2019 Potential Projects

Below is a list of potential projects and advisors in the WHOI departments and the USGS Coastal and Marine Science Center for Summer 2019. This list is not comprehensive; all Scientific and Senior Technical Staff are eligible to advise Summer Student Fellows. See also: WHOI Areas of Research and Departments, Centers and Labs.

Applied Ocean Physics and Engineering Dept.

Nearshore, Field-based Physical Oceanography

Steve Elgar
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The PVLAB team cleaning sensors at the USACE Field Research Facility, Duck, NC

The PVLAB team cleaning sensors at the USACE Field Research Facility, Duck, NC

Our (Britt Raubenheimer and Steve Elgar and the PVLAB) goal is to understand the physics of waves, currents, and sand movement across the inner continental shelf, through the shoaling region, across the surf and swash zones to the aquifer beneath the beach. We measure waves, currents, and changes to the nearshore morphology (e.g., beach erosion, dune collapse), and use the observations and numerical models to learn about the underlying physical mechanisms. Recent projects include detailed studies of (i) waves in the surfzone observed with lidar, pressure gages, and video, (ii) surf and swash zone hydrodynamics and bathymetric evolution observed during storms, (iii) groundwater fluctuations observed across a barrier island between the ocean and sound, (iv) surf and swash zone currents using remote sensing, (v) the evolution of an ocean inlet that is excavated several times yearly to drain and flush a lake adjacent to the ocean to improve water quality. Although we prefer to be in the field, we spend a lot of time in front of a computer analyzing field data.

Steve Elgar's lab

Marine Unmanned Robotics and Acoustic Sensing

Erin Fischell

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Fischell_20180829_110930_508913My lab works on the intersection of marine autonomy, signal processing including machine learning, and acoustic sensing, with an objective of developing marine systems capable of perceiving their environments and collaborating to explore those environments. Possible projects include integration of low-cost payloads with SandShark AUVs, multi-domain autonomy integration between JetYak ASVs and SandShark AUVs, or processing of high-frequency acoustic data sets to develop tools for identification and classification of features.

Erin Fischell's profile

Autonomous Underwater Exploration Robots

Yogesh Girdhar

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What's That Sound?

My lab is focused on the algorithmic and machine learning challenges in making autonomous exploration robots, and automated analyses of large datasets.  Given the sensor data, I am interested in developing techniques to extract meaning from the data so that we can develop robots that understand their surroundings at various levels of abstraction, identify interesting phenomena, and plan their mission adaptively.

Potential projects could involve development of a stereo vision based collision avoidance system for a small underwater robot; automated analysis of ambient soundscapes; development of deep neural network based techniques for characterizing seafloor imagery. Some experience and/or interest in one or more of the following is highly desirable: computer vision, machine learning, marine robotics, python, ROS.

WHOI Autonomous Robots and Perception Laboratory

Acoustical Oceanography

Andone Lavery

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My research focuses on the development and use of acoustical techniques and platforms to study the physical and biological processes in the ocean. From the perspective of physical oceanography, I am interested in developing acoustic techniques to quantify mixing by internal waves, to characterize warm-core ring intrusions onto the shelf break, the shelf break front, double-diffusive layering, and to acoustically image and quantify shear instability, buoyant plumes, salt-wedge intrusions, and hydraulic jumps. From an acoustics perspective, where there is high stratification, there is typically a strong acoustic signal. From the biological perspective, I am interested in ecosystem acoustics, that is using acoustic techniques to resolve ecosystem processes at relevant spatial-temporal scales, for example to help quantify marine diversity, behavior, patchiness, size, abundance, biogeography, migration. Pelagic ecosystems are comprised of diverse organisms spanning many trophic levels, species, sizes, and shapes. The composition and distribution of different populations are generally heterogeneous and patchy over multiple temporal and spatial scales, and differentially influenced by behavior, predator-prey interactions, physical forcing over a range of spatial scales, and anthropogenic forcing factors (such as ocean acidification or fisheries).

I am particularly motivated by 1) questions that address bio-physical interactions, 2) helping to address questions that have more immediate applications to pressing fisheries management concerns, such as stock assessment and reducing by-catch, and 3) developing new integrated acoustical and optical platforms, including AUVs and deep-towed systems, to address these questions.  I have various projects in these areas -- please contact me if you are interested in a summer of acoustical oceanography.

Andone Lavery's profile

Ocean Acoustics and Signals Lab

Applied Aquaculture

Scott Lindell

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Lindell_kelp_483273The Applied Aquaculture Research Program (Lindell Lab) is directed at researching and developing marine aquaculture for sustainably providing food and fuel. We strive to develop methods that have positive economic and ecosystem services and minimal negative social and environmental impacts. This demands a multi-disciplinary approach encompassing various subsets of biology (e.g. genetics, physiology, epidemiology), and oceanographic engineering (e.g. sensing, structural, systems). Marine aquaculture faces considerable engineering challenges, particularly in the open ocean where there are opportunities for making significant economic contributions. Marine farms need design and management to reach commercial scales that lower risk, attract investment and enhance revenue. Our program currently works with farmers (see GreenWave – greenwave.org) and engineers (see www.whoi.edu/news-release/seaweed-fuel) to research and test novel systems that support multiple commercial-scale growing structures or longlines for shellfish and seaweed.

Breeding and genetic selection applied to aquaculture species is a relatively recent phenomenon compared to agriculture. We will be coordinating the selection of a founding population of sugar kelp (Saccharina latissima) germplasm, designating crosses and families to be planted out, and evaluating the performance (phenotypes) of each family. Using a novel engineered research farm 10 minutes from our dock, we will be testing hundreds of family plots in Massachusetts, and more in New Hampshire. The project goal is to develop new strains of kelp that are better as food or animal feed sources, and that ultimately fit the production cost profile of feedstocks for biofuels.  There will be opportunities for research and mentorship in the both field (farms) and in the lab.

Scott Lindell's profile

Development of In situ Chemical Sensors

Anna Michel

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My interdisciplinary (engineering and chemistry) research focus is on advancing environmental observation through the development and deployment of novel optical sensors for measurement of key chemical species. In my lab, we design, build, and deploy advanced laser-based chemical sensors for environments ranging from the deep sea to Arctic environments. Potential projects for 2019 include developing and testing small gas sensors and working on new optical methods for detecting micro plastics.

Anna Michel's website

Nearshore Processes

Britt Raubenheimer

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Britt (right), Levi Gorrell (middle), and Bill Boyd deploying a sonar altimeter at the base of a dune in NC to measure wave runup and beach erosion during Hurricane Matthew.

Our lab (joint with Steve Elgar) is studying the physical processes that affect the coast during major hurricanes and nor'easters, including the interactions between ocean surge, waves, and infiltration-exfiltation, the groundwater,  and the sediments (pore pressures, porosity, grain size, dune and beach morphology) that contribute to erosion and flooding. We compare field observations that we collect on the beach and in the surf with numerical model simulations to evaluate the relative importance of processes, such as waves, winds, and precipitation. Summer projects could focus on: (1) wave generation in shallow water, (2) breaching and closing of an ocean inlet, (3) alongshore variability of waves and dune erosion, or (4) the role of groundwater and precipitation in coastal flooding and dune erosion on a barrier island.

Britt Raubenheimer's lab

Autonomous Surface Vessel Development

Peter Traykovski

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WHOI Engineers and scientists have recently developed the Jetyak Autonomous Surface Vessel (ASV), which has enabled interesting measurements in environments ranging from the Arctic to Coastal Estuaries.  See http://www.whoi.edu/oceanus/feature/the-jetyak. However for many applications a smaller ASV that could be launched and recovered by one person would be more suitable.  In very rough conditions (e.g. the surf zone)  the gas engine of the jetyak is problematic. Summer Student Fellow Projects that aid in the development of a smaller electric motor and battery powered ASV are possible that cover topics ranging from mechanical design to adaptive robotic control in the surfzone. Sensor integration such as bathymetric sonars or camera systems could also be part of a project  These projects would involve significant amounts of hands on engineering and field testing.

