Archive BacDiveID:10.13145/bacdive17661.20230509.8.1

Strain identifier

BacDive ID: 17661

Type strain:

Species: Nevskia soli

Strain Designation: GR15-1

Strain history: <- S.-W. Kwon, KACC, South Korea

NCBI tax ID(s): 1122604 (strain), 418856 (species)

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

General

@ref: 8139

BacDive-ID: 17661

DSM-Number: 19509

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

description: Nevskia soli GR15-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

NCBI tax id	Matching level
418856	species
1122604	strain

strain history

@ref: 8139
history: <- S.-W. Kwon, KACC, South Korea

doi: 10.13145/bacdive17661.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Nevskiales
family: Nevskiaceae
genus: Nevskia
species: Nevskia soli
full scientific name: Nevskia soli Weon et al. 2008

@ref: 8139

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Nevskiaceae

genus: Nevskia

species: Nevskia soli

full scientific name: Nevskia soli Weon et al. 2008

strain designation: GR15-1

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
32117	negative	1.75 µm	0.5 µm	rod-shaped	yes
69480					yes	92.822
69480	negative					99.999

Culture and growth conditions

culture medium

@ref: 8139
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
8139	positive	growth	28	mesophilic
32117	positive	growth	15-30
32117	positive	optimum	26.5	mesophilic

culture pH

@ref	ability	type	pH	PH range
32117	positive	growth	04-07	acidophile
32117	positive	optimum	6.5

Physiology and metabolism

oxygen tolerance

@ref: 32117
oxygen tolerance: aerobe

spore formation

@ref	spore formation	confidence
32117	no
69481	no	98
69480	no	99.989

halophily

@ref: 32117
salt: NaCl
growth: positive
tested relation: growth
concentration: <2 %

metabolite utilization

@ref: 32117
Chebi-ID: 28087
metabolite: glycogen
utilization activity: +
kind of utilization tested: carbon source

enzymes

@ref	value	activity	ec
32117	catalase	+	1.11.1.6
32117	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

isolation

@ref: 8139
sample type: soil
geographic location: Jeju Island
country: Republic of Korea
origin.country: KOR
continent: Asia

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Soil

taxonmaps

@ref: 69479
File name: preview.99_6593.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_146;96_3049;97_3828;98_4862;99_6593&stattab=map
Last taxonomy: Nevskia soli
16S sequence: EF178286
Sequence Identity:
Total samples: 2793
soil counts: 1877
aquatic counts: 338
animal counts: 333
plant counts: 245

Safety information

risk assessment

@ref: 8139
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 8139
description: Nevskia soli strain GR15-1 16S ribosomal RNA gene, partial sequence
accession: EF178286
length: 1462
database: ena
NCBI tax ID: 1122604

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Nevskia soli DSM 19509	GCA_000711955	scaffold	ncbi	1122604
66792	Nevskia soli DSM 19509	1122604.3	wgs	patric	1122604
66792	Nevskia soli DSM 19509	2565956524	draft	img	1122604

GC content

@ref: 32117
GC-content: 63.9

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	98	no
motile	yes	82.529	no
flagellated	no	72.37	no
gram-positive	no	98.625	no
anaerobic	no	98.971	yes
halophile	no	95.238	no
spore-forming	no	94.014	yes
thermophile	no	99.337	no
glucose-util	yes	74.851	no
aerobic	yes	90.579	no
glucose-ferment	no	92.324	no

External links

@ref: 8139

culture collection no.: DSM 19509, KACC 11703

straininfo link

@ref: 86652
straininfo: 406076

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	18319458	Nevskia soli sp. nov., isolated from soil cultivated with Korean ginseng.	Weon HY, Kim BY, Son JA, Song MH, Kwon SW, Go SJ, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.64994-0	2008	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Panax/growth & development, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Species Specificity, Xanthomonadaceae/*classification/genetics/isolation & purification/physiology	Genetics
Phylogeny	20584818	Nevskia terrae sp. nov., isolated from soil.	Kim SJ, Weon HY, Kim YS, Park IC, Son JA, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.021238-0	2010	DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Xanthomonadaceae/classification/genetics/*isolation & purification/metabolism	Metabolism
Phylogeny	30506271	Nevskia lacus sp. nov., a gammaproteobacterium isolated from a eutrophic lake.	Cui Y, Chun SJ, Cho AR, Wong SK, Lee HG, Oh HM, Ahn CY	Antonie Van Leeuwenhoek	10.1007/s10482-018-1206-6	2018	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Eutrophication, Fatty Acids/chemistry/metabolism, Lakes/chemistry/microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Xanthomonadaceae/classification/genetics/isolation & purification/metabolism	Metabolism

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
8139	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19509)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-19509
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
32117	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	28362	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)
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
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
86652	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID406076.1	StrainInfo: A central database for resolving microbial strain identifiers