Leveraging Microbial Phosphorus Miners in Soil

The goal of our project is to help farmers make strategic use of the natural capacity of soil to supply phosphorus (P) to plants. The natural capacity of a soil to supply plant P comes from microbial activity (or ‘biological P supply’) that recycles inaccessible forms of P, stored in minerals and organic matter, to plant available forms. The supply of biological P depends on which soil microbiota are present (all are not equally effective), whether conditions support their activity, and whether effective microbes have had time to establish sufficient biomass to convert relevant amount of P to a plant usable form. Using prior data, we will identify 6 farm fields where populations of P mining microbes are depleted. We will establish small in-field test plots where we will reintroduce the populations of microbes and compare changes in plant P availability against reference soils where no biofertilizer was added. The summer researcher will help prepare and spread bioinoculants, collect soil and plant samples, and perform DNA extractions and downstream analyses.

Expected outcomes: Information on which bioinoculants perform best, and under which circumstances.

Expectations: Interest in field and lab research. Experience in microbiology preferred, but not required. Experience with molecular biology preferred, but not required.

Roland (Roli) Wilhelm, Agronomy

Interface between metabolism and chromosome biology

Undergraduate Research Opportunity in interface between metabolism and chromosome biology. Student will conduct primary hypothesis-based research, learn to design experiments and interpret results. Student will utilize genetic, biochemical, or molecular strategies to assess functions of evolutionarily conserved metabolic enzymes and how their metabolic products influence chromatin, gene expression or responses to DNA damage using the budding yeast model organism Saccharomyces cerevisiae or mammalian cell culture and microscopy.

Expectations: Completion of General Chemistry. Molecular biology/biochemistry/genetics or related background.

Ann Kirchmaier, Biochemistry

Elucidating the Role of Rhizobial tRNA-Derived Fragments in Soybean Nodule Development and Symbiotic Nitrogen Fixation

Legume root nodulation and symbiotic nitrogen fixation (SNF) are complex biological processes that require coordinated exchanges of molecular signals between rhizobia and host plants. While enormous progress has been made to decipher the molecular mechanisms evolved by host plants to control nodule numbers, it is still poorly understood how rhizobia regulate nodulation and SNF and how the processes are affected by environmental stimuli. This project integrates genomics, molecular, and biochemical tools to elucidate the mechanisms by which rhizobial small RNAs regulate nodule development and SNF,

Expected outcomes: The SORP students will get hands-on training of the state-of-the-art technologies such as tissue culturing, transformation, and genome-editing, and be involved in research experiments under the supervision of postdocs in the Ma lab and mentored by PI to gain skills in poster design, scientific presentation etc.

Expectations: Two positions are available in Summer 2025. Background in plant science, with course study in introductory genetics, is preferred.

Jianxin Ma, Agronomy

Evaluating the Toxicity of a Fluorine-Free Foam using Marine Fish

The goal of this project is to test the toxicity of a fluorosurfactant (FS)-free foam formulation being developed by Purdue researchers for use in marineships to stop fires. The sheepshead minnow, Cyprinodon variegatus, will be used as the fish model. We will expose fish embryos and larvae to different concentrations of the foam formulation for several hours to days and calculate acute and chronic toxicity reference values. We will assess survival,percent hatch, percent larvae with debilitating morphological and/or behavioral abnormalities, and size at hatch. This data will be crucial to determine the potential impacts of this novel foam in marine environments.

Expected outcomes: Prospective student will: 1) Be expected to actively participate in lab meetings and engage with several other students working on other projects; 2) Learn how to care for and breed a marine fish, Fundulus heteroclitus; 3) Learn how to run acute toxicity tests using fish embryos and larvae; and 4)Present research findings in the form of a poster and or oral presentation. If the student is interested, there can also be opportunities to publish the workin a peer-reviewed journal.

