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

University Of Rhode Island, Kingston RI

Investigators

Abstract

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.