What's Happening Archive
s part of the Ocean Molecular Ecology (OME) group’s effort to optimize eDNA collection techniques and broaden our sample collection capabilities at sea, we are conducting a study to compare a new filter produced by an American small business, the Smith-Root self preserving eDNA filter to our current filter, the Millipore sterivex capsule filter. The collection and filtration of eDNA samples at sea is limited in part by the technical skills required to filter and preserve these sensitive samples without contamination. With our current filter, the flammable preservative and low-temperature storage requirements also present a barrier to shipping and sample storage in some field applications.
The self-preserving filter, developed by a small business in Vancouver WA, is designed to capture and preserve eDNA from multicellular organisms. It has been found to perform as well as ethanol-based preservation for a 6 month period. Rather than a preservative, the Smith-Root filter utilizes a proprietary desiccating filter housing to preserve captured DNA and cells, eliminating the need for chemical preservatives. This design simplifies operation, requires less training, and streamlines shipping. However, these filters have not been tested against the sterivex filter, nor have they been tested on their ability to capture DNA from single-celled organisms. Our current study aims to address these gaps by testing the sterivex head-to-head against the Smith-Root filter using the same filter material and pore size.
For this study, Han Weinrich and Zack Gold collected water samples from local fresh and seawater sources alongside water from the Olympic Coast National Marine Sanctuary, then they filtered them in the lab - half with sterivex filters and half with the Smith-Root filters. To avoid any degradation of DNA before preservation, Han and Zack filtered the samples immediately after collection, resulting in several 12 hour days. DNA extractions at six time points, from one day to six months post-collection, will assess the preservation performance of the Smith-Root filter relative to the sterivex filter. Preliminary results from extractions conducted up to three months post-collection indicate that the Smith-Root filter preserves DNA comparably to the sterivex filter. Further analyzes will include sequencing the extractions to determine if both filters capture and preserve the same organisms at the same proportions - a critical metric for the OME as we aim to capture biodiversity at all levels of the ecosystem, from bacteria to whales.
If the Smith-Root filters perform comparably to the sterivex in meeting OME's eDNA objectives, they may offer an alternative to sterivex filters in certain field applications - saving time and space on research vessels while enabling eDNA monitoring in a broader range of environments. In addition, the National Aquatic eDNA Strategy seeks to advance eDNA sampling technologies by developing low-cost, high fidelity devices to enable large-scale collection. The Smith-Root filter could be employed in the development of a new eDNA sampler.
Since 2020, the Ocean Molecular Ecology (OME) group has collaborated with Ecosystem and Fisheries Oceanography Coordinated Investigations (EcoFOCI) to maintain a seawater environmental DNA (eDNA) time series in the U.S. Arctic. This fall, Shannon Brown participated in the annual EcoFOCI Fall Mooring cruise, which focuses on deploying and recovering oceanographic moorings and collecting shipboard biophysical samples at and between mooring locations. U.S. Arctic marine ecosystems are rapidly changing in response to climate change with accelerating ocean warming and sea ice loss leading to cascading ecosystem effects. OME leverages eDNA approaches to examine the regional biodiversity of microbes, phytoplankton, zooplankton, fishes, and mammals. By pairing eDNA analyses with physical and chemical measurements, these efforts establish critical baselines that support fisheries management and marine conservation. Additionally, in collaboration with the FWC Center for Red Tide Research, our eDNA samples contribute to studying harmful algal blooms (HABs), which can affect marine life and human industries in the region.
During this cruise, Shannon successfully filtered 110 eDNA samples collected from CTD Niskin bottles. The team also deployed an autonomous eDNA sampler at the M2 mooring site. Designed to collect samples biweekly for a year, this sampler had previously been deployed in the Chukchi Sea, where it successfully gathered 24 samples from September 2023 to July 2024. It was recovered in August by the RV Sikuliaq and immediately shipped from Nome, AK to Dutch Harbor, AK, to meet the Fall Mooring cruise.
