New faculty member studies how to leverage microbial forces to combat climate change

The air we breathe is a direct result of the dirt under our feet. Trillions upon trillions of soil bacteria break down organic matter, releasing carbon dioxide and other potent greenhouse gases; photosynthetic microbes do the opposite, pulling CO2 out of the air and releasing oxygen. This delicate balance kept Earth's atmosphere stable for eons-until human activities sent it into a tailspin. Now, without a better understanding of the basic biology of these key microbes, it's difficult to imagine a comprehensive solution to the climate crisis.

Avi Flamholz, who joins The Rockefeller University faculty in January 2025 as assistant professor and head of the Laboratory of Environmental Microbiology, is dedicated to advancing this critical research. His lab will focus on the role of soil microbes in the carbon cycle, with an emphasis on developing computational methods and technologies. By combining machine learning with experimental work, Flamholz hopes to unlock new ways to harness the power of microbes to slow down or reverse rising global temperatures.

"The power of microbes to influence our climate is immense, but we've only scratched the surface of understanding how this could work," Flamholz says. "We're now at the point where science can begin to predict environmental changes and help mitigate the effects of climate change."

Raised in the New York metropolitan area, Flamholz was drawn to science early on-his father was a physicist, and he enjoyed STEM subjects in school. As an undergraduate at Princeton, Flamholz focused mainly on computer science, only briefly studying computational biology before going on to work as a software engineer at Google.

But among the machines, Flamholz began to feel restless.

"I had been reading about climate change and challenges to food systems, and the ways in which resource constraints influence global conflict were always in the back of my mind," Flamholz says. "I was still young, wasn't married, and had no kids, so I decided to refocus my entire career, and do something involving food and climate."

Flamholz took an unbiased approach to finding his next career move. He explored doctoral programs in molecular biology, agricultural economics, plant science, and climate science; he attended conferences and cold called professors who appeared to be working on interesting projects. Flamholz was ultimately drawn to the work of Ron Milo at the Weizmann Institute in Israel, which was then working on engineering microbes to fight climate change by consuming carbon dioxide. After Flamholz traveled overseas to join his lab, Milo took Flamholz under his wing, encouraging him to take classes, pursue research projects, and publish with the group.

This stint in Milo's lab left Flamholz with a clearer vision for his life's work. After returning to the U.S. he began his PhD at University of California Berkeley in the laboratory of David Savage, where Flamholz focused in on understanding the genes that cyanobacteria use to draw carbon dioxide out of the atmosphere. Ultimately, he demonstrated that it is possible to modify the genomes of the model bacteria E. coli so that they, too, could engage in carbon fixation. Later, as a postdoctoral researcher at Caltech, Flamholz brought his computer science background into the biology lab, developing mathematical and statistical models to explore how microbes control the release of carbon from soil, one of the largest carbon reservoirs on the planet.

At Rockefeller, one of his lab's primary goals will be to investigate how microbes process nutrients and how these processes are encoded in their genomes. By analyzing microbial sequencing data from real-world environments and applying machine learning techniques, Flamholz hopes to develop predictive tools that will improve our understanding of how microbes release and absorb carbon in different environments. This deeper understanding can lead to more accurate climate models and inform strategies to manage carbon fluxes.

"The milestones along the way will also teach us many things in fundamental science-microbial physiology, applied math, and physics," Flamholz says.

The lab will additionally focus on the delicate balance between photosynthesis and microbial respiration in real ecosystems, to better understand and predict the contributions of soil microbes to carbon emissions. "The biological processes happening beneath our feet dwarf the carbon emissions we humans produce, so understanding them is key to managing climate change," he says. Flamholz also hopes to engineer microbes to replace or mitigate high emissions from agricultural processes.

Rockefeller's president, Rick Lifton, notes that faculty who met with Flamholz were impressed by his scholarship and talent as an experimentalist. "Avi's focus on the life science aspects of climate change is a timely addition to the University's research and dovetails nicely with work in a number of other laboratories on campus," he says. "He also brings exceptional strength in applied mathematics and computer science, areas that bring new strength to our community."