Name: Dyella koreensis BB4
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17454

Type strain:

Species: Dyella koreensis

Strain Designation: BB4

Culture col. no.: CCUG 50883, DSM 17803, KCTC 12359, NBRC 100831, CIP 108881

Strain history: CIP <- 2005, KCTC <- ST Lee, KAIST: strain BB4

NCBI tax ID(s): 311235 (species)

SI-ID 214844

CCUG 50883, KCTC 12359, NBRC 100831, DSM 17803, CIP 108881

Special Collections

Section

Dyella koreensis BB4 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from rhizosphere soil of bamboo plants.

Gram-negative
rod-shaped
aerobe
16S sequence
Bacteria

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	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Rhodanobacteraceae*
	Genus	*Dyella*
	Species	**Dyella koreensis**
	Full Scientific Name (LPSN)	Dyella koreensis An et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31502]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #120476]	Gram stain	negative

[Ref.: #31502]	Cell length	1.8 µm

[Ref.: #31502]	Cell width	0.35 µm

[Ref.: #31502]	Cell shape	rod-shaped
[Ref.: #120476]	Cell shape	rod-shaped

[Ref.: #31502]	Motility	no
[Ref.: #120476]	Motility	yes

[Ref.: #31502]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7194]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7194]

Culture medium growth

[Ref.: #7194]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7194]

Culture medium composition

expand / minimize

[Ref.: #120476]

Culture medium

CIP Medium 566

[Ref.: #120476]

Culture medium growth

[Ref.: #120476]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #7194]		growth	28 °C
[Ref.: #31502]		growth	10-37 °C
[Ref.: #31502]		optimum	30 °C
[Ref.: #59040]		growth	30 °C
[Ref.: #67771]		growth	28 °C
[Ref.: #120476]		growth	10-25 °C
[Ref.: #120476]	no	growth	37 °C
[Ref.: #120476]	no	growth	41 °C

	pH	Kind of pH		pH
[Ref.: #31502]			optimum	7.15
[Ref.: #31502]			growth	6.8-7.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31502]	Oxygen tolerance	aerobe
[Ref.: #59040]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #120476]	Oxygen tolerance	obligate aerobe

[Ref.: #120476]

Ability of spore formation

	Salt	Tested relation		Salt conc.
[Ref.: #31502]	NaCl		growth	4	%
[Ref.: #120476]	NaCl		growth	0-4	%
[Ref.: #120476]	NaCl	no	growth	6	%
[Ref.: #120476]	NaCl	no	growth	8	%
[Ref.: #120476]	NaCl	no	growth	10	%

[Ref.: #31502]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31502]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #31502]	acetate ChEBI	+	carbon source
[Ref.: #120476]	citrate ChEBI	-	carbon source
[Ref.: #31502]	esculin ChEBI	+	hydrolysis
[Ref.: #120476]	esculin ChEBI	+	hydrolysis
[Ref.: #31502]	fucose ChEBI	+	carbon source
[Ref.: #31502]	glucose ChEBI	+	carbon source
[Ref.: #31502]	malate ChEBI	+	carbon source
[Ref.: #31502]	maltose ChEBI	+	carbon source
[Ref.: #31502]	mannose ChEBI	+	carbon source
[Ref.: #31502]	melibiose ChEBI	+	carbon source
[Ref.: #31502]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31502]	nitrate ChEBI	+	reduction
[Ref.: #120476]	nitrate ChEBI	+	reduction
[Ref.: #120476]	nitrate ChEBI	-	respiration
[Ref.: #120476]	nitrite ChEBI	-	reduction
[Ref.: #31502]	salicin ChEBI	+	carbon source
[Ref.: #31502]	sucrose ChEBI	+	carbon source
[Ref.: #31502]	urea ChEBI	+	carbon source
[Ref.: #31502]	valerate ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #120476]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #120476]	alcohol dehydrogenase	-	1.1.1.1
[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.: #120476]	amylase	-
[Ref.: #120476]	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.: #120476]	caseinase	+	3.4.21.50
[Ref.: #31502]	catalase	+	1.11.1.6
[Ref.: #120476]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31502]	cytochrome oxidase	+	1.9.3.1
[Ref.: #120476]	DNase	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #120476]	gelatinase	+
[Ref.: #120476]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #120476]	lipase	-
[Ref.: #68382]	lipase (C 14)	+		* from API zym
[Ref.: #120476]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120476]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120476]	oxidase	+
[Ref.: #120476]	protease	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #120476]	tryptophan deaminase	-
[Ref.: #120476]	tween esterase	+
[Ref.: #31502]	urease	+	3.5.1.5
[Ref.: #120476]	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.: #120476]	11526	-	+	+	+	+	+	+	-	+	-	+	+	-	+	-	+	+	-	-	-

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

[Ref.: #7194]	Sample type/isolated from	rhizosphere soil of bamboo plants
[Ref.: #7194]	Country	Republic of Korea
[Ref.: #7194]	Country ISO 3 Code	KOR
[Ref.: #7194]	Continent	Asia

[Ref.: #59040]	Sample type/isolated from	Soil around bamboo roots
[Ref.: #59040]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #59040]	Country	Republic of Korea
[Ref.: #59040]	Country ISO 3 Code	KOR
[Ref.: #59040]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #120476]	Sample type/isolated from	Environment, Soil sample around bamboo roots
[Ref.: #120476]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #120476]	Country	Republic of Korea
[Ref.: #120476]	Country ISO 3 Code	KOR
[Ref.: #120476]	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?

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

[Ref.: #7194]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120476]	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.: #7194]	Dyella koreensis strain BB4 16S ribosomal RNA gene, partial sequence	AY884571	1486	GenBank ENA	311235 tax ID
[Ref.: #20218]	Dyella koreensis gene for 16S rRNA, partial sequence, strain: NBRC 100831	AB681264	1470	GenBank ENA	311235 tax ID	*

[Ref.: #31502]

GC-content

63.8 mol%

Availability in culture collections External links

[Ref.: #7194]

Culture collection no.

CCUG 50883, DSM 17803, KCTC 12359, NBRC 100831, CIP 108881

[Ref.: #86450]

SI-ID 214844

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dyella marensis sp. nov., isolated from cliff soil.	Lee DW, Lee SD	Int J Syst Evol Microbiol	10.1099/ijs.0.000968-0	2009	*
Phylogeny	Dyella ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea.	Jung HM, Ten LN, Kim KH, An DS, Im WT, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.64514-0	2009	*
Phylogeny	Rhodanobacter spathiphylli sp. nov., a gammaproteobacterium isolated from the roots of Spathiphyllum plants grown in a compost-amended potting mix.	De Clercq D, Van Trappen S, Cleenwerck I, Ceustermans A, Swings J, Coosemans J, Ryckeboer J	Int J Syst Evol Microbiol	10.1099/ijs.0.64131-0	2006	*
Phylogeny	Dyella koreensis sp. nov., a beta-glucosidase-producing bacterium.	An DS, Im WT, Yang HC, Yang DC, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.63695-0	2005	*

References

#7194

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17803

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#31502

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 #27800 (see below)

#59040 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 50883
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68382

Automatically annotated from API zym .

#86450

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-ID214844.1 )

#120476 Collection of Institut Pasteur ; Curators of the CIP; CIP 108881

#27800

IJSEM 1625 2005 ( DOI 10.1099/ijs.0.63695-0 , PubMed 16014492 )

* These data were automatically processed and therefore are not curated

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