The impact of environmental change on the ecological and evolutionary dynamics of symbiotic sponge communities.

Sponges are widespread heterotrophic animals in marine environments, and they perform a critical ecosystem service, i.e. filtration of seawater. Microbial communities are present within these marine animals, and the diversity of the sponge microbiome is related to the sponge species and also to the environment in which the sponges live. One of the key waste products of seawater filtration is ammonia and removal of ammonia is facilitated by microbial ammonia oxidisers such as Thaumarchaeota, as they use ammonia as a substrate for their energy generation. The relationship between sponges and their microbial symbiotic communities, including Thaumarchaeota, has been understudied. This has prevented an understanding of the factors controlling the symbiotic specificity and system stability following environmental change. However, this symbiosis is under threat as climate change has important environmental consequences for marine organisms.
Therefore, this project aims to understand the ecological mechanisms controlling for the stability (resilience and resistance) of sponge-microbe symbiosis following environmental perturbations influenced by climate change. Factors such as temperature change, water acidification and increased pollutant amendments are classical threads and several environmental perturbation experiments will be performed to understand the effect of thermal stress, toxicant exposure, substrate fluctuation or alterations of water chemistry on the sponge microbiome, and subsequently on the sponge physiology using a state-of the-art aquarium controlled mesocosm facility. The final choice of the environmental perturbation factor(s) will depend on the student interest and will be based upon literature review. The stability (resistance and resilience) of the system to these different environmental perturbations will help predict the adaptation of this symbiosis to climate change. In addition to time-series microbial community analysis (performed using 16S rRNA amplicon sequencing), metagenomics and metatranscriptomics analyses will be performed to evaluate the role of specific genes implicated in stress response, gene repair and mutation systems on the system stability.
Thaumarchaeota are one of the only archaeal phyla containing both free-living and symbiotic organisms, so this sponge-archaea model will enable analysis of the evolutionary lifestyle transition from free-living to symbiotic state in archaea. A diverse set of free-living representative genomes has been recently assembled and used to infer ancestral evolutionary history of this lineage using metagenomic assemblies, phylogenomic reconstruction and associated bioinformatic evolutionary approaches (Sheridan et al., 2020). Following sponge sampling in diverse locations (Indonesia, Spain, UK...), this project will focus on symbiotic Thaumarchaeota to reconstruct their potential metabolic capabilities and infer the rates of gene acquisition, gene duplication, gene loss and lateral gene transfer along their evolution. The student will also assess which genomic pathways have the exciting potential to enable Thaumarchaeota to respond to several environmental perturbations linked with climate change.