Mark Bradford, Improving forest regeneration from the belowground up: testing how whole-soil inocula influence oak seedling performance

Description: One challenge in eastern temperate forests can be regenerating biodiverse high value species, such as oak and hickory. The failure to regenerate oak and hickory is often attributed to site conditions, shade tolerance, or modern fire suppression but no one has examined how below-ground biotic interactions may be influencing regeneration. The desired tree species associate with ectomycorrhizal fungi (ECM), which expands their rooting network and function, allowing the trees to access nutrients in organic as well as inorganic forms. After a disturbance, ECM connectivity is sometimes limited, which may be impeding oak and hickory regeneration. One solution to redress the limitation of mycorrhizal inoculum has been to add mycorrhizal fungal inocula to regenerating species. The use of inoculants in other ecosystem types has led to commercial mycorrhizal inoculants being marketed to forest managers in temperate forests, but their effectiveness for establishing desired tree species appears untested in eastern temperate forests. Furthermore, research in other systems has suggested that transplanting a thin layer of soil, as an alternative means to inoculate beneficial organisms, may be more effective than commercial inoculum to improve regeneration success. We know from grassland systems that adding a local soil from a late successional stage grassland to a regenerating one can shift the plant community composition toward desired, later successional stages. In addition, the introduction of soil fauna through whole soil inoculation may mediate the effect of inocula through nutrient deposition from soil animal bodies and frass, by grazing on mycorrhizal hyphal networks, and indirectly through trophic cascades, thus altering the potential impact of inocula on plant growth and providing longer-term diversity and stability in the system. Comparisons of whole soil inoculant are lacking in regenerating temperate forests and must be tested for their effectiveness on high value tree species. This project tests whether whole soil inocula, by establishing the whole soil food web and changing soil function, improves natural regeneration of oak and hickory. As a SURES student, you will 1) measure a) native tree response to inocula, b) late successional soil fauna establishment, c) impacts on belowground soil function at experimental plots, and 2) analyze, interpret and write-up a component of the project following discussion and agreement with the PI and doctoral student. Over the 8 weeks, you will learn a variety of field and lab-based techniques, and begin the process of data and conceptual interpretation.

Location: New Haven, CT with weekly day trips to Yale Myers Forest for field work

Jenn Coughlan, Are incompatibility loci polymorphic?

Description: Darwin viewed hybrids as an evolutionary mystery: why would natural selection ever favor the production of unfit offspring? While there are many hypotheses for why hybrid dysfunction evolves, the dynamics of such incompatibilities are often unknown in organisms that naturally hybridize in the wild. We have uncovered a curious incidence of incompatibility between two wildflower species in which their hybrids exhibited stunted growth and an overactive immune system. We seek a highly motivated student to assist in surveying for this incompatibility in a broader set of crosses, and ultimately help us to identify the genes involved in hybrid dwarfism.

Location: New Haven, CT

Martina Dal Bello, Disentangling the relative contribution of bottom-up and top-down drivers of phage-bacterial biomass scaling laws

Description: Microbial food webs, encompassing bacteria, their resources, and their predators (viruses, protists and predatory bacteria) drive the cycling of elements and regulate the exchanges of gases with the atmosphere. While progress has been made in establishing some general rules governing the assembly of communities of heterotrophic bacteria on their resources, little is known about how assembly is shaped by the presence of predators.

Bacteriophages, i.e. viruses that prey on bacteria, are incredibly abundant and diverse, with an estimated 10³¹ virions on Earth and hundreds of phage species persisting in the human gut for years. The “virus to microbial cell ratio” (VMR) is a commonly used proxy for the strength of the relationship between phage and bacterial abundances. In aquatic habitats VMR is typically 10:1, though fluctuations in this ratio suggest that the relationship between viral and bacterial abundances is better captured by a power law, like other predator-prey systems. The human gut exhibits a very different ratio (1:1). In addition, the lytic lifestyle prevails in the ocean while lysogeny is more common in the gut, suggesting interactions between phages and bacteria might differ depending on the environment. What drives variations in VMR is largely unknown.

