Metagenomics for the bioassessment of waterbodies using mesocosm experiments

使用介观实验对水体进行生物评估的宏基因组学

• 批准号: 2368383
• 金额: --
• 依托单位: Imperial College London
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2019
• 资助国家: 英国
• 起止时间: 2019 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2368383
• 关键词: Metagenomics; bioassessment; waterbodies; using; mesocosm

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

水体及其居民的生物多样性面临污染物、病原、生物入侵和非生物应激源的风险。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，踢采样用于检索大型无脊椎动物多样性的代表性样本。使用形态学鉴定方法来鉴定物种。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。这种方法通常耗时、费力，并且需要大型无脊椎动物的专家鉴定。传统方法需要用新技术来补充。在这里，我们建议探索水体评估的新方法，这受益于（生态）宏基因组学、生物信息学和化学生物学的最新发展。最近的分子进展，包括使用从水柱中提取的环境 DNA (eDNA)，无需直接与水样相互作用即可确定水样中是否存在某种物种。这些新颖的高通量技术可以使我们能够跟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提供的中生态系统来确定化学压力源对淡水生态系统的影响。基于中宇宙的方法越来越被认为跨越了现场观察和实验室实验之间的关键差距，通过提供现实水平的生物复杂性，同时还提供一定程度的控制和实验条件的复制。通过在中生态系统中组装人工群落并提取 eDNA，元条形码可以恢复关键物种的存在和丰度，采用尖端的分子计算方法更好地利用宏基因组数据并获得最大价值。与中生态系统一样，也可以构建微观世界并用于评估中生态系统内的微生物群落。该项目的目标是开发这些技术，作为 WFD 目前提供的冗长且昂贵的方法的替代方案。特别是人们对人类衍生的化学品如何影响淡水环境的食物网感兴趣。特别感兴趣的化学品是废水中的氨和家用产品中的表面活性剂。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，对许多物种来说是致命的。此外，氨污染常常导致富营养化和溶解氧消耗。表面活性剂也引起人们的兴趣，因为它们在家庭和工业中很常见，如肥皂、洗衣粉和提高石油产量。表面活性剂是一类广泛的化学物质，可能会破坏生态系统，因为它们会干扰细胞膜、溶解蛋白质并导致细胞裂解。由于这些原因，微生物可能会受到表面活性剂的影响，这可能会影响中宇宙中微生物介导的关键生物地球化学循环的速率