research petri dish

Agribiome Science

On people’s skin and in their bodies, and within agriculture’s soil, plants and animals, is a community of microorganisms known as the microbiome. A world-class and interdisciplinary team of CSU scientists known as the CSU Microbiome Network is taking a systems approach to improving understanding of the agricultural microbiome, or agribiome, and addressing concerns of food security, food safety and the sustainability of food systems.

Spotlight: CSU leads the way in Microbiome Science 

The Wilkins Research Group

Dr. Mike Wilkins’ research group is focused on the impacts of increasingly severe wildfire on the soil microbiome, with critical implications for long-term forest health and recovery. In the past two years, the group has secured $2M in federal funding to study this topic and has established strong collaborations with the USFS Rocky Mountain Research Station in Fort Collins to ensure that their findings translate to actionable items for forest managers and other stakeholders in Colorado.

Wilkins co-organized the inaugural Front Range Microbiome Symposium in April 2022. This event hosted nearly 200 people at CSU Canvas Stadium and highlighted the breadth of microbiome research being performed along the Front Range. Attendees came from Universities of Wyoming, CU Boulder, CU Anschutz, CO School of Mines, and CSU.

The Trivedi Laboratory

The Trivedi Laboratory explores interactions between microbiome and plant environments, including plant-microbe-insect interactions, that influence the health and productivity of managed and natural systems. By providing systems-level understanding of plant microbiomes, Dr. Trivedi’s research will develop new computational tools and models that enable plant breeders and plant ecologists to achieve improved yields and plant resilience in changing environments. This work, in partnership with Universities of Pennsylvania and Florida, is already delivering benefits to the Florida citrus industry in the management of citrus greening disease.


The Wrighton Laboratory

The Wrighton Laboratory studies how microorganisms contribute to ecosystem processes, exploring microbial communities in a range of environments, including river systems, soils, the human gut, and hydraulically fractured shales. Dr. Wrighton’s research has implications for soil health, improved predictions of greenhouse gases, optimized energy recovery from hydrocarbon systems and stabilized human gastrointestinal function. Visit the Wrighton Lab to learn more.

Recent Accomplishments

USDA funded- Meagan Schimpanski and Jessica Prenni

  • Our goal is to discover the mechanism by which cover crops use to stimulate soil health, with Prenni’s lab characterizing the root exudates of different cover crops, my lab leading the experiments to characterize microbial responses, and Meagan leading on farm work.
  • Publication 2022: *co-first authors with Prenni and Wrighton Phd students

National Needs Funding

  • Lady Grant received a graduate fellowship to continue working in Agribiome science.
  • Working Erik Wardle, along with faculty Jim Ippolito and Keith Paustain
  • Our goal is to understand how different agricultural practices from conventional to regenerative tillage impact soil health and microbial contributions to this over time and across the state.
  • Publication 2022: This publication was developed using initial data collected by our undergraduate students in Research Experience Course on soil microbiome data analytics.

Improving Our Understanding of Soil Health

Working with Wilma Trujilo on microbiome data analytics. We are developing a soil health microbiome gene analysis method that Wilma can offer to her customers. Published on the software we have built with our graduate student. Currently developing an Ag microbiome component. From microbial genome sequences we will be able to ascertain roles in N mineralization, Phosphorus solubilization, N.

Microbial Roles in Carbon Sequestration

This project is collaboration with Francesca Cortrufo, where we are trying to understand microbial gene expression patterns and biomass and how this relates to formation of MAOM. We are measuring various soil types, including regenerative grazing. Our projects began this fall, and are co-mentoring a grad student begining next year.

people using equipment in mountains

What’s Next – The Aerobiome

While CSU researchers are making important discoveries in the microbiome of soils, plants, animals, and humans, microbial life found in the atmosphere has not been extensively studied.

More than a dozen scientists from five colleges at CSU are contributors to the BROADN project that will investigate how the aerobiome is altered by environmental stresses such as weather patterns, seasons, drought, agriculture and fire, and how it impacts human, animal and environmental health.