Understanding freshwater ecosystem health from a microbial perspective

淡水环境暴露在导致淡水物种、生态系统及其提供的服务衰退的压力源之下。理解这些下降的原因是复杂的，因为通常存在多种相互作用的压力。此外，这些压力可能是零星的，例如以化学污染或极端天气事件的脉冲形式出现，这使得直接测量应激源事件成为一项挑战。了解生态系统状况和确定衰退原因的一种既定方法是使用生物指标。它们通常基于鱼类、大型无脊椎动物、硅藻或大型植物群落的组成。然而，细菌、真菌和真核微生物群落无论在数量上还是在物种和遗传多样性方面都主导着淡水生物多样性。这些群落在淡水生态系统健康的运作和维护方面发挥着重要作用。它们主要负责有机物的分解，是生物地球化学循环的关键驱动力，通过光合作用固定碳，并形成水生食物网的基础。然而，我们缺乏对淡水中微生物群落结构的了解，尤其是对它们如何应对营养物质和有机污染物以及气候和水文变化等生态系统压力因素的了解。由于这些群落的功能重要性，更多地了解它们在淡水流域的组成和分布，以及探索它们揭示生态系统状况的能力是当务之急。DNA高通量测序(HTS)的进展意味着我们现在可以以前所未有的详细、低成本和高吞吐量描述整个微生物生态系统。该项目将应用环境署结构化淡水监测方案(河流监测网)收集的淡水生物膜的高温超导技术。该项目将利用RSN的现有数据，并进行现场采样和分子分析，以开发和改进方法，使分子工具能够用于常规的调节生物监测。此外，该项目将探索基于DNA的新方法来表征淡水微生物，包括长读DNA测序(PacBio或Nanopore)来表征整个群落。这些数据将以短读DNA测序方法(Illumina)为基准，该方法由环境署正在开发评估淡水生态系统健康的新方法而产生。该项目将解决以下关键研究问题：1.英格兰河流流域的淡水微生物群落(细菌、真菌和真核生物)是如何构建的？2.淡水微生物群落的不同组成部分如何响应国家范围内的物理化学和空间驱动因素？3.如何使用新的统计和机器学习方法来识别可用于确定淡水生态系统状况和识别压力源的生物指示类群？

Freshwater environments are exposed to stressors that contribute to the decline of freshwater species, ecosystems, and the services they provide. Understanding the causes of these declines is complex, as there are typically multiple, interacting pressures. Additionally, these pressures may be sporadic, for example in the form of pulses of chemical pollution or extreme weather events, which makes directly measuring stressor events a challenge. An established approach to understand both the condition of ecosystems and identify the causes of declines, is the use of bioindicators. These are typically based on the composition of fish, macroinvertebrate, diatom or macrophyte communities. However, bacterial, fungal, and eukaryotic microbial communities dominate freshwater biodiversity, both numerically and in terms of species and genetic diversity. These communities play fundamental roles in the functioning and maintenance of freshwater ecosystem health. They are primarily responsible for the decomposition of organic matter, are key drivers of biogeochemical cycles, photosynthetically fix carbon, and form the base of aquatic food webs. However, we lack an understanding of how microbial communities are structured within freshwaters and, critically, how they respond to ecosystem stressors such as nutrient and organic pollutants, and climatic and hydrological change. Due to the functional importance of these communities, it is a priority to understand more about their composition and distributions across freshwater catchments, as well as explore their ability reveal ecosystem condition.Advances in High Throughput Sequencing (HTS) of DNA mean that we now can characterise whole microbial ecosystems in unprecedented detail, at low cost and in high throughput. This project will apply HTS of freshwater biofilms collected by the Environment Agency's structured freshwater monitoring programme (the River Surveillance Network). The project will utilise both existing data from the RSN and perform field sampling and molecular analysis to develop and refine approaches to enable the utilisation of molecular tools for routine regulatory biomonitoring. In addition, this project will explore novel DNA-based approaches to characterise freshwater microbes, including long-read DNA sequencing (PacBio or Nanopore) to characterise whole communities. These data will be benchmarked against short-read DNA sequencing approaches (Illumina), generated by the Environment Agency's ongoing work into developing novel approaches for assessing freshwater ecosystem health. There will be opportunities to feed directly into regulatory policy.The project will address the following key research questions:1. How are freshwater microbial communities (bacterial, fungal, and eukaryotic) structured across river catchments in England?2. How do different components of the freshwater microbial community respond to physicochemical and spatial drivers at a national scale?3. How can novel statistical and machine learning approaches be used to identify bioindicator taxa that can be used determine freshwater ecosystem status and identify stressors?