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Determing symbiont factors that affect compatibility with a novel host

Periodic Reporting for period 1 - Symbcompat (Determing symbiont factors that affect compatibility with a novel host)

Reporting period: 2016-10-01 to 2018-09-30

Symbiosis between multicellular organisms and microbial symbionts is near universal, and it is now clear that many aspects of organismal biology in health and disease cannot be understood without reference to interactions with microbes. In insects, this includes a diverse range of heritable symbionts, which pass from a female host to her progeny. These symbionts are highly adapted to their host, and encode important properties, such as defence against natural enemies. These properties are used in control of vector borne diseases, such as transmission of the virus causing dengue fever from mosquito to humans.

In contrast to classical adaptive phenotypes, symbiont traits generally arise through a host shift event – the movement of a microbe from into a novel host species. Experimental host shift experiments indicate that there is a compatibility filter: some symbionts in novel host species cause little pathology and transmit vertically efficiently, whereas other do not. Understanding this compatibility filter will clarify the patterns through which host shifts occur in nature, and create a principled basis for manipulation of compatibility, for instance in symbiont-mediated control of vector competence.

The project ‘SYMBCOMPAT’ aimed to identify factors governing host-symbiont compatibility. For inherited bacterial symbionts of arthropods it had been established that in addition to transmission from host mother to offspring, lateral transfers between unrelated individuals (i.e. establishment of novel symbioses) also occur, both in nature and in laboratory settings. It had further been observed that some host-symbiont combinations create a good fit (low cost of symbiont in novel host, high vertical transmission fidelity) while others are not a good fit (high cost of harbouring symbiont and/or low vertical transmission efficiency). However, it had been unclear what mechanisms drive the goodness of fit between host and symbiont.
In this project, we used the natural Drosophila symbiont Spiroplasma to artificially create a novel symbiosis with a bad fit: Spiroplasma was transferred from its natural host Drosophila hydei into Drosophila melanogaster, where it causes pathogenicity, but evolves to become non-pathogenic over ~20 host generations of adaptation to the novel host. Using this experimental setting, the objectives were 1) to identify the cause of the bad fit, i.e. the initial pathogenicity, and 2) identify the genomic changes within Spiroplasma that are associated with evolution of pathogenicity loss, as factors evolving quickly after host shifts were expected to be good candidates for factors important in establishing symbiosis.

The results of this project will impact both upon our understanding of an important natural process and enable better exploitation of symbiont encoded traits in control of vector born disease.
1. We have completed the genome for the protective Spiroplasma symbiont from Drosophila hydei, and annotated this.
This analysis reveals presence of RIP genes putatively associated with protection, as well as general metabolic and other capabilities.

2. We have completed draft genomes for this strain collected at different time points.
The comparison of these genomes reveals substantial diversity between strains of Spiroplasma that all derive from a single female collected in 2002. These data indicate that Spiroplasma evolve rapidly in laboratory passage. This result is significant as it indicates a) a mutational basis for the observed capacity for rapid evolution of this symbiont. b) the heritable symbionts are widely variable in their evolutionary rate, with Spiroplasma molecular evolution being very rapid compared to other symbiotic bacteria.

3. We have transferred the symbiont from D. hydei into D. melanogaster and investigated its properties.
This experiment had an unexpected outcome. In previous work, the D. hydei Spiroplasma showed high pathogenicity in D. melanogaster, a result that had been replicated four times. However, no impact of Spiroplasma on D. melanogaster fertility/fecundity was observed during this experiment. Thus, we conclude that the transinfection phenotype of Spiroplasma has also evolved in laboratory culture, paralleling our findings on genome evolution.

4. We have passaged Spirioplasma through the novel host for 20 generations, and are currently investigating patterns of molecular evolution.
Here, we are measuring the degree to which being within a novel host accelerates evolution. This analysis is ongoing.

Dissemination and Exploitation
1. We have published two open access papers for this project to date. Three more peer reviewed papers are expected.
2. We have presented project output through talks at four conferences, within the UK, Germany and USA.
3. We have disseminated project details through local Science-Community engagement projects.
Progress beyond state of the art are both technical and conceptual.

Technical: completion of a closed symbiont genome through nanopore sequencing including the host DNA.
This process demonstrates how completed genomes can be constructed for these important partners of insects using the cheap, portable nanopore system in combination with Illumina fragment libraries. This process permits completion of the genome of virtually any symbiont of insects. This accessibility to small laboratories has potential wide implications, enabling research effort to be completed without access to expensive genome sequencing centres.

Conceptual: the recognition that bacterial symbionts may show rapid evolution in 2-10 year timescales.
This obsevation overturns the existing dogma of relatively slow evolution. It is important as it means we can no longer think of symbionts as having fixed genomes/traits in the laboratory - rather we have to embrace that they are dynamic. This poses challenges for repeating work, but also potentiates de novo evolution to novel exploitation, for instance in pest/vector control.