2026 Potential Projects

1. Interactive effects of multiple stressors on early life stages of vertebrates: The aim of this project is to understand the role of climate change stressors such as elevated carbon dioxide and hypoxia on early life stages of ecologically important fish species (e.g., Atlantic silverside). We have previously demonstrated that exposure of Atlantic silverside embryos to combined stressors (carbon dioxide and hypoxia) delayed development (time to hatch) and growth. We are currently investigating the biochemical and molecular changes underlying these phenotypes. Students will have the opportunity to participate in these studies. They will get hands on experience in conducting wet lab experiments as well as learn skills in biochemical, molecular and bioinformatic approaches.
2. Developmental neurotoxicity of environmental contaminants: The overall objective of this project is to understand the effect of exposure environmental chemicals on developing nervous system. Using zebrafish as a model system, students will have an opportunity to conduct developmental exposure experiments, use confocal imaging for quantifying changes in the nervous system and conducting gene expression analysis.

Aluru Lab website Neel Aluru's profile page

Our lab studies harmful algal blooms (HABs) and their response to environmental change. We work on developing new methods and sensor systems in lab and in field sites to understand the biology, ecology, and occurrence of the species that cause these blooms. Some projects a student may work on include: 1. Impact of ocean acidification on a toxic dinoflagellate The aim of this project is to assess how pH may impact the growth and toxin production of harmful algal bloom-causing dinoflagellates. Students working under this project may be involved in conducting a lab experiment, assisting with some field work at the nearby Cape Cod National Seashore, and/or analyze data collected from prior blooms. 2. Morphology changes throughout a bloom Dinophysis is a dinoflagellate that causes harmful algal blooms. They are “mixotrophic”, feeding on a specific prey in order to grow. This project aims to characterize visual changes (e.g., cell size, cell “fullness”, etc.) in automated microscope images across a bloom that lacks this specific prey. Students working on this project will learn how to handle large datasets in Python, and may assist with some nearby field work. 3. Effect of HAB species and toxins on shellfish Many of the harmful algal bloom species we study produce toxins that bioaccumulate in filter-feeding shellfish. This project would involve a lab experiment to expose shellfish to one or more HAB species and investigate the impact of that exposure on shellfish development, ingestion, and clearance rates. Students working on this project will be involved in developing and executing the lab experiment and analyzing its data.

Brosnahan Lab

Capt. Willy Hatch and scientist Camrin Braun deploying electronic satellite tags on an adult blue shark offshore from Cape Cod. (T. Sinclair-Taylor)

In the Marine Predator Group, we use computational, lab and field-based approaches to study how predators interact with their environment and what that can tell us about how the ocean works. In our completely unbiased opinions, we have the best jobs in the world! We get to spend our time asking questions like: How does temperature affect when and where sharks migrate? How does the highly dynamic nature of ocean physics, with all its interacting currents, drive the formation of biological ocean “hotspots”? Why do many predators dive below the ocean’s surface to the seemingly inhospitable ocean twilight zone where its dark and cold? To answer these questions we leverage a highly interdisciplinary ocean ecology toolkit that includes, for example, using and developing electronic tags, analyzing remote sensing data from satellites, and exploring data from all kinds of in situ ocean sensors carried by ships, robots, moorings and even the predators themselves! Potential projects for Summer Student Fellows might include: [1] designing your own analysis of predator tag data from our existing database of nearly 2,000 tagged animals (e.g. explore deep diving behavior by tagged mako sharks, migratory cues of tagged albacore tuna, etc); [2] building species distribution models and investigating dynamic ocean management approaches for managing highly migratory predator species (e.g. how does a fishery closure protect important shark habitat); [3] conducting lab experiments to test new approaches for less invasive animal tagging methods (e.g. do state of the art suction cups provide the necessary strength and duration of attachment for tagging sharks, tunas and billfish species). It is helpful to have skills coding in R or Python, but these are not required and some fluency with one coding language will be gained over the course of the summer regardless.

