Name: Methylocella silvestris BL2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1658

Type strain:

Species: Methylocella silvestris

Strain Designation: BL2

Culture col. no.: DSM 15510, NCIMB 13906, CIP 108128

Strain history: CIP <- 2003, NCIMB <- Max Planck Inst., Marburg, Germany: strain BL2

NCBI tax ID(s): 199596 (species)

SI-ID 128001

DSM 15510, NCIMB 13906, CIP 108128, LMG 27833

Section

Methylocella silvestris BL2 is a psychrophilic, Gram-negative, rod-shaped bacterium that was isolated from acidic cambisol under a beech-dominated forest.

Gram-negative
rod-shaped
psychrophilic
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	*Methylocella*
	Species	**Methylocella silvestris**
	Full Scientific Name (LPSN)	Methylocella silvestris Dunfield et al. 2003

Information on morphological and physiological properties Morphology

[Ref.: #23149]	Gram stain	negative
[Ref.: #122610]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #23149]	Cell length	1.2-1.5 µm

[Ref.: #23149]	Cell width	0.6-0.8 µm

[Ref.: #23149]	Cell shape	rod-shaped
[Ref.: #122610]	Cell shape	rod-shaped

[Ref.: #23149]	Motility	no
[Ref.: #122610]	Motility	no
[Ref.: #69480]	Motility	yes Confidence in %91.765

[Ref.: #23149]	Pigment production	no
[Ref.: #23149]	Pigment name	no pigments

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5968]

Culture medium

METHYLOCELLA SILVERSTRIS MEDIUM (DSMZ Medium 1181)

[Ref.: #5968]

Culture medium growth

[Ref.: #5968]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5968]

Culture medium composition

expand / minimize

[Ref.: #36692]

Culture medium

MEDIUM 579 - for Methylocella silvestris

[Ref.: #36692]

Culture medium growth

[Ref.: #36692]

Culture medium composition

expand / minimize

[Ref.: #122610]

Culture medium

CIP Medium 579

[Ref.: #122610]

Culture medium growth

[Ref.: #122610]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #5968]		growth	20 °C
[Ref.: #23149]		growth	4-30 °C
[Ref.: #23149]		optimum	15-25 °C
[Ref.: #36692]		growth	25 °C
[Ref.: #122610]		growth	15-30 °C
[Ref.: #122610]	no	growth	5 °C
[Ref.: #122610]	no	growth	37 °C
[Ref.: #122610]	no	growth	41 °C

[Ref.: #5968]	Temperature range	psychrophilic
[Ref.: #36692]	Temperature range	mesophilic
[Ref.: #122610]	Temperature range	psychrophilic
[Ref.: #122610]	Temperature range	mesophilic
[Ref.: #122610]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #23149]			optimum	5.5
[Ref.: #23149]			growth	4.5-7.0

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 %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23149]		NaCl	no	growth	>0.8	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23149]	methane ChEBI	+	carbon source
[Ref.: #23149]	methanol ChEBI	+	carbon source
[Ref.: #23149]	methylamine ChEBI	+	carbon source
[Ref.: #122610]	nitrate ChEBI	-	reduction
[Ref.: #122610]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #122610]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #122610]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #122610]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #122610]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #122610]	gelatinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122610]	oxidase	+
[Ref.: #122610]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #122610]	tryptophan deaminase	-
[Ref.: #122610]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #122610]	10908	-	-	+	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

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

[Ref.: #5968]	Sample type/isolated from	acidic cambisol under a beech-dominated forest
[Ref.: #5968]	Geographic location (country and/or sea, region)	Marburg
[Ref.: #5968]	Country	Germany
[Ref.: #5968]	Country ISO 3 Code	DEU
[Ref.: #5968]	Continent	Europe

[Ref.: #122610]	Sample type/isolated from	Environment, Acid forest cambisol
[Ref.: #122610]	Geographic location (country and/or sea, region)	Marburg
[Ref.: #122610]	Country	Germany
[Ref.: #122610]	Country ISO 3 Code	DEU
[Ref.: #122610]	Continent	Europe

[Ref.: #23149]	Sampling date	December 1999
* marker position based on {}

Isolation sources categories

#Condition

#Acidic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ491847 (>99% sequence identity) for Methylocella silvestris from Microbeatlas

Aquatic Samples	513
Soil Samples	1894
Animal Samples	308
Plant Samples	122
Total Samples	2837

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

[Ref.: #5968]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122610]	Biosafety level	1	Risk group (French classification)

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.: #5968]	Methylocella silvestris partial 16S rRNA gene, strain BL2	AJ491847	1409	ENA	395965 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methylocella silvestris BL2	GCA_000021745	complete	GenBank	395965 tax ID	*
[Ref.: #66792]	Methylocella silvestris BL2	395965.5	complete	PATRIC	395965 tax ID	*
[Ref.: #66792]	Methylocella silvestris BL2, DSM 15510	643348565	complete	JGI IMG/M	395965 tax ID	*

[Ref.: #5968]	GC-content	60 mol%
[Ref.: #23149]	GC-content	60.0 mol%	high performance liquid chromatography (HPLC)

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: Methylocella silvestris BL2 PATRIC: 395965.5
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Methylocella silvestris BL2 BL2 NCBI: GCA_000021745.1
[Ref.: #69480]	motile	yes	58.064	yes
[Ref.: #69480]	flagellated	no	81.885	no
[Ref.: #69480]	gram-positive	no	97.755	no
[Ref.: #69480]	anaerobic	no	96.352	no
[Ref.: #69480]	aerobic	yes	87.207	no
[Ref.: #69480]	halophile	no	90.473	no
[Ref.: #69480]	spore-forming	no	94.686	no
[Ref.: #69480]	thermophile	no	98.173	yes
[Ref.: #69480]	glucose-util	yes	84.475	no
[Ref.: #69480]	glucose-ferment	no	91.648	no

Availability in culture collections External links

[Ref.: #5968]

Culture collection no.

DSM 15510, NCIMB 13906, CIP 108128

[Ref.: #71305]

SI-ID 128001

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Methylocella silvestris sp. nov., a novel methanotroph isolated from an acidic forest cambisol.	Dunfield PF, Khmelenina VN, Suzina NE, Trotsenko YA, Dedysh SN	Int J Syst Evol Microbiol	10.1099/ijs.0.02481-0	2003	*

References

#5968

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15510

#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 )

#23149

Peter F. Dunfield, Valentina N. Khmelenina, Natalia E. Suzina, Yuri A. Trotsenko, Svetlana N. Dedysh: Methylocella silvestris sp. nov., a novel methanotroph isolated from an acidic forest cambisol. IJSEM 53: 1231 - 1239 2003 ( DOI 10.1099/ijs.0.02481-0 , PubMed 13130000 )

#36692 ; Curators of the CIP;

#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) .

#68382

Automatically annotated from API zym .

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#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 )

#71305

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-ID128001.1 )

#122610 Collection of Institut Pasteur ; Curators of the CIP; CIP 108128
* These data were automatically processed and therefore are not curated

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Methylocella silvestris BL2

Methylocella silvestris BL2 BL2

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