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分布的异养动物，它们提供重要的生态系统服务，即过滤海水。微生物群落存在于这些海洋动物中，海绵微生物组的多样性与海绵物种以及海绵生活的环境有关。海水过滤的主要废物之一是氨，氨的去除是由微生物氨氧化剂如Thaumarchaeota促进的，因为它们使用氨作为其能量产生的底物。海绵和它们的微生物共生群落之间的关系，包括Thaumarchaeota，一直研究不足。这阻碍了对环境变化后控制共生特异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产生了重要的环境后果，这种共生关系正受到威胁。因此，本项目旨在了解在气候变化影响的环境扰动后，控制海绵-微生物共生稳定性（恢复力和抵抗力）的生态机制。诸如温度变化，水酸化和污染物增加修正等因素是经典的线程，将进行几个环境扰动实验，以了解热应力，有毒物质暴露，基质波动或水化学变化对海绵微生物组的影响，并随后使用最先进的水族馆控制的中生态系统设施对海绵生理学的影响。环境扰动因子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16 S rRNA扩增子测序进行）、宏基因组学和元转录组学分析，以评估涉及胁迫反应、基因修复和突变系统的特定基因对系统稳定性的作用。Thaumarchaeota是唯一一个既包含自由生活的生物又包含共生生物的古菌门，因此，这种海绵-古菌模型将能够分析古菌从自由生活到共生状态的进化生活方式转变。最近已经组装了一组不同的自由生活的代表性基因组，并使用宏基因组组装、基因组重建和相关的生物信息学进化方法来推断该谱系的祖先进化历史（谢里丹等人，2020年）。在不同地点（印度尼西亚、西班牙、英国.）进行海绵取样后，该项目将重点关注共生Thaumarchaeota，以重建其潜在的代谢能力，并推断其进化沿着的基因获得，基因复制，基因丢失和横向基因转移的速率。学生还将评估哪些基因组途径具有令人兴奋的潜力，使Thaumarchaeota能够应对与气候变化有关的几种环境扰动。

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.