This project focuses on heterotrophic bacteria, their resources, and their phage predators, and asks: what determines observed variations in phage bacteria biomass ratios? We will implement a simple experimental set-up with three trophic layers: one nutrient, a primary consumer (bacterium), and a predator (phage). This allows us to tune the abundance of the bacterial host from both the bottom-up (via the type and concentration of the supplied carbon source) and the top-down (via the lifestyle of the phage, i.e., lytic or lysogenic). By measuring the phage-bacterium abundance relationships across nutrient conditions and phage lifestyles, we will assess whether there is one or multiple models (fixed-ratio or power-law model) predicting the curves based on the available nutrients, phage lifestyle, and their interaction. This will provide insights on the mechanisms underpinning observed differences in microbiome biomass scaling laws and “knobs” to tune, like nutrients, to steer communities towards desired VMRs.

This project entails isolating phages preying on natural isolates of E. coli from soil, sequencing them, and characterizing their lifestyle. We will use one E. coli strain and 2 phages exhibiting contrasting lifestyles in the experiment. If isolation proves ineffective, we will use model organism E. coli K12 and phages λ (lysogenic) and T7 (obligate lytic).

Location: New Haven, CT

Marlyse Duguid, Forests under threat: evaluating the impacts and responses of Connecticut’s forests to canopy loss from “invasive species”

Description: Beech Leaf Disease (BLD) is a quickly spreading and little-understood disease killing American Beech trees in the Northeast. BLD is caused by invasive nematodes (Litylenchus crenatae subsp. mccannii) that cause deformed or banded leaves. Severely diseased trees experience branch dieback, crown thinning, and death within 2 to 10 years. American Beech plays a critical role in Northeastern forests, where their masts support over forty wildlife species including black bears and deer. Without effective management, BLD can make American Beech functionally extinct with downstream consequences on ecosystem stability and biodiversity.

Current BLD containment is prohibitively expensive and limited at scale because it requires resource-intensive ground surveys for identifying symptoms and measuring success. Drone-based forest health monitoring solves these challenges by allowing managers to allocate resources using affordable, safe, accurate, high-resolution and spatially flexible data instead of ground surveys. Classification models using visible & non-visible light (multispectral) and laser imaging & detection (LiDAR) drone data have identified major diseases such as Pine wilt, Olive verticillium wilt, and Spruce bark beetle across large areas. However, no research has applied this modeling approach to monitor BLD. 

We will use established plots in New Haven, CT, and establish new plots in Jericho Research Forest, VT, in collaboration with UVM, CAES and the City of New Haven to collect drone multispectral and LiDAR data as well as field surveys on BLD expression. These data will train a classification algorithm to detect BLD on a tree and stand level, which can provide important insights on Beech health and inform management and restoration strategies to ensure diverse and resilient forests following nematode invasion. 

Duties: The intern will work on all aspects of data collection including mapping plots, vegetation surveys, and data entry. There may be opportunities for modeling and analysis depending on interest and timing.

Note: This internship takes place outdoors in urban and rural forests across Connecticut and Vermont, and remotely when possible. It is based in New Haven with frequent site visits, and may include a multi-day trip to Jericho Forest, Vermont. Candidates should be comfortable walking over uneven terrain and should be comfortable being outdoors for extended periods of time including in adverse weather conditions (heat, rain, etc.). The ideal candidate will be organized, adaptable, and have an interest in forest science, ecological fieldwork, and/or geospatial modeling. 

Location: New Haven, CT and Burlington, VT

Vanessa Ezenwa, Quantifying variation in parasite traits

Description: Parasitic worms infect a wide range of animals, including humans, and have important effects on the fitness and behavior of their hosts. To reach new hosts, worms release offspring, or “propagules,” into the external environment, and these propagules must survive and disperse through complex and often hostile conditions to reach new hosts; therefore, variation in propagule abundance is a key factor contributing to differences in parasite transmission success. In addition to abundance, propagule traits, like size or the ability to disperse in the environment, may also be important determinants of parasite transmission success. However, we know much less about how propagule traits vary within or between parasite species and whether this variation affects transmission. This project will examine variation in the traits of parasitic worm propagules collected from wildlife and subjected to different experimental conditions in the laboratory (e.g., high vs. low humidity). The student will quantify propagule trait variation (e.g., size, motility) within and between worm species and explore whether host or environmental factors help explain variation in these traits.

