Understanding the ecological relevance of eDNA in freshwater lotic ecosystems

要了解环境变化和土地利用变化对生物多样性的影响以及生态系统如何工作，需要全面了解社区及其生态。分子生物多样性识别正在成为传统方法的高通量和高成本效益的替代方法，尤其是环境DNA分析(EDNA)提供了以前所未有的规模在空间和时间上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指的是生物体在穿过环境或死亡和腐烂时脱落的细胞或游离DNA。EDNA正被用于各种用途，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，特别是淡水环境中检测到埃德纳。然而，了解EDNA的来源如何与具有生态和社会经济意义的重要河流生态系统中的生物多样性和相关的生态功能相关是EDNA：LOFRESH提案的核心。提高了对运动的理解，并提高了Lottic Edna的持久性，(B)使用遗传和基因组方法的不同组合来量化热带EDNA和原位群落之间的关系，(c.)使用新的生态和系统发育算法改进EDNA数据获取和解释的方法学方法，(例如)开发和测试与河流生物多样性和生态系统功能相关的新模型，以及它们在土地利用压力下的变化。在四年的时间里，班戈大学、伯明翰大学、加的夫大学和生态与水文学中心将提供五个工作包(WPS)。在WP1中，我们将在一系列实验中使用人工流道来评估一系列物理和化学驱动因素对LOTIC EDNA丢失的影响，并比较和对比评估LOTIC EDNA已知来源的遗传和基因组方法。在WP2中，我们将通过跟踪自然湖泊(即湖泊)来检验我们在WP1中的实验结果，并通过深入研究的北威尔士Conwy River研究流域的自然河流网络实验引入控制热带Edna。WP2还将评估观测到的热带EDNA与康威河选定支流的原址群落之间的关系，展示一系列物理化学特征，并经历不同的土地利用压力。WP3将与威尔士正在进行的全国调查协调，对热带埃德纳进行抽样，以将WP1和WP2的实验和集水规模的结果扩大到威尔士地貌和全国范围。WP4将提供信息学支持，但具体地说，将制定工作流程，以确定EDNA数据集中的物种水平多样性。最后，在WP5中，我们将进一步测试我们的模型发现，通过操纵模拟土地利用压力的实验河流系统，量化分解和食物网络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(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.