Monterey Bay Aquarium Research Institute

Seafloor Biology Logbook
Day 8: Analyzing samples
March 8, 2012

Today we're transiting south to the Guaymas Basin, so most of our day was spent in the lab processing and organizing samples before the next Doc Ricketts dive. There are many different ways that we look at, test, analyze, and compare what we find here. Our samples include imagery, water, sediment, organic matter, and animals. With these samples we test and evaluate various parameters like biological community structure, chemical composition, grain size, oxygen level, pH, the amount of organic matter present, and biomass (the amount of living matter) on the seafloor.

When the remotely operated vehicle (ROV) arrives back on the ship, biologists converge to gather their samples as quickly as possible. Linda Kuhnz in the "moon pool" where ROV Doc Ricketts is launched and recovered.

One of the ways we compare deep-sea biological communities is to video record long "transects" of the seafloor using high-definition cameras. When we get back to MBARI, these recordings will be reviewed and analyzed in great detail, identifying and counting each and every organism. In addition, we document the behaviors and interactions we observe, the geological features of the habitat that animals live in, and the physical properties of the overlying water. It is always quite exciting to find a deep-sea fish or invertebrate that has never been seen before. Just as we found yesterday, many larger animals live under the sediment and are not necessarily visible on video.

ROV Doc Ricketts collects high-definition video of the seafloor. Paired lasers mounted on the ROV are used as a visual scale to determine the width of the habitat in the field of view. Back at home, the transects are analyzed to measure abundance and species diversity by identifying and counting each organism.

In addition, the sediment itself holds an astounding number of small living organisms. We sample the mud to look for these animals. Our sediment cores hold about as much mud as you would find in a soda can. You'd never know just by looking at that small amount of mud, but there can be hundreds of animals inside. Most of these small organisms can only be seen under our microscopes, and include many different types of crustaceans, worms, clams, snails, and other rarer things. Imagine how many of these small organisms exist given that two-thirds of the earth is covered in deep-sea mud!

Examples of microscopic animals that live in marine sediments. Hundreds of these animals can live in a small quantity of deep-sea mud.

Some of our sediment cores are used to look at even less conspicuous constituents—chemical content and mud grain size, among others. On this day's dive, as on previous days, we collected about 30 cores. Once back on the ship they are taken from the ROV and stored in a walk-in cooler kept at a chilly five degrees Celsius (41 degrees Fahrenheit). In the R/V Western Flyer wet lab, we use open-ended syringes to take centimeter-deep (about 1/2 inch) sub-samples from the mud they contain, like miniature cores within the core. Some sub-samples are saved for later analysis; some are analyzed immediately, as we do for adenosine triphospate (ATP), a rapidly degrading molecule common to living cells, thus a measure of living biomass. ATP is chemically extracted from a small amount of mud and mixed with a luminescent compound obtained from fireflies. A sensitive meter measures the light given off when ATP reacts with firefly extract, the emitted light being proportional to the ATP present.

A few cores are kept cold and enclosed in a nitrogen-flushed glove box which helps maintain the mud's in-situ oxygen characteristics, which would be altered if exposed to air. Inside, slight finger-turns of tiny gears lower electrodes on a micro-manipulator fractions of an inch through the overlying water and into the mud. Temperature, electrical resistance, and oxygen concentration are recorded as the probes are simultaneously stepped down through the mud's upper two inches. The resulting data profile the oxygen available to the sediment community biota and movement of O2 from the water above. The mud's porosity, the O2 concentration in the water at the sediment interface, overlying water flow, and other factors control the sediment depth where the community uses—respires—all of the O2. This balance point is usually only a few millimeters below where water and mud interface. These data provide valuable context and fascinating comparison for the animals we sift from the sediments of the warm, oxygen-rich Salsipuedes Basin and the cold, oxygen-poor Guaymas Basin

—Linda Kuhnz and Chris Lovera

Patrick Whaling prepares the seawater lab so we can keep animals from the benthic respirometer system for study.
Chris Lovera and Kurt Buck analyze CO2-spiked water samples for comparison with water conditions in the benthic respirometer system (BRS).

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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: May. 16, 2012