Name: Dyella agri DKC-1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 140754

Type strain:

Species: Dyella agri

Strain Designation: DKC-1

Culture col. no.: KEMB 9005-571, KACC 19176, JCM 31925

Strain history: J. Kim; Kyonggi Univ., South Korea; DKC-1.

NCBI tax ID(s): 1926869 (species)

Special Collections

Section

Dyella agri DKC-1 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from reclaimed grassland soil.

colony-forming
Gram-negative
motile
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 agri**
	Full Scientific Name (LPSN)	Dyella agri Chaudhary and Kim 2017

Information on morphological and physiological properties Morphology

[Ref.: #43532]	Gram stain	negative

[Ref.: #43532]	Cell length	1.5-2 µm

[Ref.: #43532]	Cell width	0.5-0.8 µm

[Ref.: #43532]	Cell shape	rod-shaped

[Ref.: #43532]	Motility	yes

[Ref.: #43532]	Flagellum arrangement	polar

[Ref.: #43532]	Colony size	1-2 mm
[Ref.: #43532]	Colony color	Yellow
[Ref.: #43532]	Colony shape	circular
[Ref.: #43532]	Incubation period	5 days
[Ref.: #43532]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

		Temperature
[Ref.: #43532]	growth	20-37 °C
[Ref.: #43532]	optimum	25-35 °C
[Ref.: #67770]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #43532]			optimum	6-8
[Ref.: #43532]			growth	4.5-9

