Abstract
A mesophilic hydrogenotrophic methanogenic archaeon, strain Z-7105T, was isolated from the bottom sediments of a collector in the vicinity of a soda lake Tanatar II (Altai, Russia). The cells were motile, irregular cocci 0.2–1.2 μm in diameter. The organism was an obligate alkaliphile, growing within a pH range from 8.0 to 10.2, with the optimum at pH 9.0–9.5. It was obligately dependent on carbonates, growing at 0.5 to 1.6 M total carbonates with the optimum at 0.7–0.9 M. Sodium ions were also obligately required at concentrations from 0.9 to 3.3 M Na+ (optimum at 1.4–1.9 M). The organism was halotolerant, but Clions were not required. Hydrogen and formate were used as electron donors. Acetate was required for anabolism. The DNA G+C content was 50.2 mol %. According to the results of its 16S rRNA gene sequence analysis, the isolate belonged to the genus Methanocalculus, being the first known alkaliphilic member of this genus. Its similarity to the neutrophilic and halotolerant Methanocalculus species (M. halotolerans, M. taiwanensis, M. pumilus, and M. chunghsingensis) was 98.2–97.1%, which is within the interspecific range for this genus. The level of DNA-DNA hybridization between strain Z-7105T and the Methanocalculus type species M. halotolerans DSM 14092T was 32%. The genus Methanocalculus, including the new isolate and the previously described species, is distant from other genera of methanogens (<90% 16S rRNA gene similarity). Based on significant phenotypic differences and the results of phylogenetic analysis, including DNA-DNA hybridization, it is proposed to assign strain Z-7105T (=DSM 25006T, =VKM B-2765T) to the new species Methanocalculus natronophilus sp. nov., and to incorporate the genus into the new family Methanocalculaceae fam. nov.
Similar content being viewed by others
References
Zavarzin, G.A., Epicontinental soda lake are probable relict biotopes of terrestrial biota formation, Microbiology (Moscow), 1993, vol. 62, pp. 473–479.
Zhilina, T.N. and Zavarzin, G.A., Alkaliphilic anaerobic community at pH 10, Curr. Microbiol., 1994, vol. 28, pp. 109–112.
Zavarzin, G.A., Zhilina, T.N., and Kevbrin, V.V., The alkaliphilic microbial community and its functional diversity, Microbiology (Moscow), 1999, vol. 68, pp. 503–521.
Zavarzin, G.A. and Zhilina, T.N., Anaerobic chemotrophic alkaliphiles, in Journey to Diverse Microbial Worlds-Adaptation to Exotic Environments, Seckbach, J., Ed., The Netherlands: Kluwer Academic, 2000, pp. 191–208.
Trudy Instituta mikrobiologii im. S.N. Vinogradskogo (Proceedings of Winogradsky Institute of Microbiology), vol. 14: Alkalofil’nye mikrobnye soobshchestva (Alkaliphilic Microbial Communities), Gal’chenko, V.F., Ed., Moscow: Nauka, 2007.
Zavarzin, G.A., Evolyutsiya prokariotnoi biosfery: Mikroby v krugovorote zhizni: 120 let spustya: Chtenie im. S.N. Vinogradskogo (Evolution of the Prokaryotic Biosphere. Microbes in the Life Cycles: 120 Years Later: Lecture in Honor of S.N. Winogradsky), Kolotilova, N.N., Ed., Moscow: MAKS Press, 2011.
Zavarzina, D.G. and Zhilina, T.N., Anaerobic communities of soda lakes as analogues of Precambrian paleocontinental microbiota, Rannyaya kolonizatsiya sushi (Early Colonization of the Land), Rozhnov, S.V., Ed., Moscow: PIN RAN, 2012, pp. 69–91.
Zhilina, T.N., Zavarzina, D.G., Panteleeva, A.N., Osipov, G.A., Kostrikina, N.A., Tourova, T.P., and Zavarzin, G.A., Fuchsiella alkaliacetigena gen. nov., sp. nov., an alkaliphilic, lithoautotrophic homoacetogen from a soda lake, Int. J. Syst. Evol. Microbiol., 2012, vol. 62, pp. 1666–1673.
Zavarzin, G.A., Zhilina, T.N., and Pikuta, E.V., Secondary anaerobes in haloalkaliphilic communities in lakes of Tuva, Microbiology (Moscow), 1996, vol. 65, no. 4, pp. 480–486.
Namsaraev, B.B., Zhilina, T.N., Kulyrova, A.V., and Gorlenko, V.M., Bacterial methanogenesis in soda lakes of the southeastern Transbaikal region, Microbiology (Moscow), 1999, vol. 68, pp. 586–591.
Sorokin, D.Y., Gorlenko, V.M., Namsaraev, B.B., Namsaraev, Z.B., Lysenko, A.M., Eshinimaev, B.T., Khmelenina, V.N., and Trotsenko, Y.A., Prokaryotic communities of the north-eastern Mongolian soda lakes, Hydrobiologia, 2004, vol. 522, pp. 235–248.
Worakit, S., Boone, D.R., Mah, R.A., AbdelSamie, M.-E., and El-Halwagi, M.M., Methanobacterium alcaliphilum sp. nov., an H2-utilizing methanogen that grows at high pH values, Int. J. Syst. Bacteriol., 1986, vol. 36, pp. 380–382.
