• Image of Maddie Mettler in the laboratory.
  • Scientist handling petri dishes in the lab
  • Stack of test tubes drying in the lab.
  • Hannah Goemann in the lab working on the microscope and pipping onto a glass slide.

2024

  • #Krukenberg V, #Kohtz AJ, Jay ZJ, Hatzenpichler R. Methyl-reducing methanogenesis by a thermophilic culture of Korarchaeia. Nature, https://doi.org/10.1038/s41586-024-07829-8 (2024) (#equal contribution)
  • Murali R, Pace LA, Sanford RA, Ward LM, Lynes M, Hatzenpichler R, Lingappa UF, Fischer WW, Gennis RB, Hemp J. Diversity and evolution of nitric oxide reduction. PNAS, 121 (26) e2316422121 (2024)
  • Kohtz AJ, #Petrosian N, #Krukenberg V, #Jay ZJ, Pilhofer M, Hatzenpichler R. Cultivation and visualization of a methanogen of the phylum Thermoproteota. Nature, https://doi.org/10.1038/s41586-024-07829-8 (2024) (#equal contribution)
  • LynesMM, Jay ZJ, Kohtz AJ, Hatzenpichler R. Methylotrophic methanogenesis in the Archaeoglobi revealed by cultivation of Ca. Methanoglobus hypatiae from a Yellowstone hot spring. The ISME J, 18(1) wrae026 (2024) 
  • Wood JM, Urbaniak C, Parker C, Singh NK, Wong S, Arumugan A, Skorupa DJ, Hemmah A, Laaguiby P, Karouia F, Peyton BM, Tighe S, and Venkateswaran K. Assessing microbial diversity in Yellowstone National Park hot springs using a field deployable automated nucleic acid extraction system. Front. Ecol. Evol. 12:1306008. doi: 10.3389/fevo.2024.1306008 (2024)
  • Larson, J., Sather, B, Lu Wang, L.,  Westrum, J., Tokmina-Lukaszewska, M., Pauley, J., Copié, V, McDermott, T.R., and Bothner, B. (2024) Metalloproteomics reveals multi-level stress response in  Escherichia Coli when exposed to Arsenite.  International Journal of Molecular Sciences. Submitted Preprint: https://doi.org/10.20944/preprints202408.0690.v1
  • Malinowski, Natalia, Matthew J. Morgan, Jason Wylie, Tom Walsh, Sergio Domingos, Suzanne Metcalfe, Anna H. Kaksonen, Elliott P. Barnhart, Rebecca Mueller, Brent M. Peyton, Geoffrey J. Puzon, Prokaryotic microbial ecology as an ecosurveillance tool for eukaryotic pathogen colonisation: Meiothermus and Naegleria fowleri, Water Research, Volume 254, 2024, 121426, https://doi.org/10.1016/j.watres.2024.121426.
  • Wood JM, Camilla Urbaniak, Ceth Parker, Nitin Kumar Singh, Season Wong, Arunkumar Arumugam, Dana J Skorupa, Ashlyn Hemmah, Phoebe Laaguiby, Fathi Karouia, Brent Peyton, Scott W Tighe and Kasthuri Venkateswaran*, 2024. Assessing microbial diversity in Yellowstone National Park hot springs using a field deployable automated nucleic acid extraction system. Front. Ecol. Evol. - Population, Community, and Ecosystem Dynamics. https://doi.org/10.3389/fevo.2024.1306008
  • Heveran, Chelsea M., Robin Gerlach, Christopher J. Hernandez, Kristen Intemann, Anne S. Meyer, Caroline Ajo-Franklin, Marimikel Charrier, Wilfred V. Srubar III, Neel Joshi, Alshakim Nelson, Matthew W. Fields (2024): Unlocking the societal potential of engineered living materials. Matter. Manuscript # MATTER-D-24-00557. In Press
  • Ugur, Gizem; Rux, Kylee; Boone, John; Seaman, Rachel; Avci, Recep; Gerlach, Robin; Phillips, Adrienne; Heveran, Chelsea (2024): Bio-Trapping Ureolytic Bacteria on Sand to Improve the Efficiency of Biocementation. ACS Applied Materials & Interfaces. ACS Appl. Mater. Interfaces. 16(2) 2075–2085. DOI: acsami.3c13971

