Monterey Bay Aquarium Research Institute

California Current Logbook
Day 5: A hard day’s night
February 8, 2012

First, I should say that the Day 1, Day 2, Day 3, structure of this logbook format might be a little too rigid for how time flows out here. A “day” at sea on a research cruise is not quite as formal as a period of daylight followed by a period of darkness. Days begin when you wake, and end when you can find a long enough block of time without anything to do that you can sleep. The boat steams continuously and you work whenever you reach the next sampling station.

Case in point, last night’s CTD casts that were scheduled for midnight didn’t end up making it back up onto the deck laden with water from the depths until after 2:00 a.m. The previous night was a late one as well, so the banter around the rosette as we filled our bottles was a little befuddled. I commented on the clarity of the water streaming from the Niskin bottles, noting, not completely disingenuously, that it looked “delicious,” resulting in Tim Pennington joking that this might be my only opportunity to taste 700-meter-deep water. At 3:00 a.m. the “day” finally came to a close as the clouds wrung the last of the rain from their desiccated billows.

Twenty-three CTD casts worth of salt water have left their briney mark on Jason Smith’s boots.

The next morning, we—those who slept—awoke to the weather we’d been looking forward to: blue skies and a shiny, glassy sea. As if the weather alone weren’t triumphant enough, there were dolphins playing in the waves of the Western Flyer’s bow. I rushed to get the camera, but apparently we’d found the one shy pod of dolphins in the entire Pacific, and they were gone.

Sorry, no dolphins. How about an island?

The ocean is, as Francisco Chavez puts it, like a giant plant; it takes in carbon dioxide (CO2) from the atmosphere and produces oxygen for the atmosphere and surface seas. Like a plant, the ocean also operates as an enormous carbon reservoir—the microscopic organisms on the ocean’s surface take in carbon dioxide gas (inorganic carbon), convert it into organic carbon as it becomes part of their physical structure, and then, when these organisms die or get consumed and excreted, that carbon drifts down to the depths below.

There are a couple more key steps to this “biological pump” mechanism. One is that as the organic material from the surface sinks down into the abyss, it is decaying; this decaying process consumes oxygen. And when most or all of the oxygen in the seawater is consumed, that’s how these oxygen minimum zones I mentioned in yesterday’s log develop. In areas where you have lots of productivity on the sea surface–stable areas where there are lots of nutrients being stirred up from the depths—when that surface life dies, or otherwise begins its final journey into the deep, then all that organic material decaying as it sinks consumes a lot of oxygen, more than can be replenished.

The other thing going on here, and by “other” I mean “crucial,” is that over time, this cycle has created an equilibrium between the sea and the air; and our atmosphere—the one we know and love, the one with just the right mix of oxygen, nitrogen, CO2, etc. that makes our lives possible (and downright pleasant, all things considered)—is a result of this balance. Now, however, in addition to the normal exchange of nutrients between the sea and air, rising CO2 levels in the atmosphere have resulted in the ocean absorbing an additional two billion tons of CO2 annually.

The potential problem here is that as the level of CO2 in the ocean increases—making the ocean more “acidic”—then the ocean’s absorptive capacity diminishes—it’s no longer able to absorb as much CO2 from the atmosphere, which means that the CO2 stays in the atmosphere, which means that the planet warms up.

Tim Pennington has a look at the zooplankton Haibin Zhang pulled in on his last plankton tow.

Some of the seawater samples we are taking on this research cruise will be analyzed so that we can see how much carbon is in this part of the ocean. Our collaborator from Spain, Carmen Castro, is measuring the total organic carbon (TOC) content of the water; while Gernot Friederich analyzes the water for its dissolved inorganic carbon (DIC) content—how much CO2 and other forms of dissolved CO2 such as carbonic acid—are in the water. Gernot is able to make his measurements on the boat with a machine that he built just for this purpose. Carmen, however, will take her samples back to Spain before analyzing them, which is why she gets to play with a torch!

Carmen Castro seals her seawater samples in glass ampules. She’ll take them back to her lab in Spain to analyze them for their organic carbon content.

—Dana Lacono


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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.

