Monterey Bay Aquarium Research Institute

California Current Logbook
Day 3: How’s the water?
February 6, 2012

By nine o’clock last night both CTD rosettes were back on deck, Francisco Chavez and Haibin Zhang had finished their plankton tow, and our captain, George Gunther, set the Western Flyer’s course for an overnight steam to today’s station, “UC4.” UC4 is situated in the Outer Santa Barbara Passage, between two of the Channel Islands— Santa Catalina on the west, and San Clemente on the east.

Now, I know that I told you yesterday there might be some preliminary results for you to see regarding the present oxygen levels in the California Undercurrent in comparison to 2003. And they’re in. But before I give them to you, I’m going to take advantage of your rapt attention to explain a couple of things.

Top left: Santa Catalina off the port bow. Bottom left: And San Clemente off the starboard. Right: Nautical chart showing the Outer Santa Barbara Passage through the Channel Islands. The right point of the compass indicates the location of today’s sampling station.

The first is where the data you’re about to see come from. I’ll give you a hint: it starts with a “C” and ends with a “D” (and there’s a “T” in the middle). Mounted on the CTD—sorry, I guess I gave it away—is an oxygen sensor. This sensor is continuously taking readings (several per second) of the oxygen level in the water as the CTD travels down from the sea surface and then back up through the water column. These readings are being sent back up a thin wire nested inside the heavy-duty cable pulling the CTD up from the depths. Finally, an onboard computer decodes and records the data.

Once the oxygen-level data have been recorded, they can be processed and then compared to past data; for example, the oxygen levels from the 2003 expedition. Which I’m about to show you—I just need to tell you about one more thing first.

If you read yesterday’s blog, you probably noticed the word “meticulous” came up more than once. Yes, I did forget to bring a thesaurus, but let’s not let that diminish the importance of that attitude. And you can bet that because oxygen-levels are at the center of the research being conducted here, they’re the subject of quite a bit of meticulous attention.

In addition to the measurements made by the sensor on the CTD, after the rosette is hoisted back onto the well deck, the first samples that are taken will be analyzed for their dissolved oxygen content. It’s important that the oxygen samples are drawn from the Niskin bottles first. The deep water is “hypoxic”—very, very low in oxygen. When that water reaches the surface and is exposed to the air, which has a much higher concentration of oxygen, the oxygen in the air makes a bee-line for the water, where it’s in a much lower concentration. If too much atmospheric oxygen makes it into the seawater, the sample is no longer an accurate representation of the seawater at depth.

A.J. Limardo, a research assistant in Alex Worden’s Molecular Microbial Ecology lab, collects water samples from the CTD. A.J. is filtering the water to extract DNA from Bathycoccus—a type of phytoplankton.

Once the water is drawn from the Niskin bottles, reagents are added to measure the oxygen content in the flasks, and the flasks are then brought to Gernot Friederich, who will analyze them on the machine he built for this purpose. Later on, Gernot’s measurements will be used to verify and calibrate these data the CTD sensor returned.

Gernot Friederich built this machine automating the analysis of dissolved oxygen levels in water.

And now, since you’ve all been such patient readers—and because you now understand what lengths everyone here has gone to in order to get these data, you’ll appreciate it that much more—without further ado… here are the results of our cast at station UC2 about 80 kilometers (50 miles) due west of Pismo Beach …

Line graph showing the oxygen content at Station UC2 of samples taken in 2003 against the samples taken yesterday. The 2012 levels are significantly lower. Admit it, you never thought a data plot could be so exciting!

Tomorrow, our first cast in Mexican waters, and what the graph above says about our planet…

—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