Peter Traykovski's profile

Projects website

Antarctic Coastal Polynya Biophysical Interaction

Weifeng Gordon Zhang

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fig5_polynyas_480134This potential summer project is a part of an interdisciplinary, multi-PI National Science Foundation project to examine the connection of physical circulation with the phytoplankton and Emperor Penguin ecology in Antarctic coastal polynya regions. Coastal polynyas are isolated openings in the sea ice that are mostly formed by strong winds blowing from the continent toward the ocean. Antarctic coastal polynyas are hotspots of sea ice production and the primary source regions of Antarctic Bottom Water, the lower branch of the global overturning circulation. They sustain high levels of biological production and provide the main wintertime feeding grounds for predators, such as the iconic emperor penguins. Polynyas are thus an important component of the global ocean and a key part of the Antarctic ecosystems.

This particular summer project is i) to compile existing physical (wind, sea ice, temperature, salinity, etc.) and biological observations in a variety of Antarctic coastal polynyas from different sources and ii) to investigate the dynamical connections between the winds, sea ice formation, polynya size/location/persistence, water column stratification, and phytoplankton bloom intensity. The existing observations will include measurements taken by satellites, ships, underwater gliders, tagged seals, etc. The summer student will also be able to interact with WHOI sea ice dynamists to examine the connection between sea ice formation and stratification, and with WHOI biological oceanographers to consider incorporating the physical influences into a phytoplankton dynamical model and an emperor penguin ecological model.

Weifeng Gordon Zhang's profile

Biology Dept.

Marine Microbial (Meta)Genomics

Harriet Alexander and Maria Pachiadaki
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Sampling route and stations of the Tara Oceans Expedition. Sampling route of the Tara Oceans Expedition (green track), showing station labels and areas (blue shade) where the annual mean oxygen concentration is O2 ml/l, usually corresponding also to high CO2 concentration and low pH. Tara Ocean Expedition produced TB of sequencing data that can now be mined to explore the metabolic capabilities, distribution, and ecology of marine microorganisms. Credit: Pesant et al., 2015 (Scientific Data).

The Alexander lab focuses on the application of computational approaches to better understand the ecological roles and interactions of eukaryotic microbes (protists) in marine systems. The Pachiadaki lab studies the identity, function and activity of marine microorganisms, with emphasis on prokaryotes (bacteria and archaea).

Together we are interested in characterizing the patterns of nitrogen fixation and organic matter degradation in the oceanic water column, from the well-lit surface waters to the deep mesopelagic. Tara Oceans, a multinational consortium, organized a standardized metagenomic sampling program effort that circumnavigated the world's oceans to study marine plankton (spanning viruses to zooplankton) in their natural environment. This summer, we are recruiting an undergraduate student who would like to hone their computational biology and bioinformatic skills, while working on a project to mine the publicly available Tara Oceans metagenomic data. The goal of this project is to: 1) characterize patterns of functional gene presence and absence across oceanic regions and depths, 2) identify key microbial taxa (bacteria, archaea, and protists) that might mediate the nitrogen fixation and organic matter degradation and the encoded metabolic pathways, and 3) reveal potential cross-domain interactions that may underlie these molecular transformations.

Though not necessary, prospective students will ideally have had a basic introduction to computational biology (i.e., have run a blast search) and have some experience coding in a programming language (e.g., python, R, Matlab).

Alexander Lab

Pachiadaki publications

Mixotrophy in Marine Plankton

Rebecca Gast
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Aquatic protists, which are key mediators of planktonic food-web productivity, have traditionally been categorized as either strict autotrophs (when they contain chloroplasts) or heterotrophs (when they do not). However, mounting evidence has revealed that a large portion are mixotrophs that combine photosynthesis and ingestion of particles for growth. The miscategorization of protists as strictly autotrophic or heterotrophic has major implications for the way scientists understand the flow of carbon and nutrients through the food-web. Nutrients and energy flow differently in microbial food-webs if they are dominated by bacterivorous mixotrophs compared to strict autotrophs and heterotrophs. A high abundance of bacterivorous mixotrophs could result in more carbon sequestered at depth through the biological pump than originally predicted. There is an emerging interest in incorporating mixotrophs into food-web and biogeochemical models, but there is a lack of data on when and where it is necessary to include this nutritional strategy. Particularly lacking are studies that examine seasonal changes in mixotrophic abundance and activity.  We are investigating the seasonal and spatial variability in the dominance of mixotrophic nanoflagellate assemblages compared to heterotrophic nanoflagellate assemblages in Waquiot Bay in an effort to increase our understanding of what environmental conditions favor mixotrophic organisms. This summer we are interested in recruiting a student who would be interested in participating in the field sampling and accomplishing ingestion experiments and amplicon tag sequencing, as well as interacting with community volunteers in counting phytoplankton samples as part of an outreach activity.

Rebecca Gast profile

Seabird Ecology and Demography

Stephanie Jenouvrier
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Counting emperor penguins from space with satellite images

Jenouvrier_Penguins_5092The Jenouvrier Seabirds lab studies the effect of global change on individual and population of a community of seabirds breeding in the Southern Ocean. Specific area of interests include how climate changes and human activities affect the behaviors (e.g. foraging) and vital rates of individuals (e.g. survival and breeding success); the timing of key life cycle events (e.g. breeding phenology); and the population growth and structure.

This year, the summer student will be participating in the development of a comprehensive analysis of emperor penguin habitat suitability and population trends over the whole Antarctic continent using unique remote sensing imageries. The project is salient and fascinating in the context of climate change and the conservation of polar ecosystems.

The very high resolution (VHR) imagery allows unconstrained access to all emperor penguin colonies – indeed, constraint to certain emperor penguin populations has previously biased total population estimates low and further produced population trends that may have been biased toward colonies associated with certain habitat characteristics. Emperor penguins in particular are ideal for direct, satellite-based investigation of their distribution and numbers: emperor penguins rear chicks in the spring time when satellite images of the coastline are easily acquired, and they also leave a representative guano stain on the fast ice that indicates colony presence. The VHR imagery approach uncouples the observation process from site accessibility and has the potential to provide complete, annual counts across a species’ range. Through observations based on imagery, researchers have already determined a baseline abundance of emperor penguins for 2009 (~595,000 individuals); observed previously unseen behaviors such as breeding on glacial ice in years of poor fast ice conditions and observed apparent moving and/or relocating colony locations altogether.

The student will be in charge of defining training dataset for analysing the satellite images, but also defining the sea-ice scape in those images. This work using very high-resolution satellite imagery, remote sensing techniques, and statistical modelling, will contribute to learn about the effect of environmental conditions on the spatial (habitat suitability) and temporal (population trends) dynamics of this iconic seabird, the emperor penguin.

Jenouvrier Seabirds Lab

Biological-physical interaction and modeling

Rubao Ji

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Research in Ji's lab focuses on three interlinked biological oceanography topics, including phenology, biogeography, and connectivity of marine plankton (both holo- and mero- plankton). Phenology is the study of annually recurring phenomena in relation to climate conditions and biogeography is about the geographic distribution of organisms. The study of population connectivity focuses on the exchange of individuals between geographically separated subpopulations.  All three aspects of ecosystem dynamics are likely affected by climate-related forcing, including changes in hydrography and circulation patterns.  Coupled biological-physical modeling is the primary tool used in Ji's research group, with an aim to synthesize the data collected from laboratory experiments, in-situ observation and remote sensing. Potential projects for summer students include: 1) model-data validation and skill assessment; 2) model results processing and visualization; and 3) preliminary development of energy budget model for plankton and/or fisheries populations.

Rubao Ji's profile

Northeast U.S. Shelf Long-Term Ecological Research

Protistan Ecology and Evolution

Matthew Johnson
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All images are fluorescence micrographs. Top images show mixotrophic dinoflagellates with ingested cryptophyte algal prey (orange/yellow food vacuoles). Their chloroplasts appear as red and their nucleus is blue. Bottom images show mixotrophic ciliates that steal chloroplasts (yellow/orange) from cryptophyte algae. The ciliate on the bottom right is Mesodinium rubrum, with a large stolen prey nucleus visible in the center (green nucleolus) and one of its own nuclei next to it (pink nucleolus). This cell was labeled with two different fluorescent in situ hybridization (FISH) probes for the 18s rRNA genes of cryptophyte prey (green) and of Mesodinium (pink).

