Monterey Bay Aquarium Research Institute

Seafloor Biology Logbook
Day 5: The storm beneath
March 5, 2012

The seas slowly diminished through the night and we all had a decent night’s sleep that wasn’t like trying to sleep on a city bus running down a winding, bumpy road. We arose to calm, glassy seas in the Salsipuedes Basin and a beautiful sunrise over the islands to the east. El Norte had blown itself out, and we looked forward to light winds and calm seas. What we didn’t realize was that the rough, stormy conditions were now beneath us.

We were all quite thankful to awaken at Salispuedes where the ocean was very calm and a wonderful sunrise greeted us.

The crew deployed the benthic respirometer system (BRS) over the stern and it sank at its normal rate of 30 meters (100 feet) per minute toward the bottom of the Salsipuedes Basin, 1,600 meters (one mile) down. We followed it immediately with the remotely operated vehicle (ROV), intending to place an animal in each of the eight respiration chambers.

Deep waters in the Salsipuedes Basin and the other nearby basins in the northwestern Gulf of California are warm and oxygen-rich relative to the basins in the south. Whereas the temperature in the Guaymas Basin to the south was 5°C (37°F), down in Salsipuedes it is 11°C (51°F). Oxygen, near zero (one micromole per liter) in Guaymas Basin, was 44 at the same depth here—surface water usually contains around 300 micromoles of oxygen per liter.

The ROV Doc Ricketts descended toward the bottom and entered a thick "snowstorm" of suspended particles of detritus, sediment, and other organic debris that sinks slowly toward the seabed (marine snow). As the ROV neared the bottom, the snowstorm became thicker and thicker until it looked like we were driving through a blizzard. In the last couple of meters above the bottom, it was so thick we could barely see and was combined with suspended sediment. The bottom waters in the basin were like a thick brown soup. The pilots landed "blind" on the seabed, which we couldn’t see through the brown cloud.

With surface conditions so nice, we were dismayed when we reached the seafloor and couldn't see anything but sediment-laden water.

Why such turbid water? The very fast tidal currents that run through Salsipuedes Channel and Basin are well known, and they zip along the bottom, churning sediment up into the water column. These benthic storms are caused more by tides than winds. Either way, it presented a dilemma: it was too turbid to capture animals and place them in the respiration chambers.

We decided to pick the respirometer system up with the ROV and carry it to a shallower area toward the side of the basin, about 500 meters (one-third of a mile) to the east. We slowly made our way, moving about 50 meters shallower, which proved just enough to get us out of the brown soup and into waters clear enough to see at least some of the bottom next to the ROV.

Unlike the bottom in the Guaymas Basin—where oxygen was low, but the water was relatively clear—here in the Salsipuedes deep, there were few animals on the seabed. It must be a tough place to make a living—somewhat like living your life in a continuous dust storm. Nevertheless, there were quite a few sea stars on the otherwise mostly barren seabed, so we chose to load the chambers with one each. As we began, the tidal currents kicked into high gear and the pilots could barely hold the ROV in position to complete loading the BRS. But they are highly skilled and dedicated, and somehow figured a way to make it work. After an hour or so, they’d completed the job in the gloom of the deep-sea storm.

The underwater visibility got much better as we moved upslope onto rocky habitat. These deep-sea corals dotted the steep rock outcrops we encountered.

After that we started a video transect up the slope to observe and count animals on the seabed. The shallower we progressed up the slope, the clearer the water became. Six and one-half hours later, we had moved most of the way up the slope, which turned out to be a steep cliff about 800 kilometers (half mile) high. It was spectacular, with sheer drop-offs and rubble fields, and was covered with sponges, clams, deep-sea corals, and various other animals. Lots of filter feeders seem to thrive here where the rapid currents provide high amounts of food that simply drifts by, waiting to be captured, but it is not so turbid as the bottom of the basin.

The ROV is now on the way up, and we’ll have a long evening processing the animals and sediment cores we collected. We’ll sieve the mud to separate the "macrofauna"—worms, small shrimps, and other crustaceans, snails, and any little animals that live in and on the mud—from the sediment. Time to put on a lab coat and get muddy!

—Jim Barry

Adrianna Gaytán-Caballero and Yosse Tapia cheerfully worked well into the the night processing samples.
Previous log Next log

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: Mar. 08, 2012