Marine Predators Group website

The Coy (Biology Department) and Apprill (Marine Chemistry & Geochemistry Department) labs are seeking a student to co-advise for the 2026 summer student fellowship program. This collaborative project will combine lab themes spanning marine microbial symbioses, virology, and ecology to understand microbiome-mediated health impacts on corals. Specifically, the project will contribute to understanding on the functional role of a common bacterial genera, Endozoicomonas, that is widely distributed among marine metazoans, often dominating healthy microbiomes of hard, reef-building corals. Prospective candidates should describe how their interests align with the proposed work, their enthusiasm to work cooperatively with others, and their organizational skills. The chosen candidate will develop experience in molecular biology, microbiology, coral reef ecology, and computational analyses. There will also be opportunities for exposure to a wide range of coral reef science through participation in Reef Solutions research updates at WHOI (https://reefsolutions.whoi.edu/) as well as through assisting with ongoing projects including those involving aquaria corals. The project will focus on samples and data from corals that harbor Endozoicomonas bacterial associates which we are following over time. In the photo, two divers are measuring the health of the algal symbionts of these corals using a pulse amplitude modulated fluorometer. The student will have the opportunity to work with field-collected data from these corals, in addition to genomics-based data.

Samantha Coy

Amy Apprill

The Stegeman Lab works on the mechanistic toxicology of pollutants and natural products. We are particularly focused on the biochemistry, evolution, and regulation of cytochrome P450 enzymes and their roles in biochemical toxicology. We are interested in the metabolism and biological effects of xenobiotics, such as PCBs, and natural products, including steroid hormones, in aquatic animals. We investigate how the structure-function relationships involved in the effects of these chemicals are related to the susceptibility of developing animals, and how these relationships may have changed over the course of evolution. We have worked in the lab with animals ranging from cnidaria, molluscs, tunicates, to fish, and bioinformatically in everything from giant viruses to humans.

Potential projects for a SSF include laboratory work such as characterizing behavioral toxicity in gene-knockout zebrafish; determining the metabolism of toxic chemicals from the EPA ToxCast database; or examining the gene expression responses of pollutant-exposed mussels. Bioinformatic explorations include the analysis of genome data in interesting invertebrate taxa or computational analysis of protein-ligand interactions.
Students can expect to learn about molecular and biochemical analyses of pollutant effects, behavioral neurotoxicity, or computational biology, depending on the project. Knowledge of PCR and/or bioinformatics tools would be helpful.

Lab website: https://www2.whoi.edu/site/stegemanlab

Mixotrophy in marine food webs In marine microbial ecology, mixotrophy is defined as the combination of phagotrophy (i.e., eating) and photosynthesis occurring simultaneously in a single organism. In pelagic food webs, mixotrophy generally occurs in two major forms; constitutive mixotrophs (CM) that have their own chloroplasts but also eat, and non-constitutive mixotrophs (NCM), which e.g., steal chloroplasts from their prey to photosynthesize. Mixotrophy functions to make food webs more efficient in transferring energy and organic matter to higher trophic levels through their dual metabolic capabilities and efficient recycling. We work with a wide variety of mixotrophs, including CM dinoflagellates, chrysophytes, and cryptophytes, as well as NCMs within the ciliate Mesodinium genus. Projects could include looking at predator-prey dynamics and trait trade-offs under different treatment conditions, or working with transcriptomic data to analyze changes in organelle and nuclear expression following sequestration by Mesodinium spp. Chemical defense in diatoms Oxylipins (i.e., oxygenated lipids) are signaling compounds produced by all life that have diverse roles, from maintaining homeostasis to acting as chemical defense molecules. In diatoms, a major group of marine phytoplankton, the production of oxylipins has been linked to cell stress (e.g. from nutrient limitation), allelopathy, and exposure to grazers. Increased production of oxylipins by diatoms has been shown to interrupt copepod reproduction and to inhibit protist grazers, thereby protecting their populations from grazing mortality. We aim to better understand how oxylipins effect protist grazers and competition with other phytoplankton. We will evaluate changes in predator and competitor behavior, physiology, and gene expression using dinoflagellate grazer and diatom cultures. Results from these experiments will help us to better understand the role of oxylipin production by diatoms, and their potential impacts on trophic structure in marine food webs.

