2015 Research Highlights
Yuxin (left) slabs a core into small chunks with lab partner Henry Abrams. They later washed, filtered and dried the sediment for foraminifera picking. (Tom Kleindinst, WHOI)
Tracing Carbon Isotopes
Yuxin Zhou, University of Southern California
This summer I had the privilege of working with Dr. Delia Oppo from the Geology & Geophysics department and Dr. Jake Gebbie from the Physical Oceanography department. Under their advisement, I worked on a project to characterize the oceanic d13C Suess Effect in the deep North Atlantic water. The Suess Effect is the decrease of carbon 13 relative to carbon 12 in the atmosphere due to the burning of fossil fuels. Carbon has several isotopes. Carbon 12 is the most common one. There's also the heavier carbon 13. Plants prefer the lighter carbon 12. Fossil fuels such as oil and coal come from ancient plant. As we burn fossil fuels, we send less carbon 13 and more carbon 12 to the atmosphere. The decrease of carbon 13 relative to carbon 12 in the atmosphere is called the Suess Effect.
To detect the presence of the Suess Effect in the deep North Atlantic water, I worked with sediment cores collected from south of Iceland. I spend much time picking the shell of foraminifera, the microscopic organism that lives in the ocean and has the ability to record d13C in the ambient water. The picking requires patience and carefulness, as the dried sediment is just like ash and can be easily spilled or blown away. Whenever I felt like sneezing, I became very nervous because a sneeze would definitely blow away a whole tray of the valuable sediment. The actual picking was done under a microscope with a paint brush dipped in de-ionized water. At first, I had difficulty keep my hand steady because any small movement would be amplified under the microscope. It became easier after some practice.
Working across departments has been a unique and positive experience for me. It broadened the vision of my project but kept the project focused and efficient at the same time. The measurements I made on the foraminifera have a certain temporal resolution. Knowing that resolution helped keep my tracer simulation’s resolution at a certain degree and avoid wasting unnecessary computation time. The tracer simulation, on the other hand, predicted the general appearance time of the Suess Effect, so I could focus my measurement on a certain proportion of the cores. In this case, doing more actually enabled me to do less.
Apart from the research project, I greatly enjoyed life in Woods Hole. I especially loved the sailing classes in the Woods Hole Yacht Club. Sailing makes me more aware of things that I normally wouldn’t notice on land – the direction of the wind, how the waves are moving. The tutors there not only teach the techniques but also the related cultural knowledge, and it is a unique experience that Woods Hole has to offer.
I am deeply grateful for this wonderful fellowship opportunity and hope that one day I can go back to WHOI.
Sasha exhibits a poster on her summer research at the Biology Department summer student research symposium. (Kama Thieler, WHOI)
Investigating Phytoplankton from Space
Sasha Kramer, Bowdoin College
Most people don’t spend a lot of time thinking about microscopic phytoplankton, even though these photosynthetic organisms produce much of the oxygen that we breathe. They also form the base of the oceanic food web and are responsible for half of the drawdown of atmospheric carbon! This summer as a Summer Student Fellow in Dr. Heidi Sosik’s lab, I spent a lot of time thinking about and characterizing communities of phytoplankton in the waters around Woods Hole.
The goal of my project was to determine a more accurate estimate of phytoplankton sizes and types at the Martha’s Vineyard Coastal Observatory (MVCO) using images of the color of the ocean surface. The ocean is a huge place, and human sampling can only collect so much information about the sea. In order to make accurate estimates of oceanographic processes, we need to be able to measure qualities of the surface ocean on broad spatial and temporal scales. Fortunately, satellite remote sensing of ocean color allows for large-scale assessments of phytoplankton biomass. Recently, several papers have offered methods for determining the size of phytoplankton cells from satellite images using a measurement of remote sensing reflectance, the fraction of incident sunlight that upwells from the near surface ocean; this is also known as ocean color reflectance. These approaches can be used to understand the dominant type of cells living in the water based on the differences in optical properties depending on the size and/or shape of the phytoplankton species.
This summer, I specifically worked with a bio-optical model published by Sathyendranath et al. (2004). This algorithm was developed for use in the open waters of the Northwest Atlantic Ocean, so I began an examination of the region around the Martha’s Vineyard Coastal Observatory (MVCO), which is adjacent to the region for which the model was developed, but it more coastal and thought be more optically complex.
It is important to make use of in-water measurements to test the theoretical results of an algorithm based on satellite data. Heidi is the chief scientist at MVCO, and has overseen the development of a multi-year time series of multiple data sources—so I was lucky enough to have a rich biological and optical dataset at my disposal, just waiting to be tested. As I investigated the success of the algorithm at MVCO, it became clear that the optical properties of those waters are quite different than the conditions prescribed by the model. So using the in-water measurements taken at MVCO, I began work on the process of rebuilding the reflectance term using parameterizations of the inherent optical properties (IOPs) of the water. While the model was initially a poor predictor of species dominance at MVCO, a thorough analysis over the course of the summer of each modeled component moved the algorithm curves closer to our observations at MVCO.
