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CTD Descends into the depths to collect water samples for use with eDNA technologies.

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Ocean Chemistry and Ecosystems

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November 1, 2014 at 3:38 pm

NOAA Partners Join CalCofi to Examine the Potential of ‘Omics Research

NOAA’s Atlantic Oceanographic and Meteorological Laboratory is teaming up with NOAA’s Office of Ocean Exploration and Research, National Marine Fisheries Service, and Integrated Ocean Observing System, as well as the J.C. Venter Institute and the Scripps Institution of Oceanography to enhance ecosystem observation programs by integrating genome-enabled techniques and technologies (i.e., ‘omics) into the California Cooperative Oceanic Fisheries Investigations (CalCOFI). CalCOFI is a multi-partner, long-term ecosystem and fisheries study off the coast of California. The first quarterly CalCOFI expedition that included ‘omics recently completed at the end of November.

‘Omics is the term for a set of genome-based technologies used to examine DNA, RNA, and proteins from a variety of sample types ranging from single cells to organisms to communities in order to understand who is where, what they are doing, and how they are affected by changing environmental conditions.

The incorporation of ‘Omics into CalCOFI will help scientists better understand the diversity and functional activity of microbes in the area—enabling scientists to more accurately predict ecosystem tipping points, augment understanding of factors that enable or reduce ecosystem resiliency, and potentially unearth critical information regarding ocean response to large-scale pressures, including climate change. This project is a pilot for potential broader applications to other regions and across the NOAA fleet.

In the long term, ‘omics will ideally add to scientists’ ability to predict, monitor, and recommend responses to environmental changes and their associated effects on human health and the health of ocean and coastal ecosystems, leading to broader application to other regions and improved national efforts in ecosystem monitoring and management. Read more about other environmental microbial research in AOML features about Ocean Sampling Day and King Tide sampling on Miami Beach.

CalCOFI is a unique partnership of the California Department of Fish and Game, NOAA Fisheries Service, and the Scripps Institution of Oceanography. The organization was formed in 1949 to study the ecological aspects of the sardine population collapse off California. Today the focus has shifted to the study of the marine environment off the coast of California, the management of its living resources, and monitoring the indicators of El Nino and climate change. CalCOFI conducts quarterly cruises off southern and central California, collecting a suite of hydrographic and biological data on station and underway.

  • A CTD cast collects water samples during the CalCofi cruise.  Photo Credit: CalCofi  

     

  • The RV New Horizon is the research vessel that supported the November 2014 CalCofi cruise. Photo Credit: CalCofi

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Diatoms as seen through a microscope.

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Events, Ocean Chemistry and Ecosystems, Research Partnerships

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June 21, 2014 at 5:39 pm

NOAA Participates in International Ocean Sampling for Microbes

NOAA’s Atlantic Oceanographic and Meteorological Laboratory (AOML) participated in Ocean Sampling Day on June 21, the first global simultaneous sampling for microbes in ocean, coastal and Great Lakes waters. Over time, sampling will support international and NOAA missions to provide a snapshot of the diversity of microbes, their functions, and their potential economic benefits. Among other economic applications, microbes have been used for novel medicines, as biofuels, and to consume spilled oil. Organized and led by the European Union’s MicroB3 organization, NOAA coordinated twelve sampling sites for Ocean Sampling Day 2014 within U.S. coastal waters.

sampling in La Jolla, CA

AOML scientists Kelly Goodwin enters data from water samples from La Jolla, CA.

“Small organisms make up the majority of the ocean’s biomass and drive the cycles that sustain life on earth, but not until recently have we had the tools to reveal their diversity and function,” said Kelly Goodwin, a microbiologist at AOML. “Ocean Sampling Day and future efforts in Genomic Observatories will employ state-of-the art ‘omic technologies to uncover how the oceans are adapting to a multitude of stressors and how those changes translate up to ecosystem services – including seafood supply and healthy swimming waters and coastal habitats.”

NOAA’s Marine Microbes Working Group coordinated 12 sampling locations, part of more than 150 international sites, and supported cross-line NOAA efforts to include NOAA Research centers, including AOML, NOAA Fisheries centers, and NOAA’s National Ocean Service Sanctuary locations (Grays Reef and Humpback Whale National Marine Sanctuaries). NOAA’s Office of Ocean Exploration and Research coordinated the broader NOAA science and outreach/education aspects. Sampling sites are expected to be monitored long-term as part of the international ocean Genomic Observatories Network and the database will serve as a baseline, accessible to the research community, industry, policy makers and the public. The Smithsonian’s Global Genome Initiative will archive samples.

AOML staff, with support from a cadre of summer interns, coordinated five locations in south Florida and in California. Sites included Port Everglades, Tennessee Reef offshore of Long Key in the Florida Keys National Marine Sanctuary, and near the mouth of Tampa Bay at Fort DeSoto in Saint Petersburg. AOML collaborators from the University of Southern Mississippi conducted sampling at Horn Island offshore of the Mississippi Coast. AOML scientists also coordinated the sampling the OSD site at the Scripps Institute Pier in La Jolla, California.

FL Keys OSD sample collection

AOML student interns collect samples from the Florida Keys

Citizen Scientists all over the world also collected environmental data (water and air temperature, salinity, oxygen, etc.) to support the microbial sampling collected globally on the summer solstice. In La Jolla, CA, one of AOML’s remote employees worked with a local scout troop to guide them in collecting similar environmental data. These local efforts were designed to raise general awareness about Ocean Sampling Day.

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