Archive BacDiveID:10.13145/bacdive17457.20230509.8.1

Strain identifier

BacDive ID: 17457

Type strain:

Species: Dyella soli

Strain Designation: JS12-10

Strain history: S.-W. Kwon JS12-10.

NCBI tax ID(s): 522319 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 16737

BacDive-ID: 17457

DSM-Number: 23154

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Dyella soli JS12-10 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from forest soil.

NCBI tax id

NCBI tax id: 522319
Matching level: species

strain history

@ref	history
16737	<- KACC <- H.-Y. Weon, Rural Development Administration (RDA), Suwon, Republic of Korea; JS12-10
67770	S.-W. Kwon JS12-10.

doi: 10.13145/bacdive17457.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Lysobacterales
family: Rhodanobacteraceae
genus: Dyella
species: Dyella soli
full scientific name: Dyella soli Weon et al. 2009

@ref: 16737

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Rhodanobacteraceae

genus: Dyella

species: Dyella soli

full scientific name: Dyella soli Weon et al. 2009

strain designation: JS12-10

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
29047	negative	2.95 µm	0.45 µm	rod-shaped	yes
69480					yes	94.283
69480	negative					99.99

pigmentation

@ref: 29047
production: yes

Culture and growth conditions

culture medium

@ref: 16737
name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)
growth: yes
link: https://mediadive.dsmz.de/medium/830c
composition: Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
16737	positive	growth	28	mesophilic
29047	positive	growth	10-35
29047	positive	optimum	29	mesophilic
67770	positive	growth	30	mesophilic

culture pH

@ref	ability	type	pH	PH range
29047	positive	growth	04-08	acidophile
29047	positive	optimum	6.5

Physiology and metabolism

oxygen tolerance

@ref: 29047
oxygen tolerance: aerobe

spore formation

@ref	spore formation	confidence
29047	no
69481	no	100
69480	no	99.978

halophily

@ref	salt	growth	tested relation	concentration
29047	NaCl	positive	growth	0-2 %
29047	NaCl	positive	optimum	0.5 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
29047	17306	maltose	+	carbon source
29047	53426	tween 80	+	carbon source
29047	17632	nitrate	+	reduction

enzymes

@ref: 29047
value: acid phosphatase
activity: +
ec: 3.1.3.2

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
16737	forest soil	Jeju island	Republic of Korea	KOR	Asia
67770	Forest soil from Jeju Island		Republic of Korea	KOR	Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

Safety information

risk assessment

@ref: 16737
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 16737
description: Dyella soli strain JS12-10 16S ribosomal RNA gene, partial sequence
accession: EU604272
length: 1420
database: ena
NCBI tax ID: 522319

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Dyella soli strain KACC 12747	522319.3	wgs	patric	522319
67770	Dyella soli KACC 12747	GCA_004336905	contig	ncbi	522319

GC content

@ref	GC-content	method
16737	67.0	high performance liquid chromatography (HPLC)
29047	67
67770	67	high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
gram-positive	no	98.5	yes
anaerobic	no	99.05	no
halophile	no	95.033	yes
spore-forming	no	94.931	yes
glucose-util	yes	88.621	no
aerobic	yes	93.578	yes
thermophile	no	99.624	no
motile	yes	86.278	no
flagellated	no	72.924	no
glucose-ferment	no	91.464	no

External links

@ref: 16737

culture collection no.: DSM 23154, JCM 15423, KACC 12747

straininfo link

@ref: 86453
straininfo: 402655

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	19542132	Dyella soli sp. nov. and Dyella terrae sp. nov., isolated from soil.	Weon HY, Anandham R, Kim BY, Hong SB, Jeon YA, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.004838-0	2009	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Species Specificity, Xanthomonadaceae/classification/genetics/isolation & purification/physiology	Genetics
Phylogeny	21296929	Rhodanobacter panaciterrae sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field.	Wang L, An DS, Kim SG, Jin FX, Lee ST, Im WT	Int J Syst Evol Microbiol	10.1099/ijs.0.025718-0	2011	DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Ginsenosides/metabolism, Molecular Sequence Data, Panax/growth & development/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Xanthomonadaceae/classification/genetics/isolation & purification/metabolism	Metabolism
Phylogeny	23435246	Dyella jiangningensis sp. nov., a gamma-proteobacterium isolated from the surface of potassium-bearing rock.	Zhao F, Guo XQ, Wang P, He LY, Huang Z, Sheng XF	Int J Syst Evol Microbiol	10.1099/ijs.0.048470-0	2013	Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Potassium, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Ubiquinone, Xanthomonadaceae/classification/genetics/isolation & purification	Genetics
Phylogeny	23667147	Dyella kyungheensis sp. nov., isolated from soil of a cornus fruit field.	Son HM, Yang JE, Yi EJ, Park Y, Won KH, Kim JH, Han CK, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.051185-0	2013	Bacterial Typing Techniques, Base Composition, Cornus, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil Microbiology, Xanthomonadaceae/classification/genetics/isolation & purification	Genetics
Phylogeny	30489237	Dyella tabacisoli sp. nov., a bacterium isolated from an arable soil sample of Nicotiana tabacum L.	Li QQ, Chen X, Zhou XK, Dong LM, Xiao M, Fang BZ, Li WJ, Duan YQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003138	2019	Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Tobacco/microbiology, Ubiquinone/chemistry, Xanthomonadaceae/classification/isolation & purification	Transcriptome
Phylogeny	31454308	Dyella amyloliquefaciens sp. nov., isolated from forest soil.	Fu JC, Gao ZH, Wu TT, Chen MH, Qiu LH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003660	2019	Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Ubiquinone/chemistry, Xanthomonadaceae/*classification/isolation & purification	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
16737	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23154)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-23154
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
29047	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	25477	28776041
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
86453	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID402655.1	StrainInfo: A central database for resolving microbial strain identifiers