Wolin, E.A., Wolin, M.J., and Wolfe, R.S., Formation of methane by bacterial extracts, J. Biol. Chem., 1963, vol. 238, pp. 2882–2886.
Kevbrin, V.V. and Zavarzin, G.A., The effect of sulfur compounds on the growth of halophilic homoacetic bacterium Acetohalobium arabaticum, Microbiology (Moscow), 1992, vol. 61, pp. 563–567.
Garnova, E.S., Zhilina, T.N., Tourova, T.N., and Lysenko, A.M., Anoxynatronum sibiricum gen. nov., sp. nov. alkaliphilic saccharolytic anaerobe from cellulolytic community of Nizhnee Beloe (Transbaikal region), Extremophiles, 2003, vol. 7, pp. 213–220.
Birnboim, H.C. and Doly, J., A rapid alkaline extraction procedure for screening recombinant plasmid DNA, Nucleic Acids Res., 1979, vol. 7, pp. 1513–1523.
Lane, D.J., 16S/23S rRNA sequencing, in Nucleic Acid Techniques in Bacterial Systematics, Stackebrandt, E. and Goodfellow, M., Eds., Chichester: John Wiley & Sons, 1991, pp. 115–175.
Sanger, F., Nicklen, S., and Coulson, A.R., DNA sequencing with chain-terminating inhibitors, Proc. Natl. Acad. Sci. USA, 1977, vol. 84, pp. 5463–5467.
Gouy, M., Guindon, S., and Gascuel, O., SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building, Mol. Biol. Evol., 2010, vol. 27, pp. 221–224.
Lake, J.A., Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances, Proc. Natl. Acad. Sci. USA, 1994, vol. 91, pp. 1455–1459.
Boone, D.R. and Whitman, W.B., Proposal of minimal standards for describing new taxa of methanogenic bacteria, Int. J. Syst. Bacteriol., 1988, vol. 38, pp. 212–219.
Lai, M.C., Chen, S.C., Shu, C.M., Chiou, M.S., Wang, C.C., Chuang, M.J., Hong, T.Y., Liu, C.C., Lai, L.J., and Hua, J.J., Methanocalculus taiwanensis sp. nov., isolated from an estuarine environment, Int. J. Syst. Evol. Microbiol., 2002, vol. 52, pp. 1799–1806.
Mori, K., Yamamoto, H., Kamagata, Y., Hatsu, M., and Takamizawa, K., Methanocalculus pumilus sp. nov., a heavy-metal-tolerant methanogen isolated from a waste-disposal site, Int. J. Syst. Evol. Microbiol., 2000, vol. 50, pp. 1723–1729.
Lai, M.C., Lin, C.C., Yu, P.H., Huang, Y.F., and Chen, S.C., Methanocalculus chunghsingensis sp. nov., isolated from an estuary and a marine fishpond in Taiwan, Int. J. Syst. Evol. Microbiol., 2004, vol. 54, pp. 183–189.
Ollivier, B., Fardeau, M.-L., Cayol, J.-L., Magot, M., Patel, B.K.C., Prensier, G., and Garcia, J.-L., Methanocalculus halotolerans gen. nov., sp. nov., isolated from an oil-producing well, Int. J. Syst. Bacteriol., 1998, vol. 48, pp. 821–828.
Nolla-Ardèvol, V., Strous, M., Sorokin, D.Y., Merkel, A.Y., and Tegetmeyer, H.E., Activity and diversity of haloalkaliphilic methanogens in Central Asian soda lakes, J. Biotechnol., 2012, vol. 161, pp. 167–173.
Surakasi, A., Wani, Y., Shouche, D., and Ranade, D., Phylogenetic analysis of methanogenic enrichment cultures obtained from Lonar Lake in India: isolation of Methanocalculus sp. and Methanoculleus sp., Microb. Ecol., 2007, vol. 54, p. 697–704.
Liu, Y. and Whitman, W.B., Metabolic, phylogenetic and ecological diversity of the methanogenic archaea, Ann. N.Y. Acad. Sci., 2008, vol. 1125, pp. 171–189.
Sakai, S., Ehara, M., Tseng, I.-C., Yamaguchi, T., Brauer, S.L., Cadillo-Quiroz, H., Zinder, S.H., and Imachi, H., Methanolinea mesophila sp. nov., a hydrogenotrophic methanogen isolated from rice field soil, and proposal of the archaeal family Methanoregulaceae fam. nov. within the order Methanomicrobiales, Int. J. Syst. Evol. Microbiol., 2012, vol. 62, pp. 1389–1395.
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text © T.N. Zhilina, D.G. Zavarzina, V.V. Kevbrin, T.V. Kolganova, 2013, published in Mikrobiologiya, 2013, Vol. 82, No. 6, pp. 681–690.
Rights and permissions
About this article
Cite this article
Zhilina, T.N., Zavarzina, D.G., Kevbrin, V.V. et al. Methanocalculus natronophilus sp. nov., a new alkaliphilic hydrogenotrophic methanogenic archaeon from a soda lake, and proposal of the new family Methanocalculaceae . Microbiology 82, 698–706 (2013). https://doi.org/10.1134/S0026261713060131
Received:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S0026261713060131