CTD Rosette

The CTD measures conductivity (which helps determine salinity), temperature, and depth. This particular CTD runs profiles of the water column (surface to bottom) and along the way, collects discrete water samples (at specific predetermined depths) using the rosette of niskin bottles. Each bottle can collect a water sample. The transmissometer measures the number of particles in the water and the oxygen sensors tell us how much dissolved oxygen is present. Both of these instruments go onto the CTD rosette and give us a profile of the water column.

Optical Profiler (PRR)

The optical profiler is equipped with an hyperspectral radiometer which measures downwelling irradiance and upwelling radiance, a CTD, and two AC9's which measure absorption and beam attenuation over nine wavelengths (1 uses filtered seawater while the other uses raw seawater). It also measures backscatter at six wavelengths and fluorescence at two wavelengths.

Fast Repetition Rate Fluorometer

This unique instrument measures the photosynthetic properties of phytoplankton continuously while the ship is in motion. This greatly increases the amount of data as well as the area that can be surveyed.

Underway CTD

An underway CTD is used to map several physical parameters of the ocean's surface. As the ship travels, this instrument takes one sample every 20 seconds. The data recorded includes the ship's location, the ocean's salinity, temperature, and water clarity, and the amount of fluorescence produced by phytoplankton. By continually taking measurements, a line of values along the ship's course is created, illustrating when the ship crosses from one water type to another. The underway CTD is an important complement to the CTD rosette; because each CTD rosette deployment is miles away from the last, the data from the underway CTD measurements help to will indicate whether the rosette CTD sampling spot is representative of the area.

Underway pCO2

Like the underway CTD, the underway pCO2 continually measures the partial pressure of CO2 in the ocean along the course of the Western Flyer. "Partial pressure" is a way in which to measure the amount of CO2 in the seawater. Increasing levels of CO2 in the ocean increase the water's acidity.


R/V Western Flyer

Ian Young


George Gunther
Relief Captain, Legs 1 & 2


Matt Noyes
Chief Engineer


Andrew McKee
First Mate, Legs 1 & 2


Shaun Summer
Relief First Engineer


Paul Ban
Second Mate, Legs 1 & 2


Olin Jordan


Craig Heihn
Relief Deckhand


Jason Jordan
Relief Deckhand


Dan Chamberlain
Electronics Officer


Patrick Mitts


 Research Team

Francisco Chavez
Chief Scientist

Francisco Chavez has been managing an ocean observing program at MBARI for more than two decades, gathering a time-series of ocean parameters that have provided insight to how the ocean responds to large-scale climate variability. His work focuses on interpreting observations made locally in terms of processes that are happening globally, and he has performed comparative studies in other ocean basins.

Tim Pennington
Research Specialist

Tim works in MBARI's Biological Oceanography Group running their local shipboard programs, all of which are directed at understanding interplay between the physics, chemistry, and biology in the ocean off California. Their Monterey Bay Time Series (MBTS) cruises have been conducted in and offshore of Monterey Bay every two to three weeks since 1989. The Studies of Ecological and Chemical Responses to Environmental Trends (SECRET) cruise series extended the MBTS work 320 kilometers offshore into the California Current along CalCOFI Line 67, with more than 39 quarterly cruises since 1997. This cruise work and complimentary mooring, satellite, ROV, AUV and modelling data have enabled the development of a rich view of the biogeochemical dynamics of the coastal ocean on several spatial (Monterey Bay, upwelling system, California Current) and temporal (weather event, seasonal, interannual, even decadal) scales.

Gernot Friederich
Research Specialist

Gernot has been involved in the study of nutrient and carbon fluxes in highly productive regions of the oceans. Most of this work has been conducted in coastal upwelling regions, and he has participated in some high latitude studies. He is also interested in the chemical transformations that occur at the boundaries of oxygenated and sub-oxic or anoxic waters. To aid the study of these highly variable oceanic systems, he has developed and automated chemical methods and water sampling equipment. He has recently worked on the design and implementation of autonomous shipboard seasurface chemistry mapping systems and buoy mounted instrumentation for the measurement of the partial pressure of carbon dioxide.

Erich Rienecker
Instrumentation/Marine Operations Technician

An alum of the Biological Ocean Group, Erich now is the instrumentation technician at MBARI and will be responsible for the operation and maintenance of the scientific sampling equipment used on this cruise.