2023

  • #Lynes MM, #Krukenberg V, Jay ZJ, Kohtz AJ, Gobrogge C, Spietz RL, Hatzenpichler R. Diversity and function of Methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments. ISME Comm, 3:22 (2023) 
  • WiegandT, WilkinsonR, Santiago-FrangosA, LynesM, HatzenpichlerR, WiedenheftB. Functional and phylogenetic diversity of Cas10 proteins. The CRISPR J. DOI:10.1089/crispr.2022.0085 (2023)
  • Larson J, Tokmina-Lukaszewska M, Fausset H, Spurzem S, Cox S, Cooper G, Copié V, Bothner B. (2023) Arsenic Exposure Causes Global Changes in the Metalloproteome of Escherichia coli. Microorganisms.11(2):382. doi: 10.3390/microorganisms11020382
  • Tokmina-Lukaszewska M, Huang Q, Berry L, Kallas H, Peters JW, Seefeldt LC, Raugei S, Bothner B. Fe protein docking transduces conformational changes to MoFe nitrogenase active site in a nucleotide-dependent manner. Commun Chem. 2023 Nov 18;6(1):254. doi: 10.1038/s42004-023-01046-6. PMID: 37980448; PMCID: PMC10657360.
  • Shisler KA, Kincannon WM, Mattice JR, Larson J, Valaydon-Pillay A, Mus F, Flusche T, Kumar Nath A, Stoian SA, Raugei S, Bothner B, DuBois JL, Peters JW. Homologous acetone carboxylases select Fe(II) or Mn(II) as the catalytic cofactor. mBio. 2024 Feb 14;15(2):e0298723. doi: 10.1128/mbio.02987-23. Epub 2023 Dec 21. PMID: 38126751; PMCID: PMC10865871.
  • Alowaifeer AM, Wang Q, Bothner B, Sibert RJ, Joye SB, McDermott TR. Aerobic methane synthesis and dynamics in a river water environment. Limnol Oceanogr. 2023 Aug;68(8):1762-1774. doi: 10.1002/lno.12383. Epub 2023 Jun 14. PMID: 37928964; PMCID: PMC10624334.
  • Steward KF, Refai M, Dyer WE, Copié V, Lachowiec J, Bothner B. Acute stress reduces population-level metabolic and proteomic variation. BMC Bioinformatics. 2023 Mar 7;24(1):87. doi: 10.1186/s12859-023-05185-4. PMID: 36882728; PMCID: PMC9993721.
  • Larson J, Tokmina-Lukaszewska M, Fausset H, Spurzem S, Cox S, Cooper G, Copié V, Bothner B. Arsenic Exposure Causes Global Changes in the Metalloproteome of Escherichia coli. Microorganisms. 2023 Feb 2;11(2):382. Doi: 10.3390/microorganisms11020382. PMID: 36838347; PMCID: PMC9965246.
  • Mettler, M.K., Goemann, H.M., Mueller, R.C., Vanegas, O.A., Lopez, G., Singh, N., Venkateswaran, K. and Peyton, B.M., 2023. Development of Martian saline seep models and their implications for planetary protection. Biofilm, 5, p.100127. https://doi.org/10.1016/j.bioflm.2023.100127
  • Barnhart, E., Kinsey, S., Wright, P., Eldridge, S., Hill, V., Kahler, A., Mattioli, M., Cornman, R., Iwanowicz, D., Eddy, Z., Halonen, S., Mueller, R., Peyton, aB., Puzon, G. 2023. Naegleria fowleri detected in Grand Teton National Park Hot Springs. ACS ES&T Water, https://doi.org/10.1021/acsestwater.3c00650
  • Espinosa-Ortiz, Erika Jimena; Gerlach, Robin; Peyton, Brent M.; Roberson, Luke; Yeh, Daniel H. (2023): Biofilm reactors for the treatment of used water in space: potential, challenges, and future perspectives. Biofilm. 6:100140. DOI: 10.1016/j.bioflm.2023.100140
  • Bedard, D.L.; Van Slyke, G.; Nübel, U.; Bateson, M.M.; Brumfield, S.; An, Y.J.; Becraft, E.D.; Wood, J.M.; Thiel, V.; Ward, D.M. Geographic and Ecological Diversity of Green Sulfur Bacteria in Hot Spring Mat Communities. Microorganisms 2023, 11, 2921. https://doi.org/10.3390/microorganisms11122921
  • Kurihara, M., Thiel, V., Takahashi, H., Kojima, K., Ward, D. M., Bryant, D. A., Sakai, M., Yoshizawa, S., and Sudo Y. 2023. Identification of a functionally efficient and thermally stable outward sodium-pumping rhodopsin (BeNaR) from a thermophilic bacterium. Chem. Pharm. Bull. 71, 154-164. doi: 10.1248/cpb.c22-00774
  • Villa F, Ludwig N, Mazzini S, Scaglioni L, Fuchs AL, Tripet B, Copié V, Stewart PS, Cappitelli F. (2023) A desiccated dual-species subaerial biofilm reprograms its metabolism and affects water dynamics in limestone. Sci Total Environ 868:161666. doi: 10.1016/j.scitotenv.2023.161666. 

