NOAA’s ‘Omics Today

NOAA scientists describe the oceans by studying clues at the molecular level.

By Craig Collins

Kelly Goodwin, a microbiologist and molecular biologist at NOAA’s Atlantic Oceanographic and Meteorological Laboratory (AOML), has a simple description for the field of marine biology. She boils it down to: “knowing who is there, and what they’re doing, and how they’re adapting to changes or to stress.”

Yuan Liu (left) collects water samples for eDNA analysis in the summer of 2019, assisted by Mark Dixon (middle) and Gillian Phillips (right) at one of the aquaculture cage sites in Long Island Sound.

But the ocean ecosystem is vast, complex, poorly understood, and currently under considerable stress and change – and marine biology is quickly transforming. “In the old days,” Goodwin said, “to look at biology, you caught things and you counted them. Now, you look at their genetic code using ‘omics methods.”

Biological analyses of marine ecosystems at the molecular level, particularly molecules such as DNA, RNA, proteins and metabolites, can help to describe and characterize the way genes are programmed and expressed. These kinds of studies – i.e., genomics, proteomics and others – are known collectively by their suffixes, the ‘omics sciences. These new methods offer a snapshot of organisms in a particular place, at a particular time. When investigators want the bigger picture, ‘omics can be used to understand biological changes not only at individual scales, but also at population and ecosystem scales.

Yuan Liu filters water samples on the NOAA Ship Gordon Gunter during the fall Ecosystem Monitoring Survey.

To Goodwin and her AOML colleagues, the real potential for ‘omics lies not just in studying the genes of individual organisms, but in analyzing the heart of marine ecosystems: the microbiome, where organisms such as bacteria and phytoplankton form the base of the food web and cycle oxygen and nutrients throughout. In 2016, the laboratory launched an ‘omics program to study the health of marine organisms and ecosystems through the study of their genes and proteins.

‘Omics methods are employed for many different tasks. For example, AOML scientists are studying genes in corals that might help explain why some corals are more susceptible to bleaching or disease than others. Many coral communities are in decline, and the hope is that studying all aspects – the coral animal and its associated microbes – will give the full context needed to understand why some corals get sick and others don’t. Studies use DNA, RNA, and protein analysis of samples before, during, and after coral bleaching or disease events, and researchers hope to identify the genetic traits of the most resilient corals and their microbiomes. This knowledge could help inform future coral restoration efforts.

At NOAA, fisheries scientists have used genomics for decades to inform management of fish populations, and recently, scientists at the Southeast Fisheries Science Center and AOML have been working together to use DNA from the larvae of Atlantic bluefin tuna to distinguish between the eastern and western bluefin stocks and inform management decisions for one of the nation’s most valuable fisheries.

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In addition, NOAA investigators are using a relatively new technique to detect fish and other marine species: analyses of DNA found in a sample of water or sediment. The sampling of environmental DNA, or eDNA, is a “tissue-free” method of analysis. Goodwin says eDNA sampling allows scientists “to explore ocean habitats that are otherwise off-limits because they are too deep, too icy, too fragile, or too costly for traditional collection methods.” For example, in San Diego Bay, Goodwin and scientists from NOAA’s Southwest Fisheries Science Center found that they could use eDNA to detect the presence of endangered green sea turtles. In Southeast Alaska waters, scientists from the Alaska Fisheries Science Center’s Marine Mammal Laboratory have been able to detect genetic variation among populations of harbor porpoises, which have proved elusive to researchers looking for genetic samples.

Researchers Kyle Turner, Virginie Sonnet and Yuan Liu gather around the Niskin bottle rosette to get their portions of the seawater collected at a water sampling station during the fall 2019 Ecosystem Monitoring Survey cruise on the NOAA Ship Gordon Gunter. Tissue-free eDNA sampling allows researchers to explore ocean habitats unreachable by other means.

In many cases, uncrewed systems are being used to push past sampling limitations. Water samples collected by uncrewed underwater vehicles can be collected and analyzed on-site by environmental sample processors (ESPs), developed by the Monterey Bay Aquarium Research Institute, which can filter out genetic material and investigate biology on the molecular level in real time. ESPs can be used to identify the type and number of microorganisms and animals present in the water; monitor toxins and other biological compounds; and examine how microbes respond to climate change and seasonal variation. For example, autonomous ‘omics sampling is being used in the Great Lakes to monitor for genes of harmful algae. ‘Omics techniques such as eDNA analysis for fisheries and protected

species is a new breakthrough whose potential is still being explored. “It really is relatively recently that we’ve been able to understand and interrogate genetic sequences,” Goodwin said. Goodwin estimates that these types of studies generate huge amounts – terabytes – of genetic data, and scientists are still learning how to best apply analyses at this level. Each study requires its own set of algorithms and powerful computing capabilities, to process and make sense of terabytes of genetic data. And even then, Goodwin said, eDNA currently is best at answering the question: Who’s here? It doesn’t yet answer the equally important: How many?

“When we talk about eDNA,” said Goodwin, “I think the most exciting things to talk about are the things that are on the horizon – those we can’t quite yet do right now.”