Understanding the ecological relevance of eDNA in freshwater lotic ecosystems

要了解环境变化和土地使用变化对生物多样性的影响以及生态系统如何运作，就需要全面了解社区及其生态。分子生物多样性鉴定正在成为传统方法的高通量和成本效益的替代方法，特别是环境DNA（eDNA）的分析提供了一个机会，以前所未有的规模在空间和时间上测量生物多样性。与通过直接分析群落获得的DNA不同，eDNA是指生物体在通过环境或死亡和腐烂时脱落的细胞或游离DNA。eDNA正被应用于各种用途，如识别和监测濒危/入侵物种以及分析生物多样性。很明显，研究人员可以从各种自然环境中检测eDNA，特别是淡水环境。然而，了解这些eDNA的来源如何与生态和社会经济重要的河流生态系统中的生物多样性和相关生态功能相关是eDNA的核心：LOFRESH proposal.聚焦于一系列从地方到国家规模的实验性半自然和自然淡水集水系统，我们将（a）提高对lotic eDNA的运动和持久性的理解，（B.）使用遗传和基因组方法的不同组合量化lotic eDNA和原位群落之间的关系，（c.）用于eDNA数据获取和使用新生态学和系统发育算法解释eDNA数据的改进的方法学途径，（e.）开发和测试新的模型，将河流eDNA与河流生物多样性和生态系统功能及其对土地利用压力的变化联系起来。在4年的时间里，班戈尔大学、伯明翰大学、卡迪夫大学和生态与水文中心将提供5个工作包。在WP 1中，我们将在一系列实验中使用人工河道来评估一系列物理和化学驱动因素对lotic eDNA损失的影响，并比较和对比用于评估已知lotic eDNA来源的遗传和基因组方法。在WP 2中，我们将测试我们的实验结果从WP 1通过跟踪自然lentic（即湖）和实验引入控制lotic eDNA通过自然流网络的深入研究康威河研究集水区在北威尔士。WP 2还将评估所观察到的lotic eDNA和原位社区之间的关系，在选定的支流的康威显示一系列的理化特性，并经历不同的土地利用压力。WP 3将与威尔士正在进行的国家调查协调，对Lotic eDNA进行采样，以将WP 1和WP 2的实验和流域规模的调查结果扩大到威尔士景观和国家规模。WP 4将提供信息学支持，但具体来说，开发工作流程以识别eDNA数据集中的物种水平多样性。最后，在WP 5中，我们将进一步测试我们的模型研究结果，通过模拟土地利用压力操纵实验流系统，量化分解和食物网结构的生态系统功能，并测试与eDNA信号的联系。与广泛的利益相关者群体（政府，最终用户，环境机构）和项目合作伙伴（研究机构和专门从事eDNA，测序和信息学的学术合作伙伴）的有效参与将优化整个联盟网络中潜在变革性科学的影响和研究协同作用。

Understanding the impacts of environmental change and changing land use on biodiversity and how ecosystems work require comprehensive knowledge of communities and their ecology. Molecular biodiversity identification is emerging as a high throughput and cost effective alternative to traditional approaches and in particular, the analysis of environmental DNA (eDNA) provides an opportunity to measure biodiversity in space and time at unprecedented scales. Unlike DNA obtained through direct analysis of communities, eDNA refers to shed cells or free-DNA from organisms as they pass through an environment, or die and decay. eDNA is being applied for various uses such as identification and monitoring of endangered/invasive species and analysis of biodiversity. It is very clear that researchers can detect eDNA from a variety of natural environments and in particular, freshwater environments. However, understanding how those sources of eDNA relate to living biodiversity and associated ecological function in ecologically and socio-economically important river ecosystems is at the heart of the eDNA:LOFRESH proposal.Focusing on a range of exemplar experimental semi-natural and natural freshwater catchment systems from local to national scales, we will (a.) improve understanding of the movement, and persistence of lotic eDNA, (b.) quantify the relationship between lotic eDNA and the in situ community using different combinations of genetic and genomic approaches, (c.) improve methodological approaches for eDNA data acquisition and interpreting eDNA data using novel ecological and phylogenetic algorithms, (e.) develop and test new models relating lotic eDNA to stream biodiversity and ecosystem function and their variation in response to land use pressures. Over a 4 year period, five work packages (WPs) will be delivered by the Universities of Bangor, Birmingham, Cardiff and the Centre for Ecology and Hydrology. In WP1, we will use artificial stream channels in a series of experiments to assess the effects of a range of physical and chemical drivers on the loss of lotic eDNA and to compare and contrast genetic and genomic approaches for assessing known sources of lotic eDNA. In WP2, we will test our experimental findings from WP1 by tracking natural lentic (i.e. lake) and experimentally introduced control lotic eDNA through the natural stream network of the intensely studied Conwy River research catchment in north Wales. WP2 will also assess relationships between observed lotic eDNA and the in situ community in selected tributaries of the Conwy displaying a range of physicochemical characteristics and experiencing different land use pressures. WP3 will sample lotic eDNA in coordination with an on-going national survey in Wales to up-scale the experimental and catchment-scale findings of WP1 and WP2 to the Welsh landscape and national scales. WP4 will provide informatics support, but specifically, develop workflows to identify species level diversity in eDNA datasets. Finally, in WP5 we will further test our model findings, by manipulating the experimental stream systems with emulated land use pressures, quantify the ecosystem functions of decomposition and food web structure and test linkages with eDNA signals. Effective engagement with a broad range of stakeholder groups (government, end-users, environmental agencies) and project partners (research institutions and academic partners specialising in eDNA, sequencing and informatics) will optimise impact and research synergies of potentially transformative science throughout the consortium network.