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

Vorobev, Alexey; Boer, Wietse de; Folman, L.B.; Bodelier, Paul L. E.; Доронина, Н. В.; Suzina, N. E.; Trotsenko, Yu. A.; Dedysh, Svetlana N.

doi:10.1099/ijs.0.010074-0

Cited by 56 publications

(42 citation statements)

References 30 publications

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“…PLFAs that made up ,0.1 % of total in all organisms are not included. Data for reference taxa were taken from Dedysh et al (2000Dedysh et al ( , 2004a, Dunfield et al (2003Dunfield et al ( , 2010 and Vorob'ev et al (2009). Phospholipid fatty acid (PLFA) profiles of the novel methanotrophic isolates were highly similar to those described for methano-and methylotrophic representatives of the family Beijerinckiaceae, i.e.…”

Section: Strains Ar4mentioning

confidence: 81%

Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase

Vorobev

Baani

Доронина

et al. 2011

International Journal of Systematic and Evolutionary Microbiology

234

155

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and LAY possessed only a soluble form of methane monooxygenase (sMMO) and lacked intracytoplasmic membranes. Growth occurred only on methane and methanol; the latter was the preferred growth substrate. mRNA transcripts of sMMO were detectable in cells when either methane or both methane and methanol were available. Carbon was assimilated via the serine and ribulose-bisphosphate (RuBP) pathways; nitrogen was fixed via an oxygen-sensitive nitrogenase. Strains AR4 T , SOP9 and LAY were moderately acidophilic, mesophilic organisms capable of growth between pH 3.5 and 7.2 (optimum pH 4.8-5.2) and at 4-33 6C (optimum 20-23 6C).The major cellular fatty acid was 18 : 1v7c and the quinone was Q-10. The DNA G+C content was 55.6-57.5 mol%. The isolates belonged to the family Beijerinckiaceae of the class Alphaproteobacteria and were most closely related to the sMMO-possessing methanotrophs of the genus Methylocella (96.4-97.0 % 16S rRNA gene sequence similarity), particulate MMO (pMMO)-possessing methanotrophs of the genus Methylocapsa (96.1-97.0 %), facultative methylotrophs of the genus Methylovirgula (96.1-96.3 %) and non-methanotrophic organotrophs of the genus Beijerinckia (96.5-97.0 %). Phenotypically, strains AR4 T , SOP9 and LAY were most similar to Methylocella species, but differed from members of this genus by cell morphology, greater tolerance of low pH, detectable activities of RuBP pathway enzymes and inability to grow on multicarbon compounds. Therefore, we propose a novel genus and species, Methyloferula stellata gen. nov., sp. nov., to accommodate strains AR4 The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences and partial mmoX gene sequences of strains AR4 T , SOP9 and LAY are FR686343-FR686345 (16S rRNA gene) and FR686346-FR686348 (mmoX), respectively, and those for the partial mxaF, nifH and rbcL sequences of strain AR4T are FR686349, FR686351 and FR686352, respectively.

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Section: Strains Ar4mentioning

confidence: 81%

Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase

Vorobev

Baani

Доронина

et al. 2011

International Journal of Systematic and Evolutionary Microbiology

234

155

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“…Growth factor requirements have been only reported in two species, C. asaccharovorans ) and M. ligni (Vorob'ev et al 2009). …”

Section: Taxonomy Historical and Currentmentioning

confidence: 96%

“…In addition to these genes, the key genes of C 1 metabolism have also been widely used as phylogenetic and functional markers in a number of taxonomic and ecologic studies (Berestovskaya et al 2012;Dedysh et al 1998bDedysh et al , 2000Dedysh et al , 2001bDedysh et al , 2002Dedysh et al , 2004aDunfield et al 2003Dunfield et al , 2010Lau et al 2013;McDonald and Murrell 1997a, b;Vorob'ev et al 2009;Vorobev et al 2011).…”

