Monterey Bay Aquarium Research Institute

Deep-Sea Chemistry Logbook
Day 5: A chemical high
March 18, 2012

Different territory, different chemical activity. We spent the last few days exploring in a valley where the seafloor is spreading and found sulfur venting from the cracks. Today we moved to a transform fault—a spot where tectonic activity created cracks in the sea floor at right angles to the spreading center—and found methane and cold seeps, in addition to sulfur.

Black mud, large fields of chemosynthetic clams, and fuzzy mats of bacteria are all signs that an area has chemicals venting from below. Today we saw all these indicators and stopped to take measurements of the chemical signals using the laser Raman spectrometer. When the Raman probe was inserted into the sediment in a field of live clams and returned a signal clearly showing methane in the pore water within the sediment, a cheer went up in the control room. It was a sure sign we found the target we’ve been looking for and that all the equipment was working as expected.

The laser Raman probe was inserted into fields of live clams, left, and a fissure lined with orange and white bacteria to determine which chemicals were present. Water passes before a focused laser beam in a tiny cavity; the light that bounces back indicates what chemical components are present.

The remotely operated vehicle was on the seafloor almost 10 hours today, allowing the science team to survey a large section of the transform fault zone, to search for the most interesting sites, and to gather water and sediment samples along with data, all to be analyzed in the lab later to paint a clearer picture of the chemical activity in the area. Methane gas is a primary fuel source and huge quantities are present on Earth; in the atmosphere it is a critical heat-trapping gas. But the vast majority of methane that leaks from the interior of the Earth to the seafloor is consumed by organisms before it can ever get out of the seafloor. This is one of the fundamental processes that hold our climate in balance. These seafloor observations of the microbes and higher animals that play key roles in this balance allow us to better understand the balance of Earth’s methane budget.

This view from the main camera on the remotely operated vehicle gives an idea of the various sampling tools carried to the seafloor to conduct chemistry studies. The laser Raman probe in a specially designed tripod with a hydraulic actuator sits above a fissure lined with white and orange bacteria. In the foreground, from left are the thermistor at the end of the orange cable, used to measure the temperature of venting fluids; push core tubes used to collect mud from the seafloor; and the pump and gauges used for the precise operation of the Raman spectrometer.

As mentioned earlier in these daily logs, two Ph.D. students from the University of California, Santa Cruz, have joined the science team for this cruise. The expedition offers them a rare opportunity to go to sea with an experienced team of scientists, and gives them a chance to collect data and samples for their own research projects. Here they explain the goals of their graduate research.

From Joe Murray: My work on this cruise is focused on studying the dynamics of the nitrogen cycle in the Gulf of California. I am specifically interested in the link between fertilizer run-off from farms in the Yaqui Valley and phytoplankton blooms in the gulf. The Yaqui Valley is a region of intense agriculture along the west coast of the Mexican mainland. Previous studies using ocean-color satellite measurements have shown a strong correlation between the timing of regional irrigation and large phytoplankton blooms off the coast of the Yaqui Valley. The implication is that a significant proportion of the fertilizer applied for farming is being transported to the ocean. The Gulf of California is naturally low in essential nutrients such as nitrate, so any inputs of nitrate, such as from fertilizers, has the potential to stimulate increases in phytoplankton growth.

These satellite observations of a potential relationship between fertilizer run-off and phytoplankton blooms have not been verified by direct measurements in the field. This cruise gives me an opportunity to sample the water, then to perform various geochemical measurements to see if run-off from the Yaqui Valley is indeed an important source of nutrients to this region of the Gulf of California. The most important measurement I will be utilizing is the nitrogen and oxygen isotopic composition of dissolved nitrate. Nitrate produced from different sources have very slightly different nitrogen and oxygen isotope ratios, which means they have a slightly different chemical signature. Nitrate produced for use as fertilizer is isotopically distinct from nitrate upwelled from the deep ocean. Thus, by measuring the isotopic composition of nitrate towards shore and at depth in waters off the coast of the Yaqui Valley, I should be able to determine the relative importance of these different sources for phytoplankton growth in the area.