Marguerite Blum

Marguerite Blum is a collaborator from University of California, Santa Cruz. She is assisting Gernot Friederich and Tim Pennington with biogeochemical samples to search for differences in the pCO2, DIC, alkalinity, and macronutrients from the previous Gulf of California cruise. This will be her 41st cruise with the Chavez group.

Dana Lacono
Administrative Assistant

Dana works in the Information and Technology Dissemination (ITD) group at MBARI where he performs administrative duties and creates web pages such as the one you are looking at now. On this cruise he will be assisting the science team as needed and writing the cruise logs. This is his first research expedition, and he is as excited as can be.

A.J. Limardo
Research Assistant

A.J. Limardo received a B.S. in Biology from the University of Georgia, and is currently applying to the University of California, Santa Cruz Ocean Sciences Department to pursue a Ph.D. In the Worden Laboratory at MBARI, A.J. is currently exploring phytoplankton ecology and phylogenetics. During this cruise, he will be investigating the distribution and abundance of Bathycoccus, a genus of pico-eukaryotic algae.

Monique Messié
Postdoctoral Fellow

Monique works on phytoplankton and its links with physics and higher trophic levels, using a combination of satellite data, model outputs and in situ datasets. During the cruise she will be helping with the collection and analysis of water samples, including nutrients and oxygen measurements.

Chris Wahl
Research Technician

Chris works in the Chavez lab on moorings, gliders, and instrumentation for various projects and was recruited by MBARI's Marine Operations division to help operate the CTD for the first leg of this expedition. He received a B.S. in Mechanical Engineering from University of California, Berkeley and later a M.S. in Engineering Science from University of California, San Diego.

Haibin Zhang
Postdoctoral Fellow

Haibin works in the molecular ecology group at MBARI. He received his Ph.D. in marine biology from the Chinese Academy of Sciences, Institute of Oceanology. Haibin's research interests include ecology, evolution, and genetic conservation of marine invertebrates. He uses molecular tools to examine gene flow of natural populations in order to understand the effect of environment factors (light, pressure, oxygen, salinity, and temperature) on population diversity and genetic structure.

Carmen Castro
Higher Council for Scientific Investigations, Spain

Carmen is a chemical oceanographer from Instituto de Investigaciones Marinas from Vigo,Spain. She studies the environmental control of nutrients and carbon in the upwelling regions of NW Iberian Peninsula and California. In this cruise, she will be collecting water samples for analysing the alongshore distribution of total organic carbon.

Curt Collins
Naval Postgraduate School

Curt Collins is a sea-going descriptive physical oceanographer. Convinced by Nan Bray (now Australia's Chief of Marine Research) to make some measurements of the deep flows at the entrance to the Gulf of California in the early 1990s, Curt has since collaborated a number of times with Mexican colleagues including a Fulbright fellowship at Universidad Autónoma de Baja California in Ensenada in 1994/5. Curt is looking forward to helping to collect and analyze the CTD data during this cruise. In addition, he will conduct laboratory analyses of seawater conductivity to assure the accuracy of the team's salinity observations.

Martín Hernández Ayón
Universidad Autónoma de Baja California

Martín Hernández-Ayón is a chemical oceanographer. His research is focused on the inorganic carbon system, ocean acidification and biogeochemistry in the coastal regions of Baja California, the Sea of Cortez, the subtropical region where the oxygen minimum zone is located and, more recently, the Gulf of Mexico.

Gabriela Y. Cervantes
Graduate Student
Universidad Autónoma de Baja California

Gaby is a graduate student in the coastal oceanography program at the University of Baja California in Ensenada, Mexico. She is doing her graduate studies on the dynamics of CO2 in seawater from a coastal monitoring site known as Ensenada Station.

Jason Smith
Graduate Student
Stanford University

Jason is a fifth-year Ph.D. student at Stanford University. His work focuses on how upwelling and other factors alter the distribution and activity of the microorganisms responsible for nitrification. On this cruise Jason's work will focus on ammonium dynamics; specifically, determining the magnitude of ammonia incorporation and oxidation in the photic zone and how it alters estimates of new and regenerated production.

Last updated: Feb. 27, 2012