Fortunately, my project didn’t have to end when I left WHOI in August: now that I am back at school, I am continuing work on my summer project as a senior Honors thesis with Heidi and with my advisor at Bowdoin, Dr. Collin Roesler. I think this project is important because phytoplankton have a powerful impact on broader ecosystem function through processes such as photosynthesis, but rates of primary production and carbon drawdown are highly dependent upon both the size of the cells and the species composition. If we have an increasingly accurate understanding of phytoplankton species distribution, we could make more precise estimates of biogeochemical fluctuations and carbon export to the deep ocean—and determining these characteristics from satellite remote sensing allows us to make these estimates from space, which is pretty amazing to consider.
Claudia (right) samples at an oyster aquaculture site in West Falmouth Harbor. (Tom Kleindinst, WHOI)
Microbial Processes under Oyster Aquaculture
Claudia Mazur, Mount Holyoke College
Before I came to Woods Hole as a Summer Student Fellow, my previous research focused on paleontology and the earliest life on earth. As I continued my studies, I wanted to gain a better understanding of the interaction of organisms with their environments. This led me to an interest in microbial life and how it influences and interacts with Earth’s anoxic environments. Associate Scientist, Virginia Edgcomb gave me the opportunity to substitute a chisel and a hand lens for a pipette and a lab coat. Working in the Edgcomb Lab I gained valuable skills in microbiology and chemistry, which will be necessary in conducting my future research.
Coastal waters around Cape Cod are being damaged by high inputs nitrogen. Excess nitrogen is detrimental to the environment because it causes harmful algal blooms, which result in hypoxia, anoxia and eutrophication. Not only does additional nitrogen ruin the health of the waterway, it also has an economic impact. Cape Cod residents can be expected to pay $5 billion for wastewater treatment projects to address these problems. In an effort to reduce this cost, less expensive alternatives, such as, nutrient bio-extractions with shellfish are being considered.
Oysters modify biogeochemical cycles by filtering large quantities of organic matter from the water column and converting it to biomass. The phytoplankton that are not consumed are excreted as feces and pseudofeces, which are deposited on the sediment surface. This layer on top of the sediment creates an anoxic environment, which impacts the microbial processes with the potential of enhancing denitrification and anammox processes. The purpose of my project was to examine microbial processes that occur in sediments under oyster aquaculture cages in local ponds and estuaries, and to measure the rates of key processes associated with nitrogen removal. This project involved incubation studies with stable isotopes to measured rates of key processes, and quantitative PCR of genes specifically associated with annamox and denitrification. The ultimate goal of my research is to provide data to improve models of the nitrogen removal potential of shellfish aquaculture as a possible remediation strategy for improving the quality of these coastal waters. Not only did I get to work in a lab, I also participated in field work.
A typical day as a Summer Student Fellow began with a beautiful bike ride along the Shining Sea Bikeway. Once I got into the lab, I immediately began repeating the previous day’s quantitative PCR experiments, extracting pond water from incubation bottles and analyzing it for nutrients. As a geology student, my previous experiences with these microbiology and chemistry techniques were very minimal. Luckily, with the help of my mentor and the members of the lab, I was able to learn quickly and carry out my work with confidence.
When I wasn’t working in the lab, I went out into the field with to collect samples for my project. We collected sediment cores from various oyster aquaculture sites on Cape Cod, such as Little Pond, West Falmouth and Wellfleet. When all of our cores were collected, we carefully transported them back to the lab for processing. These days were usually the longest, but they were also the most fun.
While our research projects took up most of our days, there was still plenty of time to explore the beautiful Cape Cod area. Students gathered together to eat dinners on the beach, watch sunsets at The Knob, swim in the ocean, and sit around bonfires. On Friday nights I always enjoyed attending the Marine Biological Laboratory’s Summer Lecture Series and hearing about the various scientific research being conducted in the area. Overall, my time at WHOI was intellectually stimulating and rewarding. Being surrounded by scientists and students with a passion for studying the ocean made for an enriching experience. My time as an SSF encouraged me to work hard and continues to inspire me to study coastal and ocean sciences.
Using AUVs to Measure Gravity on the Seafloor
Jerry Fontus, Georgia Institute of Technology
One typical question that I received as I prepared for the start of my summer research at WHOI was the following, "What type of research can an electrical engineering major without any prior research experience in the ocean sciences conduct at a world-renown oceanographic research institution?" My opportunity to work in Dr. James Kinsey's lab, whose research is targeted at the intersection of robotics and the earth sciences which involves researching and developing new methods for investigating the Earth's oceans with robotic technologies, helped to show how ocean scientists from different academic research backgrounds are working together to improve our overall understanding of the ocean and how it interacts with other parts of the planet.