Research in my lab is focused on understanding the ecology and evolution of marine protists with an emphasis on their interactions and trophic role. We primarily focus on mixotrophic protists, which survive by simultaneously combining photosynthetic and phagotrophic nutritional modes. These protists can be algae that eat or protozoa that steal chloroplasts from their algal prey. Our research aims at understanding how these organisms function and how they shape microbial communities and the flow of energy and matter through them. One mixotroph that we are particularly fond of is the ciliate Mesodinium rubrum, which not only steals chloroplasts but also a transcriptionally active nucleus from its prey. This unique trophic mode, called karyoklepty, allows them to gain full access to the metabolic potential of their prey and to essentially function as phototrophs. Potential projects in my lab include (1) measuring dynamics of prey selection and plastid sequestration in marine protists, (2) assessing the role of feeding in mixotrophic marine phytoplankton under nutrient limitation, or (3) determining how phytoplankton prey phenotypes and defense mechanisms alter selection by and grazing rates of predatory protists.

Johnson Lab

Fisheries Oceanography/Larval Fish Ecology

Joel Llopiz
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Research in our lab focuses on aspects related to the early life stages of fish (e.g. feeding, growth, mortality, distribution) as well the interactions between zooplanktivorous fishes, their prey, and the physical environment. We have several ongoing projects projects that a Summer Student Fellow could be a part of, including the larval and juvenile ecology of river herring, settlement dynamics of coral reef fish larvae in the Virgin Islands, sand lance feeding dynamics on Stellwagen Bank, and diets and stable isotopes of small pelagic fishes from the NE US continental shelf. The last of these is related to our Long-term Ecological Research (LTER) project, which will be supporting one SSF who could be placed in one of several different labs (interest in this project should be mentioned in your application). Depending on the fellow’s project, there’s the likelihood of participating in research cruises, whether they are for sand lance on Stellwagen Bank and Nantucket Shoals, or plankton and fish on the continental shelf south of Martha’s Vineyard on a 6-day LTER cruise.

Joel Llopiz's Lab

Northeast US Shelf Long Term Ecological Research

Benthic Larval Ecology

Kirstin Meyer

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graphics-Kirstin_Meyer-VCL_3145-1280_468778_508414In my lab, we study the colonization and connectivity of island-like benthic invertebrate populations. We use field surveys, larval culturing, and experiments in the lab and field to understand how and why larvae of benthic invertebrates disperse and colonize where they do.

Drop any solid object into the ocean, and it will eventually become colonized by something. For example, shipwrecks are home to benthic invertebrate communities in locations where there is not “supposed to” be a hard-bottom habitat. Most benthic invertebrates reproduce via a larval stage that disperses in the water column, but why would a larva that needs to settle on a solid object disperse to an area that is “supposed to” have just sand or mud? Island-like communities may have been founded by only a few individuals that for some reason dispersed farther than others.

I am looking for a Summer Student Fellow to join my lab in 2019 and investigate what factors might cause a larva to disperse farther than other individuals of the same species. Maybe its mother had good energy reserves and added more yolk to her eggs, allowing the larva to swim for longer. Maybe the larva swam up shallower than its conspecifics and got caught in a fast current. The Fellow will collaborate with me to design and carry out an experiment examining intraspecific variation in larval provisioning and behavior, using their choice of model species. Possibilities include an anemone, a tunicate, a limpet, and a bivalve.

The Fellow’s project will begin with field collections of the target species by wading at low tide in shallow rocky habitats around Woods Hole. Females of the target species will be maintained in the laboratory at various levels of nutrition during their reproductive period, and then some will be dissected to measure larval provisioning (yolk mass or larval size). Another set of females will be allowed to spawn, and the behavior of their larvae will be observed in the laboratory using high-speed video recordings. Analysis of the video data will be conducted using the code-based program Matlab. The Fellow will gain experience in experimental design, larval culturing techniques, video analysis, and the interpretation of complex data.

Kirstin Meyer's profile

Sensory Biology and Bioacoustics

Aran Mooney

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In the Sensory Ecology and Bioacoustics lab we study how marine animals use detect and respond to the cues around them, as well as the patterns of cues, signals and noise available to the animal. Our work focuses on cephalopod hearing and use of sound, cephalopod eco-physiology (physiology and behaviors in response to local environmental conditions such as oxygen and pH), marine mammal bioacoustics, and the bioacoustics of coral reefs. We often address how stressors such as low pH or ocean noise impacts behavior and physiology.  Potential projects for the SSF include: (1) studies on coral reef soundscapes and larval responses to sound, (2) impacts of noise on cephalopods, and (3) using the ITAG to quantify the behavior and physiology of marine invertebrates.

Sensory Ecology and Bioacoustics Lab

Sensory Ecology blog

Larval Ecology, Benthic Community Resilience

Lauren Mullineaux
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MIT/WHOI JP student Carly Strasser and scientist Lauren Mullineaux work with crew aboard the R/V Atlantis to deploy deep-sea mooring. (S.W. Mills, WHOI)

Our lab studies the oceanographic and ecological processes that connect geographically separate populations and contribute to their resilience in the face of natural and human disturbance. To do this, we investigate how larvae of benthic invertebrates disperse and recruit into marine communities. We work mostly in patchy habitats, ranging from coastal bays to deep-sea hydrothermal vents, where larval dispersal is the driving process connecting populations. Students in our lab use a variety of approaches, often in collaboration with WHOI scientists in other disciplines, including coupled studies of circulation and larval ecology, manipulative benthic experimentation, laboratory study of larval behavior, and mathematical models. This coming summer, available projects for an undergraduate fellow include: (1) analyze the development of a deep-sea vent community following a catastrophic eruption on the East Pacific Rise; (2) conduct laboratory experiments on larval behavioral responses to environmental cues; or (3) explore the roles of disturbance, dispersal, and species interactions on community persistence in a metacommunity model.

Mullineaux Lab

Mathematical Ecology

Michael Neubert
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In my laboratory, we formulate and analyze mathematical models to address scientific questions that arise in the study of marine populations or communities. Many (but not all) of these questions have to do with how best to conserve or manage populations in the face of some form of stress (e.g., invasive pests, habitat disturbance, harvesting, or climate change). The project a summer student might work on in my lab will depend upon a combination of the student’s mathematical and computational training and biological interests. Examples include developing models to study (1) the efficacy of marine protected areas, (2) how best to manage the spread of an invasive species or epidemic, (3) how species persist in dynamic environments around hydrothermal vents, (4) phytoplankton population dynamics, or (5) zombies.

Michael Neubert's profile page

Marine Mammal Behavior and Communication

Laela Sayigh
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My research interests focus on behavior and communication in cetaceans (whales and dolphins), and how humans impact these aspects of cetacean societies. Student projects will largely focus on analysis of acoustic data. Possible research areas for summer 2019 include: (1) Analysis of tag data to study how bottlenose dolphins, pilot whales and blue whales use communicative signals; (2) Analysis of playback experiments to bottlenose dolphins, aimed at studying how noise impacts dolphin communication.

Laela Sayigh's profile page

Marine Mammal Physiology & Energetics

Michelle Shero
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Surveys of grey seal colonies in Nova Scotia, CA. Image courtesy of Dave Johnston.

The Shero Lab focuses on identifying critical energy ‘bottlenecks’ in marine mammal life history cycles that would make them particularly vulnerable to environmental and anthropogenic disturbance. The lab’s work also puts an emphasis on marine mammal reproductive physiology and identifying processes that are critical to successfully producing offspring.

Measuring energy dynamics in marine mammals often requires sedating and weighing the animals, which poses great limitations on our sample sizes. More minimally-invasive approaches have been also been developed, including using morphometric measurements and taking photographs of the animals to estimate total body volume and mass. While these techniques have been widely successful, they still necessitate animal disturbance. Thus, we are validating the use of unmanned aerial vehicles (UAVs; or drones) to measure energy dynamics in pinnipeds, from the air to ‘weigh whole colonies’ without ever touching or disturbing our study subjects. In combination, we will be acquiring much more information regarding the nutritional and physiologic status of individuals than would ever be possible using traditional ground survey. These methods are being applied to translate organismal-level processes to understanding patterns observed at the level of the population.

A summer intern is needed to help analyze the massive image datasets we are acquiring. The student would learn to use processing software that will stitch all the drone images back together to construct 3-dimensional models of seal colonies, and measure individuals. Potential students could choose to focus more on (1) whole-colony demography, (2) mass and photogrammetry, and/or (3) thermal regulation/IR images across different life history stages in marine mammals.

