Leslie A Day, Hans K Carlson, Dallas R Fonseca, Adam P Arkin, Morgan N Price, Adam Deutschbauer, and Kyle C. Costa (2024) High-throughput genetics enables identification of nutrient utilization and accessory energy metabolism genes in a model methanogen. BioRxiv preprint: doi:

Mohd Farid Abdul Halim, Emily H. Hanson, and Kyle C. Costa (2024) Methanococcus maripaludis. Trends in Microbiology.

Anthony J. Zmuda, Xiaojun Kang, Katie B. Wissbroecker, Katrina Freund Saxhaug, Kyle C. Costa, Adrian D. Hegeman, and Thomas D. Niehaus (2024) A universal metabolite repair enzyme removes a strong inhibitor of the TCA cycle. Nat. Comm. 15:846.

Mohd Farid Abdul Halim, Dallas R. Fonseca, Thomas D. Niehaus, and Kyle C. Costa (2024) Functionally redundant formate dehydrogenases enable formate-dependent growth in Methanococcus maripaludis. J. Biol. Chem. 300:105550.


Kyle C. Costa and William B. Whitman (2023) Model organisms to study methanogenesis, a uniquely archaeal metabolism. J. Bacteriol. 8:e00115-23.

Dallas R. Fonseca, Madison B. Loppnow, Leslie A. Day, Elisa L. Kelsey, Mohd Farid Abdul Halim, and Kyle C. Costa (2023) Random transposon mutagenesis identifies genes essential for transformation in Methanococcus maripaludisMol. Genet. Genom. 298: 537–548.


Leslie A. Day, Elisa L. Kelsey, Dallas R. Fonseca and Kyle C. Costa (2022) Interspecies formate exchange drives syntrophic growth of Syntrophotalea carbinolica and Methanococcus maripaludisAppl Environ Microbiol. 88:e01159-22.

Francisco J. Arriaza-Gallardo, Sebastian Schaupp, Yu-Cong Zheng, Mohd Farid Abdul Halim,  Pan Hui-jie , Jörg Kahnt, Georgia Angelidou, Nicole Paczia, Xile Hu,  Kyle C. Costa and Seigo Shima (2022) The function of two radical-SAM enzymes, HcgA and HcgG, in the biosynthesis of the [Fe]-hydrogenase cofactor. Angew Chem. Int. Ed. 61:e202213239.

Eric Hernandez and Kyle C. Costa (2022) The fluorescence-activating and absorption-shifting tag (FAST) enables live-cell fluorescence imaging of Methanococcus maripaludis. J Bacteriol. 204:e00120-22.

         Article selected as an "Editor's Pick."

Sebastian Schaupp, Francisco J. Arriaza-Gallardo, Hui-jie Pan, Jörg Kahnt, Georgia Angelidou, Nicole Paczia, Kyle C. Costa, Xile Hu and Seigo Shima (2022) In vitro biosynthesis of the [Fe]-hydrogenase cofactor verifies the proposed biosynthetic precursors. Angew Chem. Int. Ed. 61:e202200994.

Thomas J. Lie, Yang P. Kuo, Mara Leite, Kyle C. Costa, Caroline S. Harwood, and John A. Leigh (2022) A genetic study of nif-associated genes in a hyperthermophilic methanogen. Microbiol Spectrum 10:e02093-21.

Stefan Schulze, Heather Schiller, Jordan Solomonic, Orkan Telhan, Kyle Costa, and Mechthild Pohlschroder (2022) Advanced understanding of prokaryotic biofilm formation using a cost-effective and versatile multi-panel adhesion (mPAD) mount. Appl Environ Microbiol. 88:e02283-21.


Leslie A. Day and Kyle C. Costa (2021) Complete genome sequence of the secondary alcohol-utilizing methanogen Methanospirillum hungatei strain GP1. Microbiol Resour Announc. 10:e00708-21.

Matthew P. Holten, Dallas R. Fonseca, and Kyle C. Costa (2021) The oligosaccharyltransferase AglB supports surface-associated growth and iron oxidation in Methanococcus maripaludisAppl Environ Microbiol. 87:e00995-21.

Mohd Farid Abdul Halim, Leslie A. Day, and Kyle C. Costa (2021) Formate-dependent heterodisulfide reduction in a Methanomicrobiales archaeon. Appl Environ Microbiol. 87:e02698-20.

         Article highlighted in the Applied and Environmental Microbiology Spotlight section.


Dallas R. Fonseca*, Mohd Farid Abdul Halim*, Matthew P. Holten, and Kyle C. Costa (2020) Type IV-like pili facilitate transformation in naturally competent archaea. J Bacteriol. 202:e00355-20. *Equal contribution

         Article highlighted in the Journal of Bacteriology Spotlight section.



