Linkages between Ocean Acidification and Marine Organisms

Author: Jesus C. Compaire

We have all have heard about how ocean acidification has an important impact on marine ecosystems (if you don’t know what ocean acidification is, our colleague Jon Sharp tells you in his entry about pH onboard GOMECC-3). One of the most known effects is coral bleaching in tropical areas, but this phenomenon does not only affect the sessile organisms (who cannot run looking for better areas for their growth). At different scales, the rest of plants and animals in the ocean can also be affected by ocean acidification since this reduces the calcification in many organisms (Orr et al., 2005). Species affected include planktonic calcifiers (coccolithophores, foraminifera, pteropods), and also other animals like echinoderms, bryozoans, molluscs, crustaceans, fish, and a long etcetera.

coral infographic

But, what exactly does “reduce the calcification” mean, you might ask yourselves, and why is this a negative impact? To try to understand this phenomenon let’s see a few cases in different animals. For example it has been documented that elevated pressure of CO2 (i.e. high concentration of carbon dioxide) reduces the growth of molluscs and sea urchins, which means that compared to normal levels of CO2, the animals that grew in high CO2 conditions had smaller sizes and body weights (Shirayama & Thornton, 2005). In other experiments with crabs, the combination of increased temperature and lower pH reduced the energy for reproduction (Paganini et al., 2014). Now let’s talk about fish, and in particular about the ichthyoplankton (the eggs and larvae of fish found mainly in the upper 200 meters of the water column) of the marine coastal species. The survival of their larvae depends on them being able to find a suitable adult habitat at the end of an offshore dispersive stage that can last weeks or months. The way that they may return to adult habitats is with their ability to detect olfactory cues from these adult places. However, under experimental ocean acidification conditions it has been noted that this ability was disrupted. So if acidification continues unabated, the impairment of the sensory ability may reduce the population sustainability of many marine species, with potentially profound consequences for marine diversity (Munday et al., 2009) and impacts to wide sections of the population whose economies depend on these species.

It is for all these reasons that we are taking zooplankton samples throughout the Gulf of Mexico in this cruise (if you are not sure about what the zooplankton is, please check out this blog entry from July 29th where our colleague Lucio Loman explains this in detail). We aim to study the species composition and their abundances, and their relationships with the physical and chemical characteristics of the water column. The long-term study of the communities composition in the Gulf of Mexico will allow for the monitoring of changes and impacts due to increased sea surface temperature and ocean acidification, which in turn, will help managers to reduce this impact.


– Munday, P. L., Dixson, D. L., Donelson, J. M., Jones, G. P., Pratchett, M. S., Devitsina, G. V., & Døving, K. B. (2009). Ocean acidification impairs olfactory discrimination and homing ability of a marine fish. Proceedings of the National Academy of Sciences, 106(6), 1848-1852.

– Orr, J. C., Fabry, V. J., Aumont, O., Bopp, L., Doney, S. C., Feely, R. A., Gnanadesikan, A., Gruber, N., Ishida, A., Joos, F., et al. (2005). Anthropogenic ocean acidification over the twenty-first century and its impact on calcifying organisms. Nature 437, 681-686.

– Paganini, A. W., Miller, N. A., & Stillman, J. H. (2014). Temperature and acidification variability reduce physiological performance in the intertidal zone porcelain crab Petrolisthes cinctipes. Journal of Experimental Biology, 217(22), 3974-3980.

– Shirayama, Y., & H. Thornton (2005) Effect of increased atmospheric CO2 on shallow water marine benthos. Journal of Geophysical Research, 110, C09S08, doi: 10.1029/2004JC002618.


What is pCO2, and why do we measure it?

An Interview with Denis Pierrot

Interview by: Emma Pontes

I’m pleased to introduce Physical Chemist and Co-Chief Scientist of GOMECC-3, Denis Pierrot. On a normal day, he can be found in the computer lab overseeing CTD operations, but today, he’s kind enough to escort me to the Hydro Lab where the pCO2 Underway System lives. pCO2 is slightly different than regular CO2 concentration; it is the partial pressure of CO2 in a liquid or gas. On the Ron Brown, we have a pCO2 Underway System which Denis proudly tells me is state of the art, and the result of collaboration between several esteemed scientists around the world.

Image 1. Image credit: Emma Pontes.

