SOAR-REEU
student blog

This summer I worked with the Runck Lab under GEMS Informatics. The goal of GEMS Informatics is to collect, analyze and integrate short and long term data of agri-food systems. This research is the foundation to inform and empower scientists, farmers, legislators, economists, the public, etc so they can make actionable decisions regarding climate change influenced problems. The use of sensors as a secondary measuring instrument for properties such as evapotranspiration, soil moisture, and air temperature etc. are the basis of all projects done in the Runck lab. 

Real-time sensing can aid farmers in monitoring soil health as climate change continues to impact crops. The objective of my individual experiment is to determine the correlation between soil permittivity and soil organic matter (SOM) in annual tilled soy/corn fields and perennial zero-tilled turfgrass fields to aid in soil health evaluation. My research project began by working closely with my lab on developing and fine tuning a proposal that included creating an objective and hypothesis, methodology, and timeline for my project. Composite soil samples were taken at five randomized locations within a corn, soy, and turf field on the St. Paul Campus and then sent to the UMN Soil Testing Laboratory for SOM analysis. To measure permittivity, an Acclima TDR 315H soil sensor was inserted into three sub locations within a square meter of the randomized locations. Exploratory data analysis was performed within RStudio by coding the statistical test, ANOVA, followed by Tukey HSD post hoc test. Visualization took the form of correlation plots and boxplots from RStudio and also maps from ArcGIS. Future implementation of this protocol could lead to a more cost-effective and less labor-intensive evaluation of soil health and could lead to more environmentally conscious practices such as reducing usage of fertilizer, irrigation, and pesticides. 

When I was not working on my project I was attending lab meetings where other members of the lab gave reports on their projects. I also aided my mentor, Samikshya, in either  taking down or raising her LiCor sensors that are measuring evapotranspiration in corn, soy, and potato fields at the research farm in Becker. Alec, another undergrad researcher, and I cleaned, reorganized, and helped inventory sensors and loggers that will be sent out to golf courses this fall for the lab’s “overwinter turf kill project”. I also assisted the lab manager, Ann, with maintenance on sensors at the Becker, TROE Center, and St. Paul Farm. This involved tightening guy wires, replacing batteries, and readjusting solar panels. As agri-food systems continue to evolve under the pressure of climate change, so does the need to continuously and quickly collect, analyze, and model data. I am thankful my experience in the Runck lab has introduced me to this increasingly important sector of agriculture.

Hi everyone! This is Kylie reporting on fun research activities. This summer, I am researching the impact of alfalfa stem lignin content on roots with Jake Jungers and Hannah Rusch. Lignin in stems is often a target of alfalfa breeding programs because it impacts digestibility. Low lignin lines are more digestible to cattle, whereas high lignin is less digestible. The alteration of stem lignin content has clear impacts above-ground, but the story of the below-ground counterpart is unknown. My research aims to understand how roots are affected by varying stem lignin content in relation to carbon and nitrogen cycling, root Klason lignin, and root architecture traits. 

After a lot of planning, I started playing in the soil by collecting tap and fine roots of five alfalfa lines that vary in stem lignin content from St. Paul and Rosemount, MN. Unearthing these specimens left me with an intense sunburn (thanks for taking care of me, Aralyn) and a huge appreciation for shovels.

The second phase of my project involved scanning the fine roots using WinRHIZO to measure traits related to root architecture. This program helps identify the root sample's total length, surface area, and volume. At this stage, the variation between alfalfa lines was apparent due to the differences in biomass and traits listed above. The third step involved analyzing chemical components. I have spent the past couple of weeks resembling a stock photo scientist while mixing my ground tap root samples with various acids and bases. Only slight mishaps occurred, like spilling bases on my lab coat, but it has been an overall success.

As a final part of my project, we buried the fine roots from these alfalfa varieties to measure decomposition over time. This was a fun final field day after a lot of lab work. This summer has been super educational, and I really appreciate Hannah and Jake for helping me learn more about their research and connecting me with people to collaborate with.