Section: Molecular Analyses Ddhmentioning

confidence: 99%

“…Acidic wetlands, particularly Sphagnum peat bogs, from different sites of Russia and forest soils from Germany, Russia, and the Netherlands were the habitats from where the species of Methylocapsa, Methylocella, Methyloferula, Methylorosula, and Methylovirgula were originally isolated (Berestovskaya et al 2012;Dedysh et al 2000Dedysh et al , 2002Dedysh et al , 2004aDunfield et al 2003Dunfield et al , 2010Vorob'ev et al 2009;Vorobev et al 2011).…”

Section: Ecologymentioning

confidence: 99%

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The Family Beijerinckiaceae

Marı́n

Arahal

2014

The Prokaryotes

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“…By contrast, Methyloferula stellata grows only on methane and methanol (Vorobev et al, 2011). Finally, the genera Methylovirgula and Methylorosula accommodate facultatively methylotrophic bacteria (Vorob'ev et al, 2009;Berestovskaya et al, 2012). These methylotrophs assimilate C 1 compounds via the ribulose bisphosphate pathway.…”

mentioning

confidence: 99%

Emended description of the family Beijerinckiaceae and transfer of the genera Chelatococcus and Camelimonas to the family Chelatococcaceae fam. nov.

Dedysh

Haupt

Dunfield

2016

International Journal of Systematic and Evolutionary Microbiology

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The family Beijerinckiaceae was circumscribed in 2005 to accommodate four genera of phylogenetically related alphaproteobacteria: Beijerinckia, Chelatococcus, Methylocella and Methylocapsa. Later, four additional genera, i.e. Methylovirgula, Methyloferula, Methylorosula and Camelimonas, were described and assigned to this family, which now accommodates 21 species with validly published names. Members of this family possess strikingly different lifestyles, including chemoheterotrophy, facultative methylotrophy, obligate methanotrophy and facultative methanotrophy. Levels of 16S rRNA gene sequence similarity among most of these bacteria range from 96 to 98 %, suggesting a common evolutionary origin. The genera Chelatococcus and Camelimonas, however, are not monophyletic with the other described genera based on 16S rRNA gene sequence phylogeny, and instead form a distant cluster more closely related to the Methylobacteriaceae. Physiologically these two genera also lack several properties common to the other Beijerinckiaceae. On the other hand, the genus Rhodoblastus, presently considered a member of the Bradyrhizobiaceae, affiliates with high confidence to the Beijerinckiaceae. Here, we propose to transfer the genera Chelatococcus and Camelimonas to the family Chelatococcaceae fam. nov., and present an emended description of the family Beijerinckiaceae, including the genus Rhodoblastus.The family Beijerinckiaceae belongs to the order Rhizobiales, in the class Alphaproteobacteria. It was circumscribed in 2005 on the basis of comparative analysis of 16S rRNA gene sequences to accommodate four phylogenetically related genera, i.e. Beijerinckia, Chelatococcus, Methylocella and Methylocapsa (Garrity et al., 2005; Validation list Number 107, 2006). Later, four additional genera, i.e. Methylovirgula, Methyloferula, Methylorosula and Camelimonas, were described and assigned to this family. The Beijerinckiaceae now accommodates eight genera containing 21 species with validly published names.The type genus of this family, Beijerinckia, and the five related genera of methano-and methylotrophs, i.e. Methylocella, Methylocapsa, Methylovirgula, Methyloferula and Methylorosula, are represented by acidophilic bacteria displaying considerable phenotypic and morphological similarities. One important feature common to these bacteria is the ability to fix dinitrogen. Although possessing different lifestyles, such as chemoheterotrophy, facultative methylotrophy, facultative methanotrophy and also obligate methanotrophy, these six genera comprise a closely related phylogenetic group with pairwise 16S rRNA gene sequence similarities ranging from 96 to 98 %. A comparative genomic study performed for the generalist organotroph Beijerinckia indica, facultative methanotroph Methylocella silvestris and obligate methanotroph Methylocapsa acidiphila confirmed the common evolutionary origin of these bacteria with several phylogenetic reconstructions (Tamas et al., 2014). However, this study also noted that the genera Chelatococcus and Camelimona...

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

Cited by 56 publications

References 30 publications

Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase

Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase

The Family Beijerinckiaceae

Emended description of the family Beijerinckiaceae and transfer of the genera Chelatococcus and Camelimonas to the family Chelatococcaceae fam. nov.

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