Name: Methylovirgula ligni BW863
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1673

Type strain:

Species: Methylovirgula ligni

Strain Designation: BW863

Culture col. no.: DSM 19998, NCIMB 14408

Strain history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; BW863 <- W. de Boer

NCBI tax ID(s): 569860 (species)

SI-ID 397492

DSM 19998

Section

Methylovirgula ligni BW863 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from beechwood blocks on acidic forest soil during decay by the white-rot fungus Hypholoma fasciculare.

Gram-negative
rod-shaped
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Beijerinckiaceae*
	Genus	*Methylovirgula*
	Species	**Methylovirgula ligni**
	Full Scientific Name (LPSN)	Methylovirgula ligni Vorob'ev et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #23152]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.964

[Ref.: #23152]	Cell length	1.2-2.5 µm

[Ref.: #23152]	Cell width	0.3-0.65 µm

[Ref.: #23152]	Cell shape	rod-shaped

[Ref.: #23152]	Motility	no

[Ref.: #23152]	Pigment production	no
[Ref.: #23152]	Pigment name	no pigments

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8284]

Culture medium

METHYLOVIRGULA LIGNI MEDIUM (DSMZ Medium 1219)

[Ref.: #8284]

Culture medium growth

[Ref.: #8284]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8284]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8284]	growth	25 °C
[Ref.: #23152]	growth	4-30 °C
[Ref.: #23152]	optimum	20-24 °C

[Ref.: #8284]	Temperature range	mesophilic
[Ref.: #23152]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #23152]			optimum	4.5-5.0
[Ref.: #23152]			growth	3.1-6.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.978

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23152]		NaCl	no	growth	>0.7	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23152]	ammonium ChEBI	+	nitrogen source
[Ref.: #23152]	ethanol ChEBI	+	carbon source
[Ref.: #23152]	malate ChEBI	+	carbon source
[Ref.: #23152]	methanol ChEBI	+	carbon source
[Ref.: #23152]	nitrate ChEBI	+	nitrogen source
[Ref.: #23152]	pyruvate ChEBI	+	carbon source
[Ref.: #23152]	yeast extract	+	nitrogen source

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	vitamin B12 metabolism	91.18	31 of 34
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	purine metabolism	68.09	64 of 94
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	lipid A biosynthesis	66.67	6 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	methanogenesis from CO2	66.67	8 of 12
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	methanofuran biosynthesis	60	3 of 5
[Ref.: #66794]	pyrimidine metabolism	57.78	26 of 45
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	cholesterol biosynthesis	54.55	6 of 11
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	oxidative phosphorylation	53.85	49 of 91
[Ref.: #66794]	glycolysis	52.94	9 of 17
[Ref.: #66794]	alanine metabolism	51.72	15 of 29
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	carotenoid biosynthesis	36.36	8 of 22
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #8284]	Sample type/isolated from	beechwood blocks on acidic forest soil during decay by the white-rot fungus Hypholoma fasciculare
[Ref.: #8284]	Host species	Hypholoma fasciculare
[Ref.: #8284]	Geographic location (country and/or sea, region)	Veluwe
[Ref.: #8284]	Country	Netherlands
[Ref.: #8284]	Country ISO 3 Code	NLD
[Ref.: #8284]	Continent	Europe

[Ref.: #23152]	Sample type/isolated from	from decaying beechwood blocks incubated on an acidic forest soil
* marker position based on {}

Isolation sources categories

#Host	#Fungi	-
#Host	#Plants	#Decomposing plant
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil
#Condition	#Acidic	-

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #8284]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #8284]	Methylovirgula ligni partial 16S rRNA gene, type strain BW863T	FM252034	1402	ENA	569860 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methylovirgula ligni BW863	GCA_004135935	complete	GenBank	569860 tax ID	*
[Ref.: #66792]	Methylovirgula ligni BW863	GCA_003387225	scaffold	GenBank	569860 tax ID	*
[Ref.: #66792]	Methylovirgula ligni strain BW863	569860.6	complete	PATRIC	569860 tax ID	*
[Ref.: #66792]	Methylovirgula ligni DSM 19998	2770939601	draft	JGI IMG/M	569860 tax ID	*

[Ref.: #23152]

GC-content

61.8-62.8 mol%

Thermal denaturation, fluorometry

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Methylovirgula ligni BW863 NCBI: GCA_004135935.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Methylovirgula ligni BW863 NCBI: GCA_004135935.1
[Ref.: #69480]	motile	yes	77.531	no
[Ref.: #69480]	flagellated	no	91.076	yes
[Ref.: #69480]	gram-positive	no	96.315	yes
[Ref.: #69480]	anaerobic	no	96.064	no
[Ref.: #69480]	aerobic	yes	85.904	no
[Ref.: #69480]	halophile	no	92.64	no
[Ref.: #69480]	spore-forming	no	92.709	no
[Ref.: #69480]	glucose-util	yes	64.08	no
[Ref.: #69480]	thermophile	no	95.635	yes
[Ref.: #69480]	glucose-ferment	no	92.641	no

Availability in culture collections External links

[Ref.: #8284]

Culture collection no.

DSM 19998, NCIMB 14408

[Ref.: #71320]

SI-ID 397492

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Methylovirgula ligni gen. nov., sp. nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF gene.	Vorob'ev AV, de Boer W, Folman LB, Bodelier PL, Doronina NV, Suzina NE, Trotsenko YA, Dedysh SN	Int J Syst Evol Microbiol	10.1099/ijs.0.010074-0	2009	*

References

#8284

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19998

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#23152

Alexey V. Vorob'ev, Wietse de Boer, Larissa B. Folman, Paul L. E. Bodelier, Nina V. Doronina, Natalia E. Suzina, Yuri A. Trotsenko, Svetlana N. Dedysh: Methylovirgula ligni gen. nov., sp. nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF gene. IJSEM 59: 2538 - 2545 2009 ( DOI 10.1099/ijs.0.010074-0 , PubMed 19622650 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#71320

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID397492.1 )

* These data were automatically processed and therefore are not curated

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