Michelle Shero's profile

Michelle Shero's website

Phytoplankton Ecology

Heidi Sosik
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graphics-Flow_Cytobot-_DSC3746_sm_408473My research is focused on quantitative plankton ecology and in my lab there are a range of possible summer projects for motivated undergraduates. Most on-going projects are related to coastal ecosystems and time series observations of plankton at scales from single cells up to large areas that can be monitored with satellite remote sensing. We have on-going field work as part of the Northeast U.S. Shelf Long-Term Ecological Research (NES-LTER) program and at the Martha's Vineyard Coastal Observatory, which is a facility on the continental shelf near WHOI that is connected to shore by power and fiber optic cables. We have developed some exciting new submersible flow cytometer technologies that rapidly measure microscopic particles (mostly phytoplankton, but also protozoa), including video imaging at the micron scale. These instruments are deployed at MVCO and produce lots of data (e.g., >10000 images per hour for months to years), so projects involving these time series can span from computer science (image analysis, computer vision, and machine learning) to modeling of populations and bloom dynamics. There are also opportunities for projects involving coastal field work, laboratory experiments with plankton cultures, and instrument development.

Heidi Sosik's website

Imaging Flow Cytobot data

Northeast U.S. Shelf Long Term Ecological Research

Marine Invertebrate Physiology

Ann Tarrant
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Pleuromamma robusta, photo courtesy of L. Bercardio-Blanco.

We seek to understand how animals detect and respond to signals and stresses in the marine environment. These include responses to natural environmental signals, such as circadian rhythms or seasonal dormancy, as well as responses to stressors such as chemical pollutants. This summer, we are particularly interested in recruiting a student to conduct enzyme activity assays with migratory copepods (especially Pleuromamma xiphias). We are interested in how the metabolism of these small animals changes over 24-hour periods, in relation to their daily swimming behavior and underlying circadian cycles. Pathways to be studied include glycolysis, the citric acid cycle, anaerobic metabolism and ammonium production - you don’t have to be familiar with the details of the pathways before starting, but you do need to be willing to learn! There will be opportunities to become involved in other ongoing projects in the lab, including thermal acclimation in Nematostella, and metabolic adaptations of Antarctic copepods.

Tarrant Lab website

Tarrant Lab blog

Geology and Geophysics Dept.

Stromatolite Microbiology and Early Diagenesis

Joan M Bernhard
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Confocal Laser Scanning Microscope image of microbialite community (bright green objects) in life position. Largest bright green object is a calcareous foraminifer; sediment grains are ooids. Also note the vertically oriented filaments, which are most likely cyanobacteria. Image by JM Bernhard, unpublished.

Stromatolites are Earth’s earliest evidence of extensive life. To better understand the impact of eukaryotic evolution on the Precambrian stromatolite fossil record, we are studying modern forms and their early diagenesis (fossilization). Two projects are available this summer as part of that larger effort.

1) In stromatolites from a meromictic (permanently stratified) lake, establish microbial distributions on a sub-millimeter scale to determine eukaryotic and prokaryotic distributions with respect to chemocline geochemistry. Laser scanning confocal microscopy will be the main tool for these analyses. An opportunity exists to join field work (collections) for this project.

2) Perform an experiment using meromictic-lake stromatolites that are differentially exposed to foraminiferal protists to assess the impact of pseudopodial activity on stromatolite laminations, similar to the experiment described in Bernhard et al. (2013 PNAS). An opportunity exists to join field work (collections) for this project.

Joan M. Bernhard's home page

Assessing microfabric attributes of calcium carbonate in foraminiferal shells from Arctic methane seeps

Joan M Bernhard and Veronique Le Roux
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Single plane of a microCT scan showing cross sections of Arctic foraminiferal shells.

Because methane is a greenhouse gas, it is important to understand the history of methane emissions from the seafloor. To do this, we study the biology and fossils of foraminifera from methane seep sites in the Arctic. An important consideration is to determine if the calcite of their shells is solely biogenic or if it also has an overgrowth of carbonate precipitated after death of the foraminifer. Part of our collaborative project is to measure the wall thicknesses and other attributes of individuals from seep and non-seep sites. Individuals have already been scanned via microCT (computerized tomography) and measurements must be made using appropriate software. There will be opportunities to scan additional foraminifera as well as learn about their cell biology.

Joan M. Bernhard

Veronique Le Roux

Climate Dynamics of the Common Era

Sloan Coats

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A) Multi-model mean tropical Pacific sea surface temperature trends (SSTs) between 1900-2013 from 40 state-of-the-art climate models. B) Trends in the SST difference between Box 1 and Box 2 over the same period, the range of the climate models is in grey/black and observations in red. Determining if the differences between models and observations are real or due to uncertainties is critical to provide confidence in future projections from climate models. (Click figure to enlarge.)

The term Common Era refers to the last ~2000 years, but it also has a scientific connotation, as this is the era common to paleoclimate reconstructions, observational data, and simulations from state-of-the-art climate models. I leverage these sources of climate information to better understand variability on decadal and longer timescales—things like “megadroughts” over the Southwest and trends in tropical Pacific sea surface temperatures. My work typically involves the development and implementation of novel statistical methods, including machine learning, as well as the use of climate modelling—particularly with the National Center for Atmospheric Research models.

Examples of potential projects include: 1) Using machine learning to better understand the characteristics of heat waves and droughts in both space and time; and 2) Analyzing historical trends in the tropical Pacific ocean, a critical region for global climate with an uncertain response to human-driven climate change.

Coats WHOI profile

Coats website

Climate Modeling

Alan Condron
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A high resolution model simulation of ocean circulation during the last glaciation, 21,000 years ago.

My research uses numerical models to study the causes of climate change. I am particularly interested in whether melting ice sheets can trigger abrupt periods of climate cooling, both in the past and the future. Current projects of interest including: (1) Assessing the impact of a collapse of the West Antarctic Ice Sheet on global climate, (2) Modeling the impact of iceberg discharges on Heinrich Events and other periods of past abrupt cooling, (3) Determining the role of Arctic sea ice and freshwater on climate.

Alan Condron profile

Alan Condron website

Climate Variability: Tropical Cyclones, Sea Level and Drought

Jeff Donnelly
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Coring a coastal pond in New York following Hurricane Sandy.

The goal of my research program is to understand how climate variability changes tropical cyclone activity, alters sea levels, and affects water availability. Storms, sea-level fluctuations, and changing freshwater inputs play key roles in driving changes in many coastal systems, yet we know very little about how these environments respond to the complex interactions of these forcing mechanisms. Gaining a process-based understanding of how and why past environmental changes have occurred provides a framework for projecting future changes. We use sedimentological and stratigraphic proxy records of tropical cyclones, sea level, and drought that extend the instrumental record back millennia. Example projects include: 1) analyzing cores to characterize event deposits and reconstruct the history of tropical cyclone activity back many centuries to millennia , 2) Analyzing historical archives in order to extend the spatial and temporal coverage of records of tropical cyclone occurrence in order to examine how changing climate may have controlled activity, 3) Reconstructing wildfire frequency by analyzing charcoal preserved in sediment cores in order to examine links between fire and changing water availability and tropical cyclone disturbance.

Coastal Systems Group

Bioremediation using Oyster Aquaculture and Marine Parasites of Phytoplankton

Virginia Edgcomb
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edgcomb_pic_407053The Edgcomb laboratory studies the ecology of marine microbial populations in oxygen-depleted water columns and sediments. Our work encompasses studies of marine protists, Fungi, Bacteria and Archaea. We utilize culture-based (studies of physiology and rates of key processes) and molecular (RNA- and DNA-based genomics) approaches, and microscopy (light, EM, and FISH). There are two projects that a summer student fellow could join us in this year. One is a study of the impacts of oyster aquaculture on nitrogen removal at a coastal Cape Cod location. Several different aquaculture methods are being compared, and we are examining nitrogen removal not only by the oysters, but by microbial communities. This project involves field work and laboratory analyses and there are several aspects of the project that a SSF could get involved in! The second project is examining microbial parasites of phytoplankton and their impact on phytoplankton communities and on releases of organic carbon and nitrogen in a tidal coastal pond very near the laboratory. This project involves lots of field work and laboratory analyses.