Maria S Sepulveda, Forestry and Natural Resources

Investigating the soil health benefits of kura clover, a promising perennial legume cover crop

This project aims to investigate the soil health benefits of perennial cover crops, particularly kura clover, in midwestern corn production systems. Kura clover is known for its deep-rooted perennial nature, which can enhance soil structure, improve water infiltration, and promote nutrient cycling. The project aims to evaluate the impact of kura clover on various soil health indicators, such as organic matter content, microbial activity, and nitrogen fixation. By comparing kura clover systems to conventional cover crops or no cover crop systems, researchers will assess its potential to reduce soil erosion, enhance carbon sequestration, and support sustainable farming practices. The findings from this study will provide insights into how perennial cover crops like kura clover can contribute to long-term soil fertility and resilience, offering valuable solutions for farmers looking to improve productivity while maintaining environmental stewardship. This research has the potential to promote more sustainable agricultural systems.

Expected outcomes: The expected outcomes of this project include demonstrating improved soil health through the use of kura clover as a perennial cover crop. Key findings will likely show enhanced soil structure, increased organic matter, improved water infiltration, and higher microbial activity compared to conventional systems. Kura clover is also expected to boost nitrogen fixation and reduce soil erosion, contributing to long-term soil fertility and resilience. The study will provide valuable data for farmers and researchers, promoting the adoption of sustainable agricultural practices that enhance productivity and environmental sustainability.

Expectations: Students involved in this project should have a strong foundation in agronomy, soil science, environmental science, or related fields. A background in plant biology, ecology, or sustainable agriculture would also be beneficial. Students should have experience or interest in soil health assessments, crop management practices, and sustainable farming systems. Knowledge of cover crops, nutrient cycling, and soil microbiology is advantageous. Familiarity with field research methods, data analysis, and scientific writing will be helpful for contributing to the project's goals and understanding the environmental impacts of perennial cover crops.

Yichao Rui, Agronomy

Mechanisms of the costs and benefits of cold acclimation

Cold acclimation is common in plants throughout the temperate zones and involves dramatic metabolic, and physiological changes in response to cool autumn temperatures which increase winter freezing tolerance. Cold acclimation is energetically costly and will likely lead to reduced fitness/yield with climate change. We demonstrated that cold acclimation has a fitness/yield advantage in a seasonally freezing environment but is strongly costly in a cool but non-freezing environment (Lee et al., 2024, PNAS). We have shown that naturally occurring functional variation in a gene that encodes the transcription factor CBF2 is a major regulator of this process. Our NSF funded research connects the genotype-phenotype-fitness/yield map for cold acclimation. Many summer opportunities are possible and may include some combination of growth chamber experiments to measure growth rates, flowering time, and fitness/yield, transcriptomics, metabolomics, and the creation of loss of function mutations of CBF2 in new ecotypic backgrounds using CRISPR-Cas9.

Expected outcomes: The student will participate in a research project, analyze data, and be encouraged to present a poster. The student will also receive mentorship on applying to graduate school or pursuing other career options.

Expectations: We welcome students from any background and/or experience level. Interest in the topic and the motivation to learn the skills needed to pursue research in this area are the only requirements.

Christopher Oakley, Botany and Plant Pathology

Exploring the genetic basis of maladaptation

Despite many examples of adaptation, we know that many ecotypes/varieties are not optimally matched to their environment. Changing selection pressures due to climate change could be one explanation. Natural populations may face additional constraints including the fixation of deleterious alleles due to random genetic drift, context dependency of new mutations, and/or linkage between adaptive and maladaptive loci. In our system, we found transgressive segregation for fitness/yield near the northern edge of the native range due to large effect maladaptive QTL for reproduction. We have also documented strong heterosis in crosses between northern ecotypes, consistent with historical drift fixing deleterious recessive alleles. Many summer opportunities are possible as part of this NSF funded research to investigate the effects of non-additive genetic architecture, transgressive segregation, and linkage on maladaptation. We have a unique panel of genome-wide near isogenic lines to use in growth chamber experiments to collect fitness/yield and transcriptomic data.

Expected outcomes: The student will participate in a research project, analyze data, and be encouraged to present a poster. The student will also receive mentorship on applying to graduate school or pursuing other career options.

Expectations: We welcome students from any background and/or experience level. Interest in the topic and the motivation to learn the skills needed to pursue research in this area are the only requirements.

