Lab publications

(* undergraduate, ** graduate students)

2021
  1.  *Johnson ZJ, *Krutkin DD, Bohutskyi P, Kalyuzhnaya MG (2021) Metals and methylotrophy: Via global gene expression studies. Methods Enzymol. 650:185-213. doi: 10.1016/bs.mie.2021.01.046
  2.  **Afshin Y, **Delherbe N, Kalyuzhnaya MG (2021) Methylotenera. Bergey’s Manual of Systematics of Archaea and Bacteria (BMSAB). 
  3. Xiong W, Kalyuzhanaya MG, Henard CA (2021) Editorial: Microbial C1 Metabolism and Biotechnology. Front Microbiol. 12. 2403.  https://doi.org/10.3389/fmicb.2021.744030
  4. **Hamilton R, Nizovtseva I, Chernuskin D, Kalyuzhnaya MG (in press) C1-proteins prospect for production of industrial proteins and protein-based materials from methane.  In. Algal Biorefineries and the Circular Bioeconomy. Ed.  Mehariya S, Bhatia S, and Karthikeyan OP.  Taylor & Francis/CRC.
  5.   **McNamara JP, **Delherbe N, Kalyuzhnaya MG (in press) Methylophilus. Bergey’s Manual of Systematics of Archaea and Bacteria (BMSAB).
2020
  1. Ortega DR, Yang W, Subramanian P, Mann P, Kjær A, Chen S, Watts KJ, Pirbadian S, **Collins DA, Kooger R, Kalyuzhnaya MG, Ringgaard S, Briegel A, Jensen GJ (2020) Repurposing a chemosensory macromolecular machine. Nat Commun. 11(1):2041. doi: 10.1038/s41467-020-15736-5.
  2. **Nariya S, Kalyuzhnaya MG. (2020) Hemerythrins enhance aerobic respiration in Methylomicrobium alcaliphilum 20ZR, a methane-consuming bacterium. FEMS Microbiol Lett 1, 367(2):fnaa003. doi: 10.1093/femsle/fnaa003.
  3. Nguyen AD, Park JY, Hwang IY, **Hamilton R, Kalyuzhnaya MG, Kim D, Lee EY. 2020.  Genome-scale evaluation of core one-carbon metabolism in gammaproteobacterial methanotrophs grown on methane and methanol. Metab Eng. 57:1-12. doi: 10.1016/j.ymben.2019.10.004.
  4.   Kalyuzhanaya MG, Kumaresan D, Heimann K, Caetano NS, Visvanathan C, Karthikeyan OP  (2020). Editorial: Methane: A Bioresource for Fuel and Biomolecules.  Front. Environ. Sci.,9.  doi: 10.3389/978-2-88963-562-7c
2019
  1. Henard CA, Akberdin IR, Kalyuzhnaya MG, Guarnieri MT (2019) Muconic acid production from methane using rationally-engineered methanotrophic biocatalysts. Green Chem doi: 10.1039/C9GC03722E.
  2. Kalyuzhnaya MG, **Collins DA, Chistoserdova L (2019) Microbial Cycling of Methane. In: Schmidt, Thomas M. (ed.) Encyclopedia of Microbiology, 4th Edition. vol. 3, pp. 115- 124. UK: Elsevier.
  3. **Nariya S,  Kalyuzhna, MG 2019. Diversity, Physiology, and Biotechnological Potential of Halo(alkali)philic Methane-Consuming Bacteria. In E.Y. Lee (Ed) Methanotrophs: Microbiology Fundamentals and Biotechnological Applications (Ed.  E.Y. Lee). Springer Nature. 278 pp.
  4. Kalyuzhnaya MG, **Gomez OA, Murrell JC (2019) The Methane-Oxidizing Bacteria (Methanotrophs). In: McGenity T. (Eds) Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes. Handbook of Hydrocarbon and Lipid Microbiology. Springer, Cham. doi.org/10.1007/978-3-319-60053-6_10-1
2018
  1. **Collins D.A., Kalyuzhnaya M.G. 2018. Navigating methane metabolism: Enzymes, Compartments, and Networks. Methods Enzymol. 613:349-383. doi: 10.1016/bs.mie.2018.10.010.