Abbey Chrystal, right, helps Joe Murray process water samples for his study of agricultural run-off into the Gulf of California waters.

From Abbey Chrystal: I am interested in long-term variations in deep-ocean carbonate chemistry. The deep ocean is a large reservoir for carbon and can isolate carbon from the atmosphere for thousands of years. Any variation in the amount or length of time carbon remains in the deep ocean has the potential to impact global climate. The carbonate chemistry of the deep ocean is influenced by the amount of carbon it holds, so by reconstructing past ocean carbonate chemistry, I hope to better understand how the deep-ocean carbon reservoir has changed over time.

Benthic foraminifera are unicellular organisms that live in ocean sediments. They build a tiny calcium carbonate shell and the chemistry of their shells reflects the chemistry of the water in which they live. By analyzing the remnant shells of ancient foraminifera preserved in deep-sea sediments, I can reconstruct the chemistry of the ancient deep ocean. On this cruise, I am collecting push-cores of the seafloor sediment as well as samples of bottom water. I will use them to perform a calibration study by comparing the shell chemistry of the foraminifera that were living at the time of collection with the chemistry of the seawater around them.

Abbey uses a syringe to extract the water sample from the top of the push-core sample.

While we may have hoped for bigger, hotter, denser fields of vents, the day's discoveries were certainly rewards after exploring this seafloor valley northeast of La Paz.

Abbey takes a break from the lab to watch a pod of pilot whales.

—Nancy Barr

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Deep-Sea Chemistry

R/V Western Flyer

The R/V Western Flyer is a small water-plane area twin hull (SWATH) oceanographic research vessel measuring 35.6 meters long and 16.2 meters wide. It was designed and constructed for MBARI to serve as the support vessel for ROV operations. Her missions include the Monterey Bay as well as extended cruises to Hawaii, Gulf of California and the Pacific Northwest.

ROV Doc Ricketts

ROV Doc Ricketts is MBARI's next generation ROV. The system breaks new ground in providing an integrated unmanned submersible research platform, with many powerful features providing efficient, reliable and precise sampling and data collection in a wide range of missions.

Laser Raman spectrometer DORISS2

By bouncing a specially tuned laser beam off of almost any object or substance—solid, liquid, or gas—a laser Raman spectrometer can provide information about that object's chemical composition and molecular structure.

Push cores

A push-core looks like a clear plastic tube with a rubber handle on one end. Just as its name implies, the push core is pushed down into loose sediment using the ROV's manipulator arm. As the sediment fills up the core, water exits out the top through one-way valves. When the core is pulled up again, these valves close, which (most of the time) keeps the sediment from sliding out of the core tube. When we bring these cores back to the surface, we typically look for living animals and organic material in the sediments.

CTD Rosette

The CTD measures conductivity (which helps determine salinity), temperature, and density (which helps determine depth). This particular CTD runs profiles of the water column (surface to bottom) and along the way, collects discrete water samples (at specific predetermined depths) using the rosette of niskin bottles. Each bottle can collect a water sample. The transmissometer measures the number of particles in the water and the oxygen sensors tell us how much dissolved oxygen is present. Both of these instruments go onto the CTD rosette and give us a profile of the water column.


Vibracoring is a common technique used to obtain samples from water-saturated sediment. These corers work by attaching a motor that induces high frequency vibrations in the core liner that in turn liquefies the sediment directly around the core cutter, enabling it to pass through the sediment with little resistance.

Heat-flow probe

MBARI's heat-flow probe is mounted on the side of the ROV Doc Ricketts inside the vertical stainless steel box. This both protects the delicate probe and provide the track so that the probe can be inserted into the sediment along a totally straight path.  The probe contains five high precision platinum sensors which are used to measure the vertical temperature gradient in the sediments. This gradient along with some knowledge of the heat capacity of the sediment allows scientists to calculate the rate of heat loss from the sediments into the ocean.


