EAGER: Field-Deployed Microfluidic Trap Array for Discovery and Observation of Microbial Eukaryotes

细菌和原生动物是水生和陆地生态系统的重要组成部分，推动着生物地球化学过程，包括固碳、产氧、营养循环和人为污染物的分解。在许多生境中，细菌群落结构和净产量受到原生动物捕食的自上而下的控制；反过来，大型动物对原生动物的捕食将营养物质和污染物动员到更高的营养水平。尽管微生物真核生物包括原生动物具有重要意义，但由于传统培养方法和基因技术的限制，人们对它们的多样性、生物地理学和生态系统功能知之甚少。需要新的仪器来采样、研究和了解自然系统中更广泛的原生动物。本研究的目的是开发一种微流控现场采样和分析工具，以研究自然生境中微生物真核生物的生物地理学和功能。微流控采样器将由聚二甲基硅氧烷(PDMS)和玻璃制成，具有微米级的物理特征。取样器将被选择性地放置在不同的自然环境中，以便根据形态、行为、栖息地和猎物来源选择微生物，并能够通过光学显微镜直接观察捕获的活原生动物。对收集的真核生物和原核生物的遗传分析将有助于为分类、功能和基因组信息提供一个统一的框架。这项工作与对环境变量如pH、温度和营养浓度的共置微尺度测量一起，将使研究人员能够将微生物真核生物置于它们直接的物理和化学微生境的背景下。这项工作将使一种全新的微生物群落分析工具的开发和验证成为可能，该工具将对微生物生态学家、水中地球化学家、工程师和海洋科学家立即和实际使用。它可能有助于回答生物学中的基本问题，包括群落结构变化的相关物理规模是什么，以及原生动物物种在自然生境中在多大程度上是世界性的与地方性的？此外，更好地了解微生物群落结构和功能将有助于更好地预测生物地球化学反馈作为气候变化的作用；更好地了解微生物群落结构和功能对污染物吸收和动员的影响，并增强微生物病原体环境水库的风险模型。未来的工作将整合一套全面的传感能力，并将在更广泛的自然和工程微生物栖息地部署设备。这一项目的成果将通过同行评议的期刊和以生物用户群体为目标的会议发言来传播。这项技术的实施将通过网上发布的演示视频来实现，这些视频展示了采样器是如何在实验室中设计、创建、测试、部署和研究的。所有材料都将在http://www.cmbe.engr.uconn.edu/facultyshor.html.上在线获得

Bacteria and protozoa are critical components of aquatic and terrestrial ecosystems, driving biogeochemical processes including carbon fixation, oxygen production, nutrient cycling, and break-down of anthropogenic contaminants. In many habitats, the bacterial community structure and net production are controlled in a top-down fashion by protozoan predation; in turn, predation of protozoa by larger animals mobilizes nutrients and contaminants to higher trophic levels. Despite their importance, relatively little is known about the diversity, biogeography, and ecosystem function of microbial eukaryotes including protozoa, due to limitations of both traditional culturing methods and genetic techniques. New instrumentation is needed to sample, study and understand a broader range of protozoa in natural systems.The objective of this research is to develop a microfluidic field sampling and analysis tool to study the biogeography and function of microbial eukaryotes in natural habitats. Microfluidic samplers will be fabricated with micron-scale physical features in polydimethylsiloxane (PDMS) and glass. Samplers will be selectively baited and placed in different natural environments in order to select for microorganisms based on morphology, behavior, habitat, and prey source, and will enable direct observation of entrapped live protozoa via light microscopy. Genetic analysis of collected eukaryotes and prokaryotes will help provide a unified framework for taxonomic, functional, and genomic information. Together with co-located micro-scale measurements of environmental variables such as pH, temperature, and nutrient concentrations, this work will enable researchers to place microbial eukaryotes within the context of their immediate physical and chemical microhabitats.This work will enable development and validation of a completely new microbial community analysis tool that will be of immediate and practical use to microbial ecologists, aqueous geochemists, engineers, and marine scientists. It may help to answer fundamental questions in biology including what is the relevant physical scale of community structure variations, and to what extent are protozoan species cosmopolitan vs. endemic in natural habitats? Also, a better understanding of microbial community structure and function will permit better predictions of biogeochemical feedbacks as a function of climate change; improved understand the impacts of microbial community structure and function on contaminant uptake and mobilization, and enhanced risk models for environmental reservoirs of microbial pathogens. Future work will integrate a comprehensive suite of sensing capabilities and will deploy devices in a broader range of natural and engineered microbial habitats. The results of this project will be disseminated through peer-reviewed journals and conference presentations that target the biological user community. Implementation of the technology will be enabled by web-posted demonstration videos that illustrate how samplers are designed, created, tested, deployed, and studied back in the lab. All materials will be available online at http://www.cmbe.engr.uconn.edu/facultyshor.html.