Monterey Bay Aquarium Research Institute

Seafloor Biology Logbook
Day 7: A (not so) barren seafloor
March 7, 2012

Contrary to the forecast, the wind picked up to nearly 40 knots overnight and the captain decided to move several miles toward shore to find calmer waters. We all slept better because of it. By sunrise the wind was down near 25 knots, and we launched the ROV Doc Ricketts at around 7:00 a.m. As it descended toward the bottom 820 meters (2,700 feet) beneath the surface, we watched the video screens showing thicker and thicker marine snow. After the mud storm yesterday only 27 kilometers (17 miles) away, we were really hoping for workable conditions on the bottom. The tide was approaching a low at 8:30 a.m., and we expected that the tidal currents would be lowest during slack tide.

On the bottom, it was murky with suspended sediment and a moderate current. But it could have been worse—yesterday the current was so strong that the ROV couldn’t land on the bottom. Through the suspended sediment, we saw a mud-covered plain, with very few animals; some small octopuses, sea squirts, and a few animals known as heart urchins. While it looked very barren compared to other habitats we see, we could tell that there are actually many of these urchins living just under the sediment—their primary habitat. We began slurping up urchins visible on the surface with a suction sampler, then dropping them one by one into seven of the respiration chambers in the benthic respirometer system (BRS), closing the doors after we’d finished. We left one chamber without an urchin so that we could measure the "extra" respiration caused by the microbial community in the water and any sediment that was present in the chamber.

A heart urchin inside the suction sampler. The majority of these animals remain burrowed under the sediment and out of sight.

The most interesting features on this bottom were the many octopuses we observed. As soon as we arrived at the respirometer system, there was one sitting on the frame, appearing to have claimed this new "rock" for itself. It gave what seemed to us to be a mean stare, but it quickly backed down and hid under the frame as the five-ton ROV with huge lights approached. This octopus was a treat to see, but during the dive we found them to be quite abundant on the mostly barren seabed. We saw them nestled under the occasional sea squirt, partially buried in the sediment, and swimming or crawling over the seabed. Such curious beasts.

We’d timed the tide well, and were able to work pretty effectively, but only for a while. As time passed and the tidal phase moved into full flood, the currents picked up and we couldn’t work on the bottom. We decided to fly up to about 20 meters (65 feet) above the bottom and let the ROV and the ship drift down-current. After about 30 minutes, the pilots flew the ROV back down to the seabed and we struggled to run a video transect, zooming in on the seabed and recording video close-up as they piloted the ROV over about 300 meters (1,000 feet) of the seabed. This will allow us to measure the abundance of various animals living there. Here and there we stopped to collect some animals (urchins, tiny fish, sea squirts) and sediment core samples we’ll analyze this evening.

The seafloor looked mostly barren in the Delfin Basin except when we came along some octopuses. There are two in this picture; one is nearly 100 percent buried in the front and it was interesting to watch them interact.

As we crossed over the seabed, we hoped to stumble upon a hydrothermal vent or methane seep—features associated with tectonic motion. This dive, like nearly all others on this cruise, was located directly over the seam between tectonic plates that is tearing Baja California from mainland Mexico. We’d have recognized the vent or seep communities immediately by the typically high densities of large clams, tubeworms, and other animals—far more abundant than in any other deep-sea habitat. Many of these animals have symbiotic relationships with "chemosynthetic bacteria"—bacteria that live in their tissues.

Many clams, mussels, worms, and other animals can use chemical energy rather than sunlight to grow. We all know that plants use photosynthesis—carbon dioxide + water + energy (sunlight) are used to create sugars and other organic compounds, with oxygen as a waste product. Chemosynthesis is nearly identical, but uses chemical energy instead of sunlight. Various chemical compounds can fuel chemosynthesis, but sulfide and methane appear to be the most common for the chemosynthetic microbes at vent and seep communities. Had we found these ecosystems, we could have measured sulfide concentrations in the water near the vent and seep sites using the ISUS sulfide sensor developed by Ken Johnson, a marine chemist on this leg of the cruise. The sulfide sensor was operating nearly continuously during the cruise, but never detected sulfide during our dives. The ISUS will be used on later legs of the Gulf of California expedition, targeting known or likely locations of vent and seep systems.

The ROV was on the surface by 5:00 p.m., just in time for another big dinner. We ate and then began processing all of the cores and other samples. Considering the conditions, this was a great day. We stayed on station until 8:00 p.m., when we released the respirometer system from the bottom using the acoustic release, and by 8:30 it was on deck and the captain turned the ship south, heading back toward the Guaymas Basin near the mid-point of the Sea of Cortez. We’ll have one final dive there tomorrow before we head to La Paz on Friday.

—Jim Barry

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. 09, 2012