Metagenomics for the bioassessment of waterbodies using mesocosm experiments

水体及其生物多样性受到污染物、疾病媒介、生物入侵和非生物压力源的威胁。在欧盟，《水框架指令》（WFD）旨在提供评估、监测和管理水体的手段，以确保安全、经济和自然资源的可持续性。传统上，踢腿取样是用于检索大型无脊椎动物多样性的代表性样本。用形态学方法鉴定物种。然后根据生物多样性和物理化学因素对河流进行定性评分。这种方法通常是耗时的，劳动密集型的，并且需要大型无脊椎动物的专家鉴定。需要用新技术来补充传统方法。在此，我们建议利用（生态）宏基因组学、生物信息学和化学生物学的最新发展，探索水体评价的新方法。最近的分子进展，包括使用从水柱中提取的环境DNA (eDNA)，提供了从水样中获得存在或不存在物种的能力，而无需直接与之相互作用。这些新颖的高通量技术可以使我们追踪和描述焦点物种，以及它们所嵌入的更广泛的食物网。该项目的目的是利用eDNA和宏基因组方法以及帝国理工学院现有的中生态系统来确定化学应激源对淡水生态系统的影响。人们越来越认识到，基于介观世界的方法跨越了现场观察和实验室实验之间的关键差距，提供了现实水平的生物复杂性，同时也提供了一定程度的实验条件控制和复制。元条形码通过在中生态系统中组装人工群落和提取eDNA，恢复关键物种的存在度和丰度，采用尖端的分子计算方法，更好地利用元基因组数据，获得最大价值。与中生态系统一样，微观生态系统也可以用来评估中生态系统内的微生物群落。该项目的目的是开发这些技术，以替代世界粮食计划署目前提供的冗长而昂贵的方法。人们特别感兴趣的是，人为产生的化学物质如何影响淡水环境中的食物网。特别感兴趣的化学物质是废水中的氨和家用产品中的表面活性剂。之所以选择氨，是因为文献中有强有力的证据表明，氨的增加会导致鳃结构受损，对许多物种都是致命的。此外，氨的污染往往导致富营养化和溶解氧的消耗。表面活性剂也引起了人们的兴趣，因为它们在家庭和工业中都很常见，如肥皂、洗衣剂和增产油。表面活性剂是一类广泛的化学物质，它们会干扰细胞膜，溶解蛋白质，导致细胞裂解，从而破坏生态系统。由于这些原因，微生物可能会受到表面活性剂的影响，这可能会影响微生物在中生态系统中介导的关键生物地球化学循环的速率

Water bodies and their resident biodiversity are at risk from contaminants, disease agents, biological invasions, and abiotic stressors. In the European Union, the Water Framework Directive (WFD) is designed to provide the means to assess, monitor and manage water bodies in order to ensure safety, economic, and natural resource sustainability. Traditionally, kick sampling is applied to retrieve representative samples of macroinvertebrate diversity. Species are identified using morphological methods of identification. The river is then given a qualitative score based on biodiversity, and physicochemical factors. This methodology is often time consuming, labour intensive, and requires expert identification of macroinvertebrates. There is the need for conventional approaches to be supplemented with new technologies. Here, we propose to explore new approaches for the assessment of water bodies, which benefit from the latest developments in (eco)metagenomics, bioinformatic and chemical biology. Recent molecular advances, including the use of environmental DNA (eDNA) extracted from the water column, provide the ability to derive presence, absence of a species from a water sample without needing to directly interact with it. These novel high through-put technologies could enable us to track and describe focal species as well as the wider food web within which they are embedded. The aim of the project is to use eDNA and metagenomic approaches with the mesocosms available at Imperial College to determine the effects of chemical stressors on freshwater ecosystems. Mesocosm-based approaches are increasingly recognized as spanning the critical gap between field observations and lab experiments, by offering realistic levels of biocomplexity, whilst also affording a degree of control and replication of experimental conditions. Through the assembly of artificial communities in mesocosms and extraction of eDNA, metabarcoding can recover presence and abundance of key species, employing cutting-edge molecular computational methods to better exploit metagenomic data and derive maximum value. As well as the mesocosms, microcosms may be constructed and used to assess the microbial communities within the mesocosms. It is an aim of this project to develop these techniques as an alternative to the lengthy and costly methodology currently provided by the WFD.In particular there is an interest in how anthropogenically derived chemicals impact the food webs of freshwater environments. Particular chemicals of interest are ammonia from waste waters, and surfactants from household products. Ammonia was chosen as there is strong evidence in literature that increases in ammonia lead to damage to gill structures, fatal to many species. Furthermore, pollution of ammonia often leads to eutrophication and depletion of dissolved oxygen. Surfactants are also of interest as they are common at home and in industry, as soaps, laundry detergents, and enhanced oil production. Surfactants are a broad class of chemicals that could be disruptive to the ecosystem as they interfere with cell membranes, solubilize proteins, and cause cell lysis. Due to these reasons microbes are likely to be influenced by surfactants, this may have an impact the rates of key biogeochemical cycles that are mediated by microbes in the mesocosms