The focus of my summer research was to evaluate the ability of the thermal regulator for one of his thermally regulated autonomous underwater vehicle (AUV) gravimeters to regulate its own internal temperature. During an engineering test run in 2011, it was discovered that fluctuations in the ambient temperature of the AUV gravimeter forces changes in the device's internal temperature. These changes in the internal temperature hinder the AUV gravimeter's ability to measure the changes in gravity on the seafloor at a resolution of one part-per-million (which is about 10-6 of the earth's overall gravitational field). Given this information, my task was to conduct a series of test to understand the extent to which the ambient temperature of the AUV gravimeter affects the internal temperature of the device. In order to do this, I needed to locate all the areas on this device that were sensitive to fluctuations in the ambient temperature. Once these areas were located, I was responsible for designing and testing solutions for adding thermal insulation to minimize the detrimental effects of this ambient temperature to the device's internal temperature.
Why do we care about changes in gravity on the seafloor? Well, the measurement of gravity on the seafloor reveals valuable information regarding its density and its porosity. These measurements provide scientist with information regarding the seafloor structure without having to obtain physical samples. When gravity measurements are combined with other type of measurements, scientists are able to gain some insight into the structure of the seafloor and the processes that occur in this area. Currently, there are two methods of obtaining gravity measurements of the ocean: satellite gravimetry and surface vessel gravimetry. While these two methods are able to measure changes of gravity which provide insight to many of the processes that occur in the ocean, these two methods are limited by the magnitude of the gravity signal they are able to detect since the magnitude of a gravity signal decreases as the distance between the seafloor and the gravimeter (a device that measures gravity) increases. During the past couple of years, research has been done to create a new class of gravimeters (which are compact and have low power consumption) that can be mounted on an AUV. The ability to mount a gravimeter on an AUV allows these sensors to get closer to the seafloor which gives these devices the ability to detect these small changes in gravity that are unable to be detected by satellite and surface vessel gravimetry.
During my 11 weeks of research in the Deep Submergence Laboratory, a total of 21 experiments consisting of 9 different laboratory setups were conducted to evaluate the thermal regulator's ability to maintain a constant commanded temperature for the AUV gravimeter while protecting the device's internal temperature from fluctuations in the ambient temperature. There were a total of six thermistors that were used to monitor the temperature at various locations on the gravimeter. These six temperature sensors were also used as a basis to create the 9 different laboratory setups which were refined based on the knowledge obtained from the preceding experiments with the goal of minimizing the effect of the ambient temperature on the device's internal temperature. Near the end of my research, we were able generate a list containing some of the weaknesses in the design of the current prototype of the thermally regulated AUV gravimeter which hindered the device from negating the effects of the ambient temperature. The findings in these experiments will help to influence the design changes that will be made to the next prototype of the thermal regulated AUV gravimeter whose goal is to measure gravity at a resolution of one part-per-million.
In addition to developing my research skills under the supervision of Dr. Kinsey, I had the opportunity to take advantage of the resources that one is exposed to when spending a summer at WHOI. My first official day as a WHOI SSF started with Dr. Kinsey, giving me the privilege to board the R/V Atlantis in order to give me an in-depth tour of the ALVIN. I also had the opportunity to meet some of the WHOI engineers in the Oceanographic Systems Laboratory who designed the REMUS SharkCam which is featured on the Discovery Channel's Shark Week website. Not only did I have the opportunity to meet accomplished WHOI engineers and scientists, but I was able to interact with other students (from the WHOI SSF, Woods Hole PEP, and the MBL Summer program) who had other incredible research opportunities in the ocean sciences prior to arriving to Woods Hole. Overall, I can say that my summer at WHOI was an experience of a lifetime that I will never forget!
Structure and Circulation of the Chukchi Sea
Astrid Pacini, Yale University
This past summer I had the opportunity to work with Dr. Bob Pickart in a Physical Oceanography research project. Its goal was to examine the structure and circulation of the Chukchi Sea in late spring. The Chukchi Sea, located North of the Bering Strait, is an extremely important pathway for the flow of Pacific waters northward onto the shelf and, eventually, off the shelf break and into the Arctic Ocean. In 2011, massive phytoplankton blooms were discovered growing underneath the sea ice. It became important to understand the conditions that have made, and continue to make, these blooms possible.
