Monterey Bay Aquarium Research Institute

Seafloor Biology Logbook
Day 2: Deploying the benthic respirometer system
March 2, 2012

The second day of our leg began just as the sun snuck above the eastern horizon. We prepared the benthic respirometer system (BRS) for deployment on the back deck. This robotic system is designed to measure the rates of oxygen consumption of seafloor animals placed in each of eight glass chambers. Each chamber has an oxygen sensor, stirring pump, flush pump, and an injection pump. The BRS is deployed over the side of the ship, released from its deployment line, and sinks alone to the seafloor.

Engineer Bob Herlien programs the benthic respirometer system (at right) to measure the rates of oxygen consumption of seafloor animals placed in each of eight glass chambers. Each chamber has an oxygen sensor, stirring pump, flush pump, and an injection pump.
Kurt Buck works to ready the benthic respirometer system before launch time this morning.

We launched the BRS in the Guaymas Basin, then tracked its descent using a navigation beacon attached to its frame. The remotely operated vehicle (ROV) Doc Ricketts was then launched and followed the BRS to the bottom. The BRS landed at a depth of 979 meters (3,132 feet) on a moderately sloping undersea hillside.

Having launched the benthic respirometer system over the side of the ship, we were happy to see it waiting for us when we arrived on the seafloor with the Doc Ricketts.

The mud bottom had high densities of animals, dominated by a sea cucumber called Pannychia, lots of small anemones, shrimps, squat lobsters, sponges, various fish species, and lots of burrows. This depth is slightly below the core of the oxygen minimum zone stretching between 400-800 meters (1,280-2,560 feet) where oxygen levels begin to rise. This higher oxygen is an important factor allowing life to thrive at this depth.

Sea cucumbers known as Pannychia moselyi were very abundant on the seafloor at 979 meters (3,132 feet).

The ROV pilots used a suction sampler—a sort of vacuum cleaner hose—to gently slurp up individual animals to place into each respiration chamber. As we were scanning the seafloor for likely candidates to fill the chambers, a large deep-sea crab called Paralomis lumbered into the scene. We decided to try and get it into the chamber. We held the suction head next to its carapace—the upper section of its shell—and attached it like a suction cup. The hard part is getting this animal into the small chamber and closing the lid before it scrambles out. It fell into the chamber and the pilots hustled to get the lid closed, but the big crab was just too fast. It escaped, and then wandered away.

This Paralomis crab was easily collected, but fast enough to escape later.

We flew the ROV away several meters to find another crab. A smaller Paralomis was nestled next to a rock, but the pilots were able to slurp it up, and flew back to the BRS to try again. It fell into the chamber, but once again, scrambled out before we could close the lid. Score it Paralomis: 2, scientists: 0. We gave up and decided to try for other species.

We saw a pair of juvenile batfish lying on the seafloor and thought we’d see if our luck was better with this slow-moving fish. We were able to try again with each of the pair. We easily suctioned them onto the end of the slurp sampler, but once again failed to get them into the chambers and the lids closed. Game over – score, Batfish: 2, Scientists: 0. I thought we would eventually win in this match if we had lots of time, but the winds were increasing rapidly.

The final target was the sea cucumber Pannychia—these animals are slower than a turtle and we knew we could get the eight chambers loaded up with them quickly. With the increasing winds came larger seas, and we were almost out of dive time for the day. In about 30 minutes we loaded seven of the eight chambers with Pannychia and closed all the lids. Chamber 1 was left empty to measure the respiration rate of the microbial community in the water or any sediment that wafted into the chamber while it was open. We can subtract this value from any rates we measure in the other chambers.

The BRS will automatically measure how much oxygen is consumed in each chamber over a three-hour period. After three hours, a flushing pump will turn on, flushing the water from the chamber to renew it with fresh seawater so that the animals don’t suffocate. These cycles will repeat five times over 15 hours, to determine the ‘baseline’ rates of respiration for each animal. After that, we will inject a bit of high-oxygen water, high-CO2 water, or both into each chamber immediately after flushing, to measure how these animals will respond to higher oxygen or higher CO2 levels.

More CO2 causes some ‘ocean acidification,’ a process that is happening throughout the world ocean as our fossil fuel carbon dioxide emissions are absorbed from the atmosphere. Will Pannychia’s respiration rates be affected by changes in oxygen or CO2? Hopefully, we’ll have the answer soon.

Although the day started out calm, during our ROV dive, the winds kicked up to nearly 40 knots, forcing us to abort the dive very early. We were able to collect 10 sediment cores at the end of the dive, just prior to heading up. The BRS will stay down until at least tomorrow morning. Hopefully, we’ll have better weather. Stay tuned.

It was amazingly calm this morning, but 40-knot winds and large waves forced us to recover the remotely operated vehicle early.

—Jim Barry

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Seafloor Biology

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.

