What's Happening Archive
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.
Hello! My name is Chloe Rabinowitz, and I am an undergraduate research intern through a joint collaboration between the University of Washington (UW) EarthLab and NOAA PMEL ‘Omics Group. This summer, I sampled zooplankton from the Salish Sea and then proceeded to extract DNA and sequence species of interest. The purpose of my work has been to publish whole mitochondrial genomes to the national nucleotide database (NCBI) to enhance our understanding of zooplankton biodiversity in the region. Sequencing the full mitogenome enriches the coverage of zooplankton species by ensuring there is a reference sequence regardless of the targeted DNA amplicon. Additionally, information gained by assembling the mitochondrial genome can provide significant insight in understanding the evolutionary history of a species.
At the beginning of my internship, I worked with researchers on a Washington Ocean Acidification Center (WOAC) cruise. As we visited long-term monitored sites around the Salish Sea, I conducted vertical and oblique net tows into the ocean to a predetermined depth and pulled them up through the water to collect zooplankton samples. When I returned to land, I analyzed the zooplankton samples from previous WOAC cruises. Participating in a sampling effort allowed me to see the entire step-by-step process of my research. For the next few weeks of my internship, I worked with mentors in the Keister Lab at UW to fine-tune my zooplankton taxonomy skills. Using a microscope and my trusty forceps, I pulled out eight species of interest from the samples, seven copepods and one amphipod. Zooplankton, such as copepods and amphipods are important to the marine food web as they are the foundational food/energy source for marine invertebrates, fish, mammals, and most things in between. The health and functionality of any marine ecosystem is directly impacted by the health, diversity, and abundance of zooplankton.
Once I identified and separated out species (even up to 2000 individuals for one species), I brought my samples to the NOAA Western Regional Office to begin my work with the PMEL ‘Omics Group. In the ‘Omics lab, I photographed each species of interest, so we had physical documentation of the specimens extracted. Then, due to their small size, we used two different extraction methodologies to determine which would result in the highest DNA yield. Next, we checked the quality and quantified how much DNA was extracted from each organism with PCR gel electrophoresis and a Qubit fluorometer. We utilized a Nanopore long-read DNA sequencer to sequence the mitochondrial genome of the amphipod species, Cyphocaris challengeri. In addition, C. challengeri and four copepod species with the highest DNA yields post-extraction, were sent for Illumina NGS sequencing. With the results of the full mitochondrial genome sequences, we will gain a better understanding of the ecology and regional impacts of this species. The information we obtain will be published to enhance scientific knowledge of their ecology and evolution, improve public awareness, and allow us to detect and monitor their presence in Puget Sound.
While zooplankton might seem like small organisms, their impact is vast. Through my work during this internship and the passion/dedication I’ve seen from my mentors, it is clear that genomics is a critical tool that allows us to understand the deep complexity of important creatures in marine ecosystems that would otherwise potentially go unnoticed.
Hello, my name is Owen Yazzie, and I am a Cooperative Institute for Climate, Ocean, and Ecosystem Studies (CICOES) undergraduate research intern working at the University of Washington. This summer, I assisted the ‘Omics Group with an ongoing project in the Olympic Coast National Marine Sanctuary (OCNMS), off the outer coast of Washington state. The PMEL ‘Omics Lab is working with OCNMS to deploy autonomous environmental (e)DNA samplers in the sanctuary to study how biodiversity changes during and surrounding hypoxic events. During the 2022 field season, the group has two planned deployments scheduled, with automated samplers out for a month-long window at two sites (Teahwhit Head and Cape Elizabeth). These automated samplers collect a total of 24 samples spaced every 36 hours, eliminating the need for costly in-person sampling. I participated in the summer recovery cruise at OCNMS, and that opportunity allowed me to gain hands-on experience in the lab and in the field. Aside from the lab/research experience, there were other first time experiences for myself, such as seeing marine life outside of an enclosure.
In preparation for fieldwork, I assisted with packing gear and sterilizing equipment required for eDNA sampling. Environmental DNA samples are prone to contamination, so it was important we carefully sterilize the bottles and tubing used in the field. On the two-day recovery cruise, aboard the OCNMS vessel, the R/V Storm Petrel, we recovered both automated samplers and collected water samples using a CTD niskin array at Teahwhit Head and Cape Elizabeth. To generate occupancy models, which account for imperfect detection of organisms and to determine the probability of their true presence or absence, we collected 10 water samples near the automated sampler just prior to recovery to supplement a sliding window analysis. To do this, we started by lowering a CTD niskin array to the depth of the sampler, niskin bottles were then closed to capture water at that depth, and once returned to the ship deck, we collected the water samples in our sterilized bottles. Later we filtered the eDNA from those samples, while maintaining sterile technique to prevent contamination. I assisted with multiple steps of the filtration process, including the preservation of the eDNA samples in ethanol. I also worked alongside the OCNMS crew to recover the automated samplers. These moorings included an acoustic release mechanism, which allowed for the recovery of the entire mooring and ensured we did not leave anything behind. On both days, I helped collect the 24 samples (i.e., filters) from the automated samplers, while maintaining sterility during this process. Assisting with this project was a very rewarding experience that I am grateful to have taken part in.
