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

Dedysh, Svetlana N.; Haupt, Evan S.; Dunfield, Peter F.

doi:10.1099/ijsem.0.001167

Cited by 37 publications

(15 citation statements)

References 29 publications

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“…Weak responses to DMSP and 2-(N-morpholino)ethanesulfonic acid (MES) were unexpected, as the slag material presumably contains high quantities of lignin-derived compounds containing sulfur and methylated sulfur compounds. Considering the utilization of monosaccharides and di-/trisaccharides, the isolated strains showed a broad range of potential substrates, matched only by Methylorosula polaris (59) and the heterotroph Beijerinckia (15). Regarding organic acid utilization, we observed growth for propionate as well as pyruvate (Fig.…”

Section: Resultsmentioning

confidence: 91%

“…In comparison to this broad taxonomic distribution of methylotrophy, the family Beijerinckiaceae within the Alphaproteobacteria represents an example of high metabolic diversity over a limited evolutionary distance (approximately 4% dissimilarity of 16S rRNA gene sequences). Members of this family include heterotrophs (Beijerinckia), facultative methylotrophs (Methylovirgula), facultative methanotrophs (Methylocapsa and Methylocella), and the USC-␣ clade of atmospheric methane oxidizers (11)(12)(13)(14)(15)(16). Most methylotrophic Beijerinckiaceae have in common that they possess genes for Mxa-and Xox-type MDHs, which are central to methanol oxidation.…”

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confidence: 99%

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Lanthanide-Dependent Methylotrophs of the Family Beijerinckiaceae : Physiological and Genomic Insights

Wegner

Gorniak

Riedel

et al. 2019

Appl Environ Microbiol

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Methylotrophic bacteria use methanol and related C1 compounds as carbon and energy sources. Methanol dehydrogenases are essential for methanol oxidation, while lanthanides are important cofactors of many pyrroloquinoline quinone-dependent methanol dehydrogenases and related alcohol dehydrogenases. We describe here the physiological and genomic characterization of newly isolated Beijerinckiaceae bacteria that rely on lanthanides for methanol oxidation. A broad physiological diversity was indicated by the ability to metabolize a wide range of multicarbon substrates, including various sugars, and organic acids, as well as diverse C1 substrates such as methylated amines and methylated sulfur compounds. Methanol oxidation was possible only in the presence of low-mass lanthanides (La, Ce, and Nd) at submicromolar concentrations (>100 nM). In a comparison with other Beijerinckiaceae, genomic and transcriptomic analyses revealed the usage of a glutathione- and tetrahydrofolate-dependent pathway for formaldehyde oxidation and channeling methyl groups into the serine cycle for carbon assimilation. Besides a single xoxF gene, we identified two additional genes for lanthanide-dependent alcohol dehydrogenases, including one coding for an ExaF-type alcohol dehydrogenase, which was so far not known in Beijerinckiaceae. Homologs for most of the gene products of the recently postulated gene cluster linked to lanthanide utilization and transport could be detected, but for now it remains unanswered how lanthanides are sensed and taken up by our strains. Studying physiological responses to lanthanides under nonmethylotrophic conditions in these isolates as well as other organisms is necessary to gain a more complete understanding of lanthanide-dependent metabolism as a whole. IMPORTANCE We supplemented knowledge of the broad metabolic diversity of the Beijerinckiaceae by characterizing new members of this family that rely on lanthanides for methanol oxidation and that possess additional lanthanide-dependent enzymes. Considering that lanthanides are critical resources for many modern applications and that recovering them is expensive and puts a heavy burden on the environment, lanthanide-dependent metabolism in microorganisms is an exploding field of research. Further research into how isolated Beijerinckiaceae and other microbes utilize lanthanides is needed to increase our understanding of lanthanide-dependent metabolism. The diversity and widespread occurrence of lanthanide-dependent enzymes make it likely that lanthanide utilization varies in different taxonomic groups and is dependent on the habitat of the microbes.

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Section: Resultsmentioning

confidence: 91%

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confidence: 99%

Lanthanide-Dependent Methylotrophs of the Family Beijerinckiaceae : Physiological and Genomic Insights

Wegner

Gorniak

Riedel

et al. 2019

Appl Environ Microbiol

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“…These organisms are known to endure under fluctuations in the environment, such as variable O 2 and CH 4 availability. Their stability is owed to several strategies, including dormancy (Eller, Krüger, & Frenzel, 2005; Krause, Lüke & Frenzel, 2012; Ho et al, 2013) and ability to use different carbon substrates (Dedysh, Knief, & Dunfield, 2005; Dedysh, Haup, & Dunfield, 2016). Such versatility could confer an advantage in the floodplain environment, which may present not only temporal, but also spatial variation in CH 4 availability (Moura et al, 2008).…”

Section: Discussionmentioning

confidence: 99%

Seasonal dynamics of methane cycling microbial communities in Amazonian floodplain sediments