Kyle C. Costa, Leon S Moskatel, Lucas A Mierelles, and Dianne K. Newman (2018). PhdA catalyzes the first step of phenazine-1-carboxylic acid degradation in Mycobacterium fortuitumJ Bacteriol. 200: e00763-17.

Wei Qin, Shady A. Amin, Rachel A. Lundeen, Katherine R. Heal, Willm Martens-Habbena, Serdar Turkarslan, Hidetoshi Urakawa, Kyle C. Costa, Erik L. Hendrickson, Tony Wang, David A. C. Beck, Sonia M. Tequia, Fred Taub, Andrew D. Holmes, Todd M. Lowe, James W. Moffett, Alan H. Devol, Nitin S. Baliga, Daniel J. Arp, Luis A. Sayavedra-Soto, Murray Hackett, E. Virginia Armbrust, Anitra E. Ingalls, and David A. Stahl (2018) Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations. ISME J. 12: 508-519.

Kyle C. Costa, Nathaniel R. Glasser, Stuart J. Conway, and Dianne K. Newman (2017) Pyocyanin degradation by a tautomerizing demethylase inhibits Pseudomonas aeruginosa biofilms. Science. 355: 170-173.

Kyle C. Costa, Megan Bergkessel, Scott Saunders, Jonas Korlach, and Dianne K. Newman (2015) Enzymatic degradation of phenazines can generate energy and protect sensitive organisms from toxicity. mBio. 6: e01520-15.

Kyle C. Costa and John A. Leigh (2014) Metabolic versatility in methanogens. Curr Opin Biotechnol. 29: 70-75.

Kyle C. Costa, Thomas J. Lie, Qin Xia, and John A. Leigh (2013) VhuD facilitates electron flow from H2 or formate to Heterodisulfide reductase in Methanococcus maripaludisJ. Bacteriol. 195: 5160-5165.

Sung Ho Yoon, David J. Reiss, Min Pan, June Burn, Kyle C. Costa, Thomas J. Lie, Joseph Slagel, Robert L. Moritz, Murray Hackett, John A. Leigh, and Nitin S. Baliga (2013) A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen. Genome Res. 23: 1839-1851.

Thomas J. Lie, Kyle C. Costa, Daniel Pak, Varun Sakesan, and John A. Leigh (2013) Phenotypic evidence that the function of the [Fe]-hydrogenase Hmd in Methanococcus maripaludis requires seven hcg (hmd-cooccuring genes) but not hmdII. FEMS Microbiol. Lett. 343: 156-160.

Kyle C. Costa, Thomas J. Lie, Michael Jacobs, and John A. Leigh (2013) H2-independent growth of hydrogenotrophic methanogen Methanococcus maripaludismBio. 4: e00062-13.

Kyle C. Costa, Sung Ho Yoon, Min Pan, June A. Burn, Nitin Baliga, and John A. Leigh (2013) Effects of H2 and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludisJ. Bacteriol. 195: 1456-1462.

Thomas J. Lie*, Kyle C. Costa*, Boguslaw Lupa, Suresh Korpole, William B. Whitman, and John A. Leigh (2012) Essential anaplerotic role for the energy converting hydrogenase Eha in hydrogenotrophic methanogenesis. Proc Natl Acad Sci USA. 109: 15473-15478. *Equal contribution

Kyle C. Costa, Phoebe M. Wong, Tiansong Wang, Thomas J. Lie, Jeremy A. Dodsworth, Ingrid Swanson, June A. Burn, Murray Hackett, John A. Leigh (2010) Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase.  Proc Natl Acad Sci USA. 107: 11050-11055.

Trista J. Vick, Jeremy A. Dodsworth, Kyle C. Costa, Everett L. Shock, and Brian P. Hedlund.  (2010) Microbiology and geochemistry of Little Hot Creek, a hyperthermophilic hot spring environment in the Long Valley Caldera. Geobiology. 8: 140-154.

Kyle C. Costa, Jason B. Navarro, Everett L. Shock, Chuanlun Zhang, Debbie Soukup, and Brian P. Hedlund. (2009) Microbiology and geochemistry of Great Boiling and Mud Hot Springs in the United States Great Basin. Extremophiles. 13: 447-459.

Kyle C. Costa, Joy Hallmark, Duane P. Moser, Deborah A. Soukup, Stephanie Labahn and Brian P. Hedlund. (2008). Erratum: "Geomicrobiological changes in two ephemeral desert playa lakes in the western United States" (Geomicrobiology Journal vol. 25 (5)). Geomicrobiol. J. 25(7-8): 456.