Monitoring in the Arctic is challenging given its remoteness and the difficulty of navigating harsh sea ice and ocean conditions, making it impossible to manually sample for half the year. Autonomous eDNA samplers are an innovative solution, enabling year-round biodiversity sampling. Due to a limited number of samples and only a few deployment opportunities, we decided to collect one unit, turn it around in the field, and redeploy it for another year.
Redeploying the autonomous sampler highlighted the logistical complexity of Arctic fieldwork. Alaska, the largest U.S. state, lacks road connections between key locations like Nome and Dutch Harbor, requiring equipment to be transported by plane or boat. With only a week between cruises, the team opted to ship the sampler by air—a process fraught with delays. Unfortunately, after countless hours spent coordinating the unit transfer, the sampler missed the departure of the NOAA Ship Oscar Dyson departure date. Fortunately, Han Weinrich was still on the island and ready to receive the delayed unit. A few days after departing, the NOAA Ship Oscar Dyson returned briefly to Dutch Harbor, and the amazing crew retrieved the sampler with a small boat.
Once aboard, Shannon and the EcoFOCI team worked tirelessly to prepare the sampler for deployment within 48 hours. When a malfunction caused the unit to power down spontaneously, Shannon spent hours disassembling and reassembling components to diagnose the issue. With the help of Oscar Dyson’s Chief Engineer (a true MacGyver), foam ear plugs, and some new springs, a solution was found just three hours before the unit was successfully deployed!
Sadly, the sampler was prematurely recovered by a fishing vessel on November 24, just 11 weeks after redeployment. While it’s unclear if any samples were collected, the incident underscores the unpredictable nature of field research in the Arctic. Despite these challenges, this mission highlights the resilience and ingenuity of the scientific team. The data collected through these efforts will inform the sustainable management of Arctic marine ecosystems and improve our understanding of biodiversity in this rapidly changing region. Thanks to the crew of the NOAA Ship Oscar Dyson and the entire science party for a successful cruise!
The Phycological Society of America’s (PSA) joint meeting with the International Society of Protistology (ISOP) and International Society for Evolutionary Protistology (ISEP) brought together algae, phytoplankton and protist researchers from across the globe. During the meeting, research from carbon dioxide draw-down with kelp farms to important evolutionary questions of protists in the tree of life were presented to an international audience of academic, federal, state, and local government scientists.
Sam Setta presented on phytoplankton changes with temperature and acidification from the West Coast Ocean Acidification (WCOA) 2021 Cruise. During the meeting, Sam had the opportunity to connect with many scientists, including researchers from the Washington Department of Natural Resources and Shannon Point Marine Center at Western Washington University.
Following the conference, Sam flew to Savannah, Georgia for Dr. Holly Bik’s workshop “Telling Stories Through Data”. Unfortunately for workshop participants, this happened to coincide with Hurricane Debby’s arrival on the U.S. East Coast. While the workshop was originally planned to take place on Sapelo Island, evacuation orders meant the location changed to downtown Savannah, GA.
During the workshop (and Hurricane Debby), Sam learned new data visualization methods and best practices. In the afternoon sessions, Dr. Virginia Schutte led the group in a science communication component. Sam and workshop participants explored a variety of science communication platforms and best practices and brainstormed a future science communication plan. Graduate students to early career researchers participated in the workshop and learned data visualization and storytelling from each other while forming a community to rely on for tips and advice on “Telling Stories Through Data” in the future.
Through these two great experiences this summer, Sam was able to communicate with scientists on findings from the West Coast Ocean Acidification cruise, meet scientists with similar research, learn data visualization and science communication, and meet a wonderful group of early career researchers.
