Mode and Fidelity of Bacterial Symbiont Transmission and Its Impact on Symbiont Genome Evolution

Abstract

Mutualistic symbioses have enabled the colonization of novel habitats and niches in a large array of eukaryotic and bacterial taxa. Reliable mechanisms of symbiont transmission between host generations are necessary to stabilize these associations over evolutionary time. Historically, symbionts have been categorized as either vertically transmitted from the parents to offspring or horizontally transmitted through the environment. The route between hosts influences how symbiont populations are connected between hosts and between geographic localities. Over evolutionary time vertical transmission leads to gene loss and genome erosion. Growing evidence from diverse associations suggests that modes utilizing both horizontal and vertical strategies exist, raising the question of how these “mixed modes” influence symbiont genome evolution. The overarching goal of my dissertation was to determine whether the mode of symbiont transmission in an obligate mutualism is consistent over evolutionary time and what impact transmission mode fidelity has on symbiont genome evolution. To test these questions, I used the chemosynthetic symbiosis between the marine bivalve Solemya velum and its gammaproteobacterial symbionts, which has been reported to transmit its symbionts vertically through the ovary, but bears none of the genomic hallmarks of strict vertical transmission.

In this work, I used population genomics of S. velum subpopulations sampled from five localities along the New England coast, from Massachusetts to North Carolina, to test for evidence of horizontal transmission in the evolutionary history of this species. These analyses revealed that symbionts and mitochondria do not exhibit concordant genealogies, divergent symbiont lineages have come into contact and recombined, and symbiont genomes have experienced large-scale structural changes mediated by mobile elements and horizontal gene transfer. In total, these lines of evidence indicate that a substantial amount of horizontal transmission has occurred in the recent history of this association. The vertical transmission route through host tissues was characterized via in situ hybridization to symbiont 16S rRNA in adult host tissues and by qPCR of the rhlE gene in spawned eggs. These data showed that symbionts are present at low abundance in the ovary, associated with the supportive cells and mature oocytes, and each spawned egg contains approximately 50-100 copies of the symbiont genome. Lastly, I tested for evidence of mixed transmission modes in symbiont populations contained within host tissues (each host gill contains more than a billion symbiont cells), by deep-coverage whole genome sequencing. Using a novel variant-calling procedure, I detected low amounts of genetic variation among symbiont genomes within a host relative to between hosts. However, the variant sites that were present were correlated in position along the genome, present on the same chromosome, and segregating in the symbiont population at large, suggesting that these variants arose via recombination with a variant symbiont genotype introduced by horizontal transmission.

In total, this work supports the existence of mixed transmission modes in symbiotic associations and indicates they have distinct consequences for symbiont evolution. Mixed modes may provide a best-of-both-worlds strategy to ensure that hosts acquire symbionts every generation while maintaining opportunities for recombination and acquisition of novel genetic elements. These results are relevant to understanding the impact of symbiont transmission mode on genome evolution in associations ranging from mutualisms to pathogenic infections.