  2. Henard, C., Franklin, T., Youhenna, B*., But, S., Alexander, D., Kalyuzhnaya, M.G., Guarnieri, M. (2018). Biogas Biocatalysis: Methanotrophic Bacterial Cultivation, Metabolite Profiling, and Bioconversion to Lactic Acid. Frontiers in Microbiology. doi: 10.3389/fmicb.2018.02610.
  3. Akberdin, I., **Collins, D., *Hamilton, R., Oshchepkov, D., Shukla, A., Nicora, C., Nakayaku, E., Adkins, J., Kalyuzhanaya, M. (2018). Rare Earth Elements Alter Redox Balance in Methylomicrobium alcaliphilum 20ZR. Frontiers in Microbiology. doi: 10.3389/fmicb.2018.02735.
  4. Akberdin, I. R., **Thompson, M., *Hamilton, R., Desai, N., Alexander, D., Henard, C. A., … & Kalyuzhnaya, M. G. (2018). Methane utilization in Methylomicrobium alcaliphilum 20Z R: a systems approach. Scientific Reports, 8(1), 2512. doi: 10.1038/s41598-018-20574-z.
  5. Chistoserdova, L. & Kalyuzhnaya, M. G. (2018). Current Trends in Methylotrophy.  Trends in Microbiology, doi: 10.1016/j.tim.2018.01.011.
  6. Akberdin, I. R., **Thompson, M., & Kalyuzhnaya, M. G. (2018). Systems Biology and Metabolic Modeling of C1-Metabolism. In Methane Biocatalysis: Paving the Way to Sustainability  (Eds: Kalyuzhnaya, M.G., Xing, X.H.) Springer International Publishing. 312pp.
  7. Khmelenina V.N., Rozova O.N., Akberdin I. R., Kalyuzhnaya M. G. & Trotsenko Y. A. (2018). Pyrophosphate-Dependent Enzymes in Methanotrophs: New Findings and Views. In Methane Biocatalysis: Paving the Way to Sustainability (Eds: Kalyuzhnaya, M.G., Xing, X.H.) Springer International Publishing. 312pp.
  8. *Hamilton, R., Becken U., & Kalyuzhnaya, M. G. (2018). Growth of methanotrophic bacteria in chemostat mode in Eppendorf BioBlu 0.3f single-use vessels. Eppendorf’s Application note, 362, pdf file.
2017
  1. Osborne, K. A., Gray, N. D., Sherry, A., Leary, P., Mejeha, O., Bischoff, J., … & Talbot, H. M. (2017). Methanotroph‐derived bacteriohopanepolyol (BHP) signatures as a function of temperature related growth, survival, cell death and preservation in the geological record. Environmental Microbiology Reports. doi: 10.1111/1758-2229.12570.
  2. Frindte, K., Kalyuzhnaya, M. G., Bringel, F., Dunfield, P. F., Jetten, M. S., Khmelenina, V. N., … & Semrau, J. D. (2017). Draft Genome Sequences of Two Gammaproteobacterial Methanotrophs Isolated from Rice Ecosystems. Genome Announcements, 5(33), e00526-17. doi: 10.1128/genomeA.00526-17.
  3. Demidenko, A., Akberdin, I. R., Allemann, M., Allen, E. E., & Kalyuzhanaya, M. G. (2017). Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense 5G (B1). Frontiers in Microbiology, 7, 2167. doi: 10.3389/fmicb.2016.02167.
  4. **Collins, D.A., Akberdin, I.R., & Kalyuzhnaya, M.G. (2016). Methylobacter. Bergey’s Manual of Systematics of Archaea and Bacteria, 1-11. doi: 10.1002/9781118960608.gbm01179.pub2.