My name is Ella Crotty, and I am an undergraduate research intern through the NOAA Ernest F. Hollings Scholarship Program. I chose to work with OME for my internship because I didn't know very much about environmental DNA (eDNA), and I wanted to learn! eDNA refers to genetic material that organisms leave behind in the environment by shedding skin, releasing mucus, etc. It can be used to detect if species are present in an area of the ocean using a water sample. For my project, I worked with an automated sampler that sits in the water and collects eDNA samples at regular intervals by filtering water samples through super-fine filters.
My internship included fieldwork in the Olympic Coast National Marine Sanctuary (OCNMS). I went out to the northwest coast of Washington twice to help with sampler recovery and redeployment. I helped collect and filter eDNA samples on the boat, then after the sampler was recovered, I helped store the samples from the sampler, which had already been filtered underwater. We returned to land and spent a day sterilizing the sampler before redeploying it, which was a complicated process. I had never worked with such a big and complicated instrument before, and it was interesting to learn about the logistics of setting up and maintaining something like that without access to a full lab! We brought a lot of tools and extra parts, in case anything broke and needed to be fixed on the coast between boat days.
The main goal of my research project was to determine how the presence of different species in OCNMS changes when the amount of oxygen in the water is low. Low oxygen, also known as hypoxia, can cause stress and death in marine animals. Two mg/L of oxygen is often used as the upper limit of what counts as hypoxic. I compared the data from our eDNA samples, which told me which species were detected in the sanctuary on certain dates, with dissolved oxygen data sampled from CTD casts and moorings. In OCNMS during the summer, a process called coastal upwelling causes oxygen-poor deep water to move up from the bottom of the Pacific Ocean, which decreases oxygen levels near the coast. However, some species are more sensitive than others, and some, like larger fish, are mobile and can move away from the low-oxygen areas. So, our main research question was: which species stick around when the oxygen drops, and which can no longer be detected? This question will help us understand how seasonal changes in oxygen are impacting OCNMS waters.
It required quite a few stages of data analysis and quality-checking in order to make the environmental data and eDNA data compatible with each other. Using the programming language R, I cleaned the data and matched the species detections to the temperature and oxygen at the date and time when the eDNA samples were taken. I implemented a lot of checkpoints to ensure that the code was doing what I wanted it to. For example, I checked to make sure that everything was in the same time zone, but between the CTDs, mooring, eDNA sampler, and handwritten sample data, I had to be very vigilant about converting the time zones before combining data.
First, I focused on species that OCNMS and the coastal treaty tribes consider high priority for monitoring and management and that were detected at least 10 times. Of the 64 priority species, we detected 24 and four were detected at least 10 times. The two species with the most detection data were Pacific herring and the copepod Acartia longiremis. I didn't find any correlation between oxygen levels and the presence of these species, which suggests that seasonal hypoxia is not impacting these commonly detected taxa. Herring are known to be pretty hypoxia-tolerant, which agrees with my findings. I also investigated species outside the priority list by calculating a bunch of statistics and filtering for significant results. I found a few species that did have observable relationships with hypoxia, including two species of copepod, tiny crustaceans that are used as indicators of ecosystem health. Through this internship, I developed a code workflow that combines environmental data with eDNA data, which is useful as we continue to study how different species are affected by environmental conditions.
As the Ocean Molecular Ecology (OME) group works to make our science and lab practices open and accessible, we have prioritized standardizing and sharing our environmental DNA sample collection and processing protocols to a public repository. The Better Biomolecular Ocean Practices (BeBOP), a U.N. Decade Endorsed project under Ocean Biomolecular Observing Network (OBON), pioneered a Minimum Information about an Omics Protocol (MIOP) format to better compare practices and integrate data generated when studying ocean life. BeBOP formatted protocols are accessible, detailed, traceable, machine-readable, and standardized. Importantly, they are designed to provide the reader with all the information needed to replicate a protocol from supplies purchasing and troubleshooting to the method background and a step-by-step procedure.