Benthic tool sled

You can see the manipulator arm at the upper left side of the photo and the sample drawer with partitions in the lower left. The drawer is shown open on deck, full of rocks. Normally it is closed when the vehicle is operating and only open when a sample needs to be stowed. The partitions help us keep the rocks in order. The rocks look so much alike, all covered in manganese, it is important to know where each rock came from.

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.

Benthic respirometer system

Oxygen consumption (a measure of biological activity) of the organisms living in the sediment is measured using a benthic respirometer system (BRS). This instrument is used in situ (in place on the seafloor).

Johnson Flux Chamber System

Measures fluxes of CO2 and methane in terrestrial plant communities.

Suction samplers

This sampler acts like a vacuum cleaner sucking up samples and depositing them into buckets.

Sediment scoops

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


R/V Western Flyer

Ian Young


George Gunther
First Mate


Matt Noyes
Chief Engineer


Andrew McKee
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

Jim Barry
Chief Scientist

Jim Barry is a senior scientist at MBARI whose research program focuses on the effects of climate change on ocean ecosystems. In addition to climate change, his research interests are broad, spanning topics such as the biology and ecology of chemosynthetic biological communities in the deep sea, coupling between upper ocean and seafloor ecosystems in polar and temperate environments, the biology of deep-sea communities, and the biology of submarine canyon communities. Jim has helped inform Congress on ocean acidification, ocean carbon sequestration, and climate change by speaking at congressional hearings, briefings and meetings with congressional members.

Ken Johnson
Senior 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.

Kurt Buck
Senior Research Specialist

Kurt Buck specializes in quantitative enumeration, ecology, and imaging of marine protists and bacteria. Upper water-column communities from Antarctic and Arctic sea ice to equatorial regions were his initial focus. He is currently working with deep-sea sediment communities including those from hypoxic zones.

Bob Herlien
Senior Software Engineer

Bob Herlien is a senior software engineer at MBARI. He is project manager for the Respirometer Upgrade project, which includes the Benthic Respirometer System (BRS) being deployed on this cruise. He is also principal software designer for that system. His responsibilities on this cruise include configuring the BRS for each deployment and assuring that it's in good working shape.

Linda Kuhnz
Senior Research Technician

Linda specializes in the ecology of small animals that live in marine sediments (macrofauna), and larger invertebrates and fishes that live on the seafloor or just above it (megafauna). She conducts habitat characterization studies in benthic (seafloor) ecosystems using underwater video and by collecting deep-sea animals. She hopes to find some new and interesting animals in the unique habitats we are visiting on this cruise.

Chris Lovera
Senior Research Technician

Chris supports Jim Barry's Benthic Biology and Ecology, and Free-Ocean CO2 Enrichment research projects. On this expedition, Chris's responsibilities are varied, from collection and curation of invertebrates used in Benthic Respiration System metabolic rate and manipulative oxygen and pH studies, to Geographic Information System work, to operation of the dissolved inorganic carbon analyzer. Chris's recent work focuses on the effects of ocean acidification on invertebrate behavior.

Patrick Whaling
Senior Research Technician

Patrick has worked at MBARI since its beginning in the fall of 1987. Prior to his move to MBARI, he spent seventeen years at Duke University Marine Lab investigating heavy metals in the marine environment. He currently works with Jim Barry in the design and construction of sampling gear used on the ROV to collect benthic animals, in addition to processing benthic samples and conducting carbon-hydrogen-oxygen (CHN) analyses.

Josi Taylor
Postdoctoral Fellow

Josi is a postdoctoral fellow in Jim Barry's Benthic Biology Group. Josi's research is focused on exploring the effects of global climate change—specifically, ocean acidification and hypoxia—on the deep-sea urchin Strongylocentrotus fragilis. Josi looks for effects of environmental change on urchin physiology, behavior, and population/ community structure. During the Gulf of California expedition, Josi will investigate S. fragilis from 200-1200 meters in the Sea of Cortez to identify differences in this population's age structure, depth distribution, physiology, and behavior, as compared to S. fragilis found in the considerably different conditions of the Monterey Bay Canyon System. Josi hopes to use these comparisons of S. fragilis living in two very distinct climates, to better predict the effects of global climate change on community structure and ecosystem function.

Yossellin Tapia De la O
Graduate Student
Universidad Nacional Autónoma de México
Instituto de Ciencias del Mar y Limnología

Yossellin is working on an ecological study of ophiuroids (brittlestars) associated with bacterial mats of the cold methane seeps in the Sonora Margin of Mexico. This study will contribute information about morphological variations, abundance, biomass, and habitat preferences of the ophiuroids.

Adriana Gaytán-Caballero
Graduate Student
Universidad Nacional Autónoma de México
Instituto de Ciencias del Mar y Limnología

Adriana is a doctoral student at Posgrado en Ciencias del Mar y Limnología, UNAM. Her project looks at the abyssal distribution in the Atlantic Equatorial Belt taking as example the crustacean fauna of the asphalt volcano, Chapopote, in the southern Gulf of Mexico, with emphasis on Alvinocaris muricola and Munidopsis geyeri species.

Last updated: Oct. 04, 2012