Cooperative Institute for Research in Environmental Sciences at the University of Colorado Boulder

Big Problems, Little Solutions

Center for Microbial Exploration looks under the microscope to bolster the health of our planet and our minds


Every step we take, whether across a grassy park or down a city sidewalk, below our feet is an ecosystem teeming with life. Thousands of microbes, invisible to the naked eye, make life function as we know it. These tiny organisms play a role in everything from the sprouting of a single flower out of the dirt to regulation of the global carbon cycle. With climate change threatening to tip these processes out of balance, better understanding microbial activity could be key to humans adapting to looming crises such as drought and disease.

The Center for Microbial Exploration (CME) at the University of Colorado Boulder, founded in 2019, highlights the growing recognition that microbiology is a crucial component of many scientific fields. Center members’ research follows microbes at play in agriculture, the Arctic and even our own bodies. Despite looking at vastly different ecosystems, these scientists all want to know the same thing: what microbes are there and what are they doing? It has taken decades to arrive at even a partial answer. 

“The mysteries of the microbial world never cease to amaze. Even basic questions often remain unanswered,” said Noah Fierer, CIRES fellow and professor of ecology and evolutionary biology at the University of Colorado Boulder.

It was this knowledge gap that drew Fierer to the field of microbiology. In his 20 years of studying microbes he’s seen a lot of advances in methods, including DNA technologies that allow scientists to more easily identify organisms in a sample. Still, there are potentially thousands of undiscovered microbes with unknown capabilities to explore.

As CME director, Fierer wants to help close that gap by providing a space for collaboration across disciplines. In its first year, the center held eight meetings in which members and guests presented their research and three workshops led by graduate students.

Could Microbiology Improve Sustainable Agriculture? 

When Corinne Walsh was deciding on a research focus for her Ph.D. in Fierer’s lab, she knew she wanted to do something that could help tackle big, real world problems beyond the lab. So she turned to one of the most important cereal crops across the globe: wheat. 

Humans have studied wheat for centuries, creating a large body of work on the reactions of wheat to chemicals like fertilizers and pesticides. But there is less research into the microbiomes of these plants. 

“The microbiome angle is thinking about sustainable agriculture in terms of less chemical inputs,” said Walsh. “It’s thinking about if you can understand the biology of the system a little more and optimize it from a microbiological perspective.”

A researcher demonstrates the experiment process for exploring the relationship between microbes and wheat production.Corinne Walsh sets up an experiment to  explore the relationship between microbes and wheat production (L Panel). The three vials contain a dry dirt sample, a dirt sample mixed with water, and the wheat seeds that Walsh then applies the wet dirt "slurry" to (r panel). PHOTOS: Julia Medeiros/CIRES and CU Boulder

Walsh is investigating how the microbiome of a wheat plant is assembled. Does the wheat plant itself determine the kinds of microbes that are present, or is it more dependent on the soil? That question is critical to understanding and possibly even manipulating the relationships between microbes and plants. 

To dig into the question, Walsh collected soil samples from 200 locations across the United States. She used those samples to grow around 4,000 wheat seeds in laboratory conditions and will next analyze their DNA to find out if the different soil microbes influenced the wheat microbiomes. Defining to what extent the microbiome can be influenced will help experts understand just how much different soil microbes can potentially help strengthen the plant in times of drought and blight—something on the minds of farmers around the world as temperatures rise.

At a Loss Without Moss 

Deep in the boreal forests of the Northern Hemisphere, microbes are hard at work. Nitrogen-fixing bacteria are responsible for the growth of the mosses stretching across the forest floor. As these forests are threatened by more frequent and intense fires, scientists are investigating how moss-dwelling microbes are important not only for the health of the forest but also for the entire planet.

“These mosses are massive,” said Hannah Holland-Moritz, a Ph.D. candidate in the Ecology and Evolutionary Biology department at CU Boulder. “You can sometimes sink up to your knee in them.”

Working with a team from the University of Florida and Northern Arizona University, Holland-Moritz analyzed samples of eight boreal moss species in Fairbanks, Alaska, and found that all eight had bacterial communities capable of nitrogen fixation, despite each having diverse bacterial lineages. The team further investigated the genetic material of some lesser-known lineages to try and identify those characteristics that make them suited to living on moss, such as the processes they use to obtain nutrients.     

Knights plume moss with some Hylocomnium splendens found in Alaska. Knights plume moss (Ptillium crista-castrensis, bright green) with some Hylocomnium splendens (darker, olive green). found in Alaska, Both are well-known for nitrogen fixation. photo: Hannah Holland-Moritz/CU Boulder

Finding out which bacteria are driving the nitrogen fixation process can tell scientists more about how and where carbon is stored in boreal forests. Nitrogen input helps moss grow larger and continue to sequester carbon, but eventually it stops and dies. In a peat bog, the dead moss and the carbon within it become trapped in the wet, spongy quagmire instead of decomposing and releasing carbon dioxide into the atmosphere. 

As rising temperatures threaten to wipe out the moss and microbes of boreal forest and bogs, thousands of years of stored carbon could be released, turning the Northern Hemisphere from a carbon sink to a powerful carbon source.

Microbes on the Mind 

The study of soil microbes is not only useful for the natural world outside, but also for the one within us. Research has shown that a soil microbe called Mycobacterium vaccae, a bacterium with anti-inflammatory properties, reduces stress and fear in mice. 

For over two decades, Christopher Lowry, a professor in integrative physiology at CU Boulder and CME member, has been studying the beneficial role that bacteria like M. vaccae play in stress resilience of animals. The concept of resilience is not only about alleviating stress after the fact, but preparing for the impact before it hits.

“When we think about psychiatric disorders, we often think that it’s about the discovery of novel treatments,” said Lowry. “But we should also be thinking about how we can prevent these conditions from occuring in the first place.”

This involves exploring the microbiome-gut-brain axis—the two-way communication line between microbes in the gut and the brain. Scientists know this communication is important, but the challenge arises in determining the exact mechanisms used to facilitate it. 

Lowry has spent the majority of his career investigating how M. vaccae works within this axis. But this is only one species of thousands of bacteria that can live within the human body, interacting in many ways that may have an impact on mental health. Lowry’s work, in demonstrating that M. vaccae can have positive effects, means that it is likely other bacteria could as well, suggesting further research into the use of bacteria for treatment of depression, anxiety, and posttraumatic stress disorder. 


CIRES is a partnership of NOAA and CU Boulder.


This story was written by Julia Medeiros


contacts

Noah Fierer
CIRES fellow, CU Boulder professor of ecology and evolutionary biology
Karin Vergoth
CIRES communications
303-497-5125

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