Evidence of Genomic Diversification in a Natural Symbiotic Population Within Its Host

Abstract

Planktonic cells of the luminous marine bacterium Vibrio fischeri establish themselves in the light-emitting organ of each generation of newly hatched Euprymna scolopes bobtail squid. A symbiont population is maintained within the 6 separated crypts of the organ for the ∼9-month life of the host. In the wild, the initial colonization step is typically accomplished by a handful of planktonic V. fischeri cells, leading to a species-specific, but often multi-strain, symbiont population. Within a few hours, the inoculating cells proliferate within the organ’s individual crypts, after which there is evidently no supernumerary colonization. Nevertheless, every day at dawn, the majority of the symbionts is expelled, and the regrowth of the remaining ∼5% of cells provides a daily opportunity for the population to evolve and diverge, thereby increasing its genomic diversity. To begin to understand the extent of this diversification, we characterized the light-organ population of an adult animal. First, we used 16S sequencing to determine that species in the V. fischeri clade were essentially the only ones detectable within a field-caught E. scolopes. Efforts to colonize the host with a minor species that appeared to be identified, V. litoralis, revealed that, although some cells could be imaged within the organ, they were <0.1% of the typical V. fischeri population, and did not persist. Next, we determined the genome sequences of seventy-two isolates from one side of the organ. While all these isolates were associated with one of three clusters of V. fischeri strains, there was considerable genomic diversity within this natural symbiotic population. Comparative analyses revealed a significant difference in both the number and the presence/absence of genes within each cluster; in contrast, there was little accumulation of single-nucleotide polymorphisms. These data suggest that, in nature, the light organ is colonized by a small number of V. fischeri strains that can undergo significant genetic diversification, including by horizontal-gene transfer, over the course of ∼1500 generations of growth in the organ. When the resulting population of symbionts is expelled into seawater, its genomic mix provides the genetic basis for selection during the subsequent environmental dispersal, and transmission to the next host.

Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance

“…The uptake is often restricted to an early developmental stage ( Franke et al 2021 ), where the innate immune system has an important role in establishing symbioses in invertebrates, resulting in highly specific symbiont acquisition by the host from the environment ( Nyholm and Graf 2012 ). Additionally, the long-term host association results in low strain diversity within one host, as also observed for the marine bacterium Vibrio fischeri colonizing the squid light organ ( Bongrand et al 2022 ). We conclude that these symbioses are not open, but rather restricted, thus we term them narrow symbioses.…”

Quorum Sensing Facilitates Interpopulation Signaling by Vibrio fischeri within the Light Organ of Euprymna scolopes

“…After crypt spaces are initially colonized, the corresponding bacterial populations experience daily expulsion events, [27,28] with the majority of cells being released into the marine environment. The few cells remaining within each crypt space grow and repopulate the site, and a recent study provided evidence that these subsequent rounds of population growth promoted further diversification [29] . The model of interpopulation signaling presented here provides a potential source of selective pressure because cells must balance producing sufficient bioluminescence for the host with its energetic cost.…”

“…The few cells remaining within each crypt space grow and repopulate the site, and a recent study provided evidence that these subsequent rounds of population growth promoted further diversification. [29] The model of interpopulation signaling presented here provides a potential source of selective pressure because cells must balance producing sufficient bioluminescence for the host with its energetic cost. Exposure to a high level of autoinducer in vivo may select over time for mutants with decreased luciferase activity that compensates for the enhanced induction of the lux operon.…”

TheVibrio fischeritype VI secretion system incurs a fitness cost under host-like conditions

“…If such growth dynamics occur in the squid, one might expect to isolate more T6SS2-on genotypes when sampling the light organs of juveniles, compared to adults. Indeed, recent work has shown the potential for V. fischeri to genetically diversify within the host light organ (27), and a metagenomics study in human guts described a significantly higher proportion of Bacteroides fragilis strains contained the GA3 T6SS genotype in infant gut microbiomes, compared to adults (28), suggesting the interplay between fitness costs and selective pressure may influence the T6SS prevalence in animal-associated bacteria across diverse hosts.…”