Monterey Bay Aquarium Research Institute
2013 seafloor ecology expedition

Day 3—Corn stover and respiration experiments
October 26, 2013

We had two primary goals for today’s ROV dive. First, to deploy the benthic respiration system (BRS), then set it up to measure the oxygen consumption of some deep-sea crabs. Second, we planned to inspect a bale of “corn-stover” (like a large hay bale, except made of corn stalks) that we sank to the seafloor five years ago, to evaluate its rate of decay and effects on seafloor animals.

We started before sunrise, positioning the benthic elevator with the respiration system on the well deck, completing a final check of the system, then launching it over the stern to sink 3,206 meters to the bottom. The launch went smoothly, thanks to good teamwork and calm seas.

Next we planned to launch the ROV Doc Ricketts and dive down to the respiration system to capture squat lobsters near the corn bale and place them in the BRS chambers.

Although the ROV was ready to go, we had problems with a key piece of research equipment—a combination oxygen probe and water sampler—which we had planned to carry down with the ROV to make measurements in and around the corn bale. The probe worked well during testing yesterday evening, but failed this morning, delaying the ROV launch. We tried to repair the probe, but after 90 minutes, we removed it from the ROV and continued with the launch.

The day went pretty smoothly after the oxygen probe hiccup. We descended to the seabed and found our way to the benthic respirometer. It had drifted about 75 meters to the southwest as it sank. The BRS is light enough that the ROV could pick it up by a rope, so we moved it closer to the corn bale. This made it easier to capture animals and place them in the respiration chambers.

This large bale of “corn stover,” four feet by four feet by eight feet in size, was placed on the seafloor almost five years ago. Over the years, we have been studying the decomposition of this bale by microbes and seafloor scavengers. The little white dots are galitheid crabs, which may be living off of the corn stover.

Before placing animals in the BRS chambers, we decided to use the high definition video camera on the ROV to capture detailed video recordings of the entire exposed surface of the bale. At four feet by four feet by eight feet, the bale is quite large, and is wrapped in coarse mesh.

We discovered that the bale is largely intact. Because most deep-sea animals cannot digest the cellulose in the corn stover, it degrades quite slowly. Nevertheless, there were several species of “squat lobsters”—small crabs in the family Galatheidae—living on the bale. Some of these galatheid crabs are known to be capable of digesting cellulose, relying on bacteria in their guts to provide the proper digestive enzymes. We also noticed that white colonies of bacteria had become more abundant since our last visit two years ago.

Unlike the corn stover itself, the pine lumber used to make a frame holding the bale for deployment was highly degraded. We saw evidence of a number of scavenger species in the wood. The wood-boring clam, Xylophaga, in the bivalve family Pholadidae, was particularly obvious due to the characteristically round, large holes it bores in the wood. Roughly 75 to 85 percent of the lumber was degraded, while only about 10 to 20 percent of the corn stover appeared to have been lost.

corn bale animals

This close-up view shows a few animals clustered around the base of the corn bale. From left to right, there are an anemone, a silvery worm, and several galatheid crabs.

In addition to being consumed by crabs and other small scavengers such as snails and polychaete worms, the bale is probably being consumed by anaerobic bacteria in the interior of the bale, where there is little or no oxygen. We’d hoped to use our oxygen probe to collect water samples and measure the variation in oxygen concentrations from the outside to the inside of the bale. But that will have to wait until the probe is repaired.

After we’d inspected the corn bale and the sediment around its base, we collected about five push cores of sediment from around the bale. We will examine these cores to measure the abundance of infaunal animals—the macrofauna—mostly small crustaceans, worms, and molluscs. In addition, we’ll measure the sediment’s grain size distribution, concentration of stable isotopes of carbon and nitrogen, and ATP (energy molecule). The characteristics of cores near the bale will be compared with cores that we collected later in the day farther from the corn bale.

Next we collected galatheid crabs for the respiration chambers, as well as other types of animals for stable-isotope analyses, using the ROV’s suction sampler. This is a tricky process because the crabs can swim away when threatened. After collecting a crab in the sampler, the pilots would fly the ROV over to the respiration system on the benthic elevator and release the animal into the chamber, then try to close the chamber door quickly to prevent the crab’s escape. We placed crabs in seven of the BRS’s eight chambers. We left one chamber empty to measure the background respiration rate of the microbial community in the ambient seawater.

