Monterey Bay Aquarium Research Institute
2013 benthic ecology cruise

Day 1 – Busy first day
December 11, 2013

The R/V Western Flyer left the dock in Moss Landing on time this morning at 8:00 a.m. and departed the harbor under a brisk offshore breeze and sparkling clear skies. We headed out roughly 15 miles for the first day’s activities on a six-day research cruise. The research objectives for the day were to retrieve a benthic mooring deployed in the canyon six months ago, and to begin sampling a deep-sea urchin caging experiment that was initiated two years ago. The benthic mooring is a few instruments moored to a weight on the seafloor that measure rates of sedimentation of organic debris, current speeds, and the turbidity of the waters in the bottom of the canyon.

The robotic arm of the ROV Doc Ricketts pushes a core sampler into the muddy seafloor to collect sediment for analyses of the macrofauna (small worms and crustaceans) inhabiting the sediment. Over 60 cores were collected today, along with several fragile deep sea urchins. Our research team will use these collections to help understand the effects urchins have on the sediment-dwelling animals (macrofauna) as well as determine rates of growth and reproduction for the urchins.

The first day of a cruise is always a day to settle into the tempo and routine of a cruise. As is tradition, the required safety drill was announced by a blasting alarm bell. The nine members of the science crew hastily grabbed their survival suits (gumby suits) and headed to the designated muster location in the wet lab at the aft section of the Western Flyer. The second mate delivered a safety briefing and we discussed many of the details of the research planned for the next six days.

Not too long after the drill, we were at the benthic mooring location, where Patrick Whaling and Kurt Buck worked to communicate with the acoustic release on the mooring. In just a few minutes they reported that the acoustic release, which responds to acoustic signals sent from the surface, had released its grip on the large anchor weight that was used to sink the benthic mooring six months ago to a depth of 1,281 meters in Monterey Canyon. The mooring was now floating toward the surface. After about 30 minutes, we expected to hear the radio beacon blaring—it only transmits when the beacon is above the surface—but it never came on. We were sure the mooring was at the surface and near the ship, and after about 15 minutes we saw the yellow floats bobbing in the small swell. The crew moved the ship to the floats, grappled it, and hoisted it aboard with the winch and A-frame on the ship’s stern. Data from this mooring will be used to understand how organic material and sediment makes it way down the axis of Monterey Canyon. Once the mooring was aboard, we headed for our next station for the day.

The control room of the RV Western Flyer includes many large high-definition television screens that broadcast a live image from the seafloor. The ROV pilot and robotic arm operator are seated to the left. The science lead in the middle, and the navigator and video annotator to the right.

The remainder of the day was devoted to remotely operated vehicle (ROV) Doc Ricketts operations at 600 meter depth where we sampled an experiment designed to help us understand more about the lives and activities of deep-sea fragile sea urchins than live in abundance from depths ranging from 200 to 1,200 meters along the continental shelf of the northeast Pacific. These urchins are one of the most abundant megafauna (animals easily identified without a microscope) on the upper continental slope in this region, but we don’t know much about them. For example, what role do they play in the deep-sea benthic ecosystem? How fast do they grow and reproduce? Are they sensitive to changes in ocean conditions caused by human activities?

About two years ago, our lab group initiated an urchin caging experiment. What is that? It is an approach used commonly on land and in shallow marine waters to measure the effect of one animal on other members of its ecological community. In essence, you set up several cages on the bottom, some with the animals (in this case urchins), some without urchins, and then measure any differences that develop in the composition or abundance of other organisms inside both types of cages. Two years ago, we placed six cages (five feet by five feet by one foot high) at depths of 200, 600, and 1,000 meters just outside Monterey Bay. The cages are covered with plastic mesh. Fifteen urchins (Strongylocentrotus fragilis) were added to each of three cages at each depth. Three other cages had no urchins. We also counted all of the megafauna (remember? – big animals) in each cage, and collected 10 sediment cores (see photo above) from which we will count all of the macrofauna (the little animals). You might think that just putting the cages on the bottom could have a pretty big influence on the animals within each cage—with or without urchins. Good point. So to help understand that, we also put down three cages with no mesh, and also designated three other areas nearby with no cage at all, and sampled them in the same manner as within the cages. We’ve now returned to remove the cages, count the megafauna, and sample the sediment for macrofauna in the same way we did two years ago. Once all of this is analyzed, we should have some idea of the effects urchins have in this ecosystem.

Sediment samples, or "push cores" being transported from the just-recovered ROV Doc Ricketts. These cores were then processed in the science wet lab.

That isn’t all we are hoping to learn from this. We also hope to learn more about how fast urchins are growing at different depths. Two years ago, we soaked many of the urchins initially placed in the cages in seawater with lots of calcein, which is a fluorescent dye that urchins incorporate into their skeletons. Urchins actually have rings in their shells (called tests), much like tree-rings. The calcein should leave a fluorescent ring we will hopefully be able to see under the microscope (with UV illumination) to determine how many rings are formed each year. We expect the answer to be one ring equals one year. That information and changes in the sizes of these animals will help us understand how fast they grow, and how much that differs among depths, if at all. If so, why?

Sampling today was fantastic. Everything worked—you’d be surprised just how many things need to work together to pull off a successful ROV dive. The ship’s positioning system, the ROV winch and tether, all the computers involved, the ship navigation system, the ROV navigation system, robotic arms (we really depend on these) on the ROV, video cameras, on and on; It was like a beautiful symphony today—flawless. We were able to collect 60 sediment cores, while sampling three control locations and three cages (of nine cages at the 600 meter sites). Once all the samples were aboard, the entire science crew worked hard to process all of the samples. It will take months to get the final data set, but just getting the samples back is pretty gratifying. We’ll return here in a couple of days to continue this work.

