Methylobacterium marchantiae (DSM 21328, CCUG 56108, JT1)

Name: Methylobacterium marchantiae (DSM 21328, CCUG 56108, JT1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7193

Type strain

Strain Designation JT1

Culture col. no. DSM 21328 CCUG 56108 JT1

NCBI tax ID(s) 600331

Special Collections DSMZ CCUG Literature strains

History <- P. Kämpfer, Univ. Giessen, Germany; JT1 <- S. Schauer

Links

Methylobacterium marchantiae JT1 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from thallus of the liverwort Marchantia polymorpha L..

Gram-negative motile rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 404897

DSM 21328,CCUG 56108

@ref 20215

Last LPSN update 2026-02-09 11:19:24

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Methylobacteriaceae

Genus Methylobacterium

Species Methylobacterium marchantiae

Full scientific name Methylobacterium marchantiae Schauer et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
29827	negative	2.9 µm	1.15 µm	rod-shaped
125438	negative					96.833

Pigmentation

29827

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15615	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15615	positive	growth	28	mesophilic
29827	positive	growth	4.0-32
29827	positive	optimum	27.5	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
29827	positive	optimum	7.2
29827	positive	growth	6.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

29827

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		93.8

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29827	NaCl	positive	growth	0.0-2.0 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29827	30089 ChEBI	acetate	+	carbon source
29827	35391 ChEBI	aspartate	+	carbon source
29827	16947 ChEBI	citrate	+	carbon source
29827	16236 ChEBI	ethanol	+	carbon source
29827	15740 ChEBI	formate	+	carbon source
29827	28757 ChEBI	fructose	+	carbon source
29827	29987 ChEBI	glutamate	+	carbon source
29827	17754 ChEBI	glycerol	+	carbon source
29827	30031 ChEBI	succinate	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29827	catalase	+	1.11.1.6
29827	cytochrome oxidase	+	1.9.3.1
29827	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Plants

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Sampling date
15615	thallus of the liverwort Marchantia polymorpha L.	Marchantia polymorpha	Bergpark Wilhelmshöhe near Kassel, about 500 m above sea level, 51° 19'N 9° 24' E	Germany	DEU	Europe	51.3167	9.4167 51.3167/9.4167
60862	Phyllospere (thallus) (Marchantia polymorpha)		Kassel,Bergpark Wilhelmshöhe	Germany	DEU	Europe			2003-10-01

Taxonmaps

69479

Global distribution of 16S sequence FJ157976 (>99% sequence identity) for Methylobacterium bullatum from Microbeatlas

Aquatic Samples	3552
Soil Samples	5760
Animal Samples	8689
Plant Samples	6346
Total Samples	24347

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15615	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM4267982v1 assembly for Methylobacterium marchantiae CCUG 56108	scaffold	GCA_042679825			600331	57.71
66792	ASM2217940v1 assembly for Methylobacterium marchantiae DSM 21328	contig	GCA_022179405	600331.3	8111008557	600331	38.24

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15615	Methylobacterium marchantiae strain JT1 collection-date 2003 from Germany 16S ribosomal RNA gene, partial sequence	FJ157976	1421		600331

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methylobacterium marchantiae DSM 21328
NCBI: GCA_022179405

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.80	no
125439	motility	BacteriaNetⓘ	yes	53.40	no
125439	gram_stain	BacteriaNetⓘ	negative	89.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	83.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methylobacterium marchantiae DSM 21328
NCBI: GCA_022179405.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.83	yes
125438	anaerobic	anaerobicⓘ	no	93.93	yes
125438	aerobic	aerobicⓘ	yes	87.55	yes
125438	spore-forming	spore-formingⓘ	no	89.04	no
125438	thermophilic	thermophileⓘ	no	96.72	yes
125438	flagellated	motile2+ⓘ	yes	71.61	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment.	Kolb S, Stacheter A.	Front Microbiol	10.3389/fmicb.2013.00268	2013
	Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae.	Stepkowski T, Banasiewicz J, Granada CE, Andrews M, Passaglia LMP.	Genes (Basel)	10.3390/genes9030163	2018
Phylogeny	Methylobacterium marchantiae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the thallus of a liverwort.	Schauer S, Kampfer P, Wellner S, Sproer C, Kutschera U	Int J Syst Evol Microbiol	10.1099/ijs.0.021915-0	2010

References

#15615	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21328
#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 )
#26203	IJSEM 870 2011 ( DOI 10.1099/ijs.0.021915-0 , PubMed 20495043 )
#29827	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26203
#60862	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 56108
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Methylobacterium marchantiae (DSM 21328, CCUG 56108, JT1)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042679825

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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