Hello everyone! This summer I am working in the Jelinski Pedology and Soil Management Lab. This lab has a multitude of projects across the US with main categories being permafrost soils and urban soils. The two main urban soils projects that I have spent time on were the Shredded Cardboard Mulch Project and the Twin Cities Metro Area Urban Soil Mapping Project.

The shredded cardboard mulch project is in partnership with Urban Farm and Garden Alliance in the Twin Cities. The goal is to assess the performance of shredded cardboard mulch in urban farms and gardens due to the increase in cardboard packaging seen during the COVID-19 pandemic. The project I Twin Cities Metro Area Urban Soil Mapping is in partnership with the Natural Resources Conservation Service (NRCS) to complete a soil survey update. Much of the soil in urban areas is not mapped as anything besides “Urban Land”. This doesn't include what a profile with soil horizons would look like, or the properties of that soil. Image 1 depicts the drafted areas of interest for the project.

My specific project has been looking at the South Saint Paul Parks samples from the urban soil mapping, and quantifying the microplastics in them. To say this has been a challenge would be an understatement. After researching microplastics in soil, testing a prior protocol, and joining other UMN lab meetings focusing on quantifying microplastics, I soon realized that a standardized methodology to quantify microplastics in soil samples does not exist.

Soil samples were collected from 14 parks in South Saint Paul using a Dutch auger and going down 150cm (or as far as possible before hitting a ton of rocks). Once a profile is laid out in a gutter its color, texture, structure, effervescence, consistency and fragments are recorded for each horizon of the profile. If there are concentrations such as carbonates or redoximorphic features like iron or manganese these are also included. A description of the location is also included and one to one and a half cups of each horizon is collected for sampling.

To quantify the microplastics I have tried a variety of methods such as changing the reagents samples are in, the amount of sample used, the addition of hydrogen peroxide (to oxidize organic matter) filtration paper used, and if placed onto a slide or on filter paper. I look forward to finding out what works best for quantification and sharing that with you all! I have thoroughly enjoyed working with my PI and Mentors (they're the best!!) and am excited to dive more into the importance of soil in sustainable food systems as I continue my academic journey.

Hey, y’all. This summer I’m working with Jessica Gutknecht and Anna Cates in their respective Soil and Ecosystem Ecology for Climate Resilient Systems (SEECRS) and Soil Health labs. Their labs focus on measuring soil health and investigating management techniques that will promote more resilient agro-ecosystems. This ranges from studying soil organic matter pools and cycling to studying soil microbial ecosystem dynamics. Extension is also a big part of Dr. Cates’ work. 

My research focus area is on erosion mats. Erosion mats are 6 inch by 6 inch pieces of layered fabric that are used to measure in-field soil erosion. The idea is that water causes soil to runoff along the slopes of fields and that these amts can catch some of that sediment. Soil erosion is a huge issue for farmers since extreme weather events create more loss of topsoil and topsoil is essential for farming. It is often difficult to accurately measure how much soil is being eroded from fields. Typical techniques include edge of field monitoring, and that equipment is expensive and not widely accessible to farmers. 

This project involves working with erosion mats at different farms and comparing soil movement data from in the field with data collected from the edges. Results will help us learn more about the accuracy of the erosion mat method. One reason why monitoring erosion is important is because of programs that reward farmers for regenerative practices and carbon sequestration. If you lose topsoil due to events you can’t control, you want to account for the compensation you might lose.

The design of the project also allows us to examine the impact of different management styles and crops (e.g. Kernza - Forever Green Initiative) on soil erosion since mats were placed at different operations ranging from pasture to row crops to demonstrative cover crops. My work for this project so far has included collecting and deploying mats in the field, taking soil samples, cleaning mats and measuring soil collected, ball grinding my samples, and microscaling my samples for C:N analysis. I will get to help run the C:N analysis soon (which requires a big fancy machine that I am excited to see work).

Other work that I have done in the lab includes nitrate extractions and analyses (lots of pipetting!) and doing aggregate stability tests for a different project’s samples. I’ve gotten to see the crop services facilities and many of the resources at the disposal at the U. I’ve also enjoyed talking to the members of my labs about what they do, how they find their work meaningful, and the conditions at UMN which have been generally positive! This has been a good but challenging experience so far. I enjoy the cities and thinking about how I can work towards a career that I believe in and a world that’s more liveable.

