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Methylohalomonas lacus gen. nov., sp. nov. and Methylonatrum kenyense gen. nov., sp. nov., methylotrophic gammaproteobacteria from hypersaline lakes

¹ Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, 117811 Moscow, Russia
² Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
³ G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
⁴ Institute of Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms University, Meckenheimer Allee 168, 53115 Bonn, Germany
⁵ Center Bioengineering, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/1, 117312 Moscow, Russia

Correspondence
Dimitry Yu. Sorokin
soroc{at}inmi.host.ru
or
D.Y.Sorokin{at}tnw.tudelft.nl

Aerobic enrichment at 4 M NaCl, pH 7.5, with methanol as carbon and energy source from sediments of hypersaline chloride–sulfate lakes in Kulunda Steppe (Altai, Russia) resulted in the isolation of a moderately halophilic and obligately methylotrophic bacterium, strain HMT 1^T. The bacterium grew with methanol and methylamine within a pH range of 6.8–8.2 with an optimum at pH 7.5 and at NaCl concentrations of 0.5–4 M with an optimum at 2 M. In addition to methanol and methylamine, it can oxidize ethanol, formate, formaldehyde and dimethylamine. Carbon is assimilated via the serine pathway. The main compatible solute is glycine betaine. 16S rRNA gene sequence analysis placed the isolate as a new lineage in the family Ectothiorhodospiraceae (Gammaproteobacteria). It is proposed, therefore, to accommodate this bacterium within a novel genus and species, Methylohalomonas lacus gen. nov., sp. nov., with HMT 1^T (=DSM 15733^T =NCCB 100208^T =UNIQEM U237^T) as the type strain. Two strains were obtained in pure culture from sediments of soda lake Magadi in Kenya and the Kulunda Steppe (Russia) on a mineral medium at pH 10 containing 0.6 M total Na⁺ using methanol as a substrate. Strain AMT 1^T was enriched with methanol, while strain AMT 3 originated from an enrichment culture with CO. The isolates are restricted facultative methylotrophs, capable of growth with methanol, formate and acetate as carbon and energy sources. With methanol, the strains grew within a broad salinity range from 0.3 to 3.5–4 M total Na⁺, with an optimum at 0.5–1 M. The pH range for growth was between 8.3 and 10.5, with an optimum at pH 9.5, which characterized the soda lake isolates as obligate haloalkaliphiles. Carbon is assimilated autotrophically via the Calvin–Benson cycle. Sequence analysis of the gene coding for the key enzyme RuBisCO demonstrated that strain AMT 1^T possessed a single cbbL gene of the ‘green’ form I, clustering with members of the family Ectothiorhodospiraceae. Analysis of the 16S rRNA gene sequence showed that strains AMT 1^T and AMT 3 belong to a single species that forms a separate lineage within the family Ectothiorhodospiraceae. On the basis of phenotypic and genetic data, the novel haloalkaliphilic methylotrophs are described as representing a novel genus and species, Methylonatrum kenyense gen. nov., sp. nov. (type strain AMT 1^T =DSM 15732^T =NCCB 100209^T =UNIQEM U238^T).

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains HMT 1^T, AMT 1^T and AMT 3 are DQ834966, DQ789390 and EU006088, respectively. Those for the cbbL gene from AMT 1^T and for the mxaF gene from HMT 1^T are respectively EF152335 and EF152336.

Fatty acid compositions of isolates AMT 1^T and HMT 1^T and results of PCR amplifications of mxaF with four different primer sets from (halo)alkaliphilic methylotrophs are available as supplementary material with the online version of this paper.

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