is both syntenous and highly conserved over time and geographical distance. We also identified~250 Kb of sequence, encoding 194 dispersed orfs, that was specific to those strains that expressed the dominant colonization behavior. Taken together, the results indicate a link between the genome content of V. fischeri strains and their colonization behavior when initiating a light-organ symbiosis.

The model squid–vibrio symbiosis provides a window into the impact of strain‐ and species‐level differences during the initial stages of symbiont engagement

“…2), or to the ratio of strains within the aggregate (Supporting Information Fig. S1) (Bongrand et al, 2016).…”

“…Horizontal transmission also impacts the genetic features of the symbiont cells. For example, in model associations, such as the legume–rhizobia symbioses, specificity can be influenced by antagonistic interactions occurring between different combinations of host and symbiont genotypes, or between strains of the same symbiont species within a given host (Pellmyr and Huth, ; Frank, ; Kiers et al ., ; Sachs et al ., , Poulsen and Boomsma, ; Bongrand et al ., ). A recent study of the model symbiosis between Steinernema nematodes and Xenorhabdus bovienii (Murfin et al ., ) showed that strain‐level differences in the fitness benefits of microbial symbionts drive variation in the success of host–microbe associations, likely contributing to the maintenance of symbiotic associations over evolutionary time.…”

“…The variation in the D‐ and S‐type strains in their ability to dominate or co‐colonize the crypts under these experimental conditions revealed a dominance hierarchy among these strains. Genomic analysis revealed that the D‐strains are a recently diverged clade of V. fischeri (Bongrand et al ., ). These phenotypic and genotypic differences among V. fischeri strains render the squid–vibrio association an exceptional model system to study the impact of symbiont diversity on initiation, maintenance and persistence of host–microbe interactions.…”

“…Recent studies of the system have demonstrated that the symbiotic population in a naturally occurring E. scolopes is not clonal but, instead, contains several phenotypically and genomicly distinguishable strains of V. fischeri Ruby, 2009, 2012;Bongrand et al, 2016). In experiments where host-colonization potential was examined when strains were competed against one another, two phenotypes were noted: (i) a dominant (D-type) behaviour, in which the host organ was usually colonized by a single strain; and, (ii) a sharing (S-type) behaviour, in which more than one strain would co-colonize the same animal (Bongrand et al, 2016). The variation in the D-and S-type strains in their ability to dominate or co-colonize the crypts under these experimental conditions revealed a dominance hierarchy among these strains.…”

Phylogeographic patterns in the Philippine archipelago influence symbiont diversity in the bobtail squid–Vibrio mutualism

“…Additionally, host‐mediated factors along with abiotic variables such as water temperature and salinity have been known to shape these mutualist assemblages (McFall‐Ngai, 2014; McFall‐Ngai et al., 2012; Nishiguchi, 2000; Soto, Gutierrez, Remmenga & Nishiguchi, 2009). Collectively, either genomic comparison of closely related populations (Bongrand et al., 2016) or haplotype comparisons of allopatric populations of Indo‐west Pacific squid and their vibrio symbionts (Jones et al., 2006) do not address the connectivity of populations across physical and biogeographic barriers like those in the Philippines or across the IPB. Therefore, we examined the genetic architecture of Euprymna albatrossae (Cephalopoda: Sepiolidae) and their V. fischeri symbionts in the Philippine archipelago using a combined phylogeographic approach to determine whether host specificity or geographic location influence the distribution of symbiotic Vibrios in this region.…”