2022

  • Kohtz AJ, Jay ZJ, Lynes MM, Krukenberg V, Hatzenpichler R. Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments. ISME Comm, 2: 86 (2022)  
  • Schaible GA, Kohtz AJ, Cliff J, Hatzenpichler R. Correlative SIP-FISH-SEM-Raman-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes. ISME Comm, 2:52 (2022)
  • Reichart NJ, Bowers RM, Woyke T, Hatzenpichler R. Metagenomes and metagenome-assembled genomes from substrate-amended hot spring sediment incubations. Microbiology Resource Announcements, doi.org/10.1128/mra.01065-21 (2022)
  • Peach JT, Mueller RC, Skorupa DJ, Mesle MM, Kanta S, Boltinghouse E, Sharon B, Copié V, Bothner B, Peyton BM. Longitudinal analysis of the Five Sisters hot springs in Yellowstone National Park reveals a dynamic thermoalkaline environment. Sci Rep. Nov 4; 12(1):18707. doi: 10.1038/s41598-022-22047-w. (2022)
  • Meslé MM, Mueller RC, Peach J, Eilers B, Tripet BP, Bothner B, Copié V, Peyton BM. (2022) Isolation and Characterization of Lignocellulose-Degrading Geobacillus thermoleovorans from Yellowstone National Park. Appl. Environ. Microbiol. 88(1):e0095821. doi: 10.1128/AEM.00958-21
  • Alowaifeer AM, Clingenpeel S, Kan J, Bigelow PE, Yoshinaga M, Bothner B, McDermott TR. Arsenic and Mercury Distribution in an Aquatic Food Chain: Importance of Femtoplankton and Picoplankton Filtration Fractions. Environ Toxicol Chem. 2023 Jan;42(1):225-241. doi: 10.1002/etc.5516. Epub 2022 Dec 9. PMID: 36349954; PMCID: PMC10753857.
  • Steward KF, Payne D, Kincannon W, Johnson C, Lensing M, Fausset H, Németh B, Shepard EM, Broderick WE, Broderick JB, Dubois J, Bothner B. Proteomic Analysis of Methanococcus voltae Grown in the Presence of Mineral and Nonmineral Sources of Iron and Sulfur. Microbiol Spectr. 2022 Aug 31;10(4):e0189322. Doi: 10.1128/spectrum.01893-22. Epub 2022 Jul 25. PMID: 35876569; PMCID: PMC9431491.
  • Jesse T Peach; Rebecca C Mueller; Dana J Skorupa; Margaux M Mesle; Sutton Kanta; Eric Boltinghouse; Bailey Sharon; Valerie Copié; Brian Bothner; Brent M Peyton. (2022). "Longitudinal Analysis of the Five Sisters Hot Springs in Yellowstone National Park Reveals a Dynamic Thermoalkaline Environment" Sci Rep 12, 18707 (2022). https://doi.org/10.1038/s41598-022-22047-w
  • Goemann, Calvin L.C., Wilkinson, Royce, Henriques, William; Bui, Huyen; Goemann, Hannah M.; Carlson, Ross P.; Viamajala, Sridhar; Gerlach, Robin; Wiedenheft, Blake (2023). Genome sequence, phylogenetic analysis, and structure-based annotation reveal metabolic potential of Chlorella sp. SLA-04. Algal Research 69: 102943. DOI: 10.1016/j.algal.2022.102943 
  • Neri, U., Wolf, Y. I., Roux, S., Camargo, A. P., Lee, B. D., Kazlauskas, D., Chen, I. M., Ivanova, N., Allen, L. Z., Paez-Espino, D., Bryant, D. A., Bhaya, D., RNA Virus Discovery Consortium (including D. M. Ward), Krupovic, M., Dolja, V. V., Kyrpides, N. C., Koonin, E. V., and Gophna, U. 2022. Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell 185, 4023–4037. doi: 10.1016/j.cell.2022.08.023
  • Madigan, M.T., J. N. Absher, J.E. Mayers, M. Asao, D.O. Jung, K.S. Bender, M.L. Kempher, M.K. Hayward, S.A. Sanguedolce, A.C. Brown, S. Takaichi, K. Kurokawa, A. Toyoda, H. Mori, Y. Tsukatan, Z.-Y. Wang‑Otomo, D.M. Ward and W.M. Sattley. 2022. Allochromatium tepidum, sp. nov., a hot spring species of purple sulfur bacteria. Archiv. Microbiol. 204:115.

2021

  • Alvarez, A. L., Weyers, S.L., Goemann, H.M., Peyton, B.M., Gardner, R.D. (2021) Microalgae, soil and plants: A critical review of microalgae as renewable resources for agriculture. Algal Res., 54:102200. doi: 10.1016/j.algal.2021.102200.
  • Hammarlund, S.P., Gedeon, T., Carlson, R.P., Harcombe, W. (2021) Limitation by a shared mutualist promotes coexistence of multiple competing partners. Nat. Comm.. 12:619. doi: 10.1038/s41467-021-20922-0.
  • Hu, D., Cui, Y., Markillie, L.M., Chrisler, W.B., Wang, Q., Hatzenpichler, R., Orr, G. (2021) Counting mRNA Copies in Intact Bacterial Cells by Fluctuation Localization Imaging-Based Fluorescence In Situ Hybridization (fliFISH). Methods in Mol. Biol., 2246:237-247. doi: 10.1007/978-1-0716-1115-9_15.
  • Hunt, Kristopher A., Mallette, N., Peyton, B.M., Carlson, R. (2021) In Silico Analysis of Functionalized Hydrocarbon Production Using Ehrlich Pathway and Fatty Acid Derivatives in an Endophytic Fungus. Journal of Fungi, 7(6):435. doi: 10.3390/jof7060435
  • Marlow, J., Spietz, R. , Keun-Young, K., Ellisman, M., Girguis, P., Hatzenpichler, R. (2021) Spatially resolved correlative microscopy and microbial identification reveal dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment. Environmental Microbiology, 23(8):4756-4777. doi: 10.1111/1462-2920.15667
  • McKay, L.J., Klingelsmith, K.B., Deutschbauer, A.M., Inskeep, W.P., Fields, M.W. (2021) Draft Genome Sequence of Methanothermobacter thermautotrophicus WHS, a Thermophilic Hydrogenotrophic Methanogen from Washburn Hot Springs in Yellowstone National Park, USA. Microbiol. Resour. Announc., 10(5): e01157-20. doi: 10.1128/mra.01157-20.
  • Mueller, R.C., Peach, J.T., Skorupa, D.J., Copié, V., Bothner, B., Peyton, B.M. (2021) An emerging view of the diversity, ecology and function of Archaea in alkaline hydrothermal environments. FEMS Microbiol. Ecol.,97(2):fiaa246. doi: 10.1093/femsec/fiaa246.
  • Peyton, Brent, Dana Skorupa, “Integrating CUREs in Ongoing Research: Undergraduates as Active Participants in the Discovery of Biodegrading Thermophiles,” J. Microbiol. Biol. Educ., 2021, 22(2): e00102-21. 21-020. doi: 10.1128/jmbe.00102-21 
  • Rawle, R., Saley, T.C., Kang, Y.-S., Wang, Q., Walk, S., Bothner, B., McDermott, T.R. (2021) Introducing the ArsR-Regulated Arsenic Stimulon. Front. Microbiol., 12:630562. doi: 10.3389/fmicb.2021.630562.
  • Reichart, N., Bowers, R.M., Woyke, T., Hatzenpichler, R. (2021) High Potential for Biomass-Degrading Enzymes Revealed by Hot Spring Metagenomics. Front.Microbiol., 12:668238. doi: https://doi.org/10.3389/fmicb.2021.668238
  • Tafur Rangel, A.E., Rios, W., Mejia, D., Ojeda, C., Carlson, R., Gomez Ramirez, J.M., Gonzalez Barrios, A. F. (2021) In silico design for systems-based metabolic engineering for the bioconversion of valuable compounds from industrial by-products. Front. Genet., 12:633073. doi: 10.3389/fgene.2021.633073.
  • Wang, Q., Alowaifeer, A., Kerner, P., McDermott, T.R. (2021) Aerobic bacterial methane synthesis. PNAS,13(1):148. doi: 10.1073/pnas.2019229118.
  • Zhuang, W., Balasubramanian, N., Wang, L., Wang, Q., McDermott, T.R., Copié, V., Wang, G., Bothner, B.  (2021) Arsenate-Induced Changes in Bacterial Metabolite and Lipid Pools during Phosphate Stress.  Appl. Environ. Microbiol., 87(6):e02261-20. doi: 10.1128/AEM.02261-20.