Edgcomb Lab

Isotope Geochemical Clues about the Deep Earth

Forrest Horton
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Baffin Island lava flows contain clues about the deep Earth.

Volcanic rocks hold clues about the deep Earth and help us understand magma origins and mantle processes. Two opportunities exist to investigate the isotope geochemistry of highly unusual volcanic rocks:

Baffin Island lavas from Earth’s lowermost mantle: Lavas erupted on Baffin Island in arctic Canada are thought to derive from the deepest and most primordial mantle reservoir (and perhaps even contain material from the core!). Samples from this location are extremely important for understanding Earth’s deep interior, so we will be conducting comprehensive geochemical and isotopic analysis of these rocks. Opportunities exist to study the petrology of these samples and to conduct noble gas isotopic measurements by crushing gas-bearing olivine crystals.

Afghanistan carbonatites and the deep carbon cycle: Carbon cycling through and storage in the deep continental lithosphere remain poorly understood aspects of the global carbon cycle. Rare volcanic rocks that contain >50% carbonate minerals (carbonatites) provide insight about these processes. Khanneshin Volcano in southern Afghanistan is one of the youngest and best-preserved carbonatite volcanoes. This study will infer the origins of Khanneshin magmas based on carbon, oxygen, strontium, and boron isotopic results. Students involved will gain experience with laser ablation ICP-MS and secondary ion mass spectrometry (SIMS).

Forrest Horton homepage

What feeds Antarctic volcanoes?

Glenn Gaetani
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Mount Erebus

Antarctica is a continent covered with ice, but it is also home to many volcanoes. Ross Island is comprised of four coalesced volcanic centers: Mount Bird, Mount Terror, Hut Point Peninsula, and Mount Erebus, the world’s southernmost active volcano and home to a persistently active lava lake. Understanding volcanic hazards at Mount Erebus is particularly important considering that the volcano is located only 25 miles from McMurdo Station, Antarctica’s largest research base and home to ~1000 people during the austral summer. Constraining the depths at which magmas are stored beneath these volcanoes and how much H2O and CO2 they contain prior to ascending and erupting is especially critical to understanding the dynamics of future eruptions. However, the solubility of H2O and CO2 in magmas drops substantially during ascent to the surface, leading to extensive degassing and loss of these volatile components. This makes determining the pre-eruptive H2O and CO2 contents of magmas particularly challenging. Small packets of magma that become trapped within growing olivine crystals (olivine-hosted melt inclusions) are our most important source of information on the H2O and CO2 contents of magmas prior to eruption. The strength of the host olivine protects the included melt from the decompression experienced by the entraining magma, allowing melt inclusions to retain their pre-eruptive volatiles. We are looking for a summer student fellow to determine magma reservoir depths beneath Ross Island and the pre-eruptive concentrations of H2O and CO2 of the magmas using olivine-hosted melt inclusions. The study will combine state of the art microanalytical techniques such as Raman spectroscopy and secondary ion mass spectrometry.

Glenn Gaetani's profile

Climate and Landscapes

Liviu Giosan
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Discussing around a sediment core containing the story of the Indus civilization collapse 4000 years ago written in mud.My research seeks to uncover the millennia-long story of human interactions with the climate and the landscapes around them as written in ocean and continental sediments. Current projects available to summer visitors include reconstructions for: (1) the monsoon in the Indian Ocean and its effects on civilizations since the Bronze Age; (2) floods along large rivers like the Danube and the Mississippi prior and after the construction of engineered protection structures; (3) hydrological changes associated with of the rapid warming of the Arctic as expressed by sedimentary records along large rivers such as the Mackenzie and Yukon; (4) large delta evolution across the world in natural and anthropogenic conditions to prepare to “design” our deltas to withstand sea level rise.

Liviu Giosan's profile

Physical Volcanology

Yang Liao
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I’m a physical volcanologist and fluid dynamist with a broad range of research interest. I typically develop quantitative models based on continuum physics, but I’m also setting up a laboratory to test some of my models and to explore more physical processes using small-scale, ‘counter-top’ experiments. One research opportunity for an undergraduate summer fellow is to join me in developing and conducting some experiments relevant to magma reservoir in earth crust. Specifically, the experiments are based on using analogue materials (e.g., water, corn syrup, gelatin), one camera, and (perhaps) 3D printed molds. We will explore the behaviors of magma chambers and volcanic dikes in the crust, especially when crystals are abundant and the system is ‘mushy’.

Yang Liao's profile

Paleoceanography: Past Changes in DeepOcean Ventilation

Olivier Marchal
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The deep ocean is renewed, or “ventilated”, when surface waters present at high latitudes become sufficiently cold and dense to sink. These waters then spread laterally, filling the various deep oceanic basins, and eventually return to the sea surface. Ventilation is therefore the very process by which the deep ocean communicates with our atmosphere and is thought to play an important role in climate. This project will seek to estimate changes in deep ocean ventilation which took place during the last deglaciation – the largest manifestation of natural climate change that remains relatively well preserved in the geologic record. To this end, we will analyze existing measurements of the radiocarbon concentration of fossil biogenic carbonates (benthic foraminifera and deep-sea corals) present in sediments. As ocean surface waters sink at high latitudes, they carry with them a certain amount of radiocarbon to the deep sea. The radiocarbon in these waters decays radioactively as these waters spreads laterally through the abyssal ocean. Thus, the higher the supply of surface waters to the deep sea, the higher the supply of radiocarbon to the deep sea, and the higher the concentration of radiocarbon of deep-sea waters and of any material formed from carbon present in these waters, such as calcium carbonate. Fossil biogenic carbonates in deep-sea sediments therefore provide an archive of past changes in deep ocean ventilation rates.

Olivier Marchal's profile


Delia Oppo
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We use a variety of techniques, often in collaboration with other scientists at WHOI and elsewhere, to study past changes in ocean circulation and the earth's climate history. Some of our current projects focus on abrupt climate events of the last glacial cycle, deglacial climate evolution, and Holocene trends and variations (including detailed reconstructions of the last millennia).

Delia Oppo's homepage

Geophysics of Hot Springs and Volcanoes

Rob Sohn
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Sohn_Attach_anchor_508394I am a geophysicist who studies hydrothermal and volcanic systems. My expertise is primarily in seismology and time-series analysis. Most recently I have been doing extensive work in Yellowstone Lake, which straddles the 640 ka Yellowstone Caldera and hosts several lake floor hydrothermal vent fields. I have a number of datasets in hand that are suitable for summer research projects, including lake floor seismic data, wave gauge data, near vent thermal time-series data, thermistor chain data, CTD data, and current profile data. These datasets provide unique opportunities to study the lake floor hydrothermal systems and the hydrodynamic behavior of a large, alpine lake.

Project website - Hydrothermal Dynamics of Yellowstone Lake

Marine Chemistry and Geochemistry Dept.

Marine Radiochemistry

Ken Buesseler
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Our lab uses naturally occurring radionuclides, mostly from the decay of uranium and thorium in the ocean to look at several processes, such as the removal of carbon and associated nutrients and trace elements from the surface ocean. We also track man-made, or artificial radionuclides from sources such as the disaster at Fukushima Dai-ichi in 2011, and ongoing releases from weapons testing sites including the Marshall Islands. Students would work on existing samples and/or data from one of these projects. Given that radioactivity levels are those found in the natural ocean environment, no special radioprotection procedures are needed. In fact, the levels of many of these compounds are higher in basements in Falmouth (radon), or drinking water (plutonium) than found in the deep sea. We take advantage of the known inputs of these radionuclides at trace levels to quantify mixing rates, ages, and fluxes of many chemicals that are part of the ocean’s biological and physical environment.

Ken Buessler's group - Café Thorium

Isotope Biogeochemistry

Tristan Horner
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Ben Geyman (2016 SSF), Tristan Horner, and Maureen Auro inspecting a trace-metal sample in the clean room. (Tom Kleindinst, WHOI)

Marine sediments are valuable historical archives that document the evolution of the Earth System. However, relating the geochemistry of certain sedimentary deposits back to the environment in which they formed is not necessarily straightforward, since the information recorded can be ‘blurred’ by additional processes taking place during and after deposition (e.g., biomineralization artifacts, overprinting by diagenesis, misidentified control variable). Thus, it is imperative to conduct studies in diverse modern marine environments to fully appreciate how the chemistry of the geological record is ‘written’.

