Name: Methylorubrum extorquens ID 585-99
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7147

Type strain:

Species: Methylorubrum extorquens

Strain Designation: ID 585-99, isolate F

Culture col. no.: DSM 13060

Strain history: <- A. M. Pirttilä, Dept. of Biology/Botany and Dept. of Biochemistry, University of Oulu, Finland; isolate F

NCBI tax ID(s): 882800 (strain), 408 (species)

SI-ID 87937

DSM 13060

Other strains from Methylorubrum extorquens

Section

Methylorubrum extorquens ID 585-99 is a mesophilic, motile bacterium that was isolated from pine tissue cultures from meristems of trees.

motile
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	*Methylobacteriaceae*
	Genus	*Methylorubrum*
	Species	**Methylorubrum extorquens**
	Full Scientific Name (LPSN)	Methylorubrum extorquens (Urakami and Komagata 1984 ex Bassalik 1913) Green and Ardley 2018

	Synonym	Protomonas extorquens
	Synonym	Methylobacterium extorquens

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #69480]	Motility	yes Confidence in %92.155

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4891]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #4891]

Culture medium growth

[Ref.: #4891]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4891]

Culture medium composition

expand / minimize

[Ref.: #4891]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #4891]

Culture medium growth

[Ref.: #4891]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4891]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4891]			growth	25 °C

[Ref.: #4891]

Temperature range

mesophilic

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 %100

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

[Ref.: #4891]	Sample type/isolated from	pine (Pinus sylvestris) tissue cultures from meristems of trees
[Ref.: #4891]	Host species	Pinus sylvestris
[Ref.: #4891]	Geographic location (country and/or sea, region)	northern part
[Ref.: #4891]	Country	Finland
[Ref.: #4891]	Country ISO 3 Code	FIN
[Ref.: #4891]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Stem (Branch)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF267912 (>99% sequence identity) for Methylorubrum from Microbeatlas

Aquatic Samples	23711
Soil Samples	23280
Animal Samples	47578
Plant Samples	16159
Total Samples	110728

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

[Ref.: #4891]

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.: #4891]	Methylobacterium extorquens 16S ribosomal RNA gene, partial sequence	AF267912	1448	ENA	882800 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methylorubrum extorquens DSM 13060	GCA_000243435	contig	GenBank	882800 tax ID	*
[Ref.: #66792]	Methylobacterium extorquens DSM 13060	882800.3	wgs	PATRIC	882800 tax ID	*
[Ref.: #66792]	Methylorubrum extorquens DSM 13060	2507262015	draft	JGI IMG/M	882800 tax ID	*

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: Methylobacterium extorquens DSM 13060 PATRIC: 882800.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Methylobacterium extorquens DSM 13060 PATRIC: 882800.3
[Ref.: #69480]	motile	yes	89.087	no
[Ref.: #69480]	flagellated	no	70.122	no
[Ref.: #69480]	gram-positive	no	97.646	no
[Ref.: #69480]	anaerobic	no	96.78	no
[Ref.: #69480]	halophile	no	92.186	no
[Ref.: #69480]	spore-forming	no	92.233	no
[Ref.: #69480]	thermophile	no	99.321	no
[Ref.: #69480]	glucose-util	yes	87.164	no
[Ref.: #69480]	aerobic	yes	84.115	no
[Ref.: #69480]	glucose-ferment	no	87.912	no

Availability in culture collections External links

[Ref.: #4891]

Culture collection no.

DSM 13060

[Ref.: #76601]

SI-ID 87937

Literature:

Topic	Title	Authors	Journal	DOI	Year
Stress	The meristem-associated endosymbiont Methylorubrum extorquens DSM13060 reprograms development and stress responses of pine seedlings.	Koskimaki JJ, Pohjanen J, Kvist J, Fester T, Hartig C, Podolich O, Fluch S, Edesi J, Haggman H, Pirttila AM	Tree Physiol	10.1093/treephys/tpab102	2022	*
Genetics	The intracellular Scots pine shoot symbiont Methylobacterium extorquens DSM13060 aggregates around the host nucleus and encodes eukaryote-like proteins.	Koskimaki JJ, Pirttila AM, Ihantola EL, Halonen O, Frank AC	mBio	10.1128/mBio.00039-15	2015	*
Metabolism	Interaction with ectomycorrhizal fungi and endophytic Methylobacterium affects nutrient uptake and growth of pine seedlings in vitro.	Pohjanen J, Koskimaki JJ, Sutela S, Ardanov P, Suorsa M, Niemi K, Sarjala T, Haggman H, Pirttila AM	Tree Physiol	10.1093/treephys/tpu062	2014	*

References

#4891

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13060

#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 )

#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) .

#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 )

#76601

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-ID87937.1 )

* These data were automatically processed and therefore are not curated

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Methylobacterium extorquens DSM 13060

Methylobacterium extorquens DSM 13060

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