2020

  • Hartman, R., Biewenga, L., Munson-McGee, J., Refai, M., Boyd, E.S., Bothner, B., Lawrence, C.M., Young, M. (2020) Discovery and Characterization of Thermoproteus Spherical Piliferous Virus 1: a Spherical Archaeal Virus Decorated with Unusual Filaments. Virol., 94(11):e00036-20. doi: 10.1128/JVI.00036-20.
  • Hatzenpichler, R., Krukenberg, V., Spietz, R.L., Jay, Z.J. (2020) Next-generation physiology approaches to study microbiome function at the single cell level. Rev. Microbiol., 18:241-256. doi: 10.1038/s41579-020-0323-1.
  • Hulkova, M., Soulkupova, J., Carlson, R.P., Marsalek, B. (2020) Interspecies interactions can enhance Pseudomonas aeruginosa tolerance to surfaces functionalized with silver nanoparticles. in Colloids and Surfaces B: Biointerfaces. 192: 111027. doi: 10.1016/j.colsurfb.2020.111027
  • Jay, Z.J., Hunt, K.A., Chou, K.J., Schut, G.J., Maness, P.-C., Adams, M.W.W., Carlson, R.P. (2020) Integrated thermodynamic analysis of electron bifurcating [FeFe]-hydrogenase to inform anaerobic metabolism and H2. Biochim. Biophys. Acta Bioenerg., 1861(1):148087. doi: 10.1016/j.bbabio.2019.148087.
  • Lawrence, C. Martin. (2020) A moonlighting nuclease puts CRISPR in its place. J. Biol. Chem., 295(11):3415-3416. doi: 10.1074/jbc.H120.012897.
  • Mahout, M., Carlson, R.P., Peres, S. (2020) Answer Set Programming for computing constraints-based elementary flux. Processes, 8(12):1649. doi: 10.3390/pr8121649 
  • McGill, S.L.,Yung, Y., Hunt, K.A., Henson, M.A., Hanley, L., Carlson, R.P. (2020) Pseudomonas aeruginosa reverse diauxie is a multidimensional, optimized, resource utilization strategy. Scientific Reports, 11:1457. doi:  10.1038/s41598-020-80522-8
  • Murray, A.E., Freudenstein, J., Gribaldo, S., Hatzenpichler, R., Hugenholtz, P., Kämpfer, P., Konstantinidis, K.T., Lane, C.E., Papke, R.T., Parks, D.H., Rossello-Mora, R., Stott, M.B., Sutcliffe, I.C., Thrash, J.C., Venter, S.N.,  Whitman, W.B., Acinas, S.G., Amann, R.I., Anantharaman, K., Armengaud, J., Baker, B.J., Barco, R.A., Bode, H.B., Boyd, E.S., Brady, C.L., Carini, P., Chain, P.S.G., Colman, D.R., DeAngelis, K.M., de los Rios, M.A., Estrada-de los Santos, P., Dunlap, C.A., Eisen, J.A., Emerson, D., Ettema, T.J.G., Eveillard, D., Girguis, P.R., Hentschel, U., Hollibaugh, J.T., Hug, L.A., Inskeep, W.P., Ivanova, E.P., Klenk, H-P, Li, W-J, Lloyd, K.G., Löffler, F.E., Makhalanyane, T.P., Moser, D.P., Nunoura, T., Palmer, M., Parro, V., Pedrós-Alió, C., Probst, A.J., Smits, T.H.M., Steen, A.D.,  Steenkamp, E.T.,  Spang, A., Stewart,  F.J., Tiedje, J.M., Vandamme, P., Wagner, M.,  Wang, F-P, Hedlund, B.P., Reysenbach, A-L. (2020) Roadmap for naming uncultivated Archaea and Bacteria. Nat. Microbiol., 5:987-994. doi: 10.1038/s41564-020-0733-x.
  • Park, H., Patel, A., Hunt, K.A., Henson, M.A., Carlson, R.P. (2020) Artificial consortium demonstrates emergent properties of enhanced cellulosic-sugar degradation and biofuel synthesis. npj Biofilms and Microbiomes, 6:59. doi: 10.1038/s41522-020-00170-8 
  • Reichart, N.J., Jay, Z.J., Krunkenberg, V., Parker, A.E., Spietz, R.L., Hatzenpichler, R. (2020) Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment. Isme J., 14:2851-2861. doi: 10.1038/s41396-020-00749-1.
  • Steward, K.F., Eilers, B., Tripet, B., Fuchs, A., Dorle, M., Rawle, R., Soriano, B., Balasubramanian, N., Copié, V., Bothner, B., Hatzenpichler, R. (2020) Metabolic Implications of Using BioOrthogonal Non-Canonical Amino Acid Tagging (BONCAT) for Tracking Protein Synthesis. Microbiol., 11:197.doi: 10.3389/fmicb.2020.001970.
  • Urbaniak, C., Wong, S., Tighe, S., Arumugam, A., Liu, B., Parker, C.W., Wood, J.M., Singh, N.K., Skorupa, D.J., Peyton, B.M.,  Jenson, R., Karouia, F., Dragon, J., Venkateswaran, K. (2020) Validating an Automated Nucleic Acid Extraction Device for Omics in Space Using Whole Cell Microbial Reference Standards. Front. Microbiol., 11:1909. doi: 10.3389/fmicb.2020.01909.
  • Zhang, T., Parker, A., Stewart, P.S., Klapper, I. (2020)  Multiscale Flux-Based Modeling of Biofilm Communities. Multiscale Model. Simul., 18(2):1025-1052. doi: 10.1137/18M1234096.