I’m Cameron, working alongside my PI and mentor to study sustainable agriculture practices. Our lab focuses on developing integrated pest management (IPM) solutions for organic farming systems. We are currently investigating the effectiveness of mulch soil covers as a pest management method. Our experiment involves four Brassica species: Novantina broccoli (Brassica rapa), Gypsy broccoli (B. oleracea var. italica), White Russian Kale and Red Russian Kale (B. napus). This selection allows us to account for variability among different cultivars used in field conditions. We’re testing three treatments: reflective cover, black plastic, and bare soil. Mulch covers are expected to keep pest damage away from crops. The field trial evaluates two main insect groups using a scoring system: flea beetles and moths (cabaggeworm, cabbage looper and diamondback moth). The latter one being counted by the number of larvae (caterpillars) spotted on the crops.

Our tasks alternate throughout the week: documenting caterpillars on Tuesdays, harvesting on Thursdays, and weeding on Fridays. I've also spent considerable time at the Student Organic Farm (SOF). When not in the SOF, I am dedicated to entering collected data into Google Sheets in the lab. Tools like JMP, R, and Python facilitate quick data entry and analysis. In addition to my work in the Rogers lab, I've been assisting mentor Jonathon Dregni and his student Grayshalie Melendez. We collect Swede Midge traps from local gardens in the Twin Cities area and analyze the collected sticky cards in the laboratory.

As a newcomer to natural science research, much of what I'm currently studying and experimenting with is new to me. The SOAR-REE program allows me to apply my data analysis and statistical skills to address horticultural issues that negatively impact our food production. My favorite aspect has been utilizing my data analysis skills in horticulture and then constructing a narrative based on the statistical results.

Hello everyone! This summer, I am working in a plant pathology lab that focuses on Sclerotinia sclerotiorum which is a type of fungus that causes white mold in over 400 species of plants. White mold is a disease that can significantly decrease crop yields when conditions are favorable (the fungus prefers cool, moist conditions). Lettuces, brassicas, common beans, and other legumes are most at risk due to their high canopy cover. In conducive conditions, yield loss can exceed 20 percent due to the mold. For my research, I am working to evaluate the efficacy of biocontrol agents in managing this mold in canola. Canola, also known as rapeseed, is a Brassica with heavy canopy cover and harvested for its oil-rich seeds.

We are interested in looking at methods to manage the mold outside of chemical applications because S. sclerotiorum has been described to build resistance to fungicides when applied in low doses for prolonged periods of time. Furthermore, biocontrol methods are often better for the environment than their chemical counterparts. Biocontrol has been proven to be effective in other crops in the past, but little research has looked into their efficacy in canola. A few of the biocontrol agents we are testing are Coniothyrium minitans (Contans) which is another fungus, Bacillus amyloliquefaciens (Double Nickle LC), and Bacillus subtilis (Serenade OPTI) which are both types of bacteria.

Some of the activities I have been doing in the lab are for my project, but I also help with different aspects of other projects in the lab such as weeding the bean fields, cleaning soybean seedlings, sterilizing samples, and entering data into excel. Much of the work I have done in the lab has been to prepare me for the lab protocols I will be doing with my project. So far, I have made multiple protocols for the field portion of the project such as an apothecia scouting protocol and a disease assessment protocol. Apothecia are the little mushrooms that grow from sclerotia in the soil, and the sclerotia are the hard structures of the fungus.

Apothecia are the little mushrooms that grow from sclerotia in the soil, and the sclerotia are the hard structures of the fungus. Sclerotia can live in the soil for up to 5 years, and when conditions are favorable, apothecia will germinate from the sclerotia and produce ascospores that get carried via wind and infect other plants. We scout for these little guys because we want to see if the sclerotia is germinating. In the lab, I have made PDA media, sterilized the sclerotia samples, plated the sclerotia on cultures, and assessed their viability. I plated them on PDA (potato dextrose agar) so we can look to see sclerotinia mycelium growth (the white fuzzy part) or any other growth of a different organism that may be present.

Overall, I have learned so much already and I really enjoy working in this lab. I hope everyone has been adjusting to their lab okay and I can't wait to hear about other's projects!

