Abstract
Using a previously developed primer system, nifH gene fragments 450 nucleotides long were amplified, cloned, and sequenced for representatives of nitrogen-fixing methanotrophic bacteria of the genera Methylococcus, Methylocystis, and Methylosinus. Fragments of nifH genes were also detected and sequenced in representatives of the genera Methylomonas and Methylobacter, which were not considered diazotrophs until recently. Phylogenetic analysis revealed the remoteness of nifH gene sequences of methanotroph types I and II. At the same time, a close relationship was found between nifH of type I methanotrophs and representatives of γ-proteobacteria and between nifH genes of type II methanotrophs and representatives of α-proteobacteria. The results obtained in this study are in good accordance with the data of phylogenetic analysis based on 16S rRNA sequence comparison with the only exception being Methylococcus capsulatus strains, whose nifH genes proved to be closely related to nifH genes of Methylocystis and Methylosinus representatives. Our findings extend the database of primary sequences of nifH genes and allow the contribution of methanotrophs to the process of nitrogen fixation to be estimated.
Similar content being viewed by others
REFERENCES
Ben-Porath, J. and Zehr, J.P., Detection and Characterization of Cyanobacterial nifH Genes, Appl. Environ. Microbiol., 1994, vol. 60, pp. 880–887.
Ueda, T., Suga, Y., Yashiro, N., and Matsuguchi, T., Remarkable N2-Fixing Bacterial Diversity Detected in Rice Roots by Molecular Evolutionary Analysis of nifH Gene Sequences, J. Bacteriol., 1995, vol. 177, pp. 1414–1417.
Zehr, J.P., Mellon, M., Braun, S., Litaker, W., Steppe, T., and Paerl, H.W., Diversity of Heterotrophic Nitrogen Fixation Genes in a Marine Cyanobacterial Mat, Appl. Environ. Microbiol., 1995, vol. 61, pp. 2527–2532.
Zani, S., Mellon, M.T., Collier, J.L., and Zehr, J.P., Expression of nifH Genes in Natural Microbial Assemblages in Lake George, New York, Detected by Reverse Transcriptase PCR, Appl. Environ. Microbiol., 2000, vol. 66, pp. 3119–3124.
Hanson, R.S. and Hanson, T.E., Methanotrophic Bacteria, Microbiol. Rev., 1996, vol. 60, pp. 439–471.
Harper, H.J., The Effect of Natural Gas on the Growth of Microorganisms and Accumulation of Nitrogen and Organic Matter in Soil, Soil Sci., 1939, vol. 48, pp. 461–453.
Davis, J.B., Coty, V.F., and Stanley, J.P., Atmospheric Nitrogen Fixation by Methane-Oxidizing Bacteria, J.?Bacteriol., 1964, vol. 88, pp. 468–472.
De Bont, J.A., Lee, K.K., and Boudin, D.F., Bacterial Oxidation of Methane in the Rice Paddy, Ecol. Bull., 1978, vol. 26, pp. 91–97.
Chistyakova, I.K., Kalininskaya, T.A., and Miller, Yu.M., Methane as a Source of Carbon and Energy for Nitrogen-Fixing Bacteria in Soils under Rice, Izv. Akad. Nauk SSSR, Ser. Biol., 1982, no. 3, pp. 428–432.
Dalton, H. and Whittenbury, R., The Acetylene Reduction Technique as Assay for Nitrogenase Activity in the Methane Oxidizing Bacterium Methylococcus capsulatus Strain Bath, Arch. Microbiol., 1976, vol. 109, pp. 147–151.
De Bont, J.A. and Mulder, E.G., Nitrogen Fixation and Co-Oxidation of Ethylene by Methane-Utilizing Bacteria, J. Gen. Microbiol., 1976, vol. 83, pp. 113–119.
Romanovskaya, V.A., Lyudvichenko, E.S., Sokolov, I.G., and Malashenko, Yu.R., Fixation of Molecular Nitrogen by Methane-Oxidizing Bacteria, Mikrobiol. Zh., 1980, vol. 42, pp. 683–692.
Green, P.N., Overview of the Current State of Methylotroph Taxonomy, Microbial Growth on C1 Compounds, Murrel, J.C. and Kelly, D.P., Eds., Andover: Intercept Ltd., 1993, pp. 253–265.
Auman, A.J., Speake, C.C., and Lidstrom, M.E., nifH Sequences and Nitrogen Fixation in Type I and Type II Methanotrophs, Appl. Environ. Microbiol., 2001, vol. 67, pp. 4009–4016.
Marusina, A.I., Boulygina, E.S., Kuznetsov, B.B., Tourova, T.P., Kravchenko, I.K., and Gal'chenko, V.F., A System of Oligonucleotide Primers for the Amplification of nifH Genes of Different Taxonomic Groups of Prokaryotes, Mikrobiologiya, 2001, vol. 70, pp. 86–91.
Gal'chenko, V.F., Andreev, L.V., and Trotsenko, Yu.A., Taksonomiya i identifikatsiya obligatnykh metanotrofnykh bakterii (Taxonomy and Identification of Obligate Methanotrophic Bacteria), Kalakoutskii, L.V., Ed., Pushchino: NTsBI, 1986, pp. 1–96.
Sambrook, J., Fritsch, E.F., and Maniatis, T., Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor: Cold Spring Harbor Lab., 1989.
Birnboim, H.C. and Doly, J., A Rapid Alkaline Extraction Procedure for Screening Recombinant Plasmid DNA, Nucleic Acids Res., 1979, vol. 7, no. 6, pp. 1513–1523.
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.
Zhilina, T.N., Garnova, E.S., Tourova, T.P., Kostrikina, ?N.A., and Zavarzin, G.A., Amphibacillus fermentum sp. nov. and Amphibacillus tropicus sp. nov., New Alkaliphilic, Facultatively Anaerobic, Saccharolytic Bacilli from Lake Magadi, Mikrobiologiya, 2001, vol. 70, pp. 825–837.
Van de Peer, Y. and De Wachter, R., TREECON for Windows: A Software Package for the Construction and Drawing of Evolutionary Trees for the Microsoft Windows Environment, Comput. Appl. Biosci., 1994, vol. 10, pp. 569–570.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Boulygina, E.S., Kuznetsov, B.B., Marusina, A.I. et al. A Study of Nucleotide Sequences of nifH Genes of Some Methanotrophic Bacteria. Microbiology 71, 425–432 (2002). https://doi.org/10.1023/A:1019893526803
Issue Date:
DOI: https://doi.org/10.1023/A:1019893526803