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Indiana University Bloomington

Department of Biology

Faculty & Research

Faculty Profile

Jake McKinlay

Photo of Jake McKinlay
Research Images
Research photo by Jake McKinlay

R. palustris is the Swiss army knife of the bacterial kingdom. The versatility of its metabolism allows it to use the right metabolic tools for the right environment and presents a variety of options for applications using a single organism. 

Research photo by Jake McKinlay

Metabolic flux maps obtained from performing 13C-labeling experiments on R. palustris. Arrow thickness indicates the amount of metabolic flow through a pathway. In the absence of H2 production (left) excess reducing power is diverted to the Calvin cycle resulting in a high level of CO2 fixation (green arrows). When H2 is produced (right) reducing power is naturally diverted away from the Calvin cycle towards H2 production (yellow). This effect can be enhanced by genetically eliminating CO2 fixation.

Contact Information
By telephone: 812-855-0359/5-9332(lab)
JH A309 / A308 (lab)

McKinlay Lab website

Research Areas
  • Genomics and Bioinformatics
  • Microbial Cell Biology and Environmental Responses
  • Microbial Interactions and Pathogenesis

Ph.D., Michigan State University, 2006
Postdoctoral Fellow, University of Washington, 2007-2011


Indiana University Trustees Teaching Award, 2015

ORAU Ralph E. Powe Junior Faculty Enhancement Award, 2012

US Department of Energy Early Career Award, 2012-2017

Research Description

The McKinlay lab has diverse interests in the physiology and metabolism of bacteria. Much of our work is focused on bacteria having traits that can benefit society, for example through the production of biofuels. With help from our excellent colleagues and facilities at IU, we use a variety of approaches in our research including genetics, biochemistry, analytical chemistry, 13C-guided metabolic modeling, genomics, and microscopy. The information we gather provides unique insights into how bacteria interact with their environment and each other and guides the engineering of bacteria and synthetic communities to perform useful tasks.

The metabolism, ecology, and evolution of microbial communities. In nature, individual microbial species can engage in cooperative relationships to occupy a niche that they otherwise could not occupy alone. Synthetic microbial communities are useful systems for characterizing these interactions and determining how they evolve. The synergistic attributes of some cooperative relationships can also be harnessed to benefit society. However, progress with such consortia has been hampered by the challenge of maintaining stable relationships that yield reproducible results. 

Using defined mutations and environmental conditions we have developed a stable coculture between fermentative bacteria (e.g., Escherichia coli) and phototrophic bacteria (e.g., Rhodopseudomonas palustris). The two bacteria exist in a relationship wherein one species cannot grow without the other. Together, the two species convert sugars into H2 gas, a potential biofuel. We are using this synthetic community as a model system to explore the metabolism, ecology, evolution, and applications of microbial consortia.

The coordination of competing metabolic modules. Bacteria are typically equipped with an array of metabolic modules. Individual modules can have overlapping resource demands and thus have the potential to compete against one another. Our lab examines how different electron-requiring pathways are coordinated in biofuel-producing bacteria. Two areas of focus are (i) the coordination of CO2 fixation and H2 production in phototrophic purple nonsulfur bacteria and (ii) the coordination of N2 fixation and ethanol production in Zymomonas mobilis – a potential bacterial rival to yeast for ethanol production.

Integration of light harvesting with metabolic activities. Purple nonsulfur bacteria use specialized photosynthetic organelles to convert light energy into a proton motive force. These organelles are composed of intracellular membranes that harbor the light harvesting complexes and reaction centers. Purple nonsulfur bacteria are also some of the most metabolically versatile bacteria ever described, and are able to thrive under a wide array of environmental conditions. We are examining how the development of these organelles is coordinated with other cell processes and how they form a dynamic response to fluctuations in cellular energy demands.

Select Publications
Kremer, TA*, B LaSarre*, AL Posto, and JB McKinlay. 2015. N2 gas is an effective fertilizer for bioethanol production by Zymomonas mobilis. Proceedings of the National Academy of Sciences USA. 112: 2222-2226. * equal contribution.  [article]
McKinlay, JB, Y Oda, M Rühl, AL Posto, U Sauer, CS Harwood. 2014. Non-growing Rhodopseudomonas palustris increases the hydrogen gas yield from acetate by shifting from the glyoxylate shunt to the tricarboxylic acid cycle. J. Biol. Chem. 289: 1960-1970.  [article]
Gordon, GC and JB McKinlay. 2014. Calvin cycle mutants of photoheterotrophic purple non-sulfur bacteria fail to grow due to an electron imbalance rather than toxic metabolite accumulation. J. Bacteriol. doi:10.1128/JB.01299-13  [article]
McKinlay, JB and CS Harwood. 2011. Calvin cycle flux, pathway constraints and substrate redox state together determine the H2 biofuel yield in photoheterotrophic bacteria. mBio. 2: e00323-10. doi:10.1128/mBio.00323-10.
McKinlay, JB and CS Harwood. 2010. Carbon dioxide fixation as a central redox cofactor recycling mechanism in bacteria. Proceedings of the National Academy of Sciences USA. 107: 11669-11675.
McKinlay, JB and CS Harwood. 2010. Mini-review. Photobiological production of hydrogen gas as a biofuel. Current Opinion in Biotechnology. 21: 244-251.
Huang, JJ, EK Heiniger, JB McKinlay, and CS Harwood. 2010. Production of hydrogen gas from light and the inorganic electron donor thiosulfate by Rhodopseudomonas palustris. Applied and Environmental Microbiology. 76: 7717-7722.
McKinlay, JB, M Laivenieks, BD Schindler, AA McKinlay, S Siddaramappa, JF Challacombe, SR Lowry, A Clum, AL Lapidus, KB Burkhart, V Harkins and C Vieille. 2010. A genomic perspective on the potential of Actinobacillus succinogenes for industrial chemical production. BMC Genomics. 11: 680.
McKinlay, JB, Y Shachar-Hill, JG Zeikus, and C Vieille. 2007. Determining Actinobacillus succinogenes metabolic pathways and fluxes by NMR and GC-MS analysis of 13C-labeled metabolic product isotopomers. Metabolic Engineering. 9: 177-192.
McKinlay, JB, C Vieille, and JG Zeikus. 2007. Mini-review. Prospects for a bio-based succinate industry. Applied Microbiology and Biotechnology. 76: 727-740.

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