Studying microbes in the deep and seafloor lava flows
Day 5: Communicating in the deep-sea
July 17, 2011

Location: Ashes hydrothermal vent field at Axial Seamount
Latitude: 45.9333° N
Longitude: 130.0138° W

The ROV pilots worked well into the evening of Day 4 to repair the ROV's damaged tether, and by 6:30 a.m. Doc Ricketts was being lowered into the moon pool for today's dive. The first order of business was to connect the ROV with the Deep-ESP, which was by now overdue for recharging. This Deep-ESP has been fitted with a mass spectrometer, which functions much like a mechanical "nose," continuously sniffing for compounds critical for life on this volcanic seabed.

Mass spectrometry is a technique that allows us to detect different molecules and calculate their abundance, all at the same time. In our case, we are interested in the gas composition of the fluids coming out of cracks in the seafloor. In particular, methane is important because it can originate from geological processes or be produced/consumed by the microorganisms living on and in the seafloor. Measuring the gas composition at different sites allows us to better understand the dynamics of these gases and characterize the environment that the microorganisms are experiencing.

Deploying this kind of instrument in situ on the seafloor has many advantages, including continuous data recording, real-time data, and a virtually unlimited number of samples. But the mass spectrometer requires a lot of power. And when the instrument runs on batteries, this is a big problem. For the deployment here at Juan de Fuca with the Deep-ESP, additional batteries and an extensive recharging plan have to be used. When the ROV tether failed, we could not recharge the battery as planned. We therefore had to shut down the mass spectrometer to preserve enough power for the Deep-ESP. Today, once we finally connected the ROV, we restarted the mass spectrometer, made sure that the shutdown had not damaged it, and started collecting data again. I could see that the water sampled from the crack contained methane and carbon dioxide, while the water away from the crack had much lower carbon dioxide and very little methane.

ROV Doc Ricketts swaps external battery packs for the Deep-ESP each day

We scheduled four hours of dive time to recharge the Deep-ESP from the ROV, but this stretched to six, due to our having missed charging the day before. To make even more power available, the ROV swaps external battery packs for the Deep-ESP each day. Each evening, one of these two, identical, external packs is recharged on board the ship.

After servicing the Deep-ESP, we drove north of Ashes to a flow never before sampled and collected a piece of lava. Then the ROV ascended the 130 meter caldera wall and took a rock from a lava flow at the top. There, we tried to sample the sediment with push cores containing metal "core catchers" of differing stiffnesses. These sediments are comprised largely of volcanic sands whose layering records the history of explosive eruptions since the caldera collapsed. Unfortunately, none of the corers pictured below worked very well. We are now thinking we might need to design much larger, wider corers for our next visit.

Sampling the sediment with push cores containing metal "core catchers."

Another surprise for us was that the lava flow we found at the rim of the caldera wall appeared to have flowed into the caldera. We think that this indicates it originated from a fissure on the volcano's flank rather than from within the caldera.

The ROV returned to the Western Flyer at about 6:00 p.m. carrying rock samples, push cores, and a depleted external battery pack from the Deep-ESP. About then, one of the scientists began having misgivings about the data from the Deep-ESP, and became concerned that it had not been behaving correctly during the previous day. Sure enough, close examination of the logs we had obtained from it while connected with the ROV agreed with previously run simulation traces, both of which showed that the Deep-ESP had not properly processed some of the water samples it had recently taken on the seafloor.

The problem turned out to be an easily corrected programming error for which we quickly verified a fix on our simulated ESP running on a computer aboard the ship. However, the bug would continue to affect operations until we corrected the copy of the software actually running the Deep-ESP. Rather than wait until the next day's charging session with the ROV, we decided to try to send a patch down to the Deep-ESP via an acoustic modem. This is a device that converts binary data into a sound beam using the same basic principles that dolphins and whales use to communicate. As one might imagine, it is very slow and unreliable compared to the high bandwidth network connection we would get via the ROV's fiber optic tether. Fortunately the software "patch" required was quite small. After a few tries, we managed to squawk it down to the seafloor and verify its proper functioning.