The shelf exhibited high quantities of winter water— a water mass with a temperature close to freezing and with a high nutrient content. Vertical sections of the water column demonstrated that the shelf can be characterized as a two-layer system during this time of year, with weakly stratified surface mixed layers above well mixed bottom layers. The height of the bottom boundary layers varied according to bottom slope and according to upwelling versus downwelling conditions, all consistent with previous theories. The density jump separating the surface and bottom mixed layers was generally very weak, prompting an investigation into how quickly the water column would overturn due to re-freezing in a lead or small polynya, prevalent throughout the study region. Using a polynya model that calculates a negative freshwater flux due to brine rejection during ice formation, and a one-dimensional mixed layer model that analyzes how forcings affect mixed layers, overturn time was computed for each station. The results from this investigation reveal that during this time of year, the Chukchi Sea is poised for overturning and thus for stirring nutrients from the sediments into the water column, which in turn would promote phytoplankton growth throughout the shelf.
In addition to working on this fascinating research project, the Summer Student Fellowship at WHOI offered us many amazing resources. Every week we listened to scientists from all WHOI departments talk about their different research projects, and we had the opportunity to participate in a one day research cruise on the RV Tioga where we learned the techniques of sampling at sea. Very special additions to the experience of this past summer at WHOI were meeting and spending time with other Summer Student Fellows and Guest Students, going for long runs along the Shining Sea Bikeway, and spending time in the PO fishbowl.After the twelve weeks at Woods Hole, my mentor gave me the incredible opportunity to participate in a research cruise around Iceland. Onboard, I worked as an ADCP (Acoustic Doppler Current Profiler) watchstander and learned about other oceanographic measurements. During the two week cruise we launched gliders, recovered and deployed moorings, performed CTD casts, and ate very large quantities of fish. I want to thank WHOI Summer Student Fellowship and my mentor, Dr. Bob Pickart, for the most incredible summer in research I could ever have hoped for.
Salt Marsh Biogeochemistry: Changes during Restoration
Maggie Capooci, University of Scranton
Did you know that tidal salt marshes perform a multitude of functions in coastal ecosystems? They provide erosion control, house juvenile fish, and play a role in carbon sequestration. Despite the services they provide, tidal salt marshes are vulnerable to human activities such as urban and agricultural development. In the process of development, some tidal salt marshes get diked or dammed which results in the loss of tidal excursion to the salt marsh on the landward side of the dike or dam. Over time, that side of the marsh turns into a freshwater marsh due to the lack of saltwater intrusion.
Recently, there has been a push to restore marshes that have been affected by diking and damming. The restoration process involves placing a culvert where the restriction was in order to reintroduce tidal excursion to the marsh. Once the salt water enters the freshwater marsh, freshwater plants begin to die off and the salt-tolerant plants colonize the marsh. The microbial community changes from methanogens to sulfur-reducers. There are additional changes that occur in sediment deposition and porewater chemistry.
This summer I worked with Dr. Amanda Spivak to investigate the biogeochemical changes that occur after restoration. There are two main questions regarding marsh restoration: “How long does it take?” and “Do marshes regain the biogeochemical characteristics they had prior to being impacted?” Our study addresses these questions by utilizing a chronosequence approach. We have field sites that have been restored between 0-14 years ago, natural marshes, and non-restored marshes. The variety of sites will allow us to see how the biogeochemistry changes in a restored marsh over a period of 14 years, with the non-restored and natural marshes serving as beginning and ending points, respectively.
A typical field sampling day could begin anywhere between 4:00 am and 10:00 am. At each site, we set up plots on both the natural and restored side of the marsh. In each of these plots, we evaluated plant community composition and collected aboveground biomass, a geochemical core, and a bulk density core. Collecting a core was probably the hardest, yet most rewarding aspect of the fieldwork. After hammering a PVC tube 30-cm into the ground (and hoping that there was not a difficult root to go through in my path), I had to carefully extract the core from the ground using a shovel and some upper arm strength. I always ended up muddy, but happy that the core remained intact through the process.
In lab, I helped out with processing the samples that we collected in the field. I filtered and aliquoted surface water into vials for various chemical analyses. I also helped process the geochemical cores. These lab days were often the longest and the hardest. The cores had to be placed in an anaerobic hood, sectioned, and spun in a centrifuge in order to collect water from the sections. Then the porewater was filtered and aliquoted into vials. It took me a long time to adjust to the glove box! My other responsibilities in lab included: running DIC samples in a coulometer, properly washing glassware, and labelling vials – lots of vials!
Even though my summer at WHOI ended, I am fortunate enough to continue working on my summer project for my Honors thesis. I will be analyzing some of the data I helped collect during the summer, in addition to contacting conservation agents to inquire about the history of the salt marshes I studied this summer. This information will allow me to better understand the processes that occurred prior to, during, and after restoration.
Additionally, this experience at WHOI has enabled me participate in the process of conducting research, from planning and data collection to data analysis and paper-writing. I realized that I love studying about marsh restoration and biogeochemistry, which prompted me to apply to graduate school to continue conducting research in these fields. I also was given the opportunity to meet, befriend, and learn from other people in the SSF program. Through the WHOI softball league, I met members of the greater WHOI community. Overall, it was a summer that I will never forget.