Genetic innovations in animal-microbe symbioses

Abstract

Animal hosts have initiated myriad symbiotic associations with microorganisms and often have maintained these symbioses for millions of years, spanning drastic changes in ecological conditions and lifestyles. The establishment and persistence of these relationships require genetic innovations on the parts of both symbionts and hosts. The nature of symbiont innovations depends on their genetic population structure, categorized here as open, closed or mixed. These categories reflect modes of inter-host transmission that result in distinct genomic features, or genomic syndromes, in symbionts. Although less studied, hosts also innovate in order to preserve and control symbiotic partnerships. New capabilities to sequence host-associated microbial communities and to experimentally manipulate both hosts and symbionts are providing unprecedented insights into how genetic innovations arise under different symbiont population structures and how these innovations function to support symbiotic relationships.

Figure 1:. Symbiont genetic population structure

Genetic population structure refers to the organization of genetic variation (alleles) in a population, as a consequence of evolutionary processes including gene flow, genetic drift, and natural selection. The genetic population structure of symbionts is shaped by features of the symbiotic relationship, including the symbiont transmission mode and population bottlenecks during host colonization. These features influence the diversity of strains found within hosts, the amount of genetic recombination that symbionts undergo, and the ability of purifying selection to purge deleterious mutations that arise. Differences in genetic population structure result in different evolutionary patterns that can be categorized as open, closed, and mixed symbioses, illustrated in the lower panel. In open symbioses, such as between the bobtail squid Euprymna scolopes (red) and strains of symbiotic Aliivibrio from the sea water, horizontal transmission and recombination are frequent. In closed symbioses, such as between Hodgkinia cicadicola and the cicada Magicicada tredecim (green), symbionts are vertically transmitted and clonal. In mixed symbioses, such as between Hamiltonella defensa and the aphid Acyrthosiphon pisum (blue), transmission is mostly vertical but occasionally horizontal across divergent hosts, as H. defensa is present and vertically transmitted in the whitefly Bemisia tabaci (purple).

Figure 2.. Genomic features of bacterial species that have evolved under open, closed, and mixed symbioses.

For each bacterial species, two strains were selected to identify core (shared) and accessory (unique) genes, to calculate a pairwise ratio of the nonsynonymous to synonymous substitution rate (dN/dS) for core genes, and to visualize intergenomic synteny. Coding sequences (CDS) are displayed for both strains, and GC content is displayed for the upper strain only (the dashed lines represent 50% GC content). Host names are given in parentheses. A) Symbionts in open communities retain large genomes mainly composed of protein-coding genes under strong purifying selection (dN/dS < 0.1). They possess an average or high GC content (>30%). Their genomes are mostly syntenic, although a large inversion has occurred in G. apicola. B) Symbionts in closed communities possess reduced genomes and few genes, which are under very relaxed purifying selection (dN/dS > 0.2). Their GC content is low (20 – 27% GC for B. aphidicola strains, 11–17% for S. capleta strains). Their genomes are highly syntenic. (C) Symbionts in mixed communities possess genomes with varying levels of reduction, many accessory genes, and weak purifying selection (dN/dS > 0.1). They possess an average or high GC content (>30%), and their genomes possess many rearrangements and inversions.

Figure 3:. Symbiont phylogenetic patterns depend on the frequency of horizontal transmission.

A) Symbionts that are strictly vertically transmitted, as in closed symbioses, exhibit co-cladogenesis with their host after long timescales (top). For example, Sulcia has codiversified with insects in the suborder Auchenorrhyncha, including cicadas (bottom). B) In mixed symbioses, symbionts are predominantly vertically transmitted, but occasional horizontal transmission results in mismatch of host and symbiont phylogenies over long time scales (top). For example, Wolbachia undergoes vertical transmission in many arthropods but shows little signal of codiversification with hosts (bottom). A simplified insect phylogeny (based on data from ref) is provided for reference. Part A is adapted with permission from ref , National Academy of Sciences. Part B is adapted with permission from ref , CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/).

Figure 4:. Common features and mechanisms of innovation in open symbiotic communities.

Bacteria in open symbiotic communities face diverse selection pressures shaped by: abiotic perturbations, such as changes to diet (top left), antibiotics (bottom left), and temperature; interactions between co-residing microbes, such as phage-mediated antagonism (top right) and T6SS-mediated antagonism (bottom right); and host social behaviors and immune response. In these communities, innovation to maintain the symbiosis, or to adapt to changing conditions, is commonly accomplished through the introduction of new strains (bottom left), through mutation (bottom centre), and through recombination (including horizontal gene transfer), which can be mediated by extracellular vesicles, transformation, transfection, or conjugation (bottom right); strong natural selection acts on the resulting variants.

Figure 5:. Common features and mechanisms of innovation in closed symbiotic communities.

Closed symbiotic communities are clonal and face population bottlenecks when transmitted to offspring. As a consequence, bacteria in closed communities accumulate deleterious mutations that they are unable to purge, and their genomes degrade with time (top). To maintain degrading symbionts, hosts innovate by acquiring bacterial genes from other bacteria, by acquiring additional symbionts, or by replacing degraded symbionts altogether (bottom). HGT, horizontal gene transfer.

Figure 6:. Common features and mechanisms of innovation in mixed symbiotic communities.

Mixed symbiotic communities are mainly clonal because of ongoing vertical transmission, but symbionts are also occasionally acquired from other hosts or the environment. Symbionts that co-infect a host can recombine and exchange genes through horizontal gene transfer (HGT), which is often mediated by phage (top left). Successful symbionts in mixed systems possess innovations that have helped them to infect new hosts and spread in host populations (top right). These innovations include the ability to manipulate host reproduction in a way that favors symbiont-bearing hosts (for example, cytoplasmic incompatibility, whereby infected males induce sterility of non-infected females), or to provide a benefit that increases host survival or reproduction (for example, by providing defense against parasitic wasps). Hosts can innovate by acquiring novel symbionts (bottom left), and symbionts are known to innovate through horizontal gene transfer (bottom right). These mechanisms of innovation are illustrated by the symbiosis between Drosophila flies and their defensive Spiroplasma symbionts. RIP, ribosome-inactivating protein

Figure 7:. Commonly used tools for the study of symbiont genetics.

Symbionts that live intracellularly often possess reduced genomes and are difficult to culture or genetically engineer, limiting the study of symbiont genetics. Some common strategies have been applied to overcome these limitations. Certain symbionts can be cultured in eukaryotic cell lines, and others can be transferred from infected to uninfected hosts. Where sequencing has uncovered variation in gene content across symbiont strains, symbiont culture or symbiont transfer has been used to validate the role of certain host-beneficial genes. Lastly, symbiont gene function can be studied by heterologous expression, that is, expression of symbiont genes in genetically tractable bacteria or hosts.