Listen to an audio clip of a similar acoustic "conversation" between the ship and Deep-ESP.

— Brent Roman

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Leg 1

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.

Deep ESP

The ESP is a self-contained robotic laboratory that collects samples of seawater and tests these samples for different types of microorganisms, either their genetic material, such as DNA, or proteins they may secrete, such as toxins from a harmful algae bloom. Because of the immense pressure in the deep sea, MBARI's researchers had to build a special pressure housing to protect the delicate instrument. They also had to design and build an automated system to "depressurize" seawater before it could be introduced into the ESP.

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.

Niskin bottles

Niskin bottles are used to collect water samples as well as the tiny bacteria and plankton in that volume. The caps at both ends are open until the bottles are tripped, when the caps snap closed.


The box fits in a partition in the sample drawer. It is shown open, with an animal being placed into it by the ROV's manipulator. When the lid is closed, the box will hold water to protect the animals inside.

Rock crusher

This device is used to collect volcanic glass fragments from the surface of a flow. It is made of about 450kg of lead and steel and is launched over the stern of the ship on a wire. Fragments of rock that break off of the lava flow on impact are trapped in wax-tipped cones mounted around the crusher. The wax is melted in the lab to liberate the rock particles for analysis.

Benthic toolsled/
Manipulator arm/
Sample drawer with partitions

The benthic toolsled is attached to the bottom of the ROV for our geology dives. Its components are the manipulator arm and the sample drawer. The sample drawer is shown open on deck, full of rocks. Normally it is closed when the vehicle is operating and is opened only when a sample needs to be stowed. Partitions in the drawer help us keep the rocks in order. The rocks often look alike, but the conditions and chemistries of the eruptions are different so it is important that we know where each came from.

Glass suction sampler

This equipment is used to vacuum glass particles and larval animals from cracks and crevices. The carousel of small plastic jars fitted with wire mesh will be mounted in the benthic toolsled. The hose will be held by the ROV's manipulator and a suction will be drawn by the pump.

Sediment scoops

Canvas bags on a T-handle for collecting gravel or other materials that fall out of a push-core.

Temperature probe

Mounted on the D-ESP, the wire on the right is placed into the fluid emitted from a hydrothermal vent to record the temperature.


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.


R/V Western Flyer

Ian Young


George Gunther
First Mate


Lance Wardle
Chief Engineer


Andrew McKee
Second Mate


Paul Tucker
First Engineer


Olin Jordan


Vincent Nunes


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 Girguis
Chief Scientist
Harvard University

Peter Girguis is currently a John L. Loeb Associate Professor of Natural Sciences at Harvard University, and an adjunct research engineer at MBARI. His research focuses the ecological physiology of microbes that live in extreme environments. He is particularily interested in the physiological and biochemical adaptations to life in anaerobic environments. His research lies at the intersection of biology and geochemistry, and he develops and uses a variety of tools (high-pressure systems, in situ mass spectrometers, in situ microbial fuel cells) to address the aforementioned issues. He received his B.Sc. from UCLA and his Ph.D. from the University of California Santa Barbara, where he worked with Dr. James Childress on the physiological and biochemical adaptations of deep sea hydrothermal vent tubeworms and their microbial symbionts to the vent environment. He did postdoctoral research at the Monterey Bay Aquarium Research Institute with Dr. Edward Delong on the growth and population dynamics of anaerobic methanotrophs.

David Clague
Chief Scientist

Dave's research interests are nearly all related to the formation and degradation of oceanic volcanoes, particularly Hawaiian volcanoes, mid-ocean ridges, and isolated seamounts. Topics of interest include: compositions of mantle sources for basaltic magmas and conditions of melting; volatile and rare-gas components in basaltic magmas and their degassing history; chronostratigraphic studies of eruption sequence and evolution of lava chemistry during volcano growth; subsidence of ocean volcanoes and its related crustal flexure, plate deformation, and magmatic activity; geologic setting of hydrothermal activity; origin of isolated seamounts; and monitoring of magmatic, tectonic, and hydrothermal activity at submarine and subaerial volcanoes.