2016
  1. Rush, D., Osborne, K. A., Birgel, D., Kappler, A., Hirayama, H., Peckmann, J., … Kalyuzhnaya, M., Sidgwick, F. R.&Talbot, H.M. (2016). The Bacteriohopanepolyol Inventory of Novel Aerobic Methane Oxidising Bacteria Reveals New Biomarker Signatures of Aerobic Methanotrophy in Marine Systems. PloS one, 11(11), e0165635. doi:10.1371/journal.pone.0165635
  2. Kalyuzhnaya, M.G. (2016). Methylomicrobium. Bergey’s Manual of Systematics of Archaea and Bacteria, 1-10. 
  3. Kalyuzhnaya, M.G. (2016). Methylosarcina.Bergey’s Manual of Systematics of Archaea and Bacteria, 1-7. 
  4. Strong, P. J., Kalyuzhnaya, M., Silverman, J., & Clarke, W. P. A methanotroph-based biorefinery: Potential scenarios for generating multiple products from a single fermentation. Bioresource technology, 215, 314-323. doi: 10.1016/j.biortech.2016.04.099
  5. Henard, C.A., Smith, H., Dowe, N., Kalyuzhnaya, M.G., Pienkos, P.T., Guarnieri, M.T. Bioconversion of methane to lactate by an obligate methanotrophic bacterium. Scientific Reports,  6, 21585. doi: 10.1038/srep21585.
  6. Kalyuzhnaya M.G. Methane biocatalysis: selecting the right microbe. In. Biotechnologies for biofuel production and optimization (Ed. By C. Eckert and C.T.Trinh).
  7. *Flynn, J, Hirayama, H., Sakai, Y., Dunfield, P.F., Klotz, M.G., Knief, C., Op den Camp, H.J.M., … Kalyuzhnaya, M.G. Draft genomes of gammaproteobacterial methanotrophs isolated from marine ecosystems. Genome Announcements,  4(1), e01629-15. doi: 10.1128/genomeA.01629-15
2015
  1. *Hamilton, R., Kits, K. D., Ramonovskaya, V. A., Rozova, O. N., Yurimoto, H., Iguchi, H., … & Kalyuzhnaya, M. G. (2015). Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems. Genome Announcements, 3(3). doi: 10.1128/genomeA.00515-15
  2. de la Torre, A., *Metivier, A., Chu, F., Laurens, L.M.L., Beck, D.A.C., Pienkos, P.T., Lidstrom, M.E. and Kalyuzhnaya, M.G. (2015). Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1). Microbial Cell Factories, 14:188.  doi: 10.1186/s12934-015-0377-3
  3. Kalyuzhnaya, M. G., Puri, A. W., & Lidstrom, M. E. (2015). Metabolic engineering in methanotrophic bacteria. Metabolic Engineering, 29, 142-152. doi: 10.1016/j.ymben.2015.03.01
  4. Smalley, N. E., Taipale, S., De Marco, P., Doronina, N. V., Kyrpides, N., Shapiro, N., … & Kalyuzhnaya, M. G. (2015). Functional and genomic diversity of methylotrophic Rhodocyclaceae: description of the new species Methyloversatilis discipulorum sp. nov. IJSEM  ijs-0. doi: 10.1099/ijs.0.000190
  5. Good, N. M., Lamb, A., Beck, D. A., Martinez-Gomez, N. C., & Kalyuzhnaya, M. G. (2015). C1-Pathways in Methyloversatilis universalis FAM5: genome wide gene expression and mutagenesis studies. Microorganisms, 3(2), 175-197. doi: 10.3390/microorganisms3020175
Other (2015)
  1. Sharp, C. E., Smirnova, A. V., Kalyuzhnaya, M. G., Bringel, F., Hirayama, H., Jetten, M. S., … & Dunfield, P. F. (2015). Draft genome sequence of the moderately halophilic methanotroph Methylohalobius crimeensis strain 10Ki. Genome Announcements, 3(3), e00644-15. doi: 10.1128/genomeA.00644-15
  2. Kalyuzhnaya, M. G., Lamb, A. E., McTaggart, T. L., Oshkin, I. Y., Shapiro, N., Woyke, T., & Chistoserdova, L. (2015). Draft genome sequences of gammaproteobacterial methanotrophs isolated from Lake Washington sediment.Genome Announcements, 3(2), e00103-15. doi: 10.1128/genomeA.00103-15
  3. Dedysh, S. N., Naumoff, D. G., Vorobev, A. V., Kyrpides, N., Woyke, T., Shapiro, N., … & Dunfield, P. F. (2015). Draft genome sequence of Methyloferula stellata AR4, an obligate methanotroph possessing only a soluble methane monooxygenase. Genome Announcements, 3(2), e01555-14. doi: 10.1128/genomeA.01555-14
  4. McTaggart, T. L., Beck, D. A., Setboonsarng, U., Shapiro, N., Woyke, T., Lidstrom, M. E., … & Chistoserdova, L. (2015). Genomics of methylotrophy in gram-positive methylamine-utilizing bacteria. Microorganisms, 3(1), 94-112. doi:10.3390/microorganisms3010094
  5. Beck, D. A., McTaggart, T. L., Setboonsarng, U., Vorobev, A., Goodwin, L., Shapiro, N., … & Chistoserdova, L. (2015). Multiphyletic origins of methylotrophy in Alphaproteobacteria, exemplified by comparative genomics of Lake Washington isolates. Environmental Microbiology, 17(3), 547-554. doi: 10.1111/1462-2920.12736
  6. But, S. Y., Khmelenina, V. N., Reshetnikov, A. S., Mustakhimov, I. I., Kalyuzhnaya, M. G., & Trotsenko, Y. A. (2015). Sucrose metabolism in halotolerant methanotroph Methylomicrobium alcaliphilum 20Z. Archives of Microbiology, 197(3), 471-480. doi: 10. 1007/ s00203-015-1080-9
Other (selected)
  1. Yang, S., Matsen, J.B., Konopka, M., Green-Saxena, A., Clubb, J., Sadilek, M., Orphan, V.J., Beck, D., & Kalyuzhnaya, M.G. 2013. Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. Metabolomics and 13C-labeling study. Front. Microbiol.,  doi: 10.3389/fmicb.2013.00070.
  2. Matsen, J.B., Yang, S., Stein, L.Y., Beck, D., & Kalyuzhnaya, M.G. 2013. Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part I. Transcriptomic study. Front. Microbiol.,  doi: 10.3389/fmicb.2013.00040.
  3. Konopka, M., Strovas, T. J., Ojala, D.S., Chistoserdova, L., Lidstrom, M.E., & Kalyuzhnaya, M.G. 2011. Respiration response imaging for real time detection of microbial function at the single cell level.Appl. Environ. Microbiol., 77 (1): 67-72. doi: 10.1128/AEM.01166-10.
  4. Ojala, D.S., Beck, D.A.C. & Kalyuzhnaya, M. G. 2011. Genetic systems for moderately halo(alkali)philic bacteria of the genus Methylomicrobium. Methods Enzymol., 495: 99-118.
  5. Latypova, E., Y.S. Wang, T. Wang, M. Hackett, H. Schafer, & Kalyuzhnaya, M. G. 2010. Genetics of the glutamate-mediated methylamine utilization pathway in the facultative methylotrophic beta-proteobacterium Methyloversatilis universalis FAM5. Mol.Microbiol., 75(2): 426-439. doi:  10.1111/j.1365-2958.2009.06989.x
  6. Kalyuzhnaya, M.G., Lapidus, A., Ivanova, N., Copeland, A.C., McHardy, A.C., Szeto, E. Salamov, A., Grigoriev, I.V., Suciu, D., Levine, S.R., Markowitz, V.M., Rigoutsos, I., Tringe, S.G., Bruce, D.C., Richardson, P.M., Lidstrom, M.E., & L. Chistoserdova. 2008. High-resolution metagenomics targets specific functional types in complex microbial communities. Nature Biotech. , 26: 1029 – 1034. doi: 10.1038/nbt.1488.
  7. Kalyuzhnaya, M.G., Beck, D.A.C., Suciu, D., Pozhitkov, A., M.E. Lidstrom & L. Chistoserdova. 2009. Functioning in situ: gene expression in Methylotenera mobilis in its native environment as assessed through transcriptomics. The ISME Journal. 4: 388–398. doi: 10.1038/ismej.2009.117.
  8. Kalyuzhnaya, M.G., Lidstrom, M.E. & L. Chistoserdova. 2008. Real-time detection of actively metabolizing microbes via redox sensing as applied to methylotroph populations in Lake Washington. The ISME J., 2: 696-706. doi: 10.1038/ismej.2008.32.