The 'Omics Group received a major upgrade to their lab infrastructure, a portable lab in a shipping container, commonly referred to as a lab van. This past week, the lab van was installed at NOAA's Western Regional Office and will serve as a clean lab for the group to process environmental (e)DNA samples. The lab van significantly increases the in-house sample processing capabilities for the group and decreases the cost of outsourcing several steps of the eDNA library prep process. The 'Omics Group was previously limited in their ability to process eDNA samples due to a lack of appropriate workspace, so the scientists are eager to begin using this dedicated space.
Environmental e(DNA) samples are highly prone to contamination risks; therefore, samples must be processed in designated clean areas kept separate from other types of molecular work and free from potential airborne contaminants. One of the main sterilization features of the Omics lab van is the UV lighting system that can irradiate the entire working space after each use. In addition, the built-in HEPA filters work to eliminate the risk of airborne contaminants. The workspace includes two Class II Biosafety cabinets, one for DNA extraction and one for PCR amplifications and sequencing library prep. The biosafety cabinets are enclosed, ventilated laboratory workspaces used for processing low biomass molecular samples. Other key features of the Omics lab van include a reverse osmosis (RO) system, ample secure storage, and a double entryway to maintain a sterile/positive pressure environment. The 'Omics Group employs eDNA to monitor biodiversity shifts in the Northeast Pacific and Alaska waters. Their biological data is then comparatively examined with physical and chemical oceanographic parameters to study ecosystem biodiversity and ocean health. Once their lab van is officially commissioned, the 'Omics Group will immediately take advantage of this new resource and eDNA samples for sequencing from the 2021 and current 2022 field seasons.
David collecting water samples from CTD Rosette on the R/V Carson
My name is David Garcia-Prieto, and I’m interning in PMEL 'Omics Lab for the summer. My current funding source, NOAA-LMRCSC, is part of NOAA’s Educational Partnership Programs & Minority Serving Institutions. This program supports doctoral students through graduate school and provides students with professional experience. As part of the program, NOAA’s Experiential Research and Training Opportunities (NERTO) gives students the opportunity to work alongside NOAA scientists for a 12 week internship. The internship allows me to gain experience in a government facility and to familiarize myself with NOAA culture, all while gaining more practical scientific experience. When searching for a home base for my NERTO internship, I found that ‘Omics Lab does genomic work complementary to my Ph.D. research. We are interested in using environmental DNA (eDNA) as a tool to study the microbial and zooplankton communities in seawater and their response to changing physical ocean conditions.
At the beginning of the I performed literature reviews, familiarized myself with the lab's protocols & SOPs, gained hands-on experience with PCRs, and worked in RStudio. I then had the privilege of participating in a 5-day research cruise around the Salish Sea. The cruise was one of the Washington Ocean Acidification Centers’ (WOAC) expeditions to help monitor the Puget Sound’s health by taking measurements like dissolved inorganic carbon (DIC) and oxygen content, things that can impact microbe and zooplankton populations. WOAC is a collaborative effort between U.W. scientists and interns to sample and analyze resulting data. Amongst other things, WOAC provides water quality monitoring of six shellfish hatcheries and rearing areas. The monitoring helps inform hatchery farmers when seawater requires treatment due to changing ocean chemistry.
We sailed aboard the R/V Rachel Carson where I collected 1-liter water samples from 11 sites at various depths (surface, middle and near bottom) of the water column to look at microbial and zooplankton community composition through eDNA. After collecting the samples, I filtered the water samples across a small filter in a sterile environment with a portable peristaltic pump. These filters catch most organic material, including microbes. Next, DNA was preserved with ethanol and stored in a freezer. Back in the lab, we extracted the DNA from these filters, PCR amplified target markers, and quantified the product. With a Nanopore-long read DNA sequencer, the DNA was sequenced, and the resulting data was run through an RStudio pipeline which helped visualize the recovered community composition.
This research is important as it allows us to understand the microbial and zooplankton composition of the water column as they are the base of the ecosystem. Microbes and other small, “simple” life forms are some of the first to acclimate to a changing environment, so we can use them as a biomarker to monitor a changing system. For my project, we are interested in examining the seasonality of microbe communities. In spring, blooms in phytoplankton occur due to the winter mixing, whereas in the summer months, the water becomes stratified, likely driving zooplankton closer to the surface. Seasonal changes are important for us to monitor and can help us understand the system in terms of long-term changes. The sheer abundance of microbes and zooplankton makes them important in biogeochemical cycling. Examining their community structure across time allows us to estimate carbon and nutrient cycling by looking at the metabolic potentials of the organisms. Seeing orcas on my cruise reminded me of the trophic energy transfer that occurs in the Salish Seas. While it may take millions of microbes and zooplankton being eaten by bigger fish until an orca comes by and eats them, studying the trends of lower trophic levels allows for a better understanding and appreciation of the entire ecosystem.