In the last four years, OME has collected over 2,800 eDNA samples from coastal stations off the western coast of North America in the Northeastern Pacific Ocean, Bering Sea, and Arctic Ocean. Since 2023, we’ve extracted over 1,200 samples and sequenced/processed over a thousand. As we pushed through our backlog, we fine-tuned our standard operating procedures for all in-house lab work, including eDNA collection, extraction, and PCR amplification. Our published protocols are written for reproducibility so a new lab could replicate our efforts. We aim to continue our efforts to encompass all field and lab protocols performed by OME over the next year. These protocols are archived, version-controlled, and citable in Zenodo repositories.
Dr. Jane Lubchenco (blue jacket), White House OSTP’s Deputy Director for Climate and Environment, with eDNA researchers at CHOW. Dr. Lubchenco delivered remarks at CHOW and the 3rd National Marine eDNA Workshop and moderated a session on the unveiling of the White House Strategy.
One major challenge of studying marine and aquatic ecosystems is obtaining an accurate map of the type and number of species within the environment. The United States is home to a wide range of aquatic ecosystems, including estuaries, lakes, and oceans with one of the largest exclusive economic zones in the world. Biodiversity drives the health, functioning, and services provided by freshwater and marine ecosystems and has substantial cultural and economic significance, making accurate maps of biodiversity so important. Advancements in biomolecular technology now allow scientists to detect DNA shed by marine life into the water, a technique called environmental DNA (eDNA). eDNA approaches provide a powerful, non-destructive, and cost effective tool that gives us the ability to monitor life in our marine and aquatic environments.
The White House Office of Science, Technology, and Policy (OSTP) recognized the power of this tool and the importance of studying ecosystem biodiversity across the nation with the release of the 'National Strategy for Aquatic Environmental DNA' as part of a larger OSTP effort to advance sustainable ocean management. This strategy empowers federal agencies and partners to effectively harness eDNA as a detection tool for mapping and monitoring biodiversity. It also calls other public and private agencies to action as we work to unite science and entrepreneurial efforts to collaboratively improve the eDNA research and operations space. Importantly, NOAA has been leading the research and development of eDNA tools for the past decade to transition to operational marine biodiversity monitoring.
For the past 7 years, the Ocean Molecular Ecology (OME) Program at PMEL has been employing eDNA to study coastal ecosystems along the U.S. West Coast as well as the Bering Sea and Arctic Ocean. This national strategy is a call to action for continuing our efforts to develop and implement eDNA tools to monitor marine biodiversity at scale. In particular the strategy highlights the need for OME’s work to standardized, reproducible eDNA sampling practices, improve and deploy autonomous eDNA samplers, and fill eDNA reference databases. OME will continue to invest in the research, development, and application of eDNA science within NOAA in support of key agency missions from harmful algal bloom monitoring to protected species management to climate resilient fisheries and ecosystem management.
Read more about White House strategy to capitalize on the immense power of eDNA at NOAA Research.
Over 62 scientists from PMEL, including researchers from NOAA’s Cooperative Institutes and the University of Washington's Cooperative Institute for Climate, Ocean, & Ecosystem Studies (CICOES) and Oregon State University's Cooperative Institute for Marine Resources Studies (CIMRS) attended the Ocean Sciences Meeting in New Orleans from February 18-23. The 2024 Ocean Sciences Meeting served as a conference that unified the ocean community and brought researchers together to share findings, make connections, and advance science. Five members of the Ocean Molecular Ecology group were in attendance.
Sean McAllister presented results from the 2021 West Coast Ocean Acidification (WCOA) Cruise, which was in collaboration with PMEL Ocean Carbon. During the cruise, 525 unique environmental DNA (eDNA) samples were collected from Vancouver Island, BC to Southern California. Our eDNA samples captured diverse marine communities (e.g., phytoplankton, fish, marine mammals) across a large spatial gradient. When analyzed alongside chemical and physical parameters, we were able to draw preliminary conclusions regarding community structure in relation to warming, ocean acidification, and low-oxygen events (hypoxia) along this expansive spatial gradient. Further analysis is underway to identify key indicator species for use in monitoring and predicting ecosystem health in our changing oceans.