2019

  • Borrel, G., Adam, P.S., McKay, L.J., Chen L.-X., Sierra-Garcia, I.N., Sieber, C.M.K., Anderson, G.L., Li, W-J, Hallam, S.J., Muyzer, G., de Oliveira, V.M., Inskeep, W.P., Banfield, J.F., Gribaldo, S. (2019) Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nature Microbiology, 4:603-613. doi: 10.1038/s41564-019-0363-3.
  • Davis¸ K.J., Platt, G.A., Barnhart, E.P., Hiebert, R., Hyatt, R., Fields, M.W., Gerlach, R. (2019) Biogenic coal-to-methane conversion can be enhanced with small additions of algal amendment in field-relevant upflow column reactors. Fuel, 256:115905. doi: 10.1016/j.fuel.2019.115905.
  • Dong, Y., Sanford, R.A., Inskeep, W.P., Srivastava, V., Bulone, V., Fields, C.J., Yau, P.M., Sivaguru, M., Ahren, D., Fouke, K.W., Weber, J., Werth, C.R., Cann, I.K., Keating, K.M., Khetani, R.S., Hernandez, A.G., Wright, C., Band, M., Imai, B.S., Fried, G.A., Fouke, B.W. (2019) Physiology, metabolism, and fossilization of hot-spring filamentous microbial mats. Astrobiology, 19:1442-1458. doi: 10.1089/ast.2018.1965.
  • Hartman, R., Munson-McGee, J., Young, M.J., Lawrence, C.M. (2019) Survey of high-resolution archaeal virus structures. Curr. Opin. Virol., 36:74-83. doi: 10.1016/j.coviro.2019.05.008.
  • Hartman, Ross, Eilers, B.J., Bollschweiler, D., Munson-McGee, J.H., Engelhardt, H., Young, M.J., Lawrence, C.M. (2019) The Molecular Mechanism of Cellular Attachment for an Archaeal Virus. Structure, 27(11):1634-1646.e3. doi: 10.1016/j.str.2019.09.005. 
  • Mohamed, A., Ha, P.T., Peyton, B.M., Mueller, R., Meagher, M., Beyenal, H. (2019) In Situ Enrichment of Microbial Communities on Polarized Electrodes Deployed in Alkaline Hot Springs. Power Sources, 414:547-556. doi: 10.1016/j.jpowsour.2019.01.027.
  • Park, H., McGill, S.L., Arnold, A.D., Carlson, R.P. (2019) Pseudomonad reverse carbon catabolite repression, interspecies metabolite exchange, and consortial division of labor. Cellular and Molecular Life Sciences. 77:395-413. doi: 10.1007/s00018-019-03377-x.
  • McKay, L.J., Dlakić, M., Fields, M.W., Delmont, T.O., Eren, A.M., Jay, Z.J., Klingelsmith, K.B., Rusch, D.B., Inskeep, W.P. (2019) Co-occurring genomic capacity for anaerobic methane metabolism and dissimilatory sulfite reduction discovered in the Korarchaeota. Nature Microbiology, 4:614-622. doi: 10.1038/s41564-019-0362-4.
  • Rawle, R.A., Kang, Y.S., Bothner, B., Wang, G., McDermott, T.R. (2019) Transcriptomics analysis defines global cellular response of Agrobacterium tumefaciens 5A to arsenite exposure regulated through the histidine kinases PhoR and AioS. Microbiol., 21(8):2659-2676. doi: 10.1111/1462-2920.14577.
  • Rollins, MaryClare F., Saikat Chowdhury, Joshua Carter, Sarah M. Golden, Heini M. Miettinen, Andrew Santiago-Frangos, Dominick Faith, C. Martin Lawrence, Gabriel C. Lander, Blake Wiedenheft. (2019) Structure Reveals a Mechanism of CRISPR-RNA-Guided Nuclease Recruitment and Anti-CRISPR Viral Mimicry. Mol. Cell., 74(1):132-142.e5. doi: https://doi.org/10.1016/j.molcel.2019.02.001.
  • Schepens, D., Carlson, R.P., Heys, J., Beck, A.E., Gedeon, T. (2019) Role of resource allocation and transport in emergence of cross-feeding in microbial consortia. Journal of Theoretical Biology, 467:150-163. doi: 10.1016/j.jtbi.2019.01.030.
  • Skorupa, D.J., Akyel, A., Fields, M.W., Gerlach, R. (2019) Facultative and anaerobic consortia of haloalkaliphilic ureolytic micro‐organisms capable of precipitating calcium carbonate. Journal of Applied Microbiology, 127:1479-1489. doi: 10.1111/jam.14384.

