REU: Systems Biology of Plant and Microbiome

Center for Root and Rhizobiome Innovation  –

For information contact

Nicole Busboom

Outreach Coordinator, Nebraska EPSCoR


2018 Plant & Microbiome students at the REU picnic
2018 Plant & Microbiome students at the REU picnic

Who should apply

Related fields

  • Plant Science
  • Biochemistry
  • Biology
  • Agronomy and Horticulture
  • Biology Systems Engineering
  • Chemistry
  • Genetics


Participation in the Nebraska Summer Research Program is limited to students who meet the following criteria:
  • U.S. Citizen or Permanent Resident
  • Current undergraduate with at least one semester of coursework remaining before obtaining a bachelor's degree

See Eligibility for more information.

How to apply

Follow the application steps to submit the following materials.

About the Program

The Center for Root and Rhizobiome Innovation (CRRI) will establish and develop tools and technologies for more rapid, precise, and predictable crop genetic improvement that complement methods currently used by biotechnologists and plant breeders.  These innovations are needed because of the urgency and enormity of challenges facing global agriculture, including the need to feed a rapidly growing population in the face of extreme climate variations and limitations in water and soil vitality.  

CRRI research will be structured around a systems and synthetic biology core to generate and iteratively improve network models of plant metabolism for predictable outcomes from genetic modifications.  CRRI’s systems and synthetic biology research will be applied to the study of root metabolism and its influence on root-interactions with soil microbes for improved plant health.    

Undergraduate students studying maize roots.
Undergraduate students studying maize roots.

Research will focus on root metabolism in maize, a plant genetic model and important crop species, but findings will be broadly applicable to other plants and crop species.  CRRI will develop and use fundamental knowledge to create translational products with far-reaching impact on plant and microbial biology and global agriculture.


  • Competitive stipend: $5,000
  • Suite-style room and meal plan
  • Travel expenses to and from Lincoln
  • Campus parking and/or bus pass
  • Full access to the Campus Recreation Center and campus library system
  • Wireless internet access

Learn more about academic and financial benefits.


  • Department seminars and presentations
  • Professional development workshops (e.g., applying to graduate school, taking the GRE)
  • Welcome picnic
  • Day trip to Omaha's Henry Doorly Zoo
  • Outdoor adventures
  • Research symposium

Mentors and Projects

Dr. Tomas Helikar Biochemistry

Students would work with multiscale computational models of plant systems can enable better understanding of metabolic processes, relationships between genotype and phenotype, and impact of cellular and environmental factors. We have developed a comprehensive multi-scale metabolic model of maize root and its mutualistic soil microbe community. Simulation results predict the uptake of maize root secretions by soil microbes and vice versa. Transcriptomic analyses of maize root under varying nutrient conditions and root regions with highly expressed genes unveil more flux carrying reactions than lowly expressed genes. The REU student(s) will work with our team to 1) use the model to design novel hypotheses about manipulating microbial metabolism to improve the maize growth, and 2) develop computational models of additional soil microbes.

Dr. Marc Libault Agronomy and Horticulture

Student will be working on a single root cell transcriptomic approach to better understand the unique regulation of gene expression occurring in the different cells and cell-types composing the maize root system. This fundamental knowledge is needed in order to better understand the molecular response of maize roots to soil microbes. This knowledge will also enhance our understanding of the contribution of the different maize root cells types in producing a specific set of exudates, molecules used by the plant to communicate with the soil microbiome. This project is relevant to on-going CRRI efforts such as the analysis of the biochemical composition of maize root exudates and the need to enhance systems biology of the maize root system. As part of this summer experience, the student will develop skills in cell biology, molecular biology and bioinformatics. The student will first work on the isolation of each cell/nucleus compositing the maize root. Upon successful isolation, the student will use droplet systems to create DNA libraries reflecting the transcriptomic composition of each cell/nuclei. Finally, upon sequencing of these DNA libraries, the student will be introduced to DNA sequence analysis using bioinformatics tools. 

Dr. Daniel Schachtman Agronomy and Horticulture

The student will either work on a plant related project or a microbe related project.  The microbe related project would be the functional characterization of unique soil microbes that were cultured from either low nitrogen fields or very alkaline soils.  The plant related project would be to study the changes in root architecture and morphology due to genotype or abiotic stress such as low nitrogen or drought.

Dr. James Schnable Agronomy and Horticulture

Students will experience writing computer code, employing molecular biology techniques, working with living plants in the greenhouse, and conducting fieldwork. As a result of the diverse set of collaborators we work with – applied plant breeders, biochemists, engineers, computer scientists, food scientists, and statisticians – each member of the lab also gains experience communicating both within and across scientific disciplines, as well as to diverse non-scientific audiences. This cross training produces scientists who are equipped to both understand and address the complex and far-reaching problems our world will face in coming decades. Research projects available in the Schnable Lab in summer of 2019 include A) using machine learning to teach computers how to measure different characteristics of plants using photos taken in greenhouses and from drones flying over agricultural fields (no prior computer coding experience required) B) using genome wide association study techniques (GWAS) to identify specific genes controlling variation in plants traits which have already been measured by hand or by computer and C) using comparative genomics and RNA-seq analysis to identify promoters which turn genes off or on when plants are experiencing shortages of particular essential nutrients. 

Dr. Bin Yu Biological Sciences

Student would work to understand the molecular mechanisms underlying small RNA metabolism and function. Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are 20 to 24 nucleotide (nt) RNAs that function as sequence-specific regulators of gene expression at both transcriptional and post-transcriptional levels in eukaryotes. These small RNAs are involved in numerous cellular processes including development, differentiation, proliferation, apoptosis, and stress responses. We currently employ a combination of genetic, biochemical, cell biological, and genomic approaches to identify and characterize components involved in small RNA metabolism and utilize the knowledge obtained to design tools used in synthetic biology.