In Image 1, you can see the conglomerate of wires, equilibrators, and pumps that make up the system. A water line is connected to the system which pumps surface water from outside our ship in a constant flow into the system. The equilibrator (red circle) sprays the incoming water in a thin sheet which allows the air inside to become equilibrated with the water. This means that the pCO2 of the water will equal the pCO2 of the air inside the equilibrator. This equilibrated air is then sent to a gas analyzer (yellow circle) that measures the pCO2. In this manner, the pCO2 of the water is measured indirectly (by measuring equilibrated air pCO2) and graphed neatly on the laptop attached.

Additionally, the pCO2 Underway System has a gas line (green circle) that draws in air from the bow of the ship, ensuring the cleanest air possible with no contamination from ship emissions. This line is connected to the gas analyzer and the incoming air is measured for its pCO2 directly. The goal of this system is to measure the pCO2 of the water AND the atmosphere. The interaction and difference between ocean and air pCO2 is the basis of Denis’ work.

Image 2. Image credit: Emma Pontes.

Image 2 shows a graph of the output from the pCO2 Underway System. The blue and brown dots represent pCO2 of the water, while the purple and green crosses represent pCO2 of the atmosphere (purple line). The goal here is to determine where and when the ocean acts as a source and sink of CO2. The ocean is a source of CO2 when the water pCO2 is higher than that of the atmosphere (above the purple line). Conversely, the ocean is a sink of CO2 when atmospheric pCO2 is higher than that of the water (below the purple line). Since gases always move from high to low concentration in an endless quest for equilibrium, Denis and his colleagues can tell if the ocean is releasing (source) or absorbing (sink) CO2 and at what rate. The rate of this CO2 exchange between ocean and atmosphere is called flux. Denis hopes to create an up to date flux map of the Gulf of Mexico complete with spatial and temporal attributes. Flux is constantly changing both seasonally and temporally, and is dependent on wind, ocean current, temperature, and other atmospheric factors.

One quarter of anthropogenic CO2 is dissolved into the ocean. This has important and unfavorable implications for calcifying organisms such as certain plankton, corals, sea urchins, and any other creature that relies on carbonate to build its shell or skeleton. CO2 is an acidic gas that lowers the pH of water which it is dissolved in. A lower pH means more acidic water, which also means less available carbonate for calcifying critters to utilize in their shell building. A more acidic ocean is one with fewer ecologically important corals (and other carbonate-reliant species) and fewer commercially important seafood items like shellfish. Denis is very passionate about his work, which has ecological and commercial implications under ocean acidification conditions.

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Co-Chief Scientist Denis Pierrot, hard at work in the Hydro Lab. Image credit: Emma Pontes.

Tropical Storm Franklin Reconfigures GOMECC-3 Cruise Track

Author: Leticia Barbero 

Ahoy land dwellers!

Another week gone and a fair number of stations is now under our belt. We completed the US section of our cruise and entered Mexican waters on Wednesday, August 2nd, after taking samples just outside of the Padre Islands National Park as part of our collaboration with the National Parks Service. We are now covering all new land (or rather, ocean) as far as the GOMECC cruises go. We completed the first line in Mexican waters and were halfway through the next one when the first weather reports started coming in talking about a potential cyclone. While we were at first hopeful that the system would dissipate, by Sunday it became clear that the system was not going anywhere and that Tropical Storm Franklin was determined to pay us a visit as we sailed through the Bay of Campeche.

Probability of tropical-storm-force winds as Tropical Storm Franklin goes through the Bay of Campeche. Image credit: National Hurricane Center

We are a welcoming bunch here on the GOMECC-3 cruise, but we draw the line at hurricane-force winds, so we decided to hightail it out of there and head straight for the Yucatan peninsula, initially forfeiting our Campeche line. Franklin is in for a surprise when he finally arrives at the Bay of Campeche only to find that we are not there!

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GOMECC-3 Cruise Track, Post Franklin

After playing with scenarios A, B, C, D, and who’s counting anyway, we came up with a plan that will allow us to get enough coverage of the Bay of Campeche, despite having had to give up our plan to take surface samples all along the coast. See attached map below for our new sampling strategy, which includes a shortened Yucatan line (line 7 on the map) and a new, short line 8. The ship will have to crisscross along the Yucatan platform, but we think we can get it done with no overall loss of time.

Filtering the Gulf of Mexico

Author: Gabrielle Corradino

“Why would you spend 35 days on a boat just to filter seawater?”

