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

海绵是海洋环境中广泛存在的异养动物，它们执行关键的生态系统服务，即过滤海水。这些海洋动物体内存在微生物群落，海绵微生物群落的多样性与海绵物种有关，也与海绵生活的环境有关。海水过滤的主要废物之一是氨，微生物氨氧化剂(如塔乌阿考罗塔)促进了氨的去除，因为它们使用氨作为产生能量的底物。海绵与其微生物共生群落之间的关系，包括塔乌姆考古纲，一直没有得到充分的研究。这阻碍了对环境变化后控制共生专一性和系统稳定性的因素的理解。然而，由于气候变化对海洋生物具有重要的环境后果，这种共生正受到威胁。因此，本项目旨在了解在气候变化影响的环境扰动下，海绵-微生物共生的稳定性(弹性和抵抗力)的生态机制。温度变化、水酸化和污染物修正增加等因素是经典的线索，将进行几个环境扰动实验，以了解热应激、毒物暴露、底物波动或水化学变化对海绵微生物群的影响，以及随后使用最先进的水族馆控制的中微体设施对海绵生理的影响。环境扰动因子(S)的最终选择将取决于学生的兴趣，并将基于文献综述。系统对这些不同环境扰动的稳定性(抵抗力和恢复力)将有助于预测这种共生关系对气候变化的适应。除了时间序列微生物群落分析(使用16S rRNA扩增序列)，元基因组学和元转录组学分析将被用来评估参与应激反应、基因修复和突变系统的特定基因在系统稳定性中的作用。海绵-古生物模型将能够分析古生物中从自由生活状态向共生状态的进化生活方式转变。最近组装了一组不同的自由生活的代表性基因组，并使用元基因组组装、系统基因组重建和相关的生物信息学进化方法来推断这一血统的祖先进化史(Sheridan等人，2020年)。在不同地点(印度尼西亚、西班牙、英国……)进行海绵采样后，该项目将重点放在共生的Thaumarocota上，以重建它们潜在的代谢能力，并推断它们在进化过程中的基因获取、基因复制、基因丢失和横向基因转移的速率。这名学生还将评估哪些基因组途径具有令人兴奋的潜力，使塔乌姆考古塔能够对与气候变化有关的几种环境扰动做出反应。

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.