Developing a DNA-based indicator of multitrophic diversity to assess impacts of land use on Quebec's inland waters

加拿大人管理的内陆水体比世界上任何其他国家都多，这是一种面临农业集约化日益增加的压力的关键资源。为了跟踪这些影响并评估我们内陆沃茨的生态完整性，监测计划依赖于作为水质指标的生物体，例如底栖藻类和无脊椎动物。然而，这些生物监测活动的空间和时间范围有限，主要是因为生物体的微观计数是一个耗时的过程，需要专业的分类学知识。一种新兴的技术可以解决这个问题是环境DNA（eDNA）的表征，即生物在环境中留下的DNA痕迹。例如，在河口收集的单一水样中的DNA痕迹可以揭示该河流流域中出现的数千种植物和动物。因此，通过对eDNA进行测序，原则上可以确定一个地点的物种组成，而不必用传统的劳动密集型方法来鉴定生物体。此外，由于许多遗传标记最近已被优化，以检测各种类群，现在有可能通过对同一DNA样本中的多个标记进行测序来重建水生生态系统的整个食物网（包括微生物，无脊椎动物和鱼类），这可以提供比传统监测更丰富的生物多样性趋势。我们建议开发一个多标记的eDNA监测方法的圣皮埃尔湖联合国教科文组织生物圈保护区，一个大的河流湖泊沿着圣劳伦斯河。通过与魁北克政府的三个分支机构、4个流域管理组织、一个联邦跨机构基因组学项目和一个阿本那基第一民族社区合作，我们将：1）校准一个可供该地区各利益相关者使用的综合eDNA生物监测工具; 2）评估土地利用集约化对该省生物多样性热点地区溪流和湿地的影响;和3）提供了第一个研究量化的“多营养”淡水生物多样性的流域土地利用的反应。

Canadians are the stewards of more inland water bodies than any other country in the world, a key resource that faces increasing pressures from agricultural intensification. To track these impacts and to assess the ecological integrity of our inland waters, monitoring programs rely on organisms that serve as indicators of water quality, for example bottom-dwelling algae and invertebrates. These biomonitoring activities are however limited in their spatial and temporal scope, mainly because the microscopic enumeration of organisms is a time-consuming process that requires expert taxonomic knowledge. An emergent technology that could solve this problem is the characterization of environmental DNA (eDNA), namely DNA traces left by organisms in the environment. For example, traces of DNA in a single water sample collected at the mouth of a river can reveal the thousands of plants and animals that occur in that river's watershed. Thus, by sequencing eDNA, one could in principle determine the species composition of a site without having to identify organisms with traditional, labour-intensive methods. Moreover, as many genetic markers have recently been optimized to detect various taxa, it is now possible to reconstruct the entire food web of an aquatic ecosystem (including microbes, invertebrates, and fish) by sequencing multiple markers from the same DNA sample, which could provide a richer understanding of biodiversity trends than traditional monitoring focused on a single group of organisms. We propose to develop a multimarker eDNA monitoring approach for the Lac Saint-Pierre UNESCO Biosphere Reserve, a large fluvial lake along the St-Lawrence River. In partnership with three branches of Quebec's government, 4 watershed management organizations, a federal cross-agency genomics project, and an Abenaki first nation community, we will: 1) calibrate a comprehensive eDNA biomonitoring tool that can be used by various stakeholders in the region; 2) assess impacts of land use intensification on streams and wetlands in a provincial biodiversity hotspot; and 3) provide one of the first studies quantifying the response of 'multitrophic' freshwater biodiversity to watershed land use.