Christopher Oakley, Botany and Plant Pathology

Deciphering the Mystery of Capsaicin Biosynthesis Using a Super-Pungent Chili Pepper Variety

Chili peppers, renowned for their fiery heat and wide-ranging culinary uses, are a staple in global cuisines. Capsaicinoids, particularly capsaicin and dihydrocapsaicin, are the primary compounds responsible for their signature pungency. Understanding capsaicin biosynthesis is essential to uncovering how these compounds are produced, with applications in food, medicine, and agriculture. Capsaicinoids are synthesized through the combination of two key components: a short-chain fatty acyl-CoA derived from amino acids like valine, and vanillyl amine, which originates from the phenylpropanoid pathway. Despite this knowledge, the precise mechanism by which plants synthesize vanillin, the direct precursor to vanillyl amine, remains largely unknown. This project aims to explore the synthesis of vanillin using the super-pungent Ghost pepper as a model system, leveraging its exceptionally high metabolic flux towards capsaicinoid production to shed light on this critical pathway.

Expected outcomes: The major expected outcomes of this project include better understanding of the biosynthetic routes of vanillin by performing feeding stable isotope-labeled precursors in capsaicin-synthesizing tissue and enzymatic assays using crude protein extract, and potential identification of key genes involved in vanillin biosynthesis.

Expectations: Students with strong backgrounds in biochemistry and plant science are preferred.

Natalia Dudareva, Biochemistry

Uncovering the transcriptional coordination of KAI2-mediated signaling in floral development

The coordination of hormone signaling pathways and gene expression are vital processes in plant development. Recent research has revealed that KARRIKIN INSENSITIVE 2 (KAI2)-mediated signaling is important for plant reproductive organ development by responding to a volatile signal in the stigma. Beyond this specific role, KAI2 signaling—via the degradation of the transcriptional corepressor SUPPRESSOR OF MAX2 1 (SMAX1)—also regulates the biosynthesis of ethylene, a key hormone involved in flower senescence.

Remarkably, petunia possesses four distinct KAI2 proteins and two different SMAX1s, each of which appears to function in separate biological processes. This project aims to explore the transcriptional coordination of KAI2-mediated signaling in floral development. Specifically, we will use yeast two-hybrid (Y2H) assays to identify transcription factors that interact with, the different SMAX1 proteins. Candidate transcription factors will be selected from a database of predicted interactors to uncover the regulatory mechanisms involved in KAI2 signaling.

Expected outcomes: This study aims to identify transcription factors that interact with SMAX1a, SMAX1b, or both using yeast two-hybrid (Y2H) assays. Additional assays will investigate which specific domains of the SMAX1 proteins (N, D1, M, and D2 domains) are involved in these interactions. The findings will offer foundational insights into the molecular mechanisms of KAI2-mediated signaling in petunia. These insights will also inform future transformation experiments aimed at manipulating KAI2 signaling pathways in petunia to better understand how it coordinates with other hormone signaling pathways during plant development.

Expectations: Biochemistry background is preferred but not required.

Natalia Dudareva, Biochemistry

Transporters involved in terpenoid crosstalk in plants

Terpenoids, responsible for the aromas and flavors of fruits, vegetables, and herbs, are essential for plant processes like respiration, growth, and photosynthesis. They are synthesized from two five-carbon building blocks, IPP and DMAPP, which are produced through distinct pathways and distributed across various cell compartments. While much is known about terpenoid biosynthesis, the transport of IPP and DMAPP across cellular membranes remains poorly understood. Our research group recently identified a membrane protein that may be involved in this transport. As a student researcher, you will investigate mutant Arabidopsis and tobacco plants (using over-expression and knock-down lines) by analyzing gene expression and terpenoid levels, including chlorophylls, carotenoids, and volatile compounds. Additionally, you will explore the effects of transport disruption by feeding stable isotopically labeled terpenoid precursors to the mutants and wild-type plants to assess carbon flow through the terpenoid pathways.

Expected outcomes: The findings will offer foundational insights into the transport of metabolites between distinct terpenoid pathways. These insights will also inform future metabolic engineering experiments aimed at improving yield of high-value terpenoid compounds.

Expectations: The student has a background in either plant biology, molecular biology and/or biochemistry.