Student projects in the NIRVANA Lab will use a range of multi-element geochemical (e.g., trace element abundances) and/or stable-isotopic techniques (e.g., Ba-, Cd-, Fe-, Mo-, Tl-, V-, and Zn-isotopic analyses) to probe the ‘language’ of the geological record with the goal of using these tools to understand the evolution of primary productivity, ocean redox, and nutrient recycling through Earth History.

NIRVANA research group

Deep-Sea Microbiology

Julie Huber
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NOAA Ocean Explorer: Okeanos Explorer: Mid-Cayman Rise Expeditio

Image of an active hydrothermal vent (left) located SE of the central Von Damm hydrothermal field seen at the very end of our last dive at the MCR. Note the filaments of bacteria and hydrothermal shrimp in the immediate vicinity of the active fluid flow. Image courtesy of NOAA Okeanos Explorer Program, MCR Expedition 2011.

Julie is an oceanographer by training and is broadly interested in how basic earth processes- rocks forming, fluids moving, sediments accumulating- interact to create and maintain life in the oceans. Her research addresses some of the most central questions about the nature and extent of life on Earth in one of its least explored corners, the subseafloor habitat beneath the ocean floor. Potential projects include cultivation of microbes from deep-sea hydrothermal vents, using advanced molecular tools, including DNA and RNA sequencing, to examine microbes living beneath the seafloor, and other related microbial biogeochemistry projects.

Julie Huber's profile

Paleoclimate from Coral Skeletons

Konrad Hughen
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Coral_photo-1_447993Massive corals can grow for hundreds of years and record climatic and oceanographic conditions in the chemistry of their skeletons. Long coral drill cores provide material for a broad array of geochemical analyses that reveal information about sea surface temperature, salinity, river runoff/dust input, and human activities including land-use change and pollution. This project will involve measuring trace element (Sr/Ca and Ba/Ca) and/or oxygen isotopic ratios (d18O) in coral skeletons for reconstruction of climate in a region to be determined.

Konrad Hughen's website

Marine Chemistry, Instrumentation and Engineering

Matthew Long
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Long_photo1_508575My research explores the ways that natural and anthropogenic processes influence the structure and function of marine ecosystems through unique engineering solutions, advanced instrumentation, and technology development. Studies of biogeochemical cycling, physical transport processes, and bio-physical interactions are principle components of my research into carbon and nutrient cycling in coastal environments. These topics are significant because the long-term effects of human activities, which are rapidly altering climatic conditions and nutrient cycling, are not well understood.

Opportunities in my lab include the development of low-cost sensors through electro-mechanical engineering, development of advanced sensors and control systems, and field application and testing of sensing platforms. Advanced sensing systems collect high-frequency data (e.g. water chemistry, turbulence) which is used to calculate chemical fluxes through boundary layer exchange techniques allowing for opportunities for experience in time-series analysis, fluid mechanics, and biogeochemistry. Fellows with combined experience in engineering or biogeochemistry, and interests in electro-mechanical engineering, fluid mechanics, or ecosystem science will are encouraged to join the Machine Lab gain experience in interdisciplinary scientific research.

Long_logo_508573Matthew Long's profile

Aquatic Carbon Cycling Sensor Development

Collin Ward
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We seek a student interested in developing and characterizing a new sensor package to quantify in-situ rates of aquatic carbon cycling processes. These processes include photosynthesis, microbial respiration, and photochemical oxidation. The student would work collaboratively with Aleck Wang and Matt Long's labs, primarily focusing on optimizing the sensor package design and performance under controlled conditions (e.g., tank tests). Although not absolutely required, the ideal student would have an engineering and/or chemistry background with interests in the aquatic C cycle and environmental science.

Collin Ward's profile

CO2 Chemistry, Ocean Acidification and Sensor Development

Zhaohui Aleck Wang
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Wang_1_510093In the CO2 chemistry lab, we study seawater carbonate chemistry, coastal carbon cycle, ocean acidification (OA), and the marsh carbon cycle. Specifically, my lab group focuses on understanding how CO2, inorganic carbon species and fluxes are controlled by natural and anthropogenic factors, and how the marine CO2 system will change under climate change and ocean acidification and the effects due to these changes. We are also specialized to develop in situ sensors to measure seawater CO2 parameters and other chemical species. We use cutting-edge sensors to improve our understanding of inorganic carbon biogeochemistry in aquatic systems and impacts of ocean acidification. Potential summer projects include:

1) Developing In-situ Sensor Technology for Measurements of Dissolved Inorganic Carbon (DIC), pH pCO2 and heavy metals (e.g. As and Cd) in Aquatic Environments.
Development of robust sensors to enhance our capability to study carbon cycling and aquatic biogeochemistry has been widely recognized as a research priority in the research communities in order to improve spatial and temporal coverage of observations. The larger goal of the project is to develop a miniaturized in-situ sensor, CHANOS II, for spectrophotometric measurements of aquatic DIC, pH, pCO2 and dissolved heavy metals with high-frequency up to full water depth. The summer project will involve collaborating with engineers and scientists to test, improve, and deploy the new sensor in various coastal and freshwater environments.

2) The Role and Mechanisms of Nuclei-induced Calcium Carbonate Precipitation in the Coastal Carbon Cycle: A First In-depth Study.
One of the most important and fundamental pathways in the marine carbon cycle is formation of CaCO3 minerals (e.g., calcite and aragonite), which may occur through biological production and abiotic (chemical) precipitation of CaCO3. Understanding and quantifying the production of CaCO3 are essential to characterize the marine carbon cycle and to project responses of marine ecosystems under anthropogenic CO2 perturbations. The goal of this project is to conduct the first comprehensive, in-depth study to evaluate the significance of NICP as an in-situ biogeochemical process. The summer project will include planning and setting-up controlled lab experiments in which the effects of suspended materials (e.g. dust and river-borne particles) on the dissolved CO2 system will be studied. The summer student will also analyze and synthesize the results.

3) Development of low-cost environmental sensors for river monitoring
The impact of environmental change on riverine ecosystem requires sustained observations of the river system. Of all ecosystem impacts, the quality of the water is a serious concern as it provides water security to billions of people. Cleaning and rejuvenating the health of river ecosystems is the focal point of river basin management plans across countries. Currently, the scientific community faces a few challenges to address this issue, including poor spatial and temporal resolutions of monitoring programs, absence of integrated data fusion, and absence of on demand auto-sampling capability. The only way forward to address these challenges is to use/develop state-of-the-art in-situ river monitoring observatories that can provide real-time data. The goal of this project is to design and develop low-cost, multi-parameter, water quality monitoring platforms that would consist of several in-house developed sensors and auto sampling capability for durable and reliable real-time monitoring. The summer project is to work with a group of chemists and engineers to develop and test low-cost oxygen, pH, and conductivity sensors to be deployed in river systems. These sensors are substantially cheaper than most of commercial sensors so that we can deploy them in large quantity to significantly improve river monitoring.

Zhaohui 'Aleck' Wang's profile

Marine Policy Center

Studies of Coupled Nature-Human Systems

Porter Hoagland, Hauke Kite-Powell, Andy Solow and Di Jin

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This figure depicts the economic geography of global sea cucumber exploitation from work undertaken by 2017 SSF Kate Rawson from Mount Holyoke College. Temporal isoclines show fisheries expanding as those more proximate to the main Asian market become overexploited and fail to meet demand. Colored lines represent the global distribution of sea cucumber fisheries within a given decade; specific starting years of some fisheries are labeled over the general location of the largest city (by population) within the participating country.

Researchers at the WHOI Marine Policy Center (MPC) conduct social scientific research that integrates economics, policy analysis, and law with WHOI’s basic research in ocean sciences. While MPC’s research is based in rigorous academic disciplines, such as economics, much of it is applied in nature and motivated by current issues in coastal and marine resource management. Areas of recent research include: human responses to shoreline change; the economic effects of harmful algal blooms; the consequences of channel deepening in major estuaries; ecosystem-based fisheries management; aquaculture development and fisheries management in developing countries; and coastal and marine spatial planning. Students are offered the opportunity to choose project topics from a list of current projects or to develop their own projects. Many MPC student projects involve exploring the impacts of human activities on the coastal or marine environments by linking economic models to models of natural systems.