Tomorrow, MBARI and National Oceanic and Atmospheric Administration (NOAA) scientists aboard the Wester Flyer plan to re-visit a lost shipping container that fell from a ship during a huge storm in February of 2004. We first sampled it in March of 2011. We’re excited about observing any potential changes in the container’s condition, and any changes in faunal communities on or around it. Although thousands of these containers are thought to fall from ships each year, this is a rare opportunity to study their potential effects on the deep seafloor. In addition to all sorts of video recordings, we will collect sediment samples to test for presence of heavy metals that come from the toxic marine paint that is slowly chipping and peeling off the container.

Monterey Bay National Marine Sanctuary (MBNMS) scientists Dr. Andrew DeVogelaere and Oren Frey sieve mud to preserve animal and other larger particles.

— Jim Barry

Next log


Day 6 Day 6: Shallow water
December 16
We moved to shallow waters last night to prepare for our last cruise day, working on finishing our sampling of the urchin caging experiment.

Day 5 Day 5: Exploring unknown territory
December 15
We were all excited about today's exploration dive on Sur Ridge, a ten-mile-long submarine ridge about 20 miles due west of Pt. Sur, on the California coast.

Day 4

Day 4: A corn field on the deep-sea floor?
December 14
Our second objective for today was to visit the bale of corn stover we sank in 3,200 meter depth in 2009.

Day 3

Day 3: Hooligan fish
December 13
Sablefish were common here a couple of days ago, but today it was as if a gang of troublemakers showed up.

Day 2

Day 2: Out of sight - out of mind
December 12
An estimated 10,000 shipping containers are lost over the side of cargo ships during rough weather each year. What happens to them?

Day 1

Day 1: Busy first day
December 11
The research objectives for the day were to retrieve a benthic mooring deployed in the canyon six months ago, and to begin sampling a deep-sea urchin caging experiment that was initiated two years ago.


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.

Josi Taylor

Josi Taylor

Research Associate

Josi will continue to look at the ecological impacts of the shipping container lost to the deep sea in 2004. After analyzing data collected during a joint MBARI and Monterey Bay National Marine Sanctuary cruise in 2011, Josi is excited to see how the communities of animals on and around the container may have changed in the last two and a half years. She will also be taking samples specifically for toxicity analysis during this cruise. This information will provide a better idea of the possible effects of the thousands of shipping containers lost to the deep sea each year.

Andrew Devogelaere

Andrew DeVogelaere

Research Coordinator/SIMoN Program Director
National Marine Sanctuaries/NOAA

Andrew oversees the Monterey Bay National Marine Sanctuary's research program. This includes facilitating collaboration among over 20 research institutions in the region, providing technical information to decision makers and the Sanctuary staff, and initiating research on resource management issues. He is also leading the effort to develop the Sanctuary Integrated Monitoring Network (SIMoN), a critical program that assesses how populations of marine organisms and habitats are changing through time. He has been directly involved in a wide variety of research projects, ranging in habitats from the deep sea to estuaries. Dr. DeVogelaere has an M.S. in Marine Science and a Ph.D. in Biology.

Erica Burton

Erica Burton

Research Specialist
National Marine Sanctuaries/NOAA

As a Research Specialist, Erica Burton works on marine research issues such as ecosystem characterization, marine protected areas, and submerged cultural resources. She also spends time at sea collecting scientific data and information. Several projects include characterization of the Davidson Seamount, monitoring and characterization of deep-water fish and invertebrate assemblages, and biological characterizations at shipwreck sites. Erica also provides programatic support to the Research Activity Panel, and on the evaluation of MBNMS research permits. Erica earned a M.S. in Marine Science. Her graduate research focused on age, longevity, and growth determination of fishes, including radiometric age determination of the giant grenadier, bocaccio rockfish, Atlantic tarpon, and Atlantic sturgeon.

Chad King

Chad King

Research Specialist
National Marine Sanctuaries/NOAA

Chad has been with the Monterey Bay National Marine Sanctuary (MBNMS) since 2002, and is responsible for the collection, analyses, and dissemination of spatial data for the Sanctuary Integrated Monitoring Network (SIMoN) and MBNMS. These data help integrate past and present monitoring programs within the Sanctuary and are the foundation of decision-making tools such as interactive maps that are made available to the general public. He is also a NOAA divemaster and an active participant in subtidal research, including kelp forest and invasive species monitoring and underwater photography and videography. Additionally, he produces short outreach films and has produced significant content for the Sanctuary Exploration Center. Chad was instrumental in developing "SeaPhoto", an iOS app that features imagery and life history content of the MBNMS. Chad has a M.S. in Marine Science. His academic research focused on kelp forest ecology and subtropical ecological dynamics and genetics in the Gulf of California.

Oren Frey

Oren Frey

Research consultant
National Marine Sanctuaries/NOAA

Oren Frey has worked with the Monterey Bay National Marine Sanctuary since 2011, first as a Sea Grant fellow and then as a consultant on a variety of projects. In preparation for the MBARI/MBNMS cruise to the shipping container on Smooth Ridge in 2011, he researched the phenomenon of shipping container loss. Oren is interested to see how ecological conditions at the container site may have changed, as a means of better understanding the range of impacts that lost containers can have. Oren will be involved with sample processing and will also assist with science communication of some of the team's activities.