Understanding the ecological relevance of eDNA in freshwater lotic ecosystems

了解环境变化和不断变化的土地利用对生物多样性的影响以及生态系统是如何工作的，需要对社区及其生态学有全面的了解。分子生物多样性鉴定正在成为传统方法的高通量和高成本效益的替代方法，特别是环境DNA （eDNA）分析提供了在空间和时间上以前所未有的尺度测量生物多样性的机会。与通过直接分析群落获得的DNA不同，eDNA指的是生物体在经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，如濒危/入侵物种的识别和监测以及生物多样性的分析。很明显，研究人员可以从各种自然环境，特别是淡水环境中检测到eDNA。然而，了解这些eDNA来源与生态和社会经济重要河流生态系统中生物多样性和相关生态功能的关系是eDNA:LOFRESH提案的核心。关注从地方到国家尺度的一系列范例实验半自然和自然淡水流域系统，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与原位群落之间的关系，(c)改进eDNA数据采集和使用新的生态和系统发育算法解释eDNA数据的方法方法。(e)开发和测试与生物多样性流和生态系统功能及其对土地利用压力的变化有关的逻辑dna的新模型。在四年的时间里，班戈大学、伯明翰大学、卡迪夫大学和生态与水文中心将提供五个工作包。在WP1中，我们将在一系列实验中使用人工流通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WP2中，我们将通过跟踪自然河流（即湖泊）来测试我们在WP1中的实验结果，并通过在威尔士北部深入研究的康威河研究集水区的自然溪流网络实验引入控制性的eDNA。WP2还将评估康威河选定支流中观测到的lotic eDNA与原地群落之间的关系，显示一系列物理化学特征和经历不同的土地利用压力。WP3将与威尔士正在进行的一项全国调查协调，对lotic eDNA进行采样，以将WP1和WP2的实验和流域规模的发现扩大到威尔士景观和全国范围。WP4将提供信息学支持，但具体来说，开发工作流程来识别eDNA数据集中的物种水平多样性。最后，在WP5中，我们将通过模拟土地利用压力操纵实验溪流系统，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，进一步验证我们的模型发现。与广泛的利益相关者团体（政府、最终用户、环境机构）和项目合作伙伴（专门从事eDNA、测序和信息学的研究机构和学术合作伙伴）的有效接触，将优化整个联盟网络中潜在的变革性科学的影响和研究协同效应。

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.