How do you put a tree in a petri dish - and, more importantly, why would you do that?
For researchers at the Department of Energy's Oak Ridge National Laboratory, the answer lies in the intricate networks of bacteria and fungi hidden in the roots of towering Populus trees. These unseen communities shape plant growth, resilience and health, but their complexity has kept them largely unexplored - until now. ORNL scientists are using synthetic communities to simplify these underground populations to better understand the interactions between plants and microbes, informing the development of better crops for both domestic energy production and bioproducts for a broader bioeconomy.
Synthetic communities are lab-assembled groups of microbes designed to simulate real-world conditions. Made up of selected microbial strains, these carefully constructed communities allow scientists to simplify and study the relationships between plants and their microbial companions. Researchers can test specific interactions that would be nearly impossible to isolate in nature due to the sheer complexity of natural soil environments, which can host thousands of organisms.
"We can make synthetic communities with just two organisms or scale up to 10, 100 or more," said Dale Pelletier, leader of ORNL's Integrative Microbiomics group. "This allows us to focus on how individual microbes interact with each other and the plant." These communities help scientists study how microbes compete for resources, how some may help or hinder plant growth, and other dynamics that are much harder to explore in nature.
Exploring microbial neighborhoods in poplar
"Most microbial research focuses on two important things: our health and what we can eat," said Tomás Rush, a plant pathologist and mycologist interested in understanding chemical signals influencing fungal community organizations and behavior. "Agricultural crops are often investigated for their microbes and pathogens. At ORNL, our focus is on bioenergy crops, and we have one of the largest collections of bacteria and fungi from Populus."
Populus, or poplar trees, have immense potential as bioenergy crops due to their fast growth rate and adaptability to various environments. ORNL's collection of microbial isolates from the root environment of these trees encompasses thousands of bacterial and fungal strains.
Scientists have sequenced the genomes for a large fraction of those isolates, enabling them to handpick strains for synthetic communities based on their abundance in nature or specific genetic traits. Some microbes produce plant hormones that aid in plant growth, while others exhibit competitive behaviors or symbiotic traits of interest.
Simplifying complex communities
Creating and studying synthetic communities is no small feat. The team at ORNL conducts experiments in controlled environments, such as liquid cultures or soil mimics, to simulate plant-microbe interactions. To closely examine relationships between specific microbial strains, scientists grow them together on a gel-like surface called an agar plate. This setup acts like a microbial matchmaking zone and allows them to observe how the microorganisms interact with each other, such as whether they compete, help each other grow, or have no effect on one another.
The long-term goal is to predict microbial behavior based on genomic information. "Can we sequence a microbe's genome and accurately predict how it will interact within a community?" Pelletier added. "That's the ultimate challenge. Right now, we're gathering data to make that a reality."
Microbe relationships are inherently complex, and adding a plant into the equation makes these interactions even more difficult to study. "Microbial behavior is influenced by many factors - nutrient availability, light, humidity and environmental stresses like drought," said Rush. "When you introduce a plant, the complexity increases exponentially."
Tiny organisms, big potential
Despite the challenges, this complexity is part of what makes the research so important. Through their work with synthetic communities, ORNL researchers aim to uncover fundamental principles that govern microbial behavior. Understanding these interactions could have far-reaching implications. For example, identifying which microbes enhance plant growth, improve resilience to drought or protect against pathogens could revolutionize bioenergy crop production, strengthening the nation's energy security and the bioeconomy.
"The questions we're addressing aren't easy," said Rush. "But the complexity is part of what makes this work so exciting. It's a challenge worth pursuing."
This research is an integral part of the Plant-Microbe Interfaces Science Focus Area, which is funded by the Biological and Environmental Research program in DOE's Office of Science.
UT-Battelle manages ORNL for the Department of Energy's Office of Science, the single largest supporter of basic research in the physical sciences in the United States. The Office of Science is working to address some of the most pressing challenges of our time. For more information, please visit energy.gov/science . - Michaela Bluedorn
