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NSF Funded Research To Track Microorganisms In Michigan’s Subsurface Superhighways

Aerial view of fields and roads
Image of MSU geomicrobiologist Matt Schrenk.

MSU geomicrobiologist Matt Schrenk’s research was selected by the National Science Foundation’s 2026 Idea Machine as one of 25 projects to explore bold and potentially transformative new ideas. Credit: Matt Schrenk

With more than 11,000 lakes, including four of the Great Lakes, Michigan is rightly known as the water state. But there’s more water, and more to water, in Michigan than meets the eye. Surface water in lakes, rivers and our bathtubs make up just one percent of the total freshwater in the world; about 40 percent is held in glaciers and ice caps, and the rest? It’s flowing right beneath our feet.

When it comes to groundwater research, scientists have barely scratched the surface, but Michigan State University geomicrobiologist Matt Schrenk and members of his lab travel the world—from remote mountains in Argentina to volcanoes in the Atlantic Ocean—to investigate how subterranean microbes move across and impact the planet.

Earlier this year, Schrenk submitted a highly novel and interdisciplinary proposal, “Groundwater Microbial Communities as Sentinels of Environmental Change” which was recently selected by the National Science Foundation’s 2026 Idea Machine as one of 25 projects funded to explore bold and potentially transformative new ideas.

“I study what I like to call the subsurface superhighways for microorganisms,” said Schrenk, an assistant professor with joint appointments in the Department of Earth and Environmental Sciences and the Department of Microbiology and Molecular Genetics in the MSU College of Natural Science. “My research aims to understand how microbes get into groundwater in the first place and how human activities and the environment at the surface influence biogeochemical processes in groundwater and vice versa.”

The $300,000 grant, which began September 1, will track microbes from shallow water aquifers that fill central Michigan faucets to ancient circulation cells hundreds of meters below the land surface that hold water and microorganisms tens of thousands of years old.

“This work will develop and employ state-of-the-art tools to track and understand the quality of Michigan’s groundwater resources, which are being increasingly challenged by changes in climate, population size, the introduction of anthropogenic chemicals and land use changes,” Schrenk explained. “This toolbox will benefit communities in Michigan and other locations around the globe.”

Image of groundwater microbes.

Schrenk will use high throughput genomics tools to analyze groundwater microbes, such as those shown in this epifluorescence micrograph, and how they move and change along subsurface flow pathways in mid-Michigan. Credit: Matt Schrenk

While per- and polyfluoroalkyl substances (PFAS) grab most of the headlines, other chemicals are making their way into these subsurface water systems, including microplastics and increasing levels of pharmaceuticals. Agriculture and urbanization also influence what grows in mid-Michigan’s groundwater held in distinct, but overlapping, circulation cells.

Tapping into these cells, Schrenk will study how microbial community composition and function is affected by in situ conditions related to chemistry and hydrology as well as by disturbances at the surface such as contamination and land use changes.

“High-throughput genomics tools have come on board over the past decade and given us unprecedented insight into both the evolution and function of these hidden ecosystems,” Schrenk said. “We will tap into deep circulation cells and look at the genomes of the organisms entering the flow system at shallow depths as well as those closer to where groundwater exits, near Saginaw Bay, to understand their evolution along this flow path and how it relates to their functions.”

Scientists have yet to understand how the mixing of ancient water with modern chemicals along these subsurface superhighways, and all the cracks and fissures (detours) along the way, have transformed the microbes who travel them.

For example, are the microorganisms making or consuming methane, a potent greenhouse gas? Do they contain genes for the degradation of recent anthropogenic contaminants or for antibiotic resistance? Schrenk’s research aims to analyze the subsurface microbiome and connect it to the health of people and the planet.

“The evolutionary history and capabilities of these subterranean microorganisms are recorded in their DNA,” Schrenk said. “Analyzing them will help us understand how they are transported and change along groundwater flow pathways.”

Because the project takes place in mid-Michigan, and because water is a vital part of every Michigander’s life, Schrenk’s work has the potential both to improve Michigan’s groundwater and to flood students of all ages and local communities with engaging, interactive opportunities.

“I’m excited! Working with MSU extension and students, we will translate the data we generate into modules that can be used in K-12 classrooms and science on a sphere-like interactive data projections for the public,” Schrenk said. “This project presents a tremendous opportunity to engage people in groundwater science, something which is critical to our lives, but which most people are unaware of.”

Banner image: MSU geomicrogeologist Matt Schrenk’s novel research will explore Michigan’s groundwater resources, which are being increasingly challenged by changes in climate, population size, the introduction of anthropogenic chemicals and land use such as agriculture. Credit: Osama Alian


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