Team will use zebrafish in new study of aquatic symbioses


Fish tanks in the UO's zebrafish lab

A UO-led team of researchers spanning physics, neuroscience, molecular biology, ecology and evolution will use a new $325,000 grant to examine aquatic symbioses – the interactions between different animal species living together.

The project is funded by a 30-month award from the Gordon and Betty Moore Foundation and involves the study of zebrafish in controlled ecosystems.

The team will leverage decades’ worth of pioneering research at the UO involving zebrafish and explorations of the gut microbiome, in which vast numbers of microbes contribute to both health and disease in their hosts. UO has been a leader in zebrafish research since the 1960s, when the late biologist George Streisinger established zebrafish as an ideal model for studying human development and disease.

“We aim to develop new tools for studying these symbioses throughout the entire lifespan of zebrafish, which serves as a model aquatic animal and a model for phenomena relevant to all vertebrates, including humans,” said Raghuveer Parthasarathy, an Alec and Kay Keith Professor in the Department of Physics, a member of the UO’s Institute of Molecular Biology and Materials Science Institute, and the principal investigator on the award.

Zebrafish“The project builds on the successes of the zebrafish group here at the UO and it pushes it to the next frontier of trying to capture the whole lifespan of the animal and its ecosystem,” Parthasarathy said.

Along with Parthasarathy, the team includes Karen Guillemin, Judith Eisen and Brendan Bohannan, all professors in the Department of Biology. Guillemin is a Philip H. Knight Chair and a member of the Institute of Molecular Biology. Eisen is a member of the Institute of Neuroscience. Bohannan, the James F. and Shirley K. Rippey Chair in Liberal Arts and Sciences, is a member of the Institute of Ecology and Evolution.

The team also includes John Rawls, a professor of molecular genetics and microbiology at Duke University and the director of the Duke Microbiome Center.

Part of the Moore Foundation’s Symbiosis in Aquatic Systems Initiative, the project will contribute to a larger effort to equip the scientific community with new genetic tools, cultivation methods and other infrastructure to improve experimental capabilities in aquatic symbiosis research over the coming decade. Increasingly, researchers are recognizing that symbiotic bacteria are critical components in the processes that sculpt the evolution, ecology, development and physiology of animals, yet remarkably little is known about exactly how those processes play out.

The four UO researchers have worked together on previous projects as part of the UO’s interdisciplinary Microbial Ecology and Theory of Animals, a National Institutes of Health-funded Center of Excellence in Systems Biology. The center is funded by a $7.6 million grant and seeks to better understand the bacteria and other microorganisms that reside in the animal gut and influence many biological functions.

Building on their earlier work studying individual biological processes, the new research will explore the entire ecosystem and lifespan of zebrafish and consider food chains, population densities and other attributes. The project will serve as a bridge between more traditional model system research and field studies, opening up new frontiers in zebrafish research, Parthasarathy said.

The project involves three main areas. Investigators will:

  • Engineer environments for housing fish and prey that will allow researchers to control elements such as the delivery or removal of bacteria.
  • Develop new techniques and build on existing techniques such as the use of germ-free zebrafish or fish with controlled symbionts.
  • Address the issue of nutrition to examine questions such as how gut microbes influence metabolism, obesity and other health factors.

“We’re hoping to learn how can we both predict and control ecosystem constituents, things like food and bacteria and how can that give us healthy organisms throughout their lifespan,” Parthasarathy said. “Our approach focuses especially on better understanding nutrition and on engineering new aquatic habitats that allow controlled investigation of symbiotic interactions. We want to watch and learn from the entire process.”

The UO team will be building on a strong foundation of zebrafish research. That includes groundbreaking work by Eisen examining interactions between the nervous system, immune system and bacteria in the gut, and Guillemin’s innovative development of specialized sterile zebrafish that allow scientists to better determine the role microbes play as animals grow.

Bohannan has conducted important research on zebrafish, tracking them throughout their life cycle to see how diet, genetics and immune response affect their microbial diversity. And Parthasarathy has employed physics to better understand how gut microbes move and interact with each other, producing stunning, high-resolution, three-dimensional images and videos of gut bacteria in zebrafish using a technique known as light sheet microscopy.

Rawls, the biologist from Duke University, studies gut bacteria in zebrafish and their role in regulating digestive physiology, innate immunity and gut-brain communication.

“I think (this research) may open up a lot of ecological questions,” Parthasarathy said. “If we succeed, we can expand our methods to other species such as plants and algae and explore their interactions. I think there is lots of potential for growth.”

The project is the latest in a string of awards to UO researchers from the Moore Foundation. Earlier this year Eisen received a $2 million grant through the same symbiosis initiative to probe the relationship between symbiotic bacteria and neural development, using zebrafish as a model organism. In January, UO biologist Kelly Sutherland received a $1.1 million grant from the foundation funding her research examining the swimming mechanisms of gelatinous marine organisms.

“These awards are a testament to the exceptional research being conducted at the University of Oregon,” said Provost and Senior Vice President Patrick Phillips. “We are grateful to the Gordon and Betty Moore Foundation for their generous support of our researchers and their investment in these innovative and impactful projects, which support the foundation’s critical mission of fostering pathbreaking scientific discovery and further the UO’s commitment to enriching the human condition through creative inquiry and scientific discovery.”

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