CAS Undergraduate Research Fellowship

Mentors: Peipei Zhang

Animal Sciences

Overall Description

Food spoilage can cause food waste and economic losses. Ground beef is a very popular protein source in the United States. The shelf-life of ground beef is generally shorter than other beef products, which is attributable to its non-intact nature and consequently a relatively higher bacterial load in it than other beef products. Pseudomonas is the leading bacterial agent causing meat spoilage. Meat production environment, such as meat cutting and grinding room, is an important source of bacteria including Pseudomonas contaminating ground beef. In a separate project, we recovered various Pseudomonas isolates from ground beef products collected in seven grocery stores in Fort Collins. The present project intends to explore the factors contributing to the survival of Pseudomonas in meat processing environments. The findings generated from this study will help us to develop more effective measures to control Pseudomonas in meat production environment, which will potentially lead to extended shelf-life of ground beef.

Tasks to be completed

We will include various Pseudomonas strains (n=45) and determine their growth kinetics, biofilm forming ability, and tolerance to sanitizers in meat production-related environments.

Mentors: Jay Ham, Josh Craver, Chad Miller

Soil and Crop Science

Overall Description

It’s often said, “Colorado runs on water.” Unfortunately, our state, along with neighboring regions, is confronted with critical water resource challenges. With approximately 75% of Colorado’s direct water usage allocated to irrigation, the need to enhance irrigation management and water productivity is crucial.

Fortunately, new developments in sensor technology, data science and AI can help us address water issues. In late 2024, our team developed an innovative prototype sensor: a wireless soil moisture probe that combines research-grade precision with cost-efficiency, priced between $10-$15. This compact, hand-sized sensor avoids the traditional, cumbersome wired systems that are unpopular among growers due to the necessity of signal cables connected to dataloggers. Instead, it allows for immediate, hassle-free deployment—users can insert the sensor directly into the soil and access real-time data through a simple QR code scan, linking directly to cloud-based storage. Once a mini network of these sensors is installed, they could provide critical data to power AI-assisted irrigation decisions, enhancing water use efficiency significantly. This leads not only to water conservation but also to improvements in crop productivity and plant quality. Our goal is to make this sensor design open-source, enabling it to be continuously enhanced and mass-produced at a minimal cost. This strategy would allow our sensors to be shared globally in many regions of the world that struggle to optimize irrigation but also have limited economic resources for ag technology.

Our project is ready for a larger-scale trial. Each fall, Colorado State University’s Horticulture Center utilizes an entire greenhouse range to cultivate thousands of poinsettias under drip irrigation as part of a Greenhouse Practicum course in Horticulture. This greenhouse study provides an ideal test bed for our new soil sensors, aligning academic research with practical application and student engagement.

Moreover, this project offers an exceptional opportunity for an undergraduate research fellowship. The selected student will gain hands-on experience in IoT sensor technology within a real-world use case. They will conduct comparative analyses of water usage and plant health between areas using traditional timer-based irrigation systems and zones utilizing our sensor-driven irrigation scheduling. This direct involvement in assessing our technology not only enhances their learning but also contributes significantly to our understanding of how this sensor technology can be applied to other use cases.

This project has strong linkages to several Nutrien Showcase priorities, including: Precision Agriculture & Digital Solutions, and Sustainable Agriculture & Environmental Solutions.

Tasks to be completed

During this fellowship, the student will be actively involved in a series of hands-on tasks to support the soil sensor project, totaling approximately 150 hours. These tasks include:

• Sensor Fabrication and Testing: Participating in the construction, lab testing, and calibration of soil sensors to ensure they meet research standards.
• System Installation: Assisting in the installation of the drip irrigation system within the greenhouse.
  Cultivation Oversight: Overseeing the cultivation and monitoring of poinsettias designated for the sensor trials.
• Data Analysis: Regularly monitoring and analyzing data collected from the sensors and poinsettias. A cloud-based dashboard will be utilized to assess and report on sensor performance and irrigation efficacy.
• Collaborative Research: Engaging in regular team meetings to discuss experimental setups, troubleshoot issues, and refine research methods.
• Peer Collaboration: Working alongside student peers also involved in the Greenhouse Practicum, providing support and guidance in the use of soil sensors as needed.

Note, this list represents possible options, but the student fellow will not be expected to complete all these tasks. Once the team understands the student’s interest and career goal, the tasks will be customized and abbreviated as needed.