Marine Policy Center

Large-scale seaweed farming systems: Hauke Kite-Powell
Researchers at the WHOI Marine Policy Center (MPC) are working with scientists and engineers at WHOI and at other institutions to develop technologies for potential future large-scale ocean farming of seaweeds, including kelp and tropical species, as a feedstock for biofuel. One major challenge is to bring the cost of large-scale ocean farming down so that marine feedstocks can be competitive with land-based production. Farm location, layout, gear design, and operating paradigms all affect both the capital and operating costs of the farm, and the biological yield from the seaweed crop. This project involves the use of spreadsheet models to identify the key parameters in farm design, operations, and siting that will determine economic viability. Additional project information

Entanglement risk modeling: Hauke Kite-Powell
Researchers at the WHOI Marine Policy Center (MPC) are working with members of the protected species programs at NOAA and the New England Aquarium on ways to estimate the risk posed to North Atlantic Right Whales and other protected species by new types of ocean activities such as aquaculture. Entanglement in fishing gear is a major source of injury and mortality for marine mammals. As interest grows in farming shellfish, seaweeds, and finfish in waters off New England, understanding and managing these risks becomes critically important. The project involves working with GIS data on species abundance and spreadsheet models of entanglement risk to estimate risk from various types of aquaculture gear in locations off New England. Additional project information

Mobile shellfish hatchery systems: Hauke Kite-Powell
Researchers at the WHOI Marine Policy Center (MPC) are working with WHOI engineers and commercial shellfish hatchery operators in New England to develop a mobile shellfish hatchery system. This mobile hatchery, packaged into a standard 20 foot shipping container, can be deployed on short notice to locations where shellfish seed is needed, without the need for permanent dedicated waterfront real estate. The project involves refining the design and optimizing the economics of the mobile hatchery system in advance of anticipated prototype construction in the fall/winter of 2019. Additional project information

Physical Oceanography Dept.

Physical-biological processes in western boundary current eddies

Ke Chen
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Sea Surface Temperature (SST) showing Gulf Stream meanders and warm-core rings on May-05-2006 (a) and in the last five years on Jun-02-2011 (b), Mar-23-2012 (c), May-31-2013 (d), Jun-08-2014 (e), and Jun-11-2015 (f). Open circles in black dashed lines denote the approximate locations of WCRs. Cold-core rings are also visible at times, e.g., on 2012-03-23.

Ke Chen is a physical oceanographer broadly interested in studying processes over the continental shelf and the adjacent slope, and how the coastal ocean interacts with the large-scale atmosphere and ocean. Research topics include frontal circulation and biophysical interactions, shelf-slope exchange, heat balance, and atmosphere-ocean interaction. Research approach includes a variety of numerical models together with observations for integrated understandings.

A potential project for the summer of 2019 is the physical-biological processes in western boundary current eddies. Mesoscale eddies in the western boundary current systems include warm-core and cold-core rings. They are generated on both sides of the western boundary current, and exert significant impact on the physical and biological environments of the slope seas and marginal seas, which are major contributors to the global primary production. Compared to that of eddies in the open ocean, the role of GS WCRs in the biophysical processes of the shelf-slope system has received less attention, and contrasting results exist. This project will elucidate the key biophysical mechanisms by investigating the photoautotrophic ecosystems and the dominant physical processes controlling the vertical transport in these rings. Research activities will include analyzing satellite observations of sea surface height, sea surface temperature, and chlorophyll in both warm- and cold-core rings in the Northwest Atlantic. Depending on the progress, other western boundary current systems, e.g., Kuroshio and East Australia Current can also be included for a global-scale understanding. The analysis of satellite data will be compared with numerical simulations to better understand the dynamical processes.

Ke Chen profile

Storm Effects on Shelfbreak Frontal Variability

Glen Gawarkiewicz
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The Ocean Observatories Initiative Pioneer Array is a multi-scale inter-disciplinary shelf break observatory south of New England. A summer project examining recent storm events and the associated oceanic Shelfbreak Frontal response is encouraged. The tasks involved include downloading, processing, and analyzing oceanographic and meteorological data from the observatory, assessing frontal response in light of theories of wind forcing of fronts, and examining recent storm events in the context of climate change in comparison with storms from the past. A background in both oceanography and atmospheric science is preferred but not necessary.

Glen Gawarkiewicz profile

Evolution and Transformation of South Atlantic Water Properties

Alison Macdonald and Sachiko Yoshida
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Alison Macdonald is an observational physical oceanographer interested in the transport and variability of ocean waters and their properties. Sachiko Yoshida has worked with a variety of observations including those with regional and full basin focus, hurricanes and the Argo float program. We are seeking a student interested in joining our investigation of decadal-scale and along path changes in water mass properties in the subsurface South Atlantic.

The South Atlantic is crossroads where waters from many different regions of the World Ocean meet on their journey through global overturning circulation. In this complex setting waters are not only being transformed through mixing, but also appear to changing in time. These changes include changes in temperature and salinity, which can cause changes in sea level, as well as in anthropogenic carbon content – the basis of ocean acidification. We foresee two possible aspects of this investigation in which a student could be entrained. The first is observation based and will make use of thousands of profiling float observations of temperature and salinity to place our previously calculated estimates of property changes over approximate 10-year periods in the context of annual and sub-annual variations. The second is model-based and will use high-resolution ocean model data and particle tracking techniques to better understand the pathways of particular water masses as they traverse the subtropical South Atlantic.

Alison Macdonald's profile

Sachiko Yoshida's profile

Article: Antarctic Bottom Waters Freshening at Unexpected Rate

International Argo Project

Deep Western Boundary Current in the South Atlantic

Physical-biological interactions, upper ocean dynamics, submesoscale processes

Amala Mahadevan
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PastedGraphic-1_449973My research focusses on the physical-biological interactions within a dynamic ocean environment and asks how physical processes affect the growth and distribution of phytoplankton. The majority of oceanic phytoplankton are grazed by zooplankton, and the efficiency of the carbon cycle depends on species interactions that need to be better understood. The aim is to develop models for the collective behaviors and foraging by zooplankton and couple these to models for the growth of phytoplankton, all within a dynamic flow environment. Most ecosystem models account for grazing through phytoplankton-zooplankton co-existence and do not account for zooplankton behaviors. The project will examine the zooplankton foraging behavior on grazing rates and trophic interactions. The results will contribute to our understanding of species interactions that affect the export of particulate organic matter and biological pump.

Amala Mahadevan's lab

Sea Level Change

Christopher Piecuch
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Christopher Piecuch is a physical oceanographer interested in the physics and statistics of regional and coastal sea level variability and change. He uses a combination of computer models, mathematical theory, probabilistic methods, and observational data to identify how and why sea level has changed in the past, with the hopes of informing projections concerning future sea level change.

Potential projects would focus on understanding the observed and modeled sea level changes with a particular focus on the United States east coast. Specific research topics could include characterizing the statistical nature of recent coastal sea level changes, understanding the relationship between coastal sea level and the large-scale ocean circulation of the North Atlantic, or studying how variations in river runoff effect changes in sea level at the coast.

Christopher Piecuch's profile

Air-sea interaction and climate dynamics

Hyodae Seo
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Landfalling Atmospheric Rivers in the western US: Role of coastal ocean

AR_SSF_510013I am interested in a potential project that relates the coastal oceanic processes in the US West Coast to landfalling Atmospheric River events (ARs). ARs are characterized by strong low-level wind, transporting high water vapor content from tropical air masses to the midlatitude. When AR inflows make landfall in regions of high topographic barriers, such as in the western US, they often bring heavy precipitation accompanied by extreme streamflow events and flooding. I hypothesize that the structure of ARs and the resulting continental precipitation are modulated by the coastal oceanic conditions along their path to the western US. We will aim to identify the coastal oceans’ response and impacts by analyzing various coastal buoys and mooring arrays as well as satellite and reanalysis datasets and high-resolution model simulations. We can also attempt to diagnose the influence of decadal modes of climate variability on the probabilities of extreme rainfall events associated with ARs using long-term climate model outputs.