Matt Johnson's lab website

Climate change is causing glaciers across the world to retreat, but we don’t yet fully understand how glacial retreat impacts marine ecosystems. This Summer Student Fellow project addresses how ice – including glaciers and icebergs – impacts marine biodiversity and food webs. The Fellow will analyze a set of samples collected in Patagonia, a region of southern Chile with numerous glaciers and ice-carved fjords. Samples were collected at 11 stations extending from immediately adjacent to 3 glaciers out into open water, providing an environmental gradient and also a window into near-future polar conditions. Environmental DNA (eDNA) was filtered from surface water at each station to non-invasively capture the full diversity of fauna, flora, and microbes.

The SSF will analyze these samples, gaining hands-on lab experience with DNA protocols and analyses. Working in collaboration with experts in ecology and eDNA (Annette Govindarajan) and polar biology (Kirstin Meyer-Kaiser), the student will learn how to analyze sequence data, statistically examine biodiversity in marine systems, and assess community shifts associated with environmental gradients. Ultimately, this work will help us better understand how glacial retreat impacts marine biodiversity and aid in predicting the impacts of climate change at the poles.

Kirstin Meyer-Kaiser Annette Govindarajan

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.

Mooney Lab

The Mullineaux Benthic Ecology Lab studies the resilience of seafloor animal communities to natural disturbances such as seafloor eruptions or other major environmental changes and uses that information to understand potential impacts of human disturbances including deep-sea mining and environmental change. We have two projects for undergraduates this summer:

• Investigating the recovery of animal communities at deep-sea hydrothermal vents after a catastrophic eruption in May of 2025 (sorting samples, identifying species, analyzing images, visualizing and analyzing data)
• Describing the species composition, and helping to detect and describe new species, in a newly discovered ecosystem inhabiting hydrothermal vent features that no longer experience active venting (sorting samples, photographing specimens, categorizing potential new species, analyzing images, visualizing and analyzing data)

This research broadens our understanding of the diversity and function of seafloor communities and informs policy on deep-sea mining. Our lab group values diverse perspectives and is committed to the highest standards of professionalism, including research integrity, collaboration, and respect for colleagues at all levels.

Mullineaux Lab

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 various forms of fisheries management in the face of environmental uncertainty, (2) how best to manage the spread of an invasive species, (3) phytoplankton population dynamics, (4) the population dynamic consequences of transgenerational or maternal effects, or (5) zombies.

Michael Neubert's profile page

Northeast U.S. Shelf Long-Term Ecological Research (NES-LTER)

Research in the Benthic Ecology and Nearshore Oceanography lab addresses the factors that determine the distribution and abundance of bottom dwelling organisms. We conduct our research in temperate and tropical environments, and our research interests include investigating the consequences of environmental heterogeneity, particularly hydrodynamic phenomena, on larval behavior, larval transport, larval dispersal, settlement, recruitment, and population dynamics. Our lab is also interested in using fundamental knowledge to address societally relevant problems such as the processes most relevant to biofouling in aquaculture. This summer, students in the lab will have the opportunity to research fundamental questions in larval behavior and ocean ecology and relate their findings and understanding to problems faced by oyster farms in New England. Depending on the student's interests, specific research questions may focus on topics such as latitudinal differences in larval settlement and biofouling, native versus invasive barnacles as biofoulers, and the relationships between biofouling intensity and local environmental conditions. Depending on the question, the student may participate in weekly and monthly visits to field sites, and analysis of metadata, including survey data of oyster farmers in New England.

Pineda Lab

My lab focuses on biological-physical interactions, addressing how environment influences animal behavior and distributions in coastal ecosystems and how those interactions affect trophic dynamics of zooplankton and fish. In order to address problems across a range of temporal/spatial scales, we use active acoustics in different platforms (vessels, moorings, cabled observatories, AUVs) combined with net sampling and physical measurements. There are three potential projects for a SSF student: (1) Characterizing zooplankton aggregations patterns in response to upwelling on the Alaskan Beaufort Shelf (2) Zooplankton and fish response to shelf break front in the Northeast U.S. Shelf waters Northeast U.S. Shelf Long-Term Ecological Research (NES-LTER) (3) Characterizing squid aggregation behavior in response to changes in temperature and salinity on the Northeast U.S. Shelf. The project will be mostly computer-based analysis of existing data sets using Matlab and Echoview (software for acoustic data processing). There may be opportunities to join calibration efforts of acoustic sensors at the WHOI dock.

