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New Representative of the Species “Prosthecodimorpha hirschii” from a Methanotrophic Enrichment Culture: Phenotypic Traits and Genome Analysis

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Abstract

A dimorphic prosthecate bacterium, strain R2D2, was isolated from a methanotrophic enrichment culture obtained from freshwater pond sediments. The isolation strategy involved multiple serial dilutions in a liquid mineral medium with methane, which triggered the interest to detailed investigation of this bacterium. The 16S rRNA gene sequence of strain R2D2 displayed 99.7% similarity to that of the oligotrophic facultative methylotroph Prosthecomicrobium hirschii 16T, which was recently reclassified as a member of the novel genus “Prosthecodimorpha.” The use of hybrid sequencing approach allowed obtaining the genome sequence of strain R2D2. The genome was 6.47 Mb in size and encoded three rRNA operons and about 5700 proteins including the complete set of genes defining methylotrophic lifestyle. The search for homologs of methane monooxygenases from described methanotrophs in the genome of strain R2D2 yielded no results. The genes coding for Cu-containing propane- and butane-monooxygenases were also absent. Cultivation experiments confirmed good growth of strain R2D2 on methanol and the absence of growth on methane, which agrees well with the results of genome analysis. Apparently, members of “Prosthecodimorpha hirschii” are common satellites of methanotrophic bacteria in methane-rich habitats.

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Funding

This study was supported by the Russian Science Foundation (project 21-14-00034).

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Authors and Affiliations

  1. Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071, Moscow, Russia

    I. Yu. Oshkin, S. E. Belova & S. N. Dedysh

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  1. I. Yu. Oshkin
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Contributions

The funding was obtained by S.D. Dedysh. Isolation, identification and genome analysis of strain R2D2 were performed by I.Yu. Oshkin. Substrate utilization experiments were conducted by S.E. Belova. I.Yu. Oshkin and S.D. Dedysh wrote the manuscript.

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Correspondence to S. N. Dedysh.

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Oshkin, I.Y., Belova, S.E. & Dedysh, S.N. New Representative of the Species “Prosthecodimorpha hirschii” from a Methanotrophic Enrichment Culture: Phenotypic Traits and Genome Analysis. Microbiology 92, 129–136 (2023). https://doi.org/10.1134/S0026261722603207

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