Gontijo

Venturini

Yoshiura

et al. 2020

Preprint

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39The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional 40 hydrological and biogeochemical cycles and provide a significant contribution to the global 41 carbon balance. Unique geochemical factors may drive the microbial community composition 42 and, consequently, affect CH4 emissions across floodplain areas. Here we provide the first 43 report of the in situ seasonal dynamics of CH4 cycling microbial communities in Amazonian 44 floodplains. We asked how abiotic factors may affect both overall and CH4 cycling microbial 45 communities and further investigated their responses to seasonal changes. We collected 46 sediment samples during wet and dry seasons from three different types of floodplain forests, 47 along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-48 resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR 49 to quantify Archaea and Bacteria, as well as key functional genes indicative of the 50 methanogenic (methyl coenzyme-M reductase -mcrA) and methanotrophic (particulate51 methane monooxygenase -pmoA) metabolisms. Methanogens were found to be present in 52 high abundance in floodplain sediments and they seem to resist to dramatic seasonal 53 environmental changes. Methanotrophs known to use different pathways to oxidise CH4 were 54 3 detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic 55 diversity may be harboured in this highly variable environment. The floodplain environmental 56 variability, which is affected by the river origin, drives not only the sediment chemistry, but also 57 the composition of the microbial communities. The results presented may contribute to the 58 understanding of the current state of CH4 cycling in this region. 59 60 Quantitative PCR. 62 63 65 et al. , 2015). These ecosystems comprise diversified and dynamic landscapes, which are 66 exposed to seasonal flooding events by the expanding rivers, as a consequence of the periodic 67 excessive rainfalls. Floodplains seem to play a significant role in the regional and global C 68 72 significant process of CH4 transfer through trees (Pangala et al., 2017). Modelling studies have 73 predicted that Amazonian floodplains may contribute up to 7% of total global CH4 emissions 74 (Potter, Melack & Engle, 2014; Wilson et al., 2016). 75In anoxic environments, the CH4 is generated as the final product of the anaerobic 76 respiration by methanogenic archaea, which can use acetate, H2/CO2, formate, CO, or 77 methylated compounds as substrates (Bridgham, Cadillo-Quiroz, Keller & Zhuang, 2013). The 78 ability to use one or more substrates varies across the different methanogenic archaea taxa. 79 Hence, substrate availability, along with other factors (biotic and abiotic), affects the diversity 80 of these organisms in the environment (Barros et al., 2019).81 103 scales. For instance, the riverine origin is a very important factor, as some waters may carry 104 large amounts of inorganic suspensoids, s...

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“…This finding is consistent with studies on other acidic soils and species descriptions of acidophilic methylotrophic Beijerinckiaceae (Radajewski et al, 2000, 2002; Dedysh et al, 2001, 2006; Morris et al, 2002; Marín and Arahal, 2013 and references therein). The genera Chelatococcus and Camelimonas were excluded from all considerations on Beijerinckiaceae , since they are not capable of C 1 compound utilization (Dedysh et al, 2016). Beijerinckiaceae comprises strains with remarkably different metabolic capacities including chemoheterotrophy ( Beijerinckia ), facultative methylotrophy ( Beijerinckia, Methylorosula, Methylovirgula ), ‘restricted’ facultative methanotrophy ( Methylocella, Methylocapsa ), and obligate methanotrophy ( Methylocapsa, Methyloferula ) (Marín and Arahal, 2013 and references therein; Tamas et al, 2014; Dedysh et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Acidotolerant Bacteria and Fungi as a Sink of Methanol-Derived Carbon in a Deciduous Forest Soil

Morawe¹,

Hoeke²,

Wissenbach³

et al. 2017

Front. Microbiol.

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Methanol is an abundant atmospheric volatile organic compound that is released from both living and decaying plant material. In forest and other aerated soils, methanol can be consumed by methanol-utilizing microorganisms that constitute a known terrestrial sink. However, the environmental factors that drive the biodiversity of such methanol-utilizers have been hardly resolved. Soil-derived isolates of methanol-utilizers can also often assimilate multicarbon compounds as alternative substrates. Here, we conducted a comparative DNA stable isotope probing experiment under methylotrophic (only [13C1]-methanol was supplemented) and combined substrate conditions ([12C1]-methanol and alternative multi-carbon [13Cu]-substrates were simultaneously supplemented) to (i) identify methanol-utilizing microorganisms of a deciduous forest soil (European beech dominated temperate forest in Germany), (ii) assess their substrate range in the soil environment, and (iii) evaluate their trophic links to other soil microorganisms. The applied multi-carbon substrates represented typical intermediates of organic matter degradation, such as acetate, plant-derived sugars (xylose and glucose), and a lignin-derived aromatic compound (vanillic acid). An experimentally induced pH shift was associated with substantial changes of the diversity of active methanol-utilizers suggesting that soil pH was a niche-defining factor of these microorganisms. The main bacterial methanol-utilizers were members of the Beijerinckiaceae (Bacteria) that played a central role in a detected methanol-based food web. A clear preference for methanol or multi-carbon substrates as carbon source of different Beijerinckiaceae-affiliated phylotypes was observed suggesting a restricted substrate range of the methylotrophic representatives. Apart from Bacteria, we also identified the yeasts Cryptococcus and Trichosporon as methanol-derived carbon-utilizing fungi suggesting that further research is needed to exclude or prove methylotrophy of these fungi.

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

Cited by 37 publications

References 29 publications

Lanthanide-Dependent Methylotrophs of the Family Beijerinckiaceae : Physiological and Genomic Insights

Lanthanide-Dependent Methylotrophs of the Family Beijerinckiaceae : Physiological and Genomic Insights

Seasonal dynamics of methane cycling microbial communities in Amazonian floodplain sediments

Acidotolerant Bacteria and Fungi as a Sink of Methanol-Derived Carbon in a Deciduous Forest Soil

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