Name: Devosia geojensis BD-c194
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 6169

Type strain:

Species: Devosia geojensis

Strain Designation: BD-c194

Culture col. no.: DSM 19414, KCTC 22082

Strain history: <- CO Jeon, Gyungsang Univ.

NCBI tax ID(s): 443610 (species)

SI-ID 405479

DSM 19414

Special Collections

Section

Devosia geojensis BD-c194 is an aerobe, Gram-negative, motile bacterium that was isolated from diesel-contaminated soil.

Gram-negative
motile
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Devosiaceae*
	Genus	*Devosia*
	Species	**Devosia geojensis**
	Full Scientific Name (LPSN)	Devosia geojensis Ryu et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32428]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %96.833

[Ref.: #32428]	Cell length	1.5 µm

[Ref.: #32428]	Cell width	0.65 µm

[Ref.: #32428]	Cell shape	rod-shaped

[Ref.: #32428]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8094]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #8094]

Culture medium growth

[Ref.: #8094]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8094]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8094]	growth	30 °C
[Ref.: #32428]	growth	30-35 °C
[Ref.: #32428]	optimum	32.5 °C
[Ref.: #67771]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #32428]			optimum	8.25
[Ref.: #32428]			growth	7.5-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32428]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #32428]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %95

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32428]	esculin ChEBI	+	hydrolysis
[Ref.: #32428]	glucose ChEBI	+	carbon source
[Ref.: #32428]	maltose ChEBI	+	carbon source
[Ref.: #32428]	mannitol ChEBI	+	carbon source
[Ref.: #32428]	mannose ChEBI	+	carbon source
[Ref.: #32428]	N-acetylglucosamine ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #32428]	acid phosphatase	+	3.1.3.2
[Ref.: #32428]	alkaline phosphatase	+	3.1.3.1
[Ref.: #32428]	catalase	+	1.11.1.6
[Ref.: #32428]	cytochrome oxidase	+	1.9.3.1
[Ref.: #32428]	urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	allantoin degradation	100	9 of 9
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	lactate fermentation	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	gallate degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	degradation of sugar acids	92	23 of 25
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	degradation of hexoses	88.89	16 of 18
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	pyrimidine metabolism	86.67	39 of 45
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	degradation of pentoses	82.14	23 of 28
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	75.53	71 of 94
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	peptidoglycan biosynthesis	66.67	10 of 15
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	oxidative phosphorylation	58.24	53 of 91
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	vitamin B1 metabolism	53.85	7 of 13
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
		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.: #8094]	Sample type/isolated from	diesel-contaminated soil
[Ref.: #8094]	Geographic location (country and/or sea, region)	Geoje
[Ref.: #8094]	Country	Republic of Korea
[Ref.: #8094]	Country ISO 3 Code	KOR
[Ref.: #8094]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From contaminated soil(Diesel)
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	#Oil (Fuel)
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF575560 (>99% sequence identity) for Devosia geojensis from Microbeatlas

Aquatic Samples	771
Soil Samples	791
Animal Samples	256
Plant Samples	100
Total Samples	1918

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

[Ref.: #8094]

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.: #8094]	Devosia geojensis strain BD-c194 16S ribosomal RNA gene, partial sequence	EF575560	1449	GenBank ENA	443610 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Devosia geojensis BD-c194	GCA_000969415	contig	GenBank ENA	443610 tax ID	*
[Ref.: #66792]	Devosia geojensis strain BD-c194	443610.3	wgs	PATRIC	443610 tax ID	*
[Ref.: #66792]	Devosia geojensis BD-c194	2636415796	draft	JGI IMG/M	443610 tax ID	*

[Ref.: #8094]	GC-content	60.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #32428]	GC-content	60.8 mol%
[Ref.: #67771]	GC-content	60.83 mol%

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: Devosia geojensis strain BD-c194 PATRIC: 443610.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	95	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Devosia geojensis strain BD-c194 PATRIC: 443610.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	96.833	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.408	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.359	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	84.62	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.505	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	60.767	no

Availability in culture collections External links

[Ref.: #8094]

Culture collection no.

DSM 19414, KCTC 22082

[Ref.: #75653]

SI-ID 405479

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Devosia nitraria sp. nov., a novel species isolated from the roots of Nitraria sibirica in China.	Xu L, Zhang Y, Read N, Liu S, Friman VP	Antonie Van Leeuwenhoek	10.1007/s10482-017-0901-z	2017	*
Phylogeny	Devosia honganensis sp. nov., isolated from the soil of a chemical factory.	Zhang L, Song M, Chen XL, Xu RJ, Chen K, Li SP, Xia ZY, Jiang JD	Antonie Van Leeuwenhoek	10.1007/s10482-015-0582-4	2015	*
Phylogeny	Devosia pacifica sp. nov., isolated from deep-sea sediment.	Jia YY, Sun C, Pan J, Zhang WY, Zhang XQ, Huo YY, Zhu XF, Wu M	Int J Syst Evol Microbiol	10.1099/ijs.0.059626-0	2014	*
Phylogeny	Devosia albogilva sp. nov. and Devosia crocina sp. nov., isolated from a hexachlorocyclohexane dump site.	Verma M, Kumar M, Dadhwal M, Kaur J, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.005447-0	2009	*
Phylogeny	Devosia geojensis sp. nov., isolated from diesel-contaminated soil in Korea.	Ryu SH, Chung BS, Le NT, Jang HH, Yun PY, Park W, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.65481-0	2008	*

References

#8094

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19414

#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 )

#32428

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 #28651 (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 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#75653

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-ID405479.1 )

#28651

IJSEM 633 2008 ( DOI 10.1099/ijs.0.65481-0 , PubMed 18319469 )

* These data were automatically processed and therefore are not curated

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Devosia geojensis strain BD-c194

Devosia geojensis strain BD-c194

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