Monterey Bay Aquarium Research Institute

Faults, Vents, and Seeps Logbook
Leg 5, Day 6: Clams!
March 31, 2012

I knew it was going to be a good day when Eric made eggs benedict for breakfast. Today was a very interesting day geologically and biologically. We made two dives on either side of a giant fault. Once again, we tried to dive in locations where the sedimentary layers appeared to outcrop onto the seafloor based on the high-resolution multibeam maps from the autonomous underwater vehicle (AUV) D. Allan B. We are trying to get samples of the outcrops on both sides of the fault. We should be able to date the sediments and reconstruct the evolution of the seafloor.

One of the most exciting moments was when we finally collected some clams! These are a species of the genus Vesicomya. They are big, fat, beautiful clams that inhabit cold seeps, which are a slow source of chemical energy (in this case sulfide) leaking out of the sediment. We also tried to take sulfide measurements at the surface of the mud with the in situ ultraviolet spectrophotometer (ISUS) probe, but didn't detect any.

The clams, which were slightly buried, indicated that there was some sulfide just below the surface and so we took push cores around where they were living. Once we extruded the mud from the push core our noses told us this was a good spot! Sulfide smells a little like rotten eggs and we all could detect that!

Deep-sea clams with suction sampler (upper left), push core (lower left), and intake for sulfide sampler (thin plastic tube). The red dots are from lasers on the ROV and help us tell how big things are in the videos.

The clams house chemosynthetic bacteria that consume sulfide. A clam will stick its big foot deep into the sediment where concentrations of the sulfide are higher, and slip its siphon out of the mud to take in oxygenated water. It then pump water across its gills, which are huge and full of bacteria. The bacteria use the sulfide and oxygen to feed the clam.

These clams are interesting to us both ecologically and evolutionarily. There are several species of Vesicomya in the Gulf of California, and we are hoping to collect all of them so we can complete a molecular phylogeny of these interesting animals. From this phylogeny we will learn how these amazing animals have evolved to inhabit seeps and how they are related to one another. The Gulf of California is interesting ecologically because it contains so many species in such a diverse geological environment.

One of the clams that we brought to the surface.

At a second site we saw some beautiful carbonate outcrops covered with deep-sea corals, seapens, and huge white vase sponges. These carbonate layers are chemical precipitates that formed at an old, but now exposed, transition between the oxidation zone in the sediment and a reducing zone below.

At this transition, methane produced by methanogenic bacteria consuming organic matter combines with sulfate present in the pore waters and produces sulfides and bicarbonate. The increase in concentration of bicarbonate leads to precipitation of calcium carbonate. When bottom currents erode the soft sediment above this carbonate deposit, the massive carbonates are exposed. The carbonate outcrops are a record of a past chemical transition within the sediment.

Carbonate outcrop.
Extracting pore water from a push core to measure methane and sulfate. Here we are using the "route of desperation" method. Usually we use a tool that squeezes water from the mud. This sediment in this core was sandy and you can't "squeeze sand." Instead we used a vacuum created by the syringe to draw the water out.
Shannon Johnson and Roberto Gwiazda working on samples in the wet lab.
Luis Terán Ortega entering notes in his research notebook.

—Shannon Johnson

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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.

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.

In situ gas sampler

These are devices that are used to collect and sample gaseous gases bubbling out of seafloor vents. The way they work is by having small pressure vials (like tiny scuba tanks) from which the air is pumped out with a vacuum pump on the surface and sealed with the valve. On the bottom gases are captured underneath an overturned funnel so that a large gas headspace is developed. Then the value on the pressure vial is opened, gas is sucked into the vial, and the vial's value is re-closed. This way a sample of the gas at the high seafloor pressures is recovered.

In situ ultraviolet spectrophotometer (ISUS)

The ISUS is a sensor used to measure concentrations of dissolved chemicals directly from their Ultraviolet Absorption Spectrum. A variety of chemicals absorb light in the UV and each of these chemicals has a unique absorption spectrum. We can determine the concentration of these chemicals directly, with no chemical manipulation, by measuring the absorption spectrum of seawater in the UV and then deconvolving the spectra to yield the concentration of each component. ISUS has been used to determine nitrate concentrations while deployed on CTD/Rosette profilers, undulating towed vehicles such as a SeaSoar or SeaSciences Acrobat, and on deep-sea moorings. It has also been used to measure sulfide flux from cold seeps in Monterey Bay while deployed on the ROV Ventana.