R/V Western Flyer

Ian Young


Andrew McKee
First Mate


Matt Noyes
Chief Engineer


Cole Davis
Second Mate


Lance Wardle
First Engineer


Shaun Summer
Relief First Engineer


Olin Jordan


Craig Heihn
Relief Deckhand


Jason Jordan
Relief Deckhand


Dan Chamberlain
Electronics Officer


Patrick Mitts


ROV Doc Ricketts

Knute Brekke
Chief ROV Pilot


Mark Talkovic
Senior ROV Pilot


Randy Prickett
Senior ROV Pilot


Bryan Schaefer
ROV Pilot/Technician


Eric Martin
ROV Pilot/Technician


 Research Team

Peter Brewer
Chief Scientist

Peter has taken part in more than 30 deep-sea cruises, and has served as chief scientist on major expeditions and on more than 90 ROV dives with MBARI ships and vehicles. His research interests include the ocean geochemistry of the greenhouse gases. He has devised novel techniques both for measurement and for extracting the oceanic signatures of global change. At MBARI his current interests include the geochemistry of gas hydrates, and the evolution of the oceanic fossil fuel CO2 signal. He has developed novel techniques for deep ocean laser Raman spectroscopy, and for testing the principles and impacts of deep ocean CO2 injection.

Ed Peltzer
Senior Research Specialist

Ed is an ocean chemist who has been with MBARI since 1997. He has been involved in developing in situ laser Raman spectrometry instruments and lab based analytical techniques to study the composition of gases in gas hydrates and deep-sea vents. He has collaborated on the development of new instrumentation for the measurement of temperature and pH from ROVs and deep-sea observatories. As the group's project manager, Ed is also responsible for expedition planning and logistics.

Nancy Barr
Web/Print Project Manager

Nancy manages the editing, design, and production of the MBARI annual report and participates in a variety of editorial and communication projects. She also oversees the institute website. For this expedition she will be in charge of the daily reports that will be posted to this website and will assist with other science crew tasks.

Peter Walz
Senior Research Technician

Peter has worked as a research technician for several scientists at MBARI. For the past 10 years he has supported the research efforts of Peter Brewer and his interests regarding the ocean chemistry of greenhouse gases such as methane and carbon dioxide. Peter is responsible for the design, testing, maintenance, and deployment of the oceangoing science hardware and works closely with the marine operations group to integrate new equipment and technology with MBARI's ROVs.

Martín Hernández Ayón
Universidad Autónoma de Baja California

Martín Hernández Ayón is a chemical oceanographer. His research is focused on the inorganic carbon system, ocean acidification and biogeochemistry in the coastal regions of Baja California, the Sea of Cortez, the subtropical region where the oxygen minimum zone is located, and, more recently, the Gulf of Mexico.

Gabriela Y. Cervantes
Graduate Student
Universidad Autónoma de Baja California

Gaby is a graduate student in the coastal oceanography program at the University of Baja California in Ensenada, Mexico. She is doing her graduate studies on the dynamics of CO2 in seawater from a coastal monitoring site known as Ensenada Station.

Abbey Chrystal
Graduate Student
University of California, Santa Cruz

Abbey Chrystal is a graduate student in earth and planetary sciences at the University of California, Santa Cruz. Her research focuses on reconstructing long-term records of past ocean carbonate chemistry parameters. On this cruise she will be collecting sediment push cores and bottom water samples to help calibrate the relationship between the shell chemistry of benthic foraminifera and the chemistry of the bottom water and porewater chemistry in which they grow.

Joseph Murray
Graduate Student
University of California, Santa Cruz

Joseph Murray is a first year ocean sciences Ph.D. student in the lab of Dr. Adina Paytan at the University of California, Santa Cruz. He is interested in coastal marine chemistry and the impact of submarine groundwater discharge on marine biogeochemical cycles. His current research is focused on using oxygen and nitrogen isotopes in nitrate to study sources and cycling of nitrogen in the coastal ocean. As part of this cruise, he plans to collect samples in order to study the impact of anthropogenic fertilizer runoff from the Yaqui Valley on the marine nitrogen cycle in the Gulf of California, including assessing the role groundwater discharge plays in this process.

Last updated: Mar. 20, 2012