Feature Story | 7-Nov-2022

James McKinlay : Then and Now / 2012 Early Career Award Winner

The Early Career Research Program award allowed James to develop a defined community composed of two bacterial species

DOE/US Department of Energy


Microbes are most abundant form of life on Earth, and they are constantly interacting with each other and with their environment. These interactions include working together to acquire and utilize nutrients.

These metabolic interactions can have profound impacts. Microbes in our gut that exchange nutrients, for example, can directly influence our health. Others form nutritional networks that span the globe, affecting the flow of carbon and, thereby Earth’s climate. These microbial interactions can be engineered and harnessed to benefit society, such as in the production of biofuels from sustainable resources.

The Early Career Research Program award allowed me to develop a defined community composed of two bacterial species. The two species are locked into a relationship where one cannot grow without the other. They exchange essential nutrients and together convert plant-derived sugars into a biofuel form of hydrogen gas.

The research supported by this program also took unexpected turns that still proved fruitful. For example, we discovered that a bacterium that we expected to require a partner to use nitrogen gas as a nutrient was actually able to use nitrogen gas itself. This bacterium also naturally produces ethanol at levels that rival that of industrial ethanol-producing yeast. We estimate that, if scaled up, supporting this ethanol-producing bacterium with nitrogen gas could save an ethanol production facility over one-million US dollars per year. 

The award allowed me to recruit a talented team of graduate students and a postdoc, the latter of whom learned about my research through a press release about this award. My group used genetics, analytical chemistry, and computational modeling to identify factors that determine hydrogen gas production levels. More broadly, we identified factors that govern cooperative relationships between microbes.


James McKinlay is an associate professor of biology at Indiana University.


The Early Career Research Program provides financial support that is foundational to early career investigators, enabling them to define and direct independent research in areas important to DOE missions. The development of outstanding scientists and research leaders is of paramount importance to the Department of Energy Office of Science. By investing in the next generation of researchers, the Office of Science champions lifelong careers in discovery science.

For more information, please go to the Early Career Research Program.


Title: Metabolism and Evolution of a Biofuel‐Producing Microbial Coculture


Some microbes can convert renewable resources such as carbohydrates and sunlight into biofuels. Therefore, they offer an urgently needed alternative to non‐renewable fuels.

Most research efforts in this area have focused on genetically engineering individual microbial species to improve biofuel production. However, a lesson can be taken from nature, where multiple microbial species help each other to thrive on food sources such as plant residues that the individual species cannot use on their own. Furthermore, mixtures of specialized microbes can sometimes outperform a single engineered strain for producing chemicals of value to society.

This research will make use of a mixture of two microbial species (a coculture) that work together using sugar and energy from sunlight to produce more hydrogen gas biofuel than either microbe could by itself. A major challenge in using cocultures is ensuring that the different species maintain a long‐term cooperative relationship. This research will stabilize such cooperation by forcing each microbe to provide a nutrient that the other requires to survive. This approach enables experiments that will decipher how the metabolisms of the two species interact and thereby how they can be optimized for biofuel production. Studying the evolution of the microbes in the coculture will also lead to the discovery of traits that enhance biofuel production. This information will ultimately lead to the design and engineering of tailor‐made microbial mixtures for the economical production of hydrogen gas and other biofuels from renewable resources.


TA Kremer, B LaSarre, AL Posto, and JB McKinlay, “N2 gas is an effective fertilizer for bioethanol production by Zymomonas mobilis.” Proceedings of the National Academy of Sciences U S A 112, 2222 (2015). [DOI: 10.1073/pnas.1420663112]

B Lasarre, AL McCully, JT Lennon, and JB McKinlay, “Microbial mutualism dynamics governed by dose-dependent toxicity of cross-fed nutrients.” The ISME Journal 11, 337 (2017). [DOI: 10.1038/ismej.2016.141]

AL McCully, B LaSarre, and JB McKinlay, “Recipient-biased competition for an intracellulary generated cross-fed nutrient is required for coexistence in a bacterial mutualism.” mBio 8, e01620-17 (2017). [DOI: 10.1128/mBio.01620-17]

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