Location: New Haven, CT

Eduardo Fernandez-Duque, Behavioral ecology of owl monkeys living in a heterogeneous landscape in Argentina

Description: Primates living in heterogeneous ecosystems must manage variable ecological (e.g. different temperatures) and social (e.g. different density of individuals) conditions across the landscape. When anthropogenic activity causes heterogeneous habitats, it can be a major threat to the persistence of primate populations, but these anthropogenic effects can take generations to manifest. Naturally heterogeneous environments may allow us to see the long-term effects of anthropogenic fragmentation. In these naturally mosaic landscapes, how does heterogeneity challenge primates, and how do primates respond to survive in such environments? The Owl Monkey Project studies Azara’s Owl Monkeys (Aotus azarae) in the naturally heterogeneous Argentine Gran Chaco, where monkeys have likely thrived for hundreds of thousands of years, to answer these questions by comparing individuals living in forest “islands” with those in continuous gallery forests.

The student will participate in research comparing owl monkeys living in the gallery forest and forest “islands,” with the opportunity to carve out a small niche within this comparative framework by designing a short study of their own. The student will learn how to 1) find and follow monkeys using both traditional methods and telemetry, and they will collect basic demographic observations; 2) conduct behavioral follows with a range of methods (including scan sampling for activity budgets, all-occurrence for foraging bouts, and ranging data using GPS) and participate in playback experiments; and 3) collect abiotic data like temperature, humidity, and luminosity. 

Location: Formosa Province, Argentina

Jennifer Marlon, Assessing wildfire-induced changes in lake water quality through Earth observation data

Description: The Yale Center for Geospatial Solutions (YCGS) is seeking an enthusiastic undergraduate student to join a summer research project focused on better understanding post-fire water quality changes within the lakes and reservoirs of the American West. Recent and ongoing changes to precipitation and temperature regimes coupled with decades of unsustainable fire suppression practices have led to an unprecedented increase in wildfire activity in the American West. The effects these new fire regimes have on the complicated hydrologic systems in the region are not well understood. This study seeks to better understand these important connections.

The student will utilize novel geospatial datasets and processing methodologies to investigate the connections between wildland fire and water resources in the western United States. In particular, the student will utilize multi-source remote sensing data (e.g., Landsat, PlanetScope) with ground-based water quality measurements and burn severity products to characterize past, present, and projected fire impacts on the lakes and reservoirs of the American West. This work will greatly advance our current knowledge of how increased wildfire activity impacts water quality in the American West.

The summer internship period will provide intensive mentorship from YCGS faculty and research staff in a collaborative research setting. The student will develop technical proficiency through hands-on experience with advanced Python-based libraries for data processing and analysis, with particular emphasis on remote sensing techniques, time series analysis, and spatial analytical methods. This position represents a unique opportunity to contribute to pressing fire and water quality research while building foundational skills in the environmental geospatial sciences.

Location: New Haven, CT

Martha Muñoz, Discovering the diversity of Caribbean rain frogs

Description: Ongoing climate change presents an existential threat to biodiversity, but these threats are especially pronounced in amphibians (e.g., frogs and salamanders). As wet-skinned ectotherms, amphibians are highly vulnerable to changes in both temperature and moisture. Rain frogs (Genus Eleutherodactylus) are highly diverse, with dozens of endemic species found across the Caribbean. Yet, we know very little about the natural history and ecophysiology of these species, which are critical pieces of information needed for forecasting the vulnerability of these frogs under global change. The YIBS SURES student(s) will participate in an ongoing research project on the ecology and evolution of Eleutherodactylus frogs. First, students will visit the lab at Yale to learn how to extract and sequence DNA, which will help build a phylogenetic tree for the Eleutherodactylus frogs. Then, they will learn how to perform phylogenetic analyses using R. Following the lab training, they will join an expedition to the Dominican Republic, where they will participate in field work on these frogs. The student will collect ecological, behavioral, and environmental data while working in several natural preserves across the country. They will assist with physiological assays on the frogs, including estimation of water loss rates, metabolic rates, and heat tolerance. Through this project, the students will develop field, laboratory, analytical, and programming skills.