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

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Ability of spore formation

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Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43532]		NaCl		growth	0-3	%(w/v)
[Ref.: #43532]		NaCl		optimum	0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43532]	3-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #43532]	3-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #43532]	4-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #43532]	4-nitrophenyl beta-D-galactopyranoside ChEBI	+	assimilation
[Ref.: #43532]	adipate ChEBI	-	assimilation
[Ref.: #43532]	carboxymethylcellulose ChEBI	+	hydrolysis
[Ref.: #43532]	casein	-	hydrolysis
[Ref.: #43532]	chitin ChEBI	-	hydrolysis
[Ref.: #43532]	D-glucose ChEBI	+	assimilation
[Ref.: #43532]	D-mannitol ChEBI	-	assimilation
[Ref.: #43532]	D-mannose ChEBI	-	assimilation
[Ref.: #43532]	D-ribose ChEBI	-	assimilation
[Ref.: #43532]	D-sorbitol ChEBI	-	assimilation
[Ref.: #43532]	decanoate ChEBI	-	assimilation
[Ref.: #43532]	dna ChEBI	-	hydrolysis
[Ref.: #43532]	esculin ChEBI	+/-	hydrolysis
[Ref.: #43532]	esculin ferric citrate	+/-	fermentation
[Ref.: #43532]	gelatin ChEBI	-	assimilation
[Ref.: #43532]	gelatin ChEBI	-	hydrolysis
[Ref.: #43532]	glucose ChEBI	-	fermentation
[Ref.: #43532]	glucose ChEBI	+/-	fermentation
[Ref.: #43532]	glycogen ChEBI	-	assimilation
[Ref.: #43532]	itaconate ChEBI	-	assimilation
[Ref.: #43532]	L-alanine ChEBI	-	assimilation
[Ref.: #43532]	L-arabinose ChEBI	-	assimilation
[Ref.: #43532]	L-arginine ChEBI	-	assimilation
[Ref.: #43532]	L-fucose ChEBI	+	assimilation
[Ref.: #43532]	L-histidine ChEBI	+	assimilation
[Ref.: #43532]	L-proline ChEBI	+/-	assimilation
[Ref.: #43532]	L-rhamnose ChEBI	-	assimilation
[Ref.: #43532]	L-serine ChEBI	+	assimilation
[Ref.: #43532]	L-tryptophan ChEBI	-	assimilation
[Ref.: #43532]	lactate ChEBI	-	assimilation
[Ref.: #43532]	malate ChEBI	-	assimilation
[Ref.: #43532]	maltose ChEBI	+	assimilation
[Ref.: #43532]	melibiose ChEBI	-	assimilation
[Ref.: #43532]	myo-inositol ChEBI	-	assimilation
[Ref.: #43532]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #43532]	nitrate ChEBI	-	reduction
[Ref.: #43532]	phenylacetate ChEBI	-	assimilation
[Ref.: #43532]	potassium 2-dehydro-D-gluconate	-	assimilation
[Ref.: #43532]	potassium 5-dehydro-D-gluconate	-	assimilation
[Ref.: #43532]	potassium gluconate ChEBI	-	assimilation
[Ref.: #43532]	propionate ChEBI	+	assimilation
[Ref.: #43532]	salicin ChEBI	-	assimilation
[Ref.: #43532]	sodium acetate ChEBI	+/-	assimilation
[Ref.: #43532]	sodium citrate ChEBI	-	assimilation
[Ref.: #43532]	sodium malonate ChEBI	-	assimilation
[Ref.: #43532]	starch ChEBI	-	hydrolysis
[Ref.: #43532]	suberic acid ChEBI	-	assimilation
[Ref.: #43532]	sucrose ChEBI	-	assimilation
[Ref.: #43532]	tween 40 ChEBI	-	hydrolysis
[Ref.: #43532]	tween 80 ChEBI	-	hydrolysis
[Ref.: #43532]	tyrosine ChEBI	+/-	hydrolysis
[Ref.: #43532]	urea ChEBI	-	assimilation
[Ref.: #43532]	valerate ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43532]	acetoin ChEBI	no
[Ref.: #43532]	hydrogen sulfide ChEBI	no
[Ref.: #43532]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #43532]		acetoin ChEBI	-
[Ref.: #43532]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #43532]	acid phosphatase	+	3.1.3.2
[Ref.: #43532]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43532]	alpha-chymotrypsin	+/-	3.4.21.1
[Ref.: #43532]	alpha-fucosidase	+	3.2.1.51
[Ref.: #43532]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43532]	alpha-glucosidase	+/-	3.2.1.20
[Ref.: #43532]	alpha-mannosidase	+	3.2.1.24
[Ref.: #43532]	beta-galactosidase	+	3.2.1.23
[Ref.: #43532]	beta-glucosidase	-	3.2.1.21
[Ref.: #43532]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43532]	catalase	+	1.11.1.6
[Ref.: #43532]	cystine arylamidase	+	3.4.11.3
[Ref.: #43532]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43532]	esterase (C 4)	-
[Ref.: #43532]	esterase Lipase (C 8)	+
[Ref.: #43532]	leucine arylamidase	+	3.4.11.1
[Ref.: #43532]	lipase (C 14)	-
[Ref.: #43532]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43532]	naphthol-AS-BI-phosphohydrolase	+/-
[Ref.: #43532]	trypsin	-	3.4.21.4
[Ref.: #43532]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43532]

Fatty acid	Percentage
C16:1ω6c / C16:1ω7c	45.5
C18:1ω7c / C18:1ω6c	27.2
C16:0	13.5
C10:0 3OH	2.8
C12:0 3OH	2.3
C14:0 3OH / C16:1 iso I	1.9
C14:0	1.1

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

[Ref.: #43532]	Sample type/isolated from	reclaimed grassland soil
[Ref.: #43532]	Geographic location (country and/or sea, region)	Hwaseong
[Ref.: #43532]	Country	Republic of Korea
[Ref.: #43532]	Country ISO 3 Code	KOR
[Ref.: #43532]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Reclaimed grassland soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Hwaseong
[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	#Grassland
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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.: #43532]	Dyella agri 16S ribosomal RNA gene, partial sequence	KY313412		GenBank ENA

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GC-content

63.1 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #43532]

Culture collection no.

KEMB 9005-571, KACC 19176, JCM 31925

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dyella agri sp. nov., isolated from reclaimed grassland soil.	Chaudhary DK, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002291	2017	*

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 )

#43532

Dhiraj Kumar Chaudhary, Jaisoo Kim: Dyella agri sp. nov., isolated from reclaimed grassland soil. IJSEM 67: 4246 - 4252 2017 ( DOI 10.1099/ijsem.0.002291 , PubMed 28920848 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
* These data were automatically processed and therefore are not curated

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