Mentors: Meagan Schipanski

Soil and Crop Sciences

Overall Description

Grain crops like wheat and corn derive about half of their nitrogen from soil organic matter each year, even when fully fertilized. We lack soil tests that can predict the capacity of different soils to supply nitrogen via nitrogen mineralization. The student in this position will conduct laboratory and greenhouse assays to assess their potential to predict soil nitrogen availability across different soils.

Tasks to be completed

Student will trained in the set-up, management, and data collection of a short-term greenhouse study, including plant and soil sampling and analysis. The student will also assist with ongoing lab activities, including lab maintenance tasks.

Mentors: Aaron Prairie (Post-doc)

Soil and Crop Sciences

Overall Description

This project will advance soil science by uncovering how soil fauna influence soil organic matter (SOM) stabilization in integrated crop-livestock (ICL) systems. Using innovative methods, including stable-isotope tracing and microbiome analysis, it will reveal biological mechanisms that enhance carbon sequestration and soil health. Findings will inform sustainable agricultural practices and climate resilience strategies while providing hands-on research experience to an undergraduate assistant. Results will be shared through scientific publications, conferences, and outreach events, contributing to national efforts to promote regenerative agriculture.

Tasks to be completed

Tasks to be Completed (Approx. 150 Hours):

Sample Collection and Preparation (30 hours): Assist with collecting soil and fauna samples from field and greenhouse experiments, and prepare samples for laboratory analysis.

Microcosm Maintenance (20 hours): Support the maintenance of greenhouse microcosms, including monitoring plant growth, applying treatments, and managing environmental conditions.

Isotope Labeling Support (15 hours): Aid in setting up and maintaining isotope labeling chamber and recording data during greenhouse experiment.

Laboratory Analyses (40 hours): Assist with soil fractionation, aggregate stability tests, and processing samples for elemental and isotopic analyses.

Microfauna Extraction and Identification (20 hours): Perform microarthropod extraction using Tullgren funnels and assist in identifying and cataloging fauna.

Data Entry and Preliminary Analysis (15 hours): Enter laboratory data into spreadsheets and conduct basic data quality checks.

Outreach and Communication Support (10 hours): Assist in preparing presentation materials for outreach events and contributing to research documentation.

Mentors: Federico Martin

Agricultural Biology

Overall Description

Erratic weather patterns and extreme conditions driven by increasing global temperatures cause prolonged droughts, heat waves, or excessive precipitations. These conditions pose significant challenges to crop production around the world affecting not only plant yield, but also nutritional content and ability to withstand pest and pathogen pressure. One strategy to mitigate this burden is the development of enhanced crop varieties that can better adapt to future environmental changes. Our research focuses on understanding plant genetic diversity and stress adaptation pathways that can be used to naturally enhance plant protection. We aim to identify and characterize genes involved in defense responses against pathogens as well as high temperatures using genetics, bioinformatics and molecular biology approaches. Current projects include the identification of DNA regulatory elements and transcription factors that drive gene activation during stressful conditions and the development of assays to measure gene activity. Our overarching goal is to provide crop breeders with information and tools that can be applied to select more robust climate-ready crop varieties.

Tasks to be completed

• Introduction in to research of plant-pathogen interactions and stress adaptation.
• Application of the scientific method to generate hypothesis driven projects
• Introduction in to molecular biology methods (DNA/RNA purification, PCR, genome editing approaches, etc) and genetic approaches (Quantitative trait loci discovery, test of molecular markers) to understand genes involved in stress adaptation
• Development of transient assays to test promoter sequences and gene activity
• Introduction to lab general activities and greenhouse activities to grow plants and test stresses.

Mentors: Huey Yi Loh and Terry Engle

Animal Sciences

Overall Description

Using resources more efficiently in livestock production systems is a focal point of our laboratory. Copper sulfate is widely used in footbaths to help prevent lameness in dairy cows. Typically, used footbath contents are discharged into the premise lagoon. High levels of copper have been reported to inhibit lagoon microorganism function. Furthermore, copper can accumulate in soil and plants in areas where the lagoon effluent is applied. We have developed a laboratory scale system to remove copper from the used footbath solution and convert the extracted copper back to copper sulfate to be reused in subsequent footbaths. We are currently evaluating the efficiency of our current system and will further investigate techniques for recycling other metals in footbath waste.

Tasks to be completed

Laboratory work, on-farm sample collections, and live animal work.