The BRS will now perform experiments automatically for the next six weeks, measuring the changes in oxygen concentrations in each sealed chamber as the crabs (and microbes) consume the oxygen. Every two hours, fresh seawater is pumped into each chamber so that the crabs don’t suffocate.

benthic respirometry system

The top part of this image shows the benthic respirometry system, an automated experiment that is used to measure the oxygen consumption of seafloor animals under different conditions. The lower part of the image shows some of the experimental chambers. In the second chamber on the left, you can see a galatheid crab that we collected. On the right you can see the clear tip of the suction sampler, which the ROV pilots are using to place another crab into a chamber.

For the first day or so, the system will measure the natural oxygen consumption rate of each animal. After that, pumps will automatically inject a small amount of seawater containing extra carbon dioxide. Adding the carbon dioxide will make the seawater a bit more acidic. We will use these experiments to understand how changes in the acidity of the ocean affect the metabolic rate of the crabs.

Thus, this experiment simulates the effects of “ocean acidification”—an ongoing increase in the acidity of the world’s oceans. Ocean acidification is caused by the massive emissions of carbon dioxide to the atmosphere from fossil fuel burning by humans. The oceans absorb about one quarter of this carbon dioxide each year. This is causing seawater throughout the world ocean to become more acidic, just like the water in our test chambers.

In some chambers in the BRS, we will also inject water with lower than normal oxygen concentrations. This will simulate a decrease in oxygen in deep ocean waters that is occurring along with global warming. Thus, our BRS experiments will help us understand how marine life may respond to a variety of changes in ocean conditions caused by fossil fuel emissions.

After setting up the BRS, we flew the ROV back to the area where we were conducting our sunken log experiments. Then we gathered a few more logs to bring back to the surface for detailed study. For details on that research, see yesterday’s log. All in all, a pretty full day!

Jenna Judge and Rosemary Romero

Jenna Judge and Rosemary Romero look for animals living on pieces of wood that we brought back up from the deep seafloor today. These animals include tiny clams and limpets only a few millimeters across.

—Jim Barry

Previous log Next log


Day 5 Day 5
October 28
Squeezing in two dives on our last day

Day 4

Day 4
October 27
Collecting corn-bale animals and more logs

Day 3

Day 3
October 26
Corn stover and respiration experiments

Day 2

Day 2
October 25
Elevator to the seafloor

Day 1

Day 1
October 24
Urchin cages


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, the 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.

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).

 Research Team

jim barry

Jim Barry

Senior Scientist

Jim Barry's 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.

kurt buck

Kurt Buck

Senior Research Technician

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.

patrick whaling

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.

Chris Lovera

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.

kim fulton-bennett

Kim Fulton-Bennett

Public Information Specialist

Kim Fulton-Bennett works as a public information specialist at MBARI, writing articles and news releases for the institution's web site and working with members of the media on MBARI stories. During this cruise, he will be helping take digital notes about each dive, taking photos of the research activities on board, and helping prepare the daily expedition logs.

Craig McClain

Assistant Director of Science
National Evolutionary Synthesis Center

jenna judge

Jenna Judge

Postdoctoral Student
University of California, Berkeley

Jenna Judge is a doctoral student at University of California, Berkeley who is focusing on diversification patterns in chemosynthetic and biogenic habitats. Two years ago, she sank a collection of 10 different kinds of wood in Monterey Bay during a cruise with the Barry lab. On this trip, she hopes to recover all 28 wood bundles to see what animals have colonized them and whether there are differences between animal community richness and abundance for different wood types.

Rosemary Romero

Doctoral Student
University of California, Berkeley

Rosemary Romero is a doctoral student at University of California, Berkeley studying green tides in San Francisco Bay. She will be helping Jenna Judge recover sunken wood with Jim Barry and his lab members. She is excited for the opportunity to go to sea and to discover what animals have colonized the sunken wood since two years ago.