Jenny Paduan
Senior Research Technician

Jenny works with Dave Clague in the Submarine Volcanism project. On this expedition, Jenny will be in charge of the GIS work, including use of the recently acquired, high-resolution MBARI Mapping AUV data of our dive sites. She will also stand watches in the ROV control room, help with rock and sediment sample workup and curation once the vehicle is on deck, and coordinate these cruise logs for our group's two legs of the expedition. She is now quite solidly a marine geologist, but her degrees are in biochemistry (Smith College) and biological oceanography (Oregon State University). She is thankful for the opportunities that have led her to study volcanoes, and loves being involved with the research and going to sea. She looks forward to discovering more about how the Earth works.

Bill Ussler
Senior Research Specialist

During expeditions, Bill Ussler is primarily responsible for the operation of the custom-built, portable chemistry lab van which contains a complete analytical laboratory for the analysis of the fluids and gases contained in marine sediments. Bill studies how methane (natural gas) forms and moves within seafloor sediments.

scott jensen Scott Jensen
ESP Systems Lead Engineer

doug pargett Doug Pargett
Deep-water Operations Lead Engineer

chris preston Chris Preston
Senior Research Technician

brent roman Brent Roman
System Control Lead Engineer

Brent has been playing with computers and control systems since the late 1970s. He wrote embedded control software for video tape editing while attending the University of California at Santa Cruz, where he earned a B.S. in Computer and Information Sciences in 1985. His main technical interests are computer operating systems, languages and feedback control systems. Brent wrote most of the custom software driving the current generation of the Environmental Sample Processor. He also enjoys sailing.

Brian Dreyer
Institute of Marine Sciences
UC Santa Cruz

Brian is an isotope geologist in the Institute of Marine Sciences at UC Santa Cruz where he studies the recent magmagenesis and petrology of the Juan de Fuca Ridge. His interest in the petrology of mid-ocean ridges began during his postdoctoral fellowship with MBARI's Submarine Volcanism Group; there, he utilized uranium-series disequilibria within individual lavas of Axial Seamount to clarify eruption and petrogenetic timescales. At mid-ocean ridge systems globally, Brian is interested in a) how variability in lava morphology, geochemistry, and petrology reflect deeper mantle-melting and magmatic processes and their complex interplay with tectonism and b) improving the chronological framework of the ridge magmatic plumbing systems. Brian received his B.S. in Geology from Cal State East Bay in 2000 and PhD in Earth and Planetary Science from Washington University in St. Louis in 2007. When not on the Western Flyer this summer, Brian defends the left side of the infield for the Surfing Squirrels, MBARI's coed softball team.

Heather Olins
Graduate Student
Harvard University

Heather Olins is a graduate student at Harvard University in the Girguis Lab. Her research focuses on carbon fixation, microbe-mineral interactions, and biogeography of hydrothermal vent microbes. She is interested in the interactions of microbes with their physical environment in the deep sea, and determining the role of those interactions in global biogeochemical cycles. Heather received her B.A. and M.A. in Earth and Environmental Sciences from Wesleyan University. On this cruise Heather will be helping with the microbiology associated with the D-ESP and also deploying microbial samplers designed to investigate the impact that mineralogy has on microbial colonization and community structure in vent ecosystems.

Charles Vidoudez
Postdoctoral Fellow
Harvard University

Charles has a multidisciplinary background in plant biochemistry, biotechnology, chemical ecology, metabolomics and mass spectrometry. He obtained his Ph.D in chemical ecology at the Friedrich-Schiller University in Jena, Germany, working on developing and using metabolomics methods on diatoms. Charles's postdoctoral research focuses on combining all these techniques to better understand the deep-sea ecosystems. He currently uses and further develops in situ mass spectrometers. These instruments are a highlight of the Girguis lab and allow direct in situ characterization of the gases dissolved in the seawater, especially at hydrothermal vent sites.