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.


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.

Gravity corer

Device lowered off the ship to the seafloor on a wire which consists of a long tube that extends below a moderately heavy weight. When the device encounters the bottom, the weight forces the tube into the sediments. When it is pulled out of the bottom the tube will contain a sediment sample (i.e., core) of the upper layers of the ocean floor.


R/V Western Flyer

Ian Young


George Gunther
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


Eric Fitzgerald


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


 Leg 5 Research Team

Charlie Paull
Chief Scientist

Charlie Paull has been a marine geologist and geochemical stratigrapher at MBARI since January 1999. The central theme of Charlie's work involves investigating the fluxes of fluids and gases through continental margins. Over the past decade his primary focus has been gas hydrate research on the Blake Ridge gas hydrate field on the continental rise off of southeastern North America. Assessing the global distribution of gas hydrate and interstitial gas is a continuing interest as well as the development of new techniques to detect the presence of gas hydrate in marine sediments. Charlie's other ongoing work is focused on the geology associated with seafloor seepage sites, including investigating the deposits associated with chemosynthetic communities, determining the processes that occur at the methane-sulfate boundary, and understanding the origin of pockmarks and other potential seafloor fluid venting sites.

Ken Johnson
Chief Scientist

Ken's research interests are focused on the development of new analytical methods for chemicals in seawater and application of these tools to studies of chemical cycling throughout the ocean. Over the past 15 years, Ken's Chemical Sensor Program at MBARI has developed a variety of sensors and analyzers that operate in situ to depths of 4,000 meters. These instruments have been used to study processes ranging from the distribution of sulfide in deep-sea hydrothermal vent systems, to nitrate in coastal ponds surrounded by intensive agricultural activities.

Krystle Anderson
Research Technician

Krystle Anderson is a research technician working for Charlie Paull in the Continental Margins Lab. Krystle's background is primarily in the acquisition and processing of seafloor mapping data. She came from the California State University, Monterey Bay Seafloor Mapping Lab where she obtained her data processing and Geographic Information System (GIS) skills. Krystle spends a majority of her time processing and creating high-resolution maps of multibeam data collected from the mapping AUV. The high-resolution maps Krystle helps create will then be used to aid navigation for the ROV to explore particular areas of interest. On this expedition Krystle will assist with running the GIS system, and processing and cataloguing sediment samples and vibracores. This is Krystle's second research expedition with MBARI and she is very excited to be involved in this expedition.

Roberto Gwiazda
Research Specialist

Roberto is a geochemist by training. His interests lie at the intersection of marine geology and sediment and water chemistry. During cruises Roberto operates a custom-built, portable chemistry lab that includes a complete set of analytical platforms for measurements of fluids and gases. On this expedition, Roberto will be responsible for analytical measurements of pore water chemistry on samples taken from sediment cores. He will also be in charge of collecting gas samples emanating from fluid vents and performing hydrocarbon analyses on dissolved gases collected from pore waters, from gas vents and from seawater.

Eve Lundsten
Research Technician
Leg 5

Eve Lundsten works with Charlie Paull in the Continental Margins Lab. Eve's background is in hydrology but she uses her technical and mapping skills to help understand the processes that create the morphology we see on the seafloor. The Continental Margins Lab uses high-resolution, AUV-collected bathymetric maps to help direct research to the precise location of interest on the seafloor where samples can be collected for further analysis. Eve's responsibilities on this cruise include running the GIS mapping system, assisting with the processing of vibracores, and push cores collected on ROV dives, and documentation of the many samples collected during this leg of the cruise. Eve is very excited to participate in this cruise and is looking forward to many exciting discoveries.

Shannon Johnson
Research Technician
Leg 5

Shannon is a molecular ecologist. This means she uses genetics to solve mysteries about how invertebrates like worms, snails, mussels and clams, who live at hydrothermal vents, cold seeps, wood, and whale falls move around in the deep sea. These environments act like islands in the ocean because most of the animals that inhabit these environments depend on chemosynthetic bacteria for food. The reducing environments provide mineral-rich water that feed the bacteria, creating an abundance of life. On the cruise, Shannon will be responsible for collecting, identifying, and dissecting invertebrates as well as filtering water to study their larvae.