Natalia Dudareva, Biochemistry

Functional characterization of histone demethylases in Arabidopsis

The Ogas lab is interested in understanding how chromatin-based mechanisms contribute to gene expression, differentiation, and development in plants. Our primary focus is characterizing the molecular mechanism that govern homeostasis of a specific epigenetic mark: trimethylation of lysine 27 of histone H3 (H3K27me3). H3K27me3 contributes to transcriptional repression in plants and animals, but the machinery that contributes to its deposition and removal in each kingdom differs. This SROP project will focus on functional characterization of three H3K27 demethylases in Arabidopsis (REF6, ELF6, and JMJ13) and their contribution to genome-wide patterns of abundance of H3K27me3 in the context of other plant-specific factors that contribute to H3K27me3 homeostasis. The project will involve generation of combinatorial mutants, PCR-based characterization of mutant alleles, phenotypic characterization of plants, and RT-qPCR analysis of gene expression. Students will be encouraged to develop and test their own hypotheses during this project.

Expected outcomes: We anticipate that completion of these studies will result in authorship on a publication.

Expectations: Junior majoring in Biochemistry/Biology/Genetics familiar with standard molecular biology in the lab.

Joe Ogas, Biochemistry

Data-driven insights into enzyme reaction catalysis for green chemistry

Biocatalysis uses enzymes to catalyze a series of transformations to yield a desired small molecule, e.g., commodity chemicals, pharmaceutical agents, and agrochemicals. Enzymatic processes are greener and more selective compared to their organic counterparts. We will develop computational tools to predict enzymatic manufacturing routes for small molecules. We will also experimentally test these model predictions by enzymatically synthesizing a life-saving chemo-therapeutic that is currently in short supply because it employs organic synthesis techniques.

Expected outcomes: Group Meeting Presentation, Standard Operating Procedure Development

Expectations: Biological Engineering, Chemical Engineering, Chemistry, Biochemistry, Computer Science

Karthik Sankar, Agricultural & Biological Engineering

Understanding how plant cells communicate

The Kessler Lab studies both pollination and root development to understand the mechanisms through which cells communicate with each other and perceive the environment. During pollination, pollen grains send out a pollen tube that communicates with several different cell types of the pistil to deliver the sperm cells to the ovules so that seeds can form. During this process, the pollen tubes must communicate with their external environment so that they can find their way to the ovules. Root hairs are a good model system for studying plant communication with the environment since they are single cells that grow into the soil and they are easier to work with than pollen tubes. Our SROP project will use molecular biology, microscopy, and cell biology experiments to investigate the role that a family of plant calcium transporters play in root hair growth during responses to environmental stressors such as temperature, drought, and salinity.

Expectations: We prefer students who are majoring in biological sciences-related fields

Sharon Kessler, Botany and Plant Pathology

Harnessing the MVA pathway to produce high-value terpenoids in tomato fruits

Terpenoids are one of the largest groups of plant metabolites, with over 80,000 compounds that serve diverse functions in plant physiology. Terpenoids play an essential role in fruit flavor, aroma, and nutritional value, making them critical for enhancing tomato quality. This project will investigate the interactions between the mevalonic acid (MVA) and methylerythritol phosphate (MEP) pathways during tomato fruit ripening. Using isotope labeling and pathway specific inhibitors, we will evaluate the contribution of these pathways to extraplastidial terpenoid biosynthesis. The overall goal is to engineer tomato fruits to boost the production of high-value terpenoids via the MVA pathway without compromising carotenoid and lycopene levels. By overexpressing key enzymes from the MVA pathway and applying metabolic engineering strategies, we aim to increase the biosynthesis of terpenoid precursors, such as geranyl diphosphate (GPP) and farnesyl diphosphate (FPP), ultimately enhancing the levels of monoterpenes and sesquiterpenes.

Expected outcomes: By engineering the MVA pathway, we expect to significantly increase the production of key terpenoids, such as monoterpenes and sesquiterpenes, which contribute to flavor and aroma. The study will clarify how the MVA and MEP pathways interact and supply precursors for terpenoid biosynthesis, particularly during fruit ripening.

