With a few simple buckets of ordinary seawater, researchers at Scripps Institution of Oceanography at UC San Diego took part in an ambitious, globally coordinated project aiming to find out which organisms live in ocean water throughout the world.
Microscopic inhabitants in seawater play fundamental roles in key planetary processes, from carbon dioxide cycling to the health and well-being of humans. Now, an international group of marine biologists, with help from public “citizen scientists,” hope to create a global snapshot of the makeup of these tiny organisms and the conditions of their marine existence.
On June 21, the Ellen Brown Scripps Memorial Pier was one of more than 170 sites around the globe that made up Ocean Sampling Day, conceived as the largest sampling set in marine research acquired on a single day.
Scientists from Scripps, the National Oceanic and Atmospheric Administration (NOAA), and the J. Craig Venter Institute (JCVI) in La Jolla, Calif., coordinated the effort at the Scripps Pier. Scripps marine biologist Brian Palenik, Scripps graduate student Maitreyi Nagarkar, and Scripps staff members Emy Daniels and Mary Hilbern led Scripps Pier sampling with a group of San Diego Girl Scouts, and in doing so joined hundreds of marine biologists and public samplers from Antarctica to Hawaii to Iceland. Samples are now being sent to Europe for DNA analysis and genetic sequencing. With a smart phone app, researchers and citizen scientists also provided environmental information about their sample, from air and water temperature to wind speed and water salinity.
“With sequencing and environmental metadata, we will try to reconstruct information about what organisms are doing in the water, not just who they are,” said Palenik. “With all of these data from all over the globe the hope is to be able to try to make associations—between the organisms present and the conditions in the water.”
Palenik said such information will not only be useful in depicting conditions for healthy ecosystems, but to find clues in the seawater to monitor red tides, harmful algal blooms, and disease-causing marine pathogens.
While Ocean Sampling Day will be a single day’s glimpse of data, Palenik hopes the project catalyzes an ongoing effort of regular genomics sampling. Scripps Oceanography scientists, along with several collaborators, including NOAA, have established several vital long-term observation efforts that have led to key insights for science and society. They range from the 65-year-old California Cooperative Oceanic Fisheries Investigations (CalCOFI) providing valuable data for long-term fisheries and coastal resources management to the global Argo network of profiling floats that have greatly advanced ocean and climate research.
“I think the grand vision is that the Scripps Pier actually becomes a genomics monitoring site, with other genomics observatories coordinated jointly with NOAA, and we do this once a week, not just once a year,” said Palenik.
Palenik and his colleagues at NOAA and JCVI hope such a trove of data will aid in cutting-edge research for “omics” fields such as genomics (genetics/DNA research) and proteomics (detailed protein studies).
“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 principal investigator at NOAA’s Ocean and Atmospheric Research Line Office and co-chair of NOAA’s Marine Microbe Working Group. NOAA’s coordination with the team in Europe enabled dozens of sites around the country, including the Scripps Pier, to be included in the DNA sequencing efforts. “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,” said Goodwin.
“We are particularly excited about the possibility of extending our partnership with NOAA, Scripps Oceanography, and CalCOFI in order to more regularly examine microbes in the Southern California Bight region,” said Lisa Zeigler Allen, an assistant professor in the Microbial and Environmental Genetics Department at JCVI. Zeigler Allen said much of JCVI’s expertise in environmental genomics has been generated from its Global Ocean Sampling Expedition, which began in 2003.
Zeigler Allen’s team, including Andy Allen and Chris Dupont, is interested in factors that promote microbial diversity and function on one hand and mortality on the other.
“This includes our goal of developing omics-related technologies in order to establish new indicators of coastal ecosystem health and increase the sensitivity at which we are able to monitor the occurrence and dynamic of microbes in the ocean, including viruses and pathogens,” said Zeigler Allen.
Nagarkar, a first-year Scripps graduate student, is greatly enthused about the prospects of blending her marine genomics studies with public outreach connections.
“Ocean Sampling Day is especially exciting to me because it’s relevant to my research and my background in community outreach and citizen science,” said Nagarkar. “Because it’s so large-scale, the Girl Scouts we’re working with will have their hands in the sampling and see it in a global perspective. When the results come back, they can see how what they did fits into this bigger project—I think that’s a really cool opportunity.”
All the data obtained during Ocean Sampling Day will be made publicly available at microb3.eu/osd.
-- Mario C. Aguilera