Racing to preserve disappearing aquatic genomes
[28 Feb 2023] BATON ROUGE, La. — Breakthroughs in the preservation techniques of aquatic species genomes could aid conservation efforts and are needed to safeguard billions of dollars of investments in biomedical research, industrial production and fisheries.
It is estimated that 200 million people worldwide rely on freshwater fishes as their primary source of protein, and 60 million people rely on them for their livelihoods. Yet nearly 30% of freshwater fish species are threatened.
For more than 30 years, LSU AgCenter researcher Terrence Tiersch and his team have worked with cryopreservation to preserve fish and shellfish. He serves as professor and director of the Aquatic Germplasm and Genetic Resources Center (AGGRC) in the LSU School of Renewable Natural Resources.
"There are tens of thousands of aquatic species that are not protected by preservation of germplasm and genetic resources. It's a gigantic global problem," said Tiersch. "We built our center to try to address the problems in how to deal with all these different species."
Genetic resources can be considered as the genes that provide value at present or in the future. These may be genes with resistance to a new disease or genomes that provide biodiversity to a species.
The primary mission of the AGGRC is to preserve aquatic organisms through the development of germplasm repositories. Germplasm is any organic material used for the reproduction of offspring. In animals, this would be sperm, eggs or embryos. Cryopreservation is a way of freezing these materials, protecting them for future use and holding them for transportation.
Cryopreservation may aid in sustaining and protecting aquatic species by preserving genetically valuable genomes. The germplasm is frozen in straws and stored in a canister with liquid nitrogen. With this technology, bulk qualities can be frozen and placed in machines that can handle millions of samples per week. The frozen material is much more affordable and easier to transport.
Endangered species often go extinct because the animals lose their genetic variation. This variation ensures the survival of a population in a changing environment that may introduce new diseases, increase the risk of predation, or decrease access to resources that maintain health. By preserving genetic resources, animals can be specifically bred to maintain genetic diversity.
Selectively breeding plants and maintaining repositories of seeds has been ongoing for thousands of years. Modern livestock breeding technologies, like cryopreservation, have allowed producers to easily introduce important genes to their animals that improve health, efficiency and production.
Cryopreservation of semen is routinely used in modern livestock breeding. Researchers at the AGGRC are developing cryopreservation methods for aquatic species using novel methods, and some of the same industrial equipment used for livestock.
"There is this massive global need. We have the constraint of trying to figure out how to deal with all these different species with nowhere near the resources and focus of other animal industries," he said.
What happens with organisms that needs to be preserved as a single cell? There is a huge demand for cryopreserved microalgae, or single-cell algae, but there is not a high-throughput approach that allows for algae to be preserved in a rapid and cost-effective manner.
The current process for obtaining starter cultures of algae is costly and requires the algae to be stored in agar jelly—a common medium used in Petri dishes. Algae can be frozen on a small scale, but current freezing methods do not allow for mass quantities to be frozen for distribution, or for the frozen material to be easily characterized and linked to a database.
The AGGRC is currently working on a project with the National Center for Marine Algae and Microbiota in East Boothbay, Maine, to scale up the storage of algae and distribute it to other entities.
Tiersch, Teresa Gutierrez-Wing and Yue Liu of the AGGRC received funding from the LSU Provost’s Fund for Research to develop large-scale repositories for algae, and previously the LSU Agricultural Center Pilot Program for Enhancement of External Funding to develop cryopreservation protocols for algae.
Algae are incredibly versatile, serving as raw materials for multi-billion-dollar industries. They are used for chemicals, nutraceuticals, pharmaceuticals and biofuels. Rather than synthesizing materials, industries can isolate the qualities they need from algae and extract them.
Tiersch explains that a problem with growing algae is that it must maintain its purity. As algae grow, the sample quality can change, either due to other organisms growing with it or by genetic alterations.
Algae grow fast and new generations may populate in a few days, which also causes deviation. Because algae can change their characteristics quickly, researchers and industry need to be able to reliably start new cultures.
“Distribution of frozen samples would change the way these industries deal with their algal cultures. You wouldn’t have to worry about losing valuable time or materials because you wouldn’t have to maintain live cultures. When samples are frozen, you can go back to the original material over and over, perhaps even a thousand years from now,” he said.
Conservation of algae and other aquatic species is not the only benefit of cryopreservation. The AGGRC partners with six other national centers to support the needs of biomedical researchers. Around 20 years ago, Tiersch and colleagues started development of biomedical species repositories for the National Institutes of Health (NIH) in cooperation with U.S. Department of Agriculture.
In recent decades, many laboratories have shifted from mammals to aquatic species as models to study human disease. Zebrafish, for example, share roughly 70% of the same genetics as humans. Compared to research with mammals such as monkeys, dogs or mice, the fish use less space, have a shorter lifecycle, and are easier and cheaper to maintain, leading to quicker and more cost-effective research observations.
“We have a very clear mission at the AGGRC, to preserve aquatic genetic resources, and there are plenty of other folks out there that share that same mission, allowing us to form strong partnerships," he said. The AGGRC team has received more than $10 million in funding from the NIH over the past two decades for efforts to preserve genetic resources of aquatic model species to advance biomedical research. The Provost’s Fund for Research will provide opportunities to transfer this expertise to algae.
"Our work is interdisciplinary and relies on many people at the AGGRC, College of Agriculture and around the country. We greatly appreciate the forward thinking of the Provost's Fund for Research that supports LSU researchers to move in new directions,” said Tiersch.