2018

  • Beck, A.E., Hunt, K.A., Carlson, R.P. (2018) Measuring Cellular Biomass Composition for Computational Biology Applications. Processes, 6(5):38. doi: 10.3390/pr6050038.
  • Carlson, R.P., Beck, A.E., Phalak, P., Fields, M.W., Gedeon, T., Hanley, L., Harcombe, W.R., Henson, M.A., Heys, J.J. (2018) Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross feeding microbial consortia. Soc. Trans., 46:269-284. doi: 10.1042/BST20170242.
  • Dharmavaram, S., Rudnick, J., Lawrence, C.M., Bruinsma, R.F. (2018) Smectic viral capsids and the aneurysm instability. J. Phys. Condens. Matter, 20(20):204004. doi: 10.1088/1361-648X/aab99a.
  • Gumulya, Y., Boxall, N.J., Khaleque, H.N., Santala, V., Carlson, R.P., Kaksonen, A.H. (2018) In a Quest for Engineering Acidophiles for Biomining Applications: Challenges and Opportunities. Genes, 9(2):116. doi: 10.3390/genes9020116.
  • Hochstein, R., Bollschweiler, D., Dharmavaram, S., Lintner, N.G., Plitzko, J.M., Engelhardt, H., Young, M.J., Klug, W.S., Lawrence, C.M. (2018) Structural studies of Acidianus tailed spindle virus reveal a structural paradigm used in the assembly of spindle-shaped viruses. PNAS, 115(9):2120-2125. doi: 10.1073/pnas.1719180115.
  • Hunt, K.A., Jennings, R.M., Inskeep, W.P., Carlson, R.P. (2018) Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community. PLoS Comput. Biol., 14(9): e1006431. doi: 10.1371/journal.pcbi.1006431.
  • Jarett, J.K., Nayfach, S., Podar, M., Inskeep, W., Ivanova, N.N., Munson-McGee, J., Schulz, F., Young, M.,  Jay, Z.J., Beam, J.P., Kyrpides, N.C.,  Malmstrom, R.R.,  Stepanauskas, R., Woyke, T. (2018) Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis. Microbiome 6:161. doi: 10.1186/s40168-018-0539-8.
  • Jay, Z.J., Beam, P., Dlakić, M. , Rusch, D.B., Kozubal, M.A.,  Inskeep, W.P. (2018) Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats. Nature Microbiology, 3:732-740. doi: 10.1038/s41564-018-0163-1.
  • Kant, R., Llauró, A., Rayaprolu, V., Qazi, S., de Pablo PJ, Douglas T, Bothner B. (2018) Changes in the stability and biomechanics of P22 bacteriophage capsid during maturation. Biophys. Acta Gen. Subj., 1862(6):1492-1504. doi: 10.1016/j.bbagen.2018.03.006.
  • Wang, Q., Kang, Y.-S., Alowaifeer, A., Shi, K., Fan, X., Wang, L., Jetter, J., Bothner, B., Wang, G., McDermott, T.R. (2018) Phosphate starvation response controls genes required to synthesize the phosphate analog arsenate. Microbiol., 20(5):1782-1793. doi: 10.1111/1462-2920.14108.

