2022 Projects and Mentors

Applications for the 2022 MBARI internship (June 6 – August 12) will be accepted through February 7, 2022 at 8 am (Pacific).

Applications have to be received by 0800 hours PST (8:00 am in Pacific time zone) on February 7th, 2022. Electronic submissions to intern-application@mbari.org are preferred. Incomplete or late applications may not be considered.

Clearly identifying a specific research interest/area is an essential part of the application process. Additional projects may be added so please check this page prior to submitting your internship application. Please contact George Matsumoto if you have any questions. Links to the mentors’ home pages have been provided (when available) so that you can learn more about the various mentors, please DO NOT contact the mentor directly.

Application information can be found here. 

Note: PDF format is preferred for all documents and please put your name in the subject heading for all emails and ask those that are writing a letter for you to do the same. The letter can be addressed to the Selection Committee.

MBARI is an equal opportunity employer.

Jim Barry and Steve Litvin
Biology and Ecology of Seamount Ecosystems: Research on the biology and ecology of seamount ecosystems, including coral and sponge communities at Sur Ridge off Central California and octopus breeding colonies at hydrothermal warm springs along the foothills of Davidson Seamount are a central focus of research in our lab. Our research ranges from linkages between ocean conditions (e.g., currents, oxygen, temperature, pH, carbon flux) and coral distribution and conditions, to the biology of breeding octopuses. We use various platforms (ROVs, AUVs, oceanographic moorings) and sensors (imaging systems, current meters, chemical sensors) to observe and measure these ecosystems.  Opportunities in our lab for a summer internship would fall within this spectrum of research, including analysis of video imagery in relation to high resolution mapping data, the association of corals with current patterns across Sur Ridge,  or the biology of animals inhabiting warm springs at the base of Davidson Seamount.

Mari Bif
Chemical Sensors Program: Biogeochemical floats have been deployed in the world’s oceans for almost two decades, and provide valuable high-resolution chemical data so we can better understand changes in the marine ecosystem and make better climate-related predictions. Our group develops chemical sensors, produce biogeochemical floats to be deployed globally and process float data that become available near real-time (See go-bgc.org and soccom.princeton.edu for more information on the floats and our current projects). We invite an intern that has interest in data analysis of biogeochemical float data. This project focus in the Northeast Pacific Ocean, and will investigate the effect of marine heatwaves in the local biological carbon pump using data collected by the floats that are already operating in the region. Ideally, the candidate would have familiarity with programming language and a preference for the marine chemistry/biogeochemistry field. During this internship, the candidate will be exposed to sensor development and calibration on a daily basis and will have the opportunity to get involved in laboratory experiments, depending on the interest.

Magdalena Carranza
Turbulence-driven bio-physical interactions. Upper ocean turbulence influences the distribution of heat, biogeochemical tracers and plankton in the surface layer. Biogeochemical tracer measurements have been collected in the Monterey Bay from Spray gliders and from the Coastal Profiling Float (CPF), in development at MBARI. Recently, we have enhanced the capability of the CPF to measure ocean turbulence by adding a turbulence sensor package to the full suite of biogeochemical sensors. I am interested in hosting students with interests in advancing process understanding of bio-physical interactions that shape phytoplankton and tracer’s distributions in the upper ocean. These can span a broad range of spatio-temporal scales in ocean conditions, from diurnal driven by the sea-land breeze to atmospheric weather phenomena or several weeks associated to oceanic fronts, as well as ocean-atmosphere weather scale interactions. The project would involve analysis of the existing in situ observations from profiling floats and/or gliders in the Bay, in combination with satellite observations that can provide context, as well as exposure to field experience by assisting with deployments of the CPF in the Bay from the R/V Paragon. Some background in physical oceanography, and basic programming skills in MATLAB (R or python) would be advantageous, but not required.

Colleen Durkin
Image analysis: Carbon is sequestered in the ocean through complex ecological pathways.  First, phytoplankton fix organic carbon through primary production in the surface ocean.  This carbon can be transported away from the atmosphere and into the deep ocean through sinking particles (cells, aggregates, fecal pellets, detritus).  These particles are transformed by animals and microbes living in the deep ocean, which can either enhance or attenuate its downward transport to the seafloor, where carbon is sequestered for long time periods. This intern project will examine the microscopic details of the biology that controls carbon export using in situ imaging datasets that resolve the types of particles sinking into the deep ocean.