More at: Sato Lab

My research interests focus on behavior and communication in marine mammals. Student projects in 2025 will focus on computer-based analyses of acoustic data and will most likely not have a field component. Students will learn to use the acoustic analysis software program Raven, and may also analyze data using Matlab based software, although no prior experience with either of these programs is needed. Possible projects include:

1. Analysis of a long-term database of recordings of bottlenose dolphins aimed at addressing a range of research questions about dolphin communication.
2. Analysis of acoustic recordings made in Wellfleet, MA as part of a project aimed at developing an acoustic mass stranding alert system for dolphins.

Laela Sayigh

My 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 (NES-LTER)

European green crab, named one of the IUCN’s “World’s 100 Worst Invasive Species”.

Our lab studies how – and how quickly – marine animals can adapt to new environments. We mostly study invasive species, which are extremely good at surviving and thriving in new waters. We use a range of approaches, including genomics, ecophysiology, ecology, and parasitology, and are interested in student fellows who want to develop their skills in those areas. Current research projects include adaptation to temperature in the highly invasive European green crab (pictured here) as it rapidly spreads on the west coast, adaptation to an invasive body-snatching parasite by a native mud crab, and the distribution and adaptations of marine microparasites using public genetic data. Our lab culture emphasizes professionalism, collegiality, and baked goods.

Tepolt Lab

Two potential projects: Virus Ecology and Evolution Lab

Figure. 1: Northern Star Coral (Astrangia poculata) collected at Woods Hole

Ocean waters sustain human activities and support diverse marine life, including corals (of special interest in our lab), which constitute less than 1% of the coastal ecosystem but hosts the highest biodiversity on Earth. Surprisingly, little is known about the role of viruses especially within marine eukaryotes. To address this gap in knowledge, our lab employs a multi-prong approach that involves computational biology approaches (‘dry lab’), omics-(metaT-metaG-metaProt-metabolomic) ('wet lab') approaches. In addition, to in vivo and in situ virus-symbiont-coral co-culture experiments to qualitative and quantitative assess the impact/or roles of viruses within marine eukaryotes under various anthropogenic stresses. Our goal is to uncover the intricate relationships between viruses and various ocean life forms, shedding light on their importance in ecology, evolution, ecosystem health and resilience within the global Oceans. Project: Isolation and Characterization of viruses associated with the cold-reef coral Astrangia poculata (Northern Star) In the ocean, viruses modulate microbial lifestyle as they are abundant (10⁷ viral particles per millilitre of seawater), significant killers (20-40% bacteria die per day) and are mechanisms of gene flow (~10²⁹ genes are transduced per day by ocean viruses). Beyond these more readily understood impacts, viruses are responsible for significant metabolic reprogramming such that virus-infected cells, or virocells, are entirely different entities from uninfected cells. However, despite these advances in our knowledge of ocean viruses, this knowledge is primarily derived from viruses infecting prokaryotes in seawater. Though impactful, how viruses impact marine invertebrates, specifically in corals is unclear. This project aims to isolate and characterize (both morphologically and genomically) viruses present in the cold-water reef coral Astrangia poculata (Northern Star), found within the Woods Hole seawaters. Viruses isolated (infecting both eukaryotic and prokaryotic hosts) will serve as a foundation for future coral-virus mechanistic studies in the lab. The student’s role will include:

• Collecting corals from surrounding seawater in Woods Hole.
• Isolate viruses from corals.
• Morphologically characterizing these viral isolates.
• Maintaining viral isolates in culture.
• Performing genomic characterization & computational biology approach on a subset of viral isolates using long-read sequencing using promethion oxford nanopore technology.

Preferred skills

• Basic microbiology skills
• Comfortable working on the command line
• Scientific diving certification (optional but would be great)

The student will be immersed in a world-class, highly collaborative research environment and gain hands-on experience in culturing coral-associated viruses and utilizing the WHOI HPC grid. They will have the opportunity to develop skills in molecular virology and computational biology, while also working with real-time sequencing technologies enabled by Oxford Nanopore. This technology is emerging as the next gold standard in biological sequencing and provides an excellent opportunity to gain experience at the forefront of innovation in the sequencing space. Upon successful completion of this initial project, numerous opportunities will be available to further expand the student’s research experience.

Wainaina Lab: http://virusecologyevolutionlabwainaina.com/