Best practices in marine mammal research: developing a toolkit for sample collection and preservation
Over the last two decades, there has been huge growth in the availability of different ‘omics methods used to study marine mammals. From elusive beaked whales and near extinct vaquitas to more common dolphins and sea lions, understanding the ecology, evolution, and health of marine mammal populations around the globe is critical for conservation efforts. A new paper published in Marine Mammal Science, involving 19 scientists from around the globe, has laid out best practices for collecting and preserving marine mammal biological samples in the ‘omics era.
The branches of science known informally as omics are various disciplines in biology whose names end in the suffix -omics, such as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics.
Marine mammal scientists are working on different species, in different locations, and asking different questions, using tissue samples collected from wild marine mammals. Those tissue samples give scientists access to vast amounts of information, allowing them to answer questions ranging from a population’s recent foraging habits, health status, or contaminant load to its deeper evolutionary history or its resilience in the face of climate change. They provide scientists, and us, a window into the secret lives of these elusive animals and hints about how we can be better stewards of their ecosystems, but they come at a price – literally.
Most marine mammals live far from shore, and spend the majority of their lives underwater. To collect tissue samples from these animals, large teams of scientists will venture out onto the ocean for months at a time. Many marine mammal species have huge home ranges, such as the 9,000 mile migration range of humpback whales; simply finding them is a monumental task. Adding to the challenge, collecting samples from marine mammals is inherently invasive and scientists work under strict permits to minimize both the number of times samples need to be taken, and the impact on the animal during collection.
Phillip Morin from NOAA Southwest Fisheries Science Center, who has been working in genetics for over 35 years, understands all too well the difficulty in getting quality samples for genomics. “A good illustration is the sample used for the vaquita reference genome, which is one of only two live-cell samples ever obtained from this species. The vaquita, a member of the porpoise family, is the most endangered marine mammal in the world,” he shared. “A conservation project in 2017 took two years of extensive planning with over 90 experts from nine countries, and 11 days at sea, to try to capture vaquita for captive management. As part of that project, we worked to get the appropriate samples collected, transported quickly to the cell culture lab across the international border, and cultured to preserve live cells for DNA and RNA extraction.”
Because of all of these challenges, each tissue sample could represent an investment of tens of thousands of dollars. Caring for those samples and preserving them in a way that will allow them to be used by many generations of future scientists, and with many generations of emerging techniques, is a priority that is always at the forefront of a marine mammal scientists’ mind. “For some populations or species, decades of sampling effort have resulted in only 10s of samples, highlighting how critical it is to figure out the best collection and preservation techniques,” says Amy Van Cise, Assistant Professor at the University of Washington School of Aquatic and Fishery Sciences (SAFS).
What are some of the best practices for collecting and preserving marine mammal samples that research teams have gone through such effort to collect? This is the overarching question bringing together a team spanning 11 different institutions, including Van Cise, with the goal of creating a unifying set of guidelines that will ensure these samples can be shared among labs, analyzed with a variety of new and emerging technologies, and used for years to come. “What’s impressive about this study is that it brings together scientists examining different types of questions,” shared Amy Apprill from Woods Hole Oceanographic Institution (WHOI). Apprill’s particular focus is on microbiome analysis, which sheds insight into the health of marine mammals as a result of changing oceans and human impact.
Microbiome analysis is a great example of an emerging technology that’s revolutionizing how we study marine mammal health. Unlike humans, it’s difficult to assess the health of wild animals, and nearly impossible when those animals live in the ocean. “Wherever you are in the world, a doctor can sample and test your blood and those results are understandable and comparable around the globe,” Apprill said. Marine mammals don’t schedule regular doctor’s appointments, but emerging ‘omics technologies are making it possible to determine whether an individual is sick or healthy using tissue samples. Apprill is one of the scientists at the forefront of the effort to characterize the microbiomes of healthy and diseased individuals. “As we obtain samples from different animal health states, we’re gaining valuable data that builds a type of health metric,” Apprill said. This type of work can only be successful if researchers can examine samples collected by many scientists around the world. Similar to the way hospitals have standardized the way they test for diseases and assess human health, Apprill said that, “as scientists in marine mammal research, we need a similar system of guidelines, best practices, and protocols to follow, so that our samples have the maximum use.”
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- Kim Parsons (NOAA/ NMFS/ NWFSC) processes cetacean tissue biopsies in a makeshift lab onboard a survey vessel in Southeast Alaska.
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- Images courtesy of NOAA Fisheries, Marine Mammal Laboratory.
The gold standard for sample preservation is collecting it quickly from the animal, either when alive or recently dead before the cells start degrading, and freezing it to -80°C or colder immediately. However if this isn’t possible in the field, then what is the best alternative? The answer depends on the anticipated research needs, availability and transportability of preservatives, and time until samples reach a permanent storage site. While there is no single solution for all situations, some methods provide broader preservation characteristics, allow international transport, and/or greater stability prior to freezing.
“In science, there are a thousand ways you could conduct each step,” Apprill shared. “But you don’t want to spend valuable time, effort, and resources figuring out those steps if someone else already has the best method and protocol laid out.”
The ways we can use ‘omics techniques are rapidly expanding every year, adding another layer of importance to the need for high-quality, well-preserved samples. “Just like forensics held on to human samples from crime scenes while the world was waiting for DNA capabilities to expand, marine mammal science works the same way. As technological advancement expands really quickly, it’s imperative to preserve samples in a way that the wealth of information contained in them can be uncovered in the future,” Morin said.
The institutions involved in the best practices effort are: NOAA Northwest Fisheries Science Center, Stanford University, Woods Hole Oceanographic Institution, University of Washington, McGill University – Mila-Québec AI Institute, NOAA Southwest Fisheries Science Center, University of Exeter, and Mystic Aquarium.