Duane Edgington
Automated classification of deep-sea imagery: MBARI has a rich collection of underwater video and photographs, much of which has been professionally analyzed and curated. We are exploring state-of-the-art automated classification and analysis techniques. This intern will join us in this exploration, testing selected techniques against collections of underwater videos or images to detect and classify organisms of interest to MBARI scientists. One area we are exploring is weakly supervised methods. A background in computer science is required; coursework or experience in machine learning and computer vision would be an ideal background.

Steve Haddock
Bioluminescence and jellies: This intern will select from a range of topics related to the biodiversity, ecology, bioluminescence, and fluorescence of gelatinous zooplankton. Depending on the intern’s specific interests, the project could involve molecular biology and sequence analysis, behavior, morphology, chemistry, processing of oceanographic data, or analysis of transcriptome data from a variety of deep-sea organisms. For an interested candidate, there is also a possibility of contributing to the development of a plankton web page. Successful applicants will show a special interest in one of these sub-topics, and have a passing familiarity with the literature and subject matter. The goal for the summer is for the intern to contribute results to a publication in a peer-reviewed journal.

Lis Henderson and Francisco Chavez
Anchovy natural history: Within the California Current System (CCS) pelagic forage fish function as critical energy conduits between upwelling driven productivity and upper trophic levels (seabird, mammals, piscivorous fish). Historically, Northern anchovy and Pacific sardine have alternately dominated the region with anchovy being the current regime. We welcome an intern who is interested in a project that uses our expanding collection of genetic and morphometric anchovy data to answer questions regarding spawning seasonality, diet, and population variability.

Irene Hu and Yui Takeshita
Eddy covariance instrumentation: We are seeking an intern to aid in the development of a multi-analyte eddy covariance instrument. Eddy covariance (EC) is an in situ technique for measuring the fluxes of biogeochemicals between the seafloor and overlying water. It is typically limited to a single parameter, such as dissolved oxygen; EC of multiple analytes is rare, but it is a powerful tool for studying multiple processes at once. In this project, we are developing an O2 and pH EC system that allows for investigating both net community production and calcification dynamics over ecosystems such as coral reefs and seagrass meadows. Potential intern activities include the development of embedded C/C++ software, design and troubleshooting of electronics, mechanical design and fabrication, test deployments in MBARI’s test tank, potential field deployments, and data processing and analysis using MATLAB.

Kakani Katija, Paul Roberts, and Joost Daniels
Bioinspired Design: As organisms live and develop in a changing ocean, how do these environmental interactions impact their ecology and behavior, and how can we learn from these strategies for application to bioinspired design? Potential intern projects will use an integrated design, ecological, and engineering approach for in-situ or ex-situ methods. This includes bringing the laboratory into the ocean by developing advanced illumination, imaging, and sensing tools for remote or autonomous underwater vehicles (ROVs or AUVs) that provide insight on how marine organisms function within their natural environment. Conversely, we will bring the ocean into the laboratory through capture of imaging data on live specimens in the lab, and using advanced analysis tools to reveal their structure and function. For 2022, intern projects may involve the development or use of FathomNet to aid in machine learning technologies that leverage the image library, the capture and analysis of 3D imagery from a variety of lab, ROV, and AUV-mounted single- and multi-camera systems (e.g., DeepPIV, EyeRIS), or robotics projects that enable in situ or laboratory biological observations. Interns can gain experience in a variety of areas including image analysis, programming, machine vision, machine learning, robotics, fluid dynamics, biomechanics/ecomechanics, and mechanical/electrical/optical engineering.

Astrid Leitner and Bruce Robison
Midwater ecology: The midwater spans the water column from below the surface layer all the way down to the seafloor. This makes the midwater the largest habitat volumetrically on our planet! The animal communities that live in this habitat are important, contributing to the global carbon cycle by helping to export carbon from the surface ocean into the deep for long term storage and are made up of many animals that are key prey species for commercially important fish like tunas and rockfishes for example, and even whales. The midwater is also home to mysterious and still undiscovered animals, with so many discoveries left to make. Typically, we have several possible projects that we think are feasible for the summer’s work, and we discuss them with the intern, who can select one of them or suggest another. One current avenue of research in our lab is the influence that the canyon has on the midwater community. A potential project would focus on predator prey interactions at the canyon wall by seafloor predators like rockfishes on midwater animals like krill, shrimps, and jellies through analysis of underwater time lapse video and ROV video. This project is not suitable for a virtual program.