Hyodae Seo's website

Seasonal and Interannual Variability of Arctic Sea Ice

Michael Spall
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I am a physical oceanographer with a broad range of interests related to the oceanic general circulation and climate. I generally approach problems from an idealized perspective through the development of theories and the application of simplified numerical models. The goal is to gain a fundamental understanding of how a particular system behaves, how it depends on controlling parameters (forcing, environment), and, when possible, to test this understanding against observations of the real ocean. Sea ice thickness and areal extent in the Arctic Ocean have been in decline over the satellite era (1979-present), although the trend is not monotonic and there is significant seasonal and interannual variability. Sea ice is a crucial component of both the Arctic ecosystem and the global climate. Depending on the student’s interests, there are several potential projects for the summer of 2019 that relate to understanding and predicting this time-dependent behavior. A recently developed theory for the steady ice thickness and transport could be extended to consider time-dependence. Existing idealized computer models of the Arctic Ocean could be run under time-dependent forcing and compared with the theory and observations. Finally, satellite observations of ice motion and/or thickness, together with atmospheric reanalysis data, could be analyzed to test the steady theory or to develop a better understanding of the observed seasonal and interannual variability. Any one or a combination of theory, modeling, and observations could form the basis for a summer project on the seasonal and interannual variability of Arctic sea ice.

Michael Spall's profile

Climate Science

Caroline Ummenhofer
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Schematic of the effect of Indian Ocean sea surface temperature (SST) anomalies for rainfall in Indian Ocean rim countries in model simulations for the March-May (MAM), June-Aug. (JJA) and Sep.-Nov. (SON) seasons. Specific regions of SST anomalies (dashed boxes) are used in the model experiments. The anomalous rainfall associated with these SST regions is shown by circles around the Indian Ocean rim countries. Filled (empty) circles denote an increase (decrease) in rainfall (as percentage change), with the size of the circle reflecting the magnitude of change and the color of the circle the season.

Understanding past climate variability by synthesizing coupled climate models and paleoclimate records

Ummenhofer’s group focuses on ocean-atmosphere interactions, variability and change across different components of the climate system, and the resulting regional impacts. In particular, we aim to develop an understanding of the underlying mechanisms of the ocean’s role in regional climate, with a focus on rainfall variability, droughts, and extreme events across a range of spatial and temporal scales, from individual synoptic events to interannual, decadal variability and beyond. Research addresses both present-day climate conditions, past variability over the last millennium, as well as projected changes in a warming world.

Potential projects will address how variability in rainfall and temperature on land (e.g., in Canada, Southeast Asia, Australia) or coastal ocean regions over previous centuries are influenced by large-scale ocean variability in the Atlantic and Indian Ocean. Insights about the mechanisms behind these links gained from climate model output will be compared with paleo proxies, such as stalagmites, bivalve shells, corals, or tree-ring records, to understand long-term changes in hydroclimate and bio-physical interactions.

Caroline Ummenhofer's lab

US Geological Survey - Woods Hole Coastal and Marine Science Center

Estuarine and Wetland Processes

Neil Ganju
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Ganju_image_509037Estuaries and wetlands are dynamic environments where complex interactions between the atmosphere, ocean, watershed, ecosystems, and human infrastructure take place. They serve as valuable ecological habitat and provide numerous ecosystem services and recreational opportunities. We aim to quantify and understand estuarine and wetland processes through observations, geospatial analysis, and numerical modeling. We have several research opportunities, including: analysis of new geospatial data sets on wetland vulnerability across the United States, modeling of seagrass vulnerability to climate change, and investigating wetland geomorphic change from drone imagery. There are also opportunities to participate in fieldwork and learn oceanographic measurement techniques at Cape Cod National Seashore and other sites on the Atlantic coast as desired. These projects would benefit from a fellow with skills in quantitative analysis, Matlab/Python/R, and/or GIS, and enthusiasm for estuaries!

Estuarine Processes, Hazards and Ecosystems

Coastal Wetland Science

Meagan Eagle Gonneea
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USGS_SSF_2018_Gonnea_479853Coastal wetlands have experienced a dramatic reduction in area over the past century since they occur at the nexus of population growth and dynamic environmental change, including rising sea level and temperature and enhanced nutrient loads. Salt marshes are coastal ecosystems that provide a wealth of services, including bird and fish habitat, storm surge protection and carbon burial. This last ecosystem service is of interest due to rising atmospheric carbon dioxide (CO2) levels primarily driven by the burning of fossil fuels and land use changes. Research in the Environmental Geochemistry group at USGS focuses on how these critical habitats respond to stressors, such as sea-level rise, and management decisions, including managing hydrologic flow. We have a range of capabilities, from field sediment and water collections, to laboratory carbon and radionuclide analyses. We work collaboratively with scientists and land managers from WHOI, the Waquoit Bay National Estuarine Research Reserve, the Fish and Wildlife Service, the National Park Service and local management officials. We seek interns who are interested in coastal wetlands, with potential projects ranging from sediment coring and analysis to vegetation analysis to mapping products.

Woods Hole Coastal and Marine Science Center - Environmental Geochemistry

Coastal morphology, natural hazards, and image analysis

Chris Sherwood
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Coastal protection at Sandwich Town Neck Beach, MA. Drone image taken Feb. 14, 2017 by P. Traykovski, WHOI.

The USGS conducts research to assess natural hazards to coastal regions. Recent tools include unmanned aerial systems (drones) and multi-view photogrammetry (also known as structure from motion). We use these tools to make super-high resolution maps of beaches, dunes, and wetlands. In turn, these maps are used to evaluate susceptibility to storms, and as input into numerical models of morphological evolution and coastal erosion. Summer students have the opportunity to choose from a number of related topics using data from local beaches and wetlands. These include analysis of images using structure from motion and/or neural networks, analysis of oceanographic data (waves, currents, water levels) and their relation to coastal changes, or running and evaluation of numerical models for waves, sediment movement, and morphological change. Enthusiasm for GIS and coding (Matlab, Python) is necessary, but extensive experience with those tools is not.

USGS Woods Hole Coastal and Marine Science Center

Nearshore and Coastal Processes

John Warner
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Warner_figure_479873As a scientist at the US Geological Survey (USGSG) Coastal and Marine Science Center in Woods Hole, I focus on understanding nearshore and coastal ocean processes using observations and numerical models, concentrating on the interactions of winds, waves, and coastal currents that generate nearshore morphological changes. This research strives to understand the physical processes that cause coastal change to ultimately improve our ability to predict these changes. One area of active research is the investigations of cross-shore processes such as wave asymmetry and wave-current interaction that drive cross-shore sediment transport. Summer students would have many opportunities, depending on their interest, such as analyzing data collected recently from a series of tripods measuring waves, water levels, bottom stress, seafloor bedforms, and sediment transport at Matanzas Inlet, FL. We also utilize numerical models to downscale simulations of large scale storm events to drive focused applications of storm impacts to examine nearshore processes such as impacts from Hurricane Matthew (2016) including surge, runup, and barrier island breaching. The combinations of observations and numerical models provide a more comprehensive overview of the processes driving coastal change.

USGS Woods Hole Coastal and Marine Science Center

Coastal Change Processes Project

Coastal Processes (coastal geology, GIS, landscape ecology, civil engineering)

Sara Zeigler and Ben Gutierrez
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Barrier islands and other coastal landforms are highly dynamic systems, changing in response to wind, wave action, water levels, currents, and vegetation. A variety of disturbances are responsible for natural dynamism in these landforms, including both pulse-type, short-term perturbations (e.g., storms) and press-type, persistent forcing (e.g., sea-level rise). A variety of species have evolved within these dynamic coastal systems, developing niches that allow them to persist in changing environments. One such species is the federally threatened piping plover (Charadrius melodus), which nests along the North American Atlantic coast in recently disturbed sandy habitats. However, humans are changing this disturbance regime and the expression of disturbances throughout the species’ breeding range, which have led to population declines for this species. For example, climate change is predicted to alter the intensity and frequency of coastal storms in many parts of the world. Understanding how the storm regime is changing throughout the species’ breeding range and how that may effect the species at the population level are important for managing habitats for this threatened species. We seek an intern with experience with ArcGIS and coding (such as Matlab, R, Python) to assist with compiling (i) historical hurricane paths provided by the U.S. National Oceanic and Atmospheric Administration, National Hurricane Center and (ii) piping plover nesting and population data from the U.S. Fish and Wildlife Service.

Sara Zeigler profile

Sea-level Rise Hazards and Decision Support

Beach-dependent Shorebirds research group

Predicting Piping Plover Habitat