2017

  • Beck, A.E., Bernstein, H.C., Carlson, R.P. (2017) Stoichiometric network analysis of cyanobacterial acclimation to photosynthesis-associated stresses identifies heterotrophic niches. Processes, 5 (2), 32. doi: 10.3390/pr5020032.
  • Bollschweiler, D., Schaffer, M., Lawrence, C.M., Engelhardt, H. (2017) Cryo-electron microscopy of an extremely halophilic microbe: technical aspects. Extremophiles, 21(2):393-398. doi: 10.1007/s00792-016-0912-0.
  • Douglas, P.M.J., Stolper, D.A., Eiler, J.M., Sessions, A.L., Lawson, M., Shuai, Y., Bishop, A., Podlaha, O.G., Ferreira, A. A., Santos Neto, E.V., Niemann, M., Steen, A.S., Huang, L., Chimiak, L., Valentine, D.L., Fiebig, J., Luhmann, A.J., Seyfried, W.E. Jr., Etiope, G., Schoell, M., Inskeep, W.P., Moran, J.J., Kitchen, N. (2017) Methane clumped isotopes: Progress and potential for a new isotopic tracer. Organic Geochemistry 113: 262-282. doi: 1016/j.orggeochem.2017.07.016.
  • Jennings, R. deM., Moran, J., Jay, Z. J., Beam, J.P., Kozubal, M.A.,  Whitmore, L.M.,  Kreuzer, H., Inskeep, W.P. (2017) Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities. Microbiol. 8:88. doi: 10.3389/fmicb.2017.00088.
  • McKay, L.J., Hatzenpichler, R., Inskeep, W.P., Fields, M.W. (2017) Occurrence and expression of novel methyl-coenzyme M reductase gene (mcrA) variants in hot spring sediments. Scientific Reports, 7: 7252 doi: 10.1038/s41598-017-07354-x.
  • Meslé, M.M., Beam, J.P., Jay, Z.J., Bodle, B., Bogenschutz, E., Inskeep, W. (2017) Hydrogen Peroxide Cycling in High-Temperature Acidic Geothermal Springs and Potential Implications for Oxidative Stress Response. Mar. Sci., 4:130. doi: 10.3389/ fmars.2017.00130.
  • Moran, J.J., Whitmore, L.M., Jay, Z.J., Jennings, R. deM., Beam, J.P., Kreuzer, H.W., Inskeep, W.P. (2017) Dual stable isotopes of CH4 from Yellowstone hot-springs suggest hydrothermal processes involving magmatic CO2. Journal of Volcanology and Geothermal Research, 341:187-192. doi: 10.1016/j.jvolgeores.2017.05.011.
  • Rawle, R.A., Hamerly, T., Tripet, B.P., Giannone, R.J., Wurch, L., Hettich, R.L., Podar, M., Copié, V., Bothner, B. (2017) Multi-omics analysis provides insight to the Ignicoccus hospitalis-Nanoarchaeum equitans. Biochimica et Biophysica Acta, 1861(9):2218-2227. doi: 10.1016/j.bbagen.2017.06.001.
  • Schepens, D., Beck, A.E., Heys, J.J., Gedeon, T., Carlson, R.P. (2017) The Benefits of Resource Partitioning and Division of Labor in Microbial Consortia. In P. Amar, F. Kepes, and C.T. Trinh (Eds.), Advances in Systems and Synthetic Biology (pp. 137-148). EDP Sciences Publishing. ISBN 978-2-7598-2116-7.
  • Tokmina-Lukaszewska, M., Shi, Z., Tripet, B., McDermott, T.R., Copié, V., Bothner, B., Wang, G. (2017) Metabolic response of Agrobacterium tumefaciens 5A to arsenite. Environ Microbiol., 19(2):710-721. doi: 10.1111/1462-2920.13615.
  • Venters, M., Carlson, R.P., Gedeon, T., Heys, J. (2017) Effects of Spatial Localization on Microbial Consortia Growth. PLOS ONE, 12(1):e0168592. doi: 10.1371/journal.pone.0168592.
  • Wagner, C., Reddy, V., Asturias, F., Khoshouei, M., Johnson, J.E., Manrique, P., Munson-McGee, J., Baumeister, W., Lawrence, C.M., Young, M.J. (2017) Isolation and Characterization of Metallosphaera Turreted Icosahedral Virus, a Founding Member of a New Family of Archaeal Viruses. J. Virol., 91(20):e00925-17. doi: 10.1128/JVI.00925-17.

2016

  • Beam, J.P., Bernstein, H.C., Jay, Z.J., Kozubal, M.A., Jennings, R. deM., Tringe, S.G., Inskeep, W.P. (2016) Assembly and succession of iron oxide microbial mat communities in acidic geothermal springs. Microbiol., 7:25. doi: 10.3389/fmicb.2016.00025.
  • Beam, J.P., Jay, Z.J., Schmid, M.C., Romine, M.F., Rusch, D.B., Jennings, R. deM., Kozubal, M.A., Tringe, S.G., Wagner, M., Inskeep, W.P. (2016) Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous ‘streamer' community. ISME J. 10(1):210–224. doi: 10.1038/ismej.2015.83.
  • Beck, A.E., Hunt, K.A., Bernstein, H.C., Carlson, R.P. (2016) Interpreting and designing microbial communities for bioprocess applications, from components to interactions to emergent properties. In C.A. Eckert and C.T. Trinh (Ed.), Biotechnology for Biofuel Production and Optimization (1st, pp. 407-432). Elsevier. doi: 10.1016/B978-0-444-63475-7.00015-7.
  • Carlson, R.P., Oshota, O., Shipman, M., Caserta, J.A., Hu, P., Saunders, C.W., Xu, J., Reeder, N., Richards, A., Pettigrew, C., Peyton, B.M. (2016) Integrated molecular, physiological and in silico characterization of two Halomonas isolates from industrial brine. Extremophiles, 20(3):261-274. doi: 10.1007/s00792-015-0806-6.
  • Colman, D.R., Jay, Z.J., Inskeep, W.P., Jennings, deM. R., Maas, K.R., Rusch, D.B., Takacs-Vesbach, C.D. (2016) Novel, deep-branching heterotrophic bacterial populations recovered from thermal spring metagenomes. Microbiol., 7:304. doi: 10.3389/fmicb.2016.00304.
  • Dellas, Nikki, Snyder, J.C., Dills, M., Nicolay, S.J., Kerchner, K.M., Brumfield, S.K., Lawrence, C.M., Young, M.J., Structure-Based Mutagenesis of Sulfolobus Turreted Icosahedral Virus B204 Reveals Essential Residues in the Virion-Associated DNA-Packaging ATPase. J. Virol., 90(6):2729-2739. doi: 10.1128/JVI.02435-15.
  • Hamerly, T., Bothner, B. (2016) Investigations into the Use of a Protein Sensor Assay for Metabolite Analysis. Biochem. Biotechnol., 178(1):101-13. doi: 10.1007/s12010-015-1861-2.
  • Hochstein, R., Bollschweiler, D., Engelhardt, H., Lawrence, C.M., Young, M. (2015) Large Tailed Spindle Viruses of Archaea: a New Way of Doing Viral Business. J. Virol., 89(18):9146-9149. doi: 10.1128/JVI.00612-15.
  • Hunt, K., Jennings, R. deM., Inskeep, W.P., Carlson, R.P. (2016) Stoichiometric modelling of assimilatory and dissimilatory biomass utilization in a microbial community. Microbiol., 18:4946-4960. doi: 10.1111/1462-2920.13444.
  • Jay, Z.J., Beam, J.P., Kozubal, M.A., Jennings, R. deM., Rusch, D., Inskeep, W.P. (2016) The distribution, diversity and function of predominant Thermoproteales in high-temperature environments of Yellowstone National Park. Microbiol., 18:4755-4769. doi: 10.1111/1462-2920.13366.
  • Kan, J., Clingenpeel, S., Dow, C.L., McDermott, T.R., Macur, R.E., Inskeep, W.P., Nealson, K.H. (2016) Geochemistry and mixing drive the spatial distribution of free-living archaea and bacteria in Yellowstone Lake. Microbiol., 7:210. doi: 10.3389/fmicb.2016.00210.
  • Kang, Y.-S., Brame, K., Jetter, J., Bothner, B.B., Wang, G., Thiyagarajan, S., McDermott, T.R. (2016) Regulatory Activities of Four ArsR Proteins in Agrobacterium tumefaciens 5A. Environ. Microbiol., 82(12):3471-3480. doi: 10.1128/AEM.00262-16.
  • Klotz, M.G., Bryant, D.A., Fredrickson, J.K., Inskeep, W.P., Kuhl, M. (2016) Editorial: Systems Biology and Ecology of Microbial Mat Communities. Microbiol., 7:115. doi: 10.3389/fmicb.2016.00115.
  • Moran, J.J., Whitmore, L.M., Isern, N.G., Romine, M.F., Riha, K.M., Inskeep, W.P., Kreuzer, H.W. (2016) Formaldehyde as a carbon and electron shuttle between autotroph and heterotroph populations in acidic hydrothermal vents of Norris Geyser Basin, Yellowstone National Park. Extremophiles, 20(3):291-299. doi: 10.1007/s00792-016-0821-2.
  • Topuzlu, E., Lawrence, C.M. (2016) Recognition of a pseudo-symmetric RNA tetranucleotide by Csx3, a new member of the CRISPR associated Rossmann fold superfamily, 13(2):254-7. doi: 10.1080/15476286.2015.1130209.