Jacki Long and Yui Takeshita
Ocean productivity from bio-optical sensors on autonomous platforms: This work focuses on utilizing the interactions of light, water, and the particles within, to better characterize the base of our ocean’s food web (e.g., primary producers such as phytoplankton). With unprecedented changes occurring to our oceans, new observing systems have allowed us to fill in a global baseline for primary production, the first step in effectively monitoring changes due to anthropogenic activity. One such method of observation includes remote sensing by satellites. While near-daily global observations are achievable, many gaps still exist, especially in coastal environments. This work will help to fill gaps in those gaps by leveraging in situ data from on-going autonomous vehicle deployments equipped with bio-optical sensors along the California coastline. During the summer, the intern can be involved in a variety of different aspects of oceanographic research, including but not limited to interpreting new data from autonomous platforms such as gliders and floats, deployment and recovery in nearby field sites, comparing satellite-based products to in situ observations, and collecting in situ data during a week-long research cruise in June that will contribute to the project.

Gene Massion
Autonomous coastal profiling float (CPF): We have a broad spectrum of potential projects spanning a range of disciplines suitable for a summer intern. An overview of the project can be found at https://www.mbari.org/coastal-profiling-float/.  We are looking for an intern with some experience and a strong interest in one or more of the following topics and a particular interest in developing technology for oceanographic research applications.

1) Design and development of embedded microcontroller based systems.  The ST Microelectronics STM32 family is of particular interest.
2) Design and development of embedded C/C++ software.  Training and/or experience in rigorous software testing methodologies is of particular interest.
3) Automated test systems and web based applications using LabView.
4) Mechanical design of robotic oceanographic research equipment using Solidworks CAD tools

George Matsumoto
Intern logistical coordinator: This intern will be assisting with the MBARI intern program. This will likely include travel logistics during the program as well as coordinating some weekend educational activities. It is expected that this intern will also be working on his or her own independent research project. The successful applicant will have been a past intern in the MBARI intern program (ideally prior to 2020) and will stay in the same housing as the interns. Letter of recommendation is not required, but please elaborate in your application letter on your proposed research project for the summer (this should be discussed ahead of time with a mentor).
GO-BGC Adopt-A-Float project: This intern would be responsible for helping to coordinate the Adopt-A-Float program and assist with outreach to educators and other interested partners. This intern would be sponsored by the National Science Foundation as part of the Global Ocean Biogeochemistry Array program and in association with the NSF funded Southern Ocean Carbon and Climate Observations and Modeling (SOCCOM) project.

Monique Messie and Katie Pitz
Physical/biological variability in Monterey Bay from AUV and eDNA data: This project will explore a set of recurring surveys of Monterey Bay by an autonomous underwater vehicle (AUV) spanning the 2016-present time period. The primary dataset will be a set of environmental DNA (eDNA) samples collected by the AUV that provide information on local phytoplankton, zooplankton, and fish communities. These eDNA data consist of metabarcoding results targeting these communities; they are compositional data on the relative abundance of organisms within these water samples. Data from AUV Dorado also include physical measurements such as temperature and salinity, biological measurements such as fluorescence and bioluminescence, and derived proxies for autotrophic and heterotrophic plankton. The intern will generate products describing the biological variability in Monterey Bay as described by eDNA samples. Topics include, but are not limited to, seasonal and spatial variations, links across trophic communities, identification of environmental drivers, prediction of community composition from other AUV data using machine learning, and validation of plankton proxies. Preference will be given to applicants with experience in Matlab, R, or Python programming.

Raúl Nava and Susan von Thun
Science Communication Intern: This project is ideal for an intern with experience in translating science and technology concepts into written and visual content for the general public. The intern will work with MBARI staff, scientists, and engineers to develop stories about MBARI research. Responsibilities will include creating content from MBARI’s image and video archive and developing compelling stories about our research for our website and social media outlets. We are seeking a candidate with a background in outreach and communication, preferably with interests in science and technology. Strong writing and editing skills are required. Skills in web editing, video editing, other visual content creation (i.e. animations, infographics, illustrations) and photography are desired, but not required. Applications may include writing samples and a portfolio in addition to the other required materials.

Ed Peltzer and Bill Kirkwood
BioRaman: Recent developments with laser Raman spectroscopy (LRS) have revealed surprisingly successful applications in both biochemistry and biotechnology. Although the MBARI DORISS (Deep Ocean Raman In Situ Spectrometer) ROV deployed systems were initially developed to address chemical and geological questions, there is now considerable interest to see if this system can be adapted and modified to answer questions about the health of organisms in the marine environment. The primary objective of this summer intern project will be to take the first steps in applying laser Raman spectroscopy to study marine organisms. Among various potential applications of LRS, one priority for the internship will be to evaluate the utility of LRS in assessing the “health” or condition of marine organisms. For example, is LRS a useful tool for assessing the lipid content of coral tissues in relation to their reproductive condition (e.g., presence of eggs)?  Initially, we will be working with live marine specimens collected and returned to the laboratory with the hope of someday using the DORISS system on a ROV to conduct these studies at sea and in real time.