This was the most common question (second most common was: “Don’t you get seasick?”) that I received as I explained what I would be doing during the GOMECC trip to my friends and family. The biology component of the GOMECC trip does include lots of filtering of water onto specialty glass fiber filters, but the research does not stop there!

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Preserved copepods from CTD 47. The copepods were isolated and placed into filtered seawater and formalin. This will allow observations to be made about the individual organisms in each sample.

Team Plankton (Mrun and myself) will have filtered over 236,000ml of seawater onto 550 filters to help answer questions on microbial species diversity using both molecular and pigment profiling. While invisible to the naked eye, each of the filters will have tens of thousands of tiny organisms (phytoplankton and protozoa) retained on their surface that represent the base of the food web within the GOM. The filters, which may turn a greenish color, if phytoplankton are present (Fig 1), are frozen on ship and will be brought back to North Carolina State University or University of Louisiana for further analyses.

Each filter will be used to collect a snapshot look at microbial assemblages, the presence/absence of certain taxa (DNA signal) and their activities (RNA signal). In unison, we also use several preservation methods to obtain intact plankton for microscopy analyses (Fig 2) from the CTD, a bucket (Fig 3) or with a plankton net.

This trip is intensive, but with the guidance from our rockstar chief scientists (Leticia and Denis), we will be able to gain unique insight into the microbial biogeography, biodiversity and functionality. We believe this data will serve as an important baseline as we study the impact of ocean acidification on the Gulf of Mexico.

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Whole water surface samples being filtered through a 200µm mesh and into a carboy. This water will be used for filtering and for the on-deck grazing experiments.
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Example DNA filter from a surface water sample. The filter will be frozen and brought back to North Carolina State University to have the DNA extracted for processing.



Author: Leah Chomiak

Meet Jay & Andy – Jandy, as they are collectively known. As the most beautifully orchestrated scientific tag-team out there, these guys are responsible for the heartbeat and blood flow of our scientific endeavor out here on the Gulf: maintaining and running the CTD. The two have worked together for the past 6 years, clearly demonstrated in their friendship and mutual enthusiasm onboard. The two work at NOAA’s AOML laboratory in Miami, FL; Andy in the engineering department, and Jay in the physical oceanography department. The two love being out at sea, seeing the world from a different point of view, but most importantly “escaping Miami traffic”, as Jay puts it.

The two are CTD geniuses, knowing the ins and outs of each sensor, wire, and software program pertaining to data collection. The CTD, which stands for Conductivity, Temperature, and Depth, is the most highly regarded oceanographic instrument used to assess a water column, from the surface to the ocean floor. Lowered by a conductive wire off the starboard side of the ship, this mighty instrument serves the needs of 20 of the 24 scientists on board through means of water samples and profile data. Although the instrument is collectively termed a CTD, the actual CTD probe is merely a small part of the totality of the instrument. Within the steel cylindrical frame lie 24 Niskin bottles for sampling water at different depths, two ADCPs (Acoustic Doppler Current Profiler) for measuring the speed and direction of water currents, a transmissometer for detecting the chlorophyll maximum, and a series of sensors for measuring oxygen, temperature, and depth within the water. Prior to arriving on station, our CTD techs ensure all sensors are clean, functioning, and talking to the main computer. Sensors must be kept moist in between stations when the instrument is onboard the ship, this is done by connecting tubing filled with water to the probes. Before the CTD is deployed the techs remove the tubes and turn the sensors on. On deck, there is one CTD tech and one Survey tech suited up to deploy and successfully recover the instrument. The techs are outfitted with hard hats, steel-toed boots, a life jacket, and a tether to the ship when handling the instrument, to ensure safety as a 3000lb instrument dangles on a wire above their heads. Sitting in the main lab of the ship, the Chief and Co-Chief scientists stand by a series of computer monitors that show the output of the instrument sensors, and as the CTD is lowered through the water column, profiles of temperature, salinity, oxygen, and density appear, giving the scientists a first-hand look at the structure of the water column. The scientists use radios to communicate to the deck techs and wire operator, directing them when to lower and raise the CTD in the water. The scientists at the computer look for interesting features in the profiles shown to them on the screen. Are there any unusual temperature spikes or oxygen minimums?  Based on these features and common features of a water column (thermocline, mixed layer, oxygen minimum zone, chlorophyll maximum) the scientists tell the wire operator where to stop the CTD, and then a signal is sent through the wire to close a Niskin bottle at that depth. As the CTD works its way back up the surface, Niskin bottles are triggered to close at other specified depths. The techs then recover the CTD and bring it back on board safely, the sensors are cleaned and tubes replaced, and a plethora of data is now ready for scientists to use in their analysis. As mentioned in previous blogs, once the CTD is back on board, a sampling frenzy ensues.

