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

When using BacDive for research please cite our paper

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	09-12-2024 (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

[Ref.: #43532]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #43532]

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

[Ref.: #43532]

Oxygen tolerance

aerobe

[Ref.: #43532]

Ability of spore formation

[Ref.: #43532]

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

[Ref.: #43532]

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

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Dyella agri in external resources:
SILVA
BRENDA
PANGAEA
GBIF