RII Track-4: Visualization of Host-Microbe Interactions using CLASI-FISH

形成珊瑚礁的东部牡蛎Crassostrea virginica遍布美国东海岸，通过稳定海岸、改善水质和提供栖息地，为沿海生态系统的环境健康做出了贡献。牡蛎宿主选择性地从周围的海水中携带一种独特的微生物（称为微生物群）。尽管微生物群在介导宿主健康和生态功能方面具有潜在作用，但对其相互作用机制知之甚少。该项目将通过整合分子测序，计算生物学和显微成像的尖端技术，为牡蛎微生物群的多样性和功能提供新的见解。一个新的合作将在一个早期的职业教师和她的博士学位之间启动。他是罗得岛大学的一名学生，也是海洋生物实验室显微镜和微生物群成像方面的领先专家。这项研究将为在罗得岛（RI）管辖的公共机构中代表性不足的学生的跨学科培训提供新的机会。由于C.通过对RI沿海沃茨中的virginica的研究，该研究还将为未来的沿海生态系统中东部牡蛎的生理学、免疫反应和保护机制的研究提供深入的见解。尽管它们的过滤率很高，但东部牡蛎Crassostrea virginica保持着与周围海水不同的微生物群。然而，导致牡蛎微生物群选择性的机制在很大程度上是未知的。拟议的研究旨在通过应用最先进的显微技术来可视化不同组织类型中牡蛎相关微生物群的原位组成和空间组织来解决这个问题。显微成像将与鸟枪宏基因组测序和基于宏基因组的微生物基因组重建相结合，以实现菌株水平的探针设计和功能推断。一个早期的职业教师和她的博士学位。来自罗得岛大学的一名学生将与海洋生物实验室的成像专家进行广泛的合作访问，以获得能够对宿主组织中的微生物菌株进行特异性成像的培训。该提案代表了第一个例子，其中高通量测序将与先进的显微镜相结合，以分析与东部牡蛎相关的居民微生物群的组成，空间组织和功能。它将利用该团队在初步研究中进行的广泛的社区分析和功能分析，特别是牡蛎微生物群的新型未培养菌株的基因组重建。将显微成像与宏基因组的挖掘相结合，拟议的项目将为使用类似方法广泛调查其他宿主-微生物相互作用开辟新的机会，特别是对于河口和海洋生态系统中的非模式生物。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估来支持。

The reef-forming eastern oyster, Crassostrea virginica, is abundant across the east coast of the United States, where it contributes to the environmental health of coastal ecosystems through seashore stabilization, water quality improvement, and habitat provision. The oyster host selectively harbors a distinct composition of microorganisms (known as the microbiota) from the surrounding seawater. Despite the potential roles of microbiota in mediating host health and ecological function, little is known about their mechanism of interaction. This project will provide new insights into the diversity and function of oyster microbiota by integrating cutting-edge technologies in molecular sequencing, computational biology, and microscopic imaging. A new collaboration will be initiated between an early career faculty and her Ph.D. student at the University of Rhode Island and a leading expert in microscopy and microbiota imaging at the Marine Biological Laboratory. The research will provide new opportunities for the cross-disciplinary training of underrepresented students at a public institution of the Rhode Island (RI) jurisdiction. Due to the significant ecological and economic roles of C. virginica in coastal waters of RI, the research will also provide insights into population management by enabling future research on the mechanisms underlying the physiology, immune responses, and conservation of eastern oysters in coastal ecosystems.Suspension-feeding bivalves play critical roles in the nutrient dynamics, benthic-pelagic coupling, nitrogen cycling, and biomineralization in estuarine and marine ecosystems. Despite their high filtration rate, the eastern oyster, Crassostrea virginica, maintains distinct microbiota from surrounding seawater. However, the mechanisms leading to the selective nature of the oyster microbiota is largely unknown. The proposed research aims to address this problem by applying state-of-the-art microscopic technologies into visualizing the in-situ composition and spatial organization of oyster-associated microbiota across diverse tissue types. The microscopic imaging will be integrated with shotgun metagenomic sequencing and metagenome-based reconstruction of microbial genomes to enable strain-level probe designs and functional inferences. An early career faculty and her Ph.D. student from the University of Rhode Island will take extended collaborative visits to imaging experts at the Marine Biological Laboratory to obtain trainings that would enable the specific imaging of microbial strains in host tissues. This proposal represents a first example in which high-throughput sequencing will be combined with advanced microscopy to analyze the composition, spatial organization, and function of resident microbiota associated with the eastern oyster. It will take advantage of the extensive community profiling and functional analysis performed in the team’s preliminary research, especially the genome reconstruction of novel, uncultured strains of the oyster microbiota. Combining microscopic imaging with the mining of metagenomes, the proposed project will open up new opportunities for the broad investigation of other host-microbe interactions using similar approaches, especially for non-model organisms in the estuarine and marine ecosystems.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.