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Tag team of the CTD Tech (Andy) and Survey Tech (Josh) safely retrieving the CTD

Jay and Andy make sure the sensors are calibrated by comparing the sensor values to that manually determined through salinity and oxygen analysis, the job I do here on board. Jay and Andy are certainly the silent heroes of scientific data collection here on the Brown, keep up the good work boys!

Multiparameter Inorganic Carbon Analyzer in a Box!

Author: Ellie Hudson-Heck

The GOMECC-3 research cruise is equipped with outstanding scientists who specialize in the carbon cycling system of the oceans. The carbon system acts as the ocean’s buffer. If you think back to your high school chemistry class, a buffer is a chemical entity that controls the pH of a solution. The pH in the ocean is decreasing due to the heightened absorption of anthropogenic CO2, a process known as ocean acidification. This elevated flux of CO2 influences other components of the carbon system as well. Though small, these changes can have profound global impacts. Subtle variations in ocean chemistry demand instrumentation that can capture even the most precise changes.

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Image of MIB in the main lab on the Ron Brown. The back half of MICA is sealed off to prevent water from getting on the electronics. The tubing is used to introduce the reagents for each parameter as described above.

The carbon system is composed of four key parameters: pH, total alkalinity (TA), dissolved inorganic carbon (DIC), and CO2 fugacity. Quantifying the system in its entirety requires measurements of at least two of these parameters. Studying these four parameters collectively allows for a comprehensive understanding of how the carbon system is impacted by CO2 absorption. Wouldn’t it be incredible if all the measurements could each be made simultaneously in something the size of a carry-on-suitcase? The compact Multi-parameter Inorganic Carbon Analyzer (MICA) in a Box (MIB), can do just that!

MIB is a benchtop instrument that uses spectrophotometry to measure TA, DIC, and pH. Spectrophotometry is used to measure how much light a substance absorbs (in this case we are concerned with light in the visible spectrum). The concentration of the substance can be determined if the absorbance is known. MIB continuously pumps seawater through three optical cells, each analyzing a distinct parameter. Prior to the seawater reaching each cell, chemical reagents are introduced to alter its composition.

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MIB on a “road trip” to test out its GPS system. MIB is constantly recording its GPS location which allows the measurements to be mapped out.

The pH is measured spectrophotometrically by adding indicator dye (meta-cresol purple) to the seawater sample. The indicator dye dissociates into acid and base forms determined by the pH of the sample. The absorbance values of the dissociated chemical species are measured and pH is calculated based on these values.

Dissolved inorganic carbon includes aqueous carbon dioxide, bicarbonate, and carbonate. DIC is measured by acidifying the seawater, shifting the buffer towards aqueous carbon dioxide. A liquid core waveguide, permeable to CO2, is placed inside the optical cell. The waveguide allows CO2 from acidified seawater to equilibrate with an indicator dye reference solution. The color of the dye solution will change based on the concentration of CO2 that passes through. This color change is measured by a spectrophotometer and DIC can be calculated from that absorbance value.

The term alkaline describes a solution that is basic (pH > 7). When referring to the ocean, however, total alkalinity has little to do with the ocean being slightly basic (average pH 8.1). You can think of alkalinity as keeping track of the charges of the chemical species in seawater. Alkalinity measures the conjugate bases (negatively charged) that bind with hydrogen ions (positively charged) when a seawater sample is acidified to a pH of 3.5. MIB’s approach to measuring TA starts with the addition of indicator dye (bromo-cresol purple) to the seawater sample. This mixture is equilibrated with CO2 gas that is 30% Absorbance values of the solution are measured, and total alkalinity is calculated using the known mole fraction of gas.

MIB will enable scientists to delve deeper into the dynamic changes of the carbon system. Once on board the Ronald H. Brown, I learned very quickly that conducting oceanographic research requires teamwork. Novel, comprehensive techniques will further research in ocean science and stimulate collaboration between disciplines.

