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Methylovirgula ligni gen. nov., sp. nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF gene

¹ S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
² Netherlands Institute of Ecology, Centre for Terrestrial Ecology, 6666 ZG Heteren, The Netherlands
³ Netherlands Institute of Ecology, Centre for Limnology, 3631 AC Nieuwersluis, The Netherlands
⁴ G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region, 142292, Russia

Correspondence
Svetlana N. Dedysh
dedysh{at}mail.ru

Two strains of Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped bacteria were isolated from beechwood blocks during decay by the white-rot fungus Hypholoma fasciculare and were designated strains BW863^T and BW872. They are capable of methylotrophic growth and assimilate carbon via the ribulose-bisphosphate pathway. In addition to methanol, the novel isolates utilized ethanol, pyruvate and malate. Strains BW863^T and BW872 are obligately acidophilic, mesophilic organisms capable of growth at pH 3.1–6.5 (with an optimum at pH 4.5–5.0) and at 4–30 °C. Phospholipid fatty acid profiles of these bacteria contain unusually large amounts (about 90 %) of C_{18 : 1}7c, thereby resembling the profiles of Methylobacterium strains. The predominant quinone is Q-10. The DNA G+C content of the novel isolates is 61.8–62.8 mol%. On the basis of 16S rRNA gene sequence similarity, strains BW863^T and BW872 are most closely related to the acidophilic methanotroph Methylocapsa acidiphila B2^T (96.5–97 %). Comparative sequence analysis of mxaF, the gene encoding the large subunit of methanol dehydrogenase, placed the MxaF sequences of the two novel strains in a cluster that is distinct from all previously described MxaF sequences of cultivated methylotrophs. The identity between the MxaF sequences of the acidophilic isolates and those from known alpha-, beta- and gammaproteobacterial methylotrophs was respectively 69–75, 61–63 and 64–67 %. The data therefore suggest that strains BW863^T and BW872 represent a novel genus and species of methylotrophic bacteria, for which the name Methylovirgula ligni gen. nov., sp. nov. is proposed. Strain BW863^T (=DSM 19998^T =NCIMB 14408^T) is the type strain of Methylovirgula ligni.

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences and partial mxaF gene sequences of strains BW863^T and BW872 are respectively FM252034 and FM252035 (16S rRNA gene) and FM252036 and FM252037 (mxaF), and those for the partial nifH and cbbL gene sequences of strain BW863^T are respectively FM252038 and FM252039.

EMs contrasting the morphology of strain BW863^T and Methylocapsa acidiphila B2^T, a graph showing the growth response of strain BW863^T to pH and an extended 16S rRNA gene-sequence based neighbour-joining tree are available as supplementary material with the online version of this paper.