Hola! This week we have all been working hard in our labs, with out mentors helping us figure out our projects and really getting in-depth with it all. My project is about a pest insect called swede midge, a little fly from the Cecidomyiidae family that has been found damaging the leaves and heads of brassicas, affecting broccoli, kale, and cauliflower. As there are only chemical ways to manage swede midge, Dr Cindy Tong, my PI, has set-up mitigation kits, using cloth cages as an organic way to protect brassica crops from this pest. These are placed in small plots in community gardens and one of my goals is to figure out if they effectively keep the adult insects away from the crop by comparing damage in control plants outside and inside the mitigation kit.

Other activities in this study consist of catching swede midge in sticky traps that contain lures to attract males, and then counting them. We collect and replace traps every Monday and Friday. We aim to compare insect population from four community gardens in St. Paul: St. Anthony Park, Merriam Station, Midway Green Spirit, and Eleanor Graham from this and prior years. Sticky traps were also placed in four organic farms, two in Wisconsin and  two in Minnesota, with the intention of comparing swede midge’s population and broccoli damage against the community gardens.

Aside from my project I’ve helped Christina Perez with her swede midge colony by watering cauliflower plants, selecting healthy non-infected plants and putting them into cages where the colonies are, and rating damage made by the pest to the plants. 

I love my project, I have been learning so much about brassicas, the swede midge, meeting farmers that inspire me to work hard until I have my own farm and discovering new sights, animals and places. I’m so excited to see what everyone else is working on!

Hello! This summer I am studying blackspot bruise in potatoes. Blackspot bruise is a dark discoloration that occurs under a tuber’s skin when its cell membranes are damaged, triggering the formation of melanin. This damage is the result of handling and mechanical stress during and post-harvesting when tubers experience physical impacts. It is important to understand the development of bruise as it is a major concern of growers, costing the potato industry an estimated $298 million annually. 

My project focuses on developing a protocol that induces blackspot bruise in a time and labor efficient manner. My mentor, Fang Wang, and I are evaluating how different storage temperatures, storage durations, and tumbling times affect the development and incidence of blackspot bruise. Once the potatoes have undergone tumbling that simulates mechanical stress, they are then peeled and photographed in a lightbox. Once the protocol is optimized, the Shannon lab will implement the procedures to screen for bruise resistance in their breeding program, allowing them to make efficient selections and develop resistant varieties. This data will then be integrated into the Shannon lab’s image analysis program, TubAR, that objectively measures potato traits. By providing farmers with more bruise-resistant varieties, we hope to help mitigate losses associated with bruise. When I am not roughing up potatoes, I have been learning R programming and hope to be able to help out in the beautiful greenhouses and fields soon. 

I hope everyones’ projects are off to a positive start; I look forward to learning more about our respective interests together this summer!

Hello! I’m excited to share my first week in the Grossman lab this summer. I spent much of the first few days meeting everyone, including my mentor Gaby Hidrobo who will be guiding me throughout the research process. 

As a student in the social sciences, I have had many firsts this week. I was introduced to the “dirty” lab, where researchers process soil samples to prepare for testing, and the “clean” lab, where reagents are contained and protocols using chemicals take place. In the dirty lab, I weighed soil samples to be used in a POX-C protocol to measure the amount of labile carbon in the soil. In the clean lab, Gaby and Hannah led me through this protocol where we prepared a plate of samples to be run through a spectrophotometer. I felt like a real scientist in my lab coat! 

This process is part of the 100 Farms project which aims to assess the soil health of small-scale vegetable farms in Minnesota, particularly the prevalence of excessive phosphorus in the soil that can harm the environment. We are working with 200 samples of soil from 100 farms across the state, both from open fields and high tunnels. I am working on testing the amount of labile carbon in each sample to then look at correlations with other soil analytical tests such as organic matter content. 

Another highlight of this week was attending the dissertation defense of another grad student in the Grossman lab, Rebecca Fudge, who studied the symbiotic association between rhizobia and hairy vetch. It was an honor to witness the culmination of five years of hard work, and to see an example of everyone in the lab supporting one another’s accomplishments.