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USF students, Ellie Hudson-Heck and Jon Sharp have been collaborating with scientists at SRI international for the last year to prepare MIB for this cruise. Ellie and Jon study chemical oceanography and are both students in the Byrne lab.

Behind the Scenes

A blog post from the ships point of view

Author: ENS Marisa Gedney, Damage Control Officer, NOAA Ship Ronald H Brown

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ENS. Marisa Gedney at the DP station on the bridge of the Ron Brown, driving the ship. Photo credit Marisa Gedney.

“So what do you do on the boat?” is usually the first question people ask when they meet me aboard the NOAA Ship Ronald H Brown. My typical reply, “Oh, I drive the ship, among other things,” can elicit quite a variety of responses. Sometimes these inquisitive minds, generally those who have never been to sea before, will assume this means I am the captain (nope). More experienced sailors/scientists will recognize me as a Junior Officer. Specifically, I currently serve as the ship’s Damage Control and Safety Officer and spend two 4 hour shifts daily on the bridge (the place where the ship is steered from) doing anything and everything that is required to maintain safe operations of the vessel. This can include simply ensuring that the auto pilot is working properly during transits to driving the ship on station by hand, along with all required radio communications, maintaining a proper safety lookout, and responding to all alarms, just to scratch the surface.

Being a part of GOMECC has been a fascinating experience as the Brown usually specializes in blue water sailing. Meaning, that we typically operate many hundreds of miles from shore and spotting another vessel on occasion serves as an exciting reminder that there is still other life out there sailing the oceans. Working in the Gulf of Mexico has proven to be the exact opposite. Navigating around fishing boats, cargo vessels, and platforms galore has so far served to keep every watchstander on their toes. And being close enough to shore to acquire cell phone signal is generally unheard of, but has been a rare treat this project.

I’m often asked what it’s like to drive the ship, and the honest answer is that it’s rather fun (usually). Despite being the largest ship in the NOAA fleet, the Brown is incredibly maneuverable. Instead of the traditional propeller and rudder system that most ships have, we have two stern thrusters that can independently spin around to face any direction. Among a suite of navigational equipment on the bridge, we also utilize a dynamic positioning system which provides the ability to maintain the ship’s position on station within meter scale of accuracy. So we may not go very fast (10kts is the average cruising speed, for this project we are restricted to 7.5kts), but we can do just about anything.

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Small boat operations as part of the GOMECC-3 cruise. Photo credit Marisa Gedney.

And there isn’t as much to stopping the ship on station for a CTD deployment as people tend to think. First it just requires monitoring the ETA in order to give appropriate preparation calls to different departments. Then the biggest challenge is studying the wind and current to decide on a heading for the station. Maneuvering slightly to give yourself the best chance of stopping right on waypoint based on the weather conditions, the speed of the ship, and how big of a turn has to be made to come around to the chosen heading. Picking the correct moment to start slowing down. Maintaining control of the vessel while switching steering modes. Adjusting the rate of deceleration and turning to keep everything stable. Stopping, hopefully right on the mark. Making last minute adjustments. A final analysis to ensure that the ship is holding position as desired and that the sea state is safe for deployment. And ultimately, a call down to those standing by on deck that the ship is on station and deployment may begin. Ok, so maybe there actually is a bit of effort involved. But every station approach is different and thus each requires a high level of attention. Even after hundreds of stations it never becomes easy, but rather less difficult and hopefully more efficient.

There are a number of unique aspects that go along with working and living on a research vessel (When asked, “Where are you from?” the answer is “Seattle.” When asked “Where do you live?” the truthful answer is “This ship.”). Certainly more than can be listed here in a single blog post. It requires a certain degree of flexibility and a willingness to give up one’s love of sleep. Some nights I’ll be playing board games and bingo with the ship’s crew and the next morning I become everyone’s least favorite person as I announce the start of weekly drills and start yelling at people to report to their muster stations. But when you’re stuck within the confines of a 274ft long hunk of floating steel for a month, it becomes inevitable for all the crew and scientists aboard to begin working together in a rhythm and figuring out the best ways to support each other. Everyone goes from being colleagues to shipmates and it becomes that, more than anything else, which contributes to the successful completion of a project. It has been a pleasure working with the scientists of the GOMECC project so far, and I look forward to future adventures with them during our remaining weeks in the Gulf of Mexico.

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The Ronald H. Brown docked at the US Naval Base in Key West, FL prior to departure for GOMECC-3. Photo credit Marisa Gedney.