Expectations: Students with backgrounds in biochemistry and plant science are preferred.

Natalia Dudareva, Biochemistry

The physiological and ecological drivers of photo-symbiotic associations

The student will investigate the global physiology and resource allocation of a symbiosis as well as its isolated partners across environments. This project aims to understand the physiological and ecological drivers that lead to the emergence of symbioses between heterotrophs and photoautotrophs. The student will be exposed to some or all of the following techniques: cell culturing and isolation, cell transformation, gene cloning, growth curve analysis, light and fluorescence microscopy, quantitative proteomics, and data analysis.

Expectations: Microbiology, Physiology, Cell & Molecular Biology, Systems Biology, Mathematical Modelling

Sergio Muñoz-Gómez, Biological Sciences

Learning Agile Motion in Natural Terrains with Robot Dogs

Natural terrains are still challenging for robot dogs to maneuver through efficiently. In this project, we take inspiration from nature and animal gaits to learn effective motion patterns using reinforcement learning and Physics-aware AI. Our collection of robots dogs (Unitree Go2 and MiniPupper) will be used as testbeds for this development and validation.

Expected outcomes: Expected to contribute to a manuscript for a robotics journal and conference (ICRA and TRO). Expected to contribute to dataset curation and code base which will be released to the public using Github.

Expectations: Students with experience in Reinforcement learning, Python, AI, embedded systems, and robotics are encouraged to apply.

Upinder Kaur, Agricultural & Biological Engineering

Website

Microbiome insights into essential oil use in swine production

This project explores how essential oils impact the swine microbiome, focusing on potential benefits for animal health and productivity. By analyzing the microbiome response to essential oil supplementation, we aim to identify key interactions that could support more sustainable and efficient swine farming practices.

Expected outcomes: Students will develop practical skills in microbiome research and animal handling, as well as training in scientific research, data analysis, and writing. This experience will prepare them for careers in research or the animal science industry.

Expectations: Ideal candidates are students with a background in animal science, biology, or microbiology.

Tingting Ju, Animal Sciences

Website

Drought tolerance mechanisms in maize

Maize production in the US and around the world is increasingly negatively affected by drought. Understanding the genetic basis for drought tolerance mechanisms is critical to maintaining production. One mechanism that has not been extensively investigated in maize is turgor loss point (TLP): the water potential at which maize turgor becomes negative and therefore results in death. We will attempt to develop a protocol for rapid assessment of TLP in maize in an effort to determine the genetic basis for this trait. Work will be conducted in the Purdue HLA plant growth facility.

Expected outcomes: There is high potential for a publication on the methods and possibly results of experiments conducted during the summer.

Expectations: Students should have an interest in plant biology and feel comfortable with basic computer skills (spreadsheets, etc.).

Mike Mickelbart, Botany & Plant Pathology and Horticulture & Landscape Architecture

Website

Bioaccumulation and effects of Forever Chemicals on largemouth bass reproduction

Per- and polyfluoroalkyl substances (PFAS) in agricultural biosolids contaminate nearby ponds with complex mixtures that differ from mixtures associated with better-studied PFAS sources, like firefighting foams. Preliminary data suggest largemouth bass (Micropterus salmoides) in ponds receiving biosolids runoff have very high levels of PFAS in fillet, but replicate sites are needed to characterize biosolids-derived PFAS exposures. Although existing work suggests potential for reproductive toxicity, available studies cannot mimic exposures under field conditions. The central objectives of our work are to characterize PFAS in media/bass tissues from ponds receiving biosolid runoff, to determine whether exposure to PFAS influences reproduction under field conditions, to elucidate any underlying molecular mechanisms. Applicants will work with a collaborative research team on a large project and will gain diverse experiences in laboratory and field approaches to aquatic ecology and ecotoxicology.

Expected outcomes: Interested students who enjoy their experiences and perform well can earn opportunities for continued/expanded participation in this research; historically, summer scholars in our lab have routinely continued their research after their fellowships have ended.

Expectations: Students with coursework in biology, chemistry, environmental science, and/or related fields are preferred but not required.

Tyler Hoskins, Forestry and Natural Resources

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