What's Happening Archive
The Ocean Molecular Ecology (OME) 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 Ocean Molecular Ecology group 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.
Reviewing checklist and final preparations to deploy drifting hydrophone buoys off the coast of Oregon.
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A new video highlighting PMEL's acoustics research and eDNA innovations to study Blue Whales off the coast of Newport, Oregon has been released in the “PMEL at Work” YouTube series.
This video features PMEL’s Acoustic Program’s Bob Dziak and Angela Sremba discussing ongoing research to develop technology to better understand blue whales by simultaneously collecting environmental DNA (eDNA) samples and recording acoustic calls through deploying drifting buoys with underwater hydrophones.
Over the summer of 2021, PMEL and OSU CIMERS scientists field tested three passive-acoustic hydrophones to identify and locate blue and fin whales. These new smart hydrophones have an internal microprocessor that communicates the location of the buoys to shore. PMEL developed software for the microprocessor that will analyze the hydrophone data using a blue whale call detection algorithm. The goal for this algorithm is to register a positive blue call detection and transmit this positive detection information, as well as the position of the buoy, via satellite communication to shore to let scientists know when and where a blue whale call is recorded. When a call is detected on multiple buoys, the shore based scientists can then determine the location of the calling whale, and then inform the ship’s crew that a blue whale is nearby. The location of the whale will be correlated with the results from collected eDNA samples.
This past summer was a successful field test of the hydrophone buoys in anticipation for upcoming fieldwork in the summer of 2022 where PMEL will simultaneously collect acoustic recordings and eDNA samples of blue whales off the Oregon coast. This project will improve interpretation of eDNA results by using a time-series sampling method combined with acoustic detection for tracking and localizing highly migratory whale species in remote open ocean habitats.
This is a collaborative project between Oregon State University Marine Mammal Institute and Cooperative Institute for Marine Ecosystem and Resources Studies (CIMERS) and NOAA.
The PMEL at Work video series highlights ongoing research activities and projects supporting NOAA’s mission to understand changes in the global ocean and its impact on climate, weather and ecosystems.
Seawater samples being retrieved from a CTD during the West Coast Ocean Acidification Cruise. Photo Credit: Dave Butterfield (UW CICOES/PMEL)
On June 13, scientists aboard the NOAA Ship Ronald H. Brown set out on the West Coast Ocean Acidification Research Cruise to characterize conditions along the West Coast of North America and continue to build a unique time-series of carbon and hydrographic measurements in areas expected to be highly impacted by ocean acidification. Scientists have been collecting samples from CTDs, collecting plankton and water samples for genomics analysis, and conducting the first systematic regional survey of methane gas coming out of the thousands of seeps along the west coast.
The California Current System, running along the North American west coast from British Columbia to Baja California, is a region where seasonal upwelling brings nutrient- and carbon dioxide-rich and oxygen-poor waters to the surface. Increasing levels of carbon dioxide from upwelling and anthropogenic emissions, cause a series of chemical reactions that are ultimately increasing acidity in these waters. Because it is an area with high rates of primary production by phytoplankton, air-sea carbon dioxide exchange, and carbon export to the open ocean and sediments, it is particularly susceptible to the impacts of ocean acidification and hypoxia. Understanding the progression of ocean acidification in coastal areas in the context of these other natural processes is critical for developing management, mitigation, and adaptation strategies.
This 47-day research cruise brings together an international team of scientists from the United States, Canada, Mexico, Finland, and the Netherlands to measure acidity, temperature, oxygen, and chlorophyll from 16 transect lines stretching from British Columbia, Canada to San Diego, California. They also have deployed net tows to sample phytoplankton, zooplankton, and fish to analyze how the marine food web is being affected by acidified waters.
With data collected from this cruise, and previous ocean acidification cruises in this region, scientists are documenting the changing ocean acidification conditions and how they are impacting marine ecosystems against a backdrop of multiple stressors including warming and deoxygenation. In 2016, measurements from this cruise demonstrated, for the first time, that ocean acidification along the US Pacific Northwest coast is impacting the shells and sensory organs of some larval Dungeness crab and that pteropods sampled near the coasts of Washington and Oregon had shells 37 percent thinner than those in waters further offshore.
With the comprehensive approach taken on this year’s mission- combining detailed physical, chemical and biological measurements - we will not only better understand how our ocean is changing, but also test what new tools can be used to assess the future of these important marine ecosystems.
“A strong understanding of both the changes in chemistry and marine life allows us to make informed decisions to sustain the ecosystems, communities and industry members along the West coast,” says Libby Jewett, Director of NOAA’s Ocean Acidification Program which funds this research cruise.
Follow along scientists aboard with NOAA’s Ocean Acidification Program’s Twitter, Instagram and Facebook .
41 scientists from PMEL, including scientists from NOAA's cooperative institutes at the University of Washington's Joint Institute for the Study of the Ocean and Atmosphere (JISAO) and Oregon State University's Cooperative Institute for Marine Resources Studies (CIMRS), the National Research Council, graduate and undergraduate students are heading to the Ocean Sciences Meeting in San Diego to share their current research. Talks and posters cover a range of topics include saildrone research, ocean observing systems, marine heatwaves, Arctic, acoustics, Deep Argo, genetics and genomics, El Nino, hydrothermal vents, methane, nutrients, technologies, ocean carbon and data management.
The 2020 Oceans Science Meeting is the flagship conference for the ocean sciences and the larger ocean-connected community. As we approach the UN Decade of Ocean Science for Sustainable Development, beginning in 2021, it is increasingly important to gather as a scientific community to raise awareness of the truly global dimension of the ocean, address environmental challenges, and set forth on a path towards a resilient planet. The meeting is co-sponsored by the American Geophysical Union (AGU), the Association for the Sciences of Limnology and Oceanography (ASLO), and The Oceanography Society (TOS).
PMEL research groups that will be present at the conference are: Acoustics, Arctic including Innovative Technology for Arctic Exploration, Climate-Weather Interface, Earth-Ocean Interactions, EcoFOCI, Engineering, Genetics and Genomics, Global Tropical Moored Buoy Array, , Large Scale Ocean Physics, Ocean Carbon, Ocean Climate Stations, Pacific Western Boundary Currents, and Science Data Integration Group.