Ben Raanan and Yanwu Zhang
Multi-LRAUV Simulation Environment: Traditional ship-based methods for ocean observation are nowadays giving way to fleets of autonomous vessels that work collaboratively to capture meaningful and persistent information about the marine environment in locations and over periods never before possible. Alongside our growing fleet of AUVs, MBARI is developing tools for designing and validating next-generation robotic applications to help scale up autonomous operations and advance the ocean research they enable.
We invite you to join an interdisciplinary team of robotics and simulation experts at MBARI and Open Robotics and create simulation tools and models in Ignition to support rapid prototyping and testing algorithms and control software for multi-AUV applications. Under this project, you’ll have an opportunity to put your software engineering and computer science skills to practice, develop new multi-AUV applications for ocean exploration in a simulated environment, and deploy your final products to MBARI’s fleet of Long-Range AUVs for testing at sea. A software engineering/computer science background is preferred. Experience developing simulation tools in Gazebo/Ignition would be a plus.

John Ryan and Danelle Cline
Ocean Soundscape Research: The ocean holds a world of sound generated by marine life, the earth, and human activities.  MBARI has been recording sound in the center of Monterey Bay National Marine Sanctuary for over six years using a hydrophone (underwater microphone), a little instrument that produces big data – about 24 Terabytes per year.  Understanding the information contained within this mountain of data requires automated signal processing and machine learning methods that can be used to detect and classify specific sound sources and characterize their variation through time.  This project will offer the intern multiple opportunities in ongoing development and application of sound analysis, including studies of cetaceans, earthquakes, shipping noise, and sound occurrence patterns that emerge from statistical analyses of the sound archive.  This work may include exploring unsupervised learning for data exploration and labeling or supervised learning using convolutional neural network architectures. A background in computer science is essential. Experience with acoustic data and/or development with Tensorflow or Pytorch will be advantageous.

Ken Smith and Crissy Huffard
Climate change and deep-sea community structure:  Using a 29 year time series study at 4,000 meters depth in the eastern North Pacific, we have found significant changes in the surface ocean processes related to food supply and benthic community responses at these abyssal depths. Time-series photographs taken hourly of the sea floor have shown major shifts in population densities and biomass amongst many dominant species of megafauna. Many megafauna have shown precipitous changes in population abundance and size over the entire time series that began in 1989. This intern project will examine the latest changes in megafauna populations over the time series, in relation to on-going changes in climate and upper ocean processes determined from satellite monitoring.

Yui Takeshita and Lenka Sraj
Coastal Biogeochemical Sensing Program: The ocean absorbs approximately half of the anthropogenic (human-related) CO2 emissions each year, effectively lowering the atmospheric CO2 levels and slowing the impacts of climate change. Therefore understanding how this oceanic carbon sink will change in the future is critical in predicting the climate trajectory of our planet. Our current understanding of the ocean carbon sink is largely based on ship-board measurements of the surface ocean partial pressure of CO2 (pCO2). However, such measurements are sparse in both space and time, potentially leading to large uncertainties. Autonomous robotic platforms such as profiling floats and gliders equipped with pH sensors can be used to estimate surface pCO2, representing a powerful new tool to vastly improve the number of pCO2 observations in the ocean. This project aims to improve the accuracy of pCO2 estimated from pH sensors through a series of laboratory and field experiments. Throughout the summer, the intern will work closely with a small team of researchers, and will be expected to aid in laboratory experiments, participate in deployments of underwater gliders, analyze data from autonomous platforms, and potentially participate in a 5 day oceanographic cruise near Monterey Bay.

Giancarlo Troni
Scalable Marine Robotics: Ocean exploration has been widely developed thanks to marine robotics, whose platforms are currently being used on several applications, such as accurately mapping the seafloor in high-resolution and continuously tracking animals in midwater. However, these platforms are not scalable, many are still too expensive to build and operate, and access to scientists, and therefore ocean exploration and discovery, is limited due to underwater vehicle navigation among others. Potential intern projects will use current MBARI’s robotics platforms to enable scalable marine robotics navigation in complex terrain. Efforts include sensor calibration and alignment of sensor data and visual-inertial navigation based on simultaneous localization and mapping (SLAM) framework. The work will combine elements of estimation, computer vision, software development and data analysis. Candidates should have basic competence in C/C++ and Python programming. Experience with robotics will be advantageous.


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