Susan von Thun
Senior Research Technician
Leg 5

Susan works in the video lab at MBARI, where she is a senior research technician. Her primary role at MBARI is to help manage and annotate the remotely operated vehicle (ROV) video archive. Observations about the biology, geology, and equipment in ROV videos are logged using software designed by MBARI engineers called the Video Annotation and Reference System (VARS). On this expedition, Susan will use VARS to annotate and document video coming back to the ship from ROV Doc Ricketts. As one of the few biologists on this leg of the expedition, Susan will be busy identifying and processing biological samples.

Teresa Cardoza
Logistics Specialist
Leg 5

Teresa has worked as a Logistics Specialist in the Division of Marine Operations at MBARI for 12 years. She has spent much of the past year planning and preparing for this expedition, including obtaining scientific permits from the Mexican government, scheduling the science missions and port stops, arranging for services during port stops, and arranging visas for the scientists. During this expedition Teresa will help process samples collected with the ROV, assist in the ROV control room with video tapes and frame grabs, and other science tasks. Teresa is very excited to sail as a member of the science team and will no doubt learn a lot from both marine operations and science perspectives.

Brian Edwards
U.S. Geological Survey
Pacific Coastal and Marine Science Center

Brian specializes in sedimentary processes and stratigraphy, integrating insights gleaned from seafloor rock and sediment samples with information from remote-mapping products, such as close-up photographs of the seafloor, high-resolution bathymetric maps, and seismic-reflection profiles. His recent studies have focused on how sediment moves from the land to the deep sea, processes controlling submarine landslides, saltwater intrusion into coastal aquifer systems, marine pollution, seafloor habitats, and the Cenozoic history of the Arctic Ocean.

Juan Carlos Herguera

Juan Carlos is interested in the history of past oceans, how changes in climate and ocean circulation contribute to the ecology and biogeochemical cycling sustained by coastal environments in the California Current and the Gulf of California regions. During this cruise he will be involved in sampling benthic foraminifera to help characterize their genomic information, and, through their stable isotopic and metal compositions, to understand how these geochemical markers reflect their ambient conditions. He will further use planktonic foraminifera for dating the deep-sea cores with radiocarbon techniques, which hold important clues on the tectonic rupturing rhythm along the boundary between the North American and Pacific plates. He is fascinated by these new observation windows opened up by the ROV deployed from the Western Flyer, making possible the discovery of new vent environments along these fractured boundaries and the chemosynthetic oasis sustained by these leaky enclaves that connect the deep ocean with the lower crust and mantle dynamics.

Mary McGann
Research Geologist (Micropaleontology/Biology)
U.S. Geological Survey
Pacific Coastal and Marine Science Center

Mary's interests focus on using microbiota (primarily foraminifera but also pollen) to investigate marine sediment transport, geohazards (faulting, landslides and paleotsunamis), climate change, and the pathways and impact of invasive species introductions using sediment records and molecular analysis techniques. She also uses foraminifera in biomonitoring marine pollution sites and carbon-14 chronostratigraphy—the study of the age of rock layers in relation to time.

Luis Arturo Terán Ortega
Manager of Regional Exploration
Mexican Geological Service

As a member of the Mexican Geological Survey (SGM), Luis has conducted extensive geological research and prospective surveying mining studies focused on detecting resources with potential economic value. In 2007, the Mexican government commissioned the Mexican Geological Survey to conduct prospective efforts over the entire Mexican territory and adjacent sea to identify potential energy resources such as gas, coal, uranium, and other strategic minerals. Luis is the Manager of Regional Exploration of SGM and his prospective studies encompass Sonora, the Gulf of California, the Baja California peninsula, and the territorial Sea in the Pacific Ocean. This is his first experience on a research cruise and he hopes to gain a better understanding of the richness of the Gulf of California environment from a geologic, biologic, and mineral resources perspective. Luis is very eager to learn from and collaborate with his peers from MBARI.

Last updated: Apr. 09, 2012