Shannon Brown presented on ongoing research with autonomous eDNA samplers in the Olympic Coast National Marine Sanctuary. Changing ocean conditions, driven by climate change, are threatening the sanctuary’s marine ecosystem with increased, hypoxic events. We deployed samplers alongside oceanographic moorings to better understand how marine communities are impacted by these changing conditions. Our results captured a wide range of taxonomic diversity including species of commercial, recreational, cultural, and subsistence importance.
Zack Gold co-chaired a session on Ocean Biomolecular Observing Networks, and presented on a cross-NOAA bioinformatics effort to improve trustworthiness and reliability of eDNA data. More specifically, he outlined a suite of tools and approaches to accurately assign taxonomy when processing eDNA data to better characterize marine biodiversity. Han Weinrich presented on their honors thesis work investigating microbial prokaryotic communities associated with hydrothermal vent tube worms. Sam Setta presented on her PhD thesis work on diatom distribution and diatom diazotroph associations across nutrient regimes.
My name is Nicholas Silverson, and I am a master’s student at the University of Maryland Center for Environmental Science. My research, funded by the National Science Foundation (NSF) INTERN program and Graduate Research Fellowship (GRF), as well as the Distributed Biological Observatory (DBO), focuses on the biodiversity, community, and population structure of ocean floor animals (benthic macrofauna) in the Pacific Arctic. As part of my project, I visited NOAA PMEL and worked alongside Matthew Galaska, a principal investigator in the PMEL Ocean Molecular Ecology (OME) group, to incorporate a genomics approach to questions of biodiversity and population structure.
I had the chance to participate in two research cruises off the coast of Alaska this past summer on the Sir Wilfrid Laurier, a Canadian Coast Guard ice-capable buoy tender, and the research vessel Sikuliaq, owned by NSF. They were truly incredible experiences; in addition to witnessing enormous flocks of seabirds, pods of whales, and the aurora, I was able to engage with scientists studying this region so affected by climate change. I worked with Matthew Galaska and my thesis advisors, Jacqueline Grebmeier and Lee Cooper, to design a sampling protocol and sampled sites in the DBO, which consists of observation sites from the northern Bering to the Beaufort Seas that document and evaluate biological changes at productive hot spots. With members of my lab group, I collected a broad range of benthic macrofauna specimens and preserved them in ethanol for later study at PMEL. We are aiming to publish underrepresented cytochrome c oxidase subunit I (COI) barcodes to the National Nucleotide Database (NCBI), which will aid other studies in the accurate identification of organisms. Additionally, for two dominant clam species (Bivalvia) and a marine worm (Polychaeta), I collected 8-15 individuals to analyze their population structure and unravel any potential open ocean barriers to dispersal between Southern (Bering Sea) and Northern (Chukchi Sea) populations. This data will complement the analysis of long-term biodiversity and environmental data collected as a part of the DBO.
I spent two weeks at PMEL this past December learning the methodology for DNA extraction and PCR amplification. DNA barcoding of conserved regions of mitochondrial DNA can provide accurate identifications of animals and give insights into barriers to gene flow that morphological study alone cannot provide. Despite some early challenges with low DNA quantities, we successfully extracted DNA from 120 benthic animals and amplified their DNA using a COI primer set. The DNA will be Sanger sequenced this winter, and I’ll return to PMEL for another two weeks to bioinformatically process the data and perform the associated analyses. These data will contribute to understanding how ocean floor communities are changing with warming waters and reduced sea ice, which impacts primary production and energy flow in these seasonally productive ecosystems. My experience at PMEL will form an important part of my master’s program and has been fundamental to my growth as a scientist as I have been learning important methodologies for understanding community structure and change.