Locations: New Haven, CT and Dominican Republic

Michelle Wong, Digging belowground: measuring root exudates in northeastern temperate forests

Description: Forests play a critical role in the global carbon cycle by sequestering approximately one-third of anthropogenic carbon emissions from fossil fuels and land-use change annually. However, global change drivers – such as rising atmospheric carbon dioxide levels and warming – may be altering the carbon cycle balance in many northeastern forests. Specifically, indirect evidence suggests that more carbon is moving through plant roots and into soils as root exudates, potentially leading to soil carbon losses through increased microbial activity. The quantity of root exudates released by plants remains the largest unknown carbon flux in forests, and it is unclear what factors control the flux and the composition of root exudates. To address this large knowledge gap, the undergraduate student will have the opportunity to participate in a multi-week field campaign at Hubbard Brook Experimental Forest in New Hampshire with a larger team. This includes identifying trees across the watersheds at Hubbard Brook, tracing plant roots, quantifying fine root biomass, and collecting and measuring root exudates on a total organic carbon analyzer and quantifying composition using LC-MS at Yale. In summary, the undergraduate fellow will be able to carve out their research question of interest; learn lab, field, and project management skills; conduct data analysis; and collaborate with a larger team consisting of at least two PIs (Michelle Wong and Angela Possinger) and a postgraduate associate (Rachel Shaw). The student will be based at the Hubbard Brook Experimental Forest, a research station administered by the USDA Forest Service. Living and conducting research at Hubbard Brook, located in the beautiful White Mountains, will provide many enriching and fun opportunities to interact with many students and scientists working on different ecological questions.

Location: Hubbard Brook Experimental Forest, New Hampshire

Julie Zimmerman, Advancing the biorefinery

Description: The integrated biorefinery is an important element of sustainable industrial transformation, replacing fossil-based feedstocks with renewable carbon from biomass but also CO₂. Unlike traditional fossil refineries, biorefineries integrate biological and chemical processes to convert renewable carbon into fuels, chemicals and functional materials. For example, cultivation of algae provides a high-productivity biomass feedstock that can fix CO₂ directly via photosynthesis and be upgraded to bio-fuels, bioplastics or feedstocks; Lignin as the largest source of biogenic aromatics can be depolymerized and catalytically upgraded under mild conditions various feedstocks while retaining its aromatic character rather than losing it to de-functionalization; CO₂ itself can also become a circular feedstock through catalytic or electrochemical routes to create platform chemicals, building-block materials or polymers. Algae, lignin and CO₂ can thus be considered complementary carbon streams in an integrated biorefinery.

At the Center for Green Chemistry and Green Engineering, active research on the integrated biorefinery is carried out, and we would be more than happy to welcome an undergraduate intern in the summer of 2026 to participate in these New-Haven based research activities. Specifically, the project is centered around chemical approaches to directly convert the greenhouse gas CO₂ into useful materials. Examples include the electrochemical formation of the chemical reagent and fuel additive dimethyl carbonate from gaseous CO₂ and methanol, or the electrochemical synthesis of the simple amino acid and protein precursor glycine starting with the coupling of 2 CO₂ molecules and the subsequent addition of an amine (NH₂) group. The intern would get trained in electrochemistry as well as the necessary steps to separate and isolate reaction products, as well as their characterization and quantification using analytical techniques such as gas chromatography, liquid chromatography, nuclear magnetic resonance (NMR), and mass spectroscopy. For questions, please do not hesitate to reach out to hanno.erythropel@yale.edu.

Location: New Haven, CT

How to apply

The application process for 2026 will open on November 13th, 2025. Applications will be due on December 14th, 2025 at 11:59 PM (Eastern). For any questions or concerns regarding the application process contact yuji.torikai@yale.edu