Archive BacDiveID:10.13145/bacdive130263.20230509.8.1

Strain identifier

BacDive ID: 130263

Type strain:

Species: Variovorax guangxiensis

Strain Designation: GXGD002

Strain history: <- J.-L. Gao, Beijing Academy of Agriculture and Forestry Science; GXGD002 <- J. Chen, Beijing Academy of Agriculture and Forestry Science

NCBI tax ID(s): 1775474 (species)

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

General

@ref: 21863

BacDive-ID: 130263

DSM-Number: 27352

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Variovorax guangxiensis GXGD002 is a mesophilic bacterium that was isolated from rhizosphere soil of banana .

NCBI tax id

NCBI tax id: 1775474
Matching level: species

strain history

@ref: 21863
history: <- J.-L. Gao, Beijing Academy of Agriculture and Forestry Science; GXGD002 <- J. Chen, Beijing Academy of Agriculture and Forestry Science

doi: 10.13145/bacdive130263.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Variovorax
species: Variovorax guangxiensis
full scientific name: Variovorax guangxiensis Gao et al. 2015

@ref: 21863

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Variovorax

species: Variovorax guangxiensis

full scientific name: Variovorax guangxiensis Gao et al. 2015

strain designation: GXGD002

type strain: yes

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
21863	LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)	yes	https://mediadive.dsmz.de/medium/381	Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
21863	R2A MEDIUM (DSMZ Medium 830)	yes	https://mediadive.dsmz.de/medium/830	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 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
21863	NUTRIENT AGAR (DSMZ Medium 1)	yes	https://mediadive.dsmz.de/medium/1	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
21863	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	yes	https://mediadive.dsmz.de/medium/535	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@ref: 21863
growth: positive
type: growth
temperature: 28
range: mesophilic

Physiology and metabolism

compound production

@ref: 21863
compound: 1 aminocyclopropane-1-carboxylate deaminase

Isolation, sampling and environmental information

isolation

@ref: 21863
sample type: rhizosphere soil of banana (Musa paradisiaca)
host species: Musa paradisiaca
geographic location: Guangxi province
country: China
origin.country: CHN
continent: Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Rhizosphere

taxonmaps

@ref: 69479
File name: preview.99_2305.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_308;97_342;98_387;99_2305&stattab=map
Last taxonomy: Variovorax
16S sequence: JF495126
Sequence Identity:
Total samples: 9717
soil counts: 3106
aquatic counts: 2157
animal counts: 2122
plant counts: 2332

Safety information

risk assessment

@ref: 21863
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 21863
description: Variovorax guangxiensis strain GXGD002 16S ribosomal RNA gene, partial sequence
accession: JF495126
length: 1395
database: ena
NCBI tax ID: 1775474

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Variovorax guangxiensis DSM 27352	GCA_003952165	contig	ncbi	1775474
66792	Variovorax guangxiensis strain DSM 27352	1775474.3	wgs	patric	1775474
66792	Variovorax guangxiensis DSM 27352	2831265667	draft	img	1775474

GC content

@ref: 21863
GC-content: 67.8
method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	yes	82.951	no
gram-positive	no	98.606	no
anaerobic	no	98.859	no
aerobic	yes	95.449	no
halophile	no	96.537	no
spore-forming	no	94.328	no
thermophile	no	99.569	yes
glucose-util	yes	61.844	no
flagellated	no	57.841	no
glucose-ferment	no	90.916	no

External links

@ref: 21863

culture collection no.: DSM 27352, ACCC 05911

straininfo link

@ref: 88802
straininfo: 407207

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	25504533	Variovorax guangxiensis sp. nov., an aerobic, 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from banana rhizosphere.	Gao JL, Yuan M, Wang XM, Qiu TL, Li JW, Liu HC, Li XA, Chen J, Sun JG	Antonie Van Leeuwenhoek	10.1007/s10482-014-0304-3	2014	Bacterial Typing Techniques, Base Composition, Carbon-Carbon Lyases/metabolism, China, Cluster Analysis, Comamonadaceae/classification/enzymology/genetics/isolation & purification, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Musa, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, Soil Microbiology	Enzymology
Phylogeny	27082126	Description of Variovorax humicola sp. nov., isolated from a forest topsoil.	Nguyen TM, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001082	2016	Bacterial Typing Techniques, Base Composition, Comamonadaceae/classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil Microbiology, Ubiquinone/chemistry	Transcriptome
Phylogeny	35791077	