2015

  • Hamerly, T., Tripet, B., Wurch, L., Hettich, R.L., Podar, M., Bothner, B., Copié, V. (2015) Characterization of Fatty Acids in Crenarchaeota by GC-MS and NMR. Archaea, 472726. doi: 10.1155/2015/472726.
  • Hamerly, T., Tripet, B.P., Tigges, M., Giannone, R.J., Wurch, L., Hettich, R.L., Podar, M., Copié, V., Bothner, B. (2015) Untargeted metabolomics studies employing NMR and LC-MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis. Metabolomics, 11(4):895-907. doi: 10.1007/s11306-014-0747-6.
  • Härtig, C., Lohmayer, R., Kolb, S., Horn, M.A., Inskeep, W.P., Planer-Friedrich, B. (2014) Chemolithotrophic growth of the aerobic hyperthermophilic bacterium Thermocrinis ruber OC 14/7/2 on monothioarsenate and arsenite. FEMS Microbiology Ecology, 90(3):747–760. doi: 10.1111/1574-6941.12431.
  • Inskeep, W.P., Jay, Z.J., Macur, R.E., Clingenpeel, S., Tenney, A., Lavalvo, D., Beam, J.P., Kozubal, M.A., Shanks, W.C., Morgan, L.A., Kan, J., Gorby, Y., Yooseph, S., Nealson, K. (2015) Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: Phylogenetic and functional analyses reveal geochemical controls on microbial community structure. Microbiol., 6:1044. doi: 10.3389/fmicb.2015.01044.
  • Jay, Z.J., Beam, J.P., Dohnalkova, A., Lohmayer, R.,  Bodle, B., Planer-Friedrich, B.,  Romine, M., Inskeep, W.P. (2015) Pyrobaculum yellowstonensis Strain WP30 Respires on Elemental Sulfur and/or Arsenate in Circumneutral Sulfidic Geothermal Sediments of Yellowstone National Park. Environ. Microbiol., 81(17):5907–5916. doi: 10.1128/AEM.01095-15.
  • Swanson, K.D., Ratzloff, M.W., Mulder, D.W., Artz, J.H., Ghose, S., Hoffman, A., White, S., Zadvornyy, O.A., Broderick, J.B., Bothner, B., King, P.W., Peters, J.W. (2015) [FeFe]-hydrogenase oxygen inactivation is initiated at the H cluster 2Fe subcluster. Am. Chem. Soc.,137(5):1809-1816. doi: 10.1021/ja510169s.
  • Wang, Q., Warelow, T.P., Kang, Y.-S., Romano, C., Osborne, T.H., Lehr, C.R., Bothner, B., McDermott, T.R., Santini, J.M., Wang, G. (2015) Arsenite oxidase also functions as an antimonite oxidase. Environ. Microbiol., 81(6):1959-1965. doi: 10.1128/AEM.02981-14.

2014

  • Jennings, R deM., Whitmore, L.M., Moran, J.J., Kreuzer, H.W., Inskeep, W.P. (2014) Carbon dioxide fixation by Metallosphaera yellowstonensis and acidothermophilic iron-oxidizing microbial communities from Yellowstone National Park. Environ. Microbiol., 80:2665-2671. doi: 10.1128/AEM.03416-13.