Name: Motilibacter rhizosphaerae RS-16
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 24803

Type strain:

Species: Motilibacter rhizosphaerae

Strain Designation: RS-16

Culture col. no.: DSM 45622, KACC 16209, JCM 32087

Strain history: KACC 16209 <-- S. D. Lee; Jeju Natl. Univ., South Korea; RS-16.

NCBI tax ID(s): 598652 (species)

SI-ID 400016

DSM 45622

Special Collections

Section

Motilibacter rhizosphaerae RS-16 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil of the rhizosphere of Peucedanum japonicum Thunb..

Gram-positive
rod-shaped
aerobe
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Motilibacterales*
	Family	*Motilibacteraceae*
	Genus	*Motilibacter*
	Species	**Motilibacter rhizosphaerae**
	Full Scientific Name (LPSN)	Motilibacter rhizosphaerae Lee 2013

Information on morphological and physiological properties Morphology

[Ref.: #31110]	Gram stain	positive

[Ref.: #31110]	Cell length	1.45 µm

[Ref.: #31110]	Cell width	0.79 µm

[Ref.: #31110]	Cell shape	rod-shaped

[Ref.: #31110]	Motility	no

[Ref.: #31110]

Pigment production

yes

Multimedia content

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Caption:

Medium 553 28°C

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

ISP2 MEDIUM (DSMZ Medium 987)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

GPHF-MEDIUM (DSMZ Medium 553)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #21229]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21229]	growth	28 °C
[Ref.: #31110]	growth	20-37 °C
[Ref.: #31110]	optimum	37 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #31110]			growth	6.0-7.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31110]

Oxygen tolerance

aerobe

[Ref.: #31110]

Ability of spore formation

[Ref.: #31110]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-9(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31110]	dextrin ChEBI	+	carbon source
[Ref.: #31110]	esculin ChEBI	+	hydrolysis
[Ref.: #31110]	maltose ChEBI	+	carbon source
[Ref.: #31110]	melibiose ChEBI	+	carbon source
[Ref.: #31110]	raffinose ChEBI	+	carbon source
[Ref.: #31110]	ribitol ChEBI	+	carbon source
[Ref.: #31110]	xylitol ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #31110]	acid phosphatase	+	3.1.3.2
[Ref.: #31110]	alkaline phosphatase	+	3.1.3.1
[Ref.: #31110]	catalase	+	1.11.1.6

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	flavin biosynthesis	93.33	14 of 15
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	dTDPLrhamnose biosynthesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	pyrimidine metabolism	80	36 of 45
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	degradation of sugar acids	68	17 of 25
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	oxidative phosphorylation	59.34	54 of 91
[Ref.: #66794]	carotenoid biosynthesis	59.09	13 of 22
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	lipid metabolism	51.61	16 of 31
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	alginate biosynthesis	50	2 of 4
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	41.18	7 of 17
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
		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.: #21229]	Sample type/isolated from	soil of the rhizosphere of Peucedanum japonicum Thunb.
[Ref.: #21229]	Host species	Peucedanum japonicum
[Ref.: #21229]	Geographic location (country and/or sea, region)	Jeju, Mara Island
[Ref.: #21229]	Country	Republic of Korea
[Ref.: #21229]	Country ISO 3 Code	KOR
[Ref.: #21229]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Rhizosphere soil of a wild plant (Peucedanum japonicum Thunb.) on Mara Island in Jeju
[Ref.: #67770]	Host species	Peucedanum japonicum
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FM998018 (>99% sequence identity) for Motilibacter rhizosphaerae subclade from Microbeatlas

Aquatic Samples	9
Soil Samples	131
Animal Samples	9
Plant Samples	4
Total Samples	153

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

[Ref.: #21229]

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.: #21229]	Motilibacter rhizosphaerae strain RS-16 16S ribosomal RNA gene, partial sequence	FM998018	1423	GenBank ENA	598652 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Motilibacter rhizosphaerae DSM 45622	GCA_004216915	scaffold	GenBank ENA	598652 tax ID
[Ref.: #66792]	Motilibacter rhizosphaerae strain DSM 45622	598652.3	wgs	PATRIC	598652 tax ID	*
[Ref.: #66792]	Motilibacter rhizosphaerae DSM 45622	2799112218	draft	JGI IMG/M	598652 tax ID	*

[Ref.: #21229]	GC-content	73.1 mol%
[Ref.: #67770]	GC-content	73.1 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Motilibacter rhizosphaerae DSM 45622 NCBI: GCA_004216915.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	82	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Motilibacter rhizosphaerae strain DSM 45622 PATRIC: 598652.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	88.791	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	93.979	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	52.138	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	77.729	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.318	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	61.75	no

Availability in culture collections External links

[Ref.: #21229]

Culture collection no.

DSM 45622, KACC 16209, JCM 32087

[Ref.: #88625]

SI-ID 400016

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Proposal of Motilibacteraceae fam. nov., with the description of Motilibacter rhizosphaerae sp. nov.	Lee SD	Int J Syst Evol Microbiol	10.1099/ijs.0.052357-0	2013	*

References

#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 )

#21229

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45622

#31110

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 #27439 (see below)

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

#88625

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-ID400016.1 )

#27439

IJSEM 3818 2013 ( DOI 10.1099/ijs.0.052357-0 , PubMed 23667142 )

* These data were automatically processed and therefore are not curated

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Motilibacter rhizosphaerae DSM 45622

Motilibacter rhizosphaerae strain DSM 45622

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