The PMEL Ocean Molecular Ecology group collaborated with the PMEL Earth-Ocean Interactions Program (EOI) in March-April 2023 in an ocean exploration effort to identify and describe new hydrothermal sites along the Mid-Atlantic Ridge. The expedition took place on the Schmidt Ocean Institute's new vessel the RV Falkor (too).
The group found a suite of never before documented hydrothermal vent fields. Sean McAllister, a member of Ocean Molecular Ecology, participated through the collection of environmental (e)DNA samples in transects over the sites of hydrothermal venting, ultimately providing a picture of biodiversity of microbial to macrofauna communities. Individual tissue samples were also taken to enhance reference barcode databases and improve eDNA taxonomic assignment accuracy. In addition, while underway, Sean was able to extract and sequence the eDNA samples collected using a Nanopore long-read DNA sequencer to generate near real-time characterizations of the microbial and invertebrate communities at the hydrothermal vent sites. Visit the expedition website, view the cruise log which includes science blog posts and a highlights, and check out the dive stream for all ROV dives to learn more about these exploratory efforts.
Annual Ecosystems & Fisheries-Oceanography Coordinated Investigations (EcoFOCI) Survey in the Bering Sea encounters sea ice (right images) for the first time since 2012. The map (left) shows sea ice extent in the region on April 24, 2023. Photo Credits: Shaun Bell
April 21 - May 8 - NOAA PMEL oceanographers and colleagues continue leading an annual effort to collect key data in understanding the Bering Sea. This important research cruise provides key insights to monitor events such as sea-ice loss and the cold pool in the region and how these are impacting the Arctic ecosystem. This year’s cruise started out a bit different!
For the first time since 2012, the ice extent in the Bering Sea is impacting the survey and researchers had to alter their cruise plan as the ice is at and around several of the mooring and sampling sites. While not thick ice, lead scientist and NOAA oceanographer Phyllis Stabeno was surprised. “I did not expect to see ice this late on the shelf,” she said. In this region, ice arrives in the Bering Sea in the fall and typically melts and recedes in spring, - limiting when research vessels can be in the area.
2012 was a record breaking year. The melt season of 2012 started out at a sluggish pace. Around mid-April, sea ice extent was close to the 1979–2000 average for that time of year (the maximum ice extent typically occurring in March). However, soon after that the decline began to accelerate rapidly.
Stabeno took this as a unique and unexpected opportunity to safely sample around the ice edge. Most vessels are not made to break ice - but they can go near this melting ice region. As the ice continues to melt, the science team will resume their planned research.
This spring mooring cruise brings together scientists from NOAA’s PMEL and Alaska Fisheries Science Center, the University of Washington, US Fish and Wildlife, and the University of Alaska. While aboard the NOAA Ship Oscar Dyson, the scientists will service a biophysical mooring array. They will also collect water samples of conductivity (salinity), temperature, depth (CTD) profiles, zooplankton, ichthyoplankton, nutrients and chlorophyll samples. As well as conduct collaborative research including on harmful algal blooms, omics, and zooplankton machine learning. Results from these observations and experiments will help describe important ecosystem linkages among climate, plankton, fishes, birds and mammals.
EcoFOCI will be field testing and using several innovations this spring. Innovations and technologies such as these aim to enhance shipboard and mooring research with advanced and increased data collection. These include the deployment of a modified ‘high-latitude’, more robust surface mooring at M2 and a shallow-water glider. This is the 29th consecutive year the M2 mooring will be deployed. In 2022 a combination of the pandemic, sea ice, and a storm provided researchers a new perspective from NOAA’s longest operating biophysical mooring site in the US Arctic. Learn more about that in a NOAA Story Map (https://storymaps.arcgis.com/stories/1b413464b13c4aa381b48ecd5c89ed50).
This is the first of five NOAA EcoFOCI program research cruises planned between April and October in the Alaska region.
Learn more about mooring arrays and the EcoFOCI spring cruise on NOAA Fisheries 2022 blog.