Lab publications

(* undergaduate student)

2020
  1. Nariya S.,  Kalyuzhnaya M.G. (2020) Hemerythrins enhance aerobic respiration in Methylomicrobium alcaliphilum 20ZR, a methane-consuming bacterium. FEMS Microbiol. Let. (in press).
2019
  1. Kalyuzhnaya M.G., Collins D.A., Chistoserdova L. (2019) Microbial Cycling of Methane. In: Schmidt, Thomas M. (ed.) Encyclopedia of Microbiology, 4th Edition. vol. 3, pp. 115- 124. UK: Elsevier.
  2. Nariya, S.,  Kalyuzhnay, M.G. 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.
  3. Nguyen, A.D., Park, J.Y., Hwang, I.Y., Hamilton, R., Kalyuzhnaya, M.G., Kim, D., Lee, E.Y. 2019.Genome-Scale Evaluation of Core One-Carbon Metabolism in Gammaproteobacterial Methanotrophs Grown on Methane and Methanol. Metab Eng. 7176: 30307-6. doi: 10.1016/j.ymben.2019.10.004. 
  4. Kalyuzhnaya, M.G., Gomez, O.A., Murrell, J.C. (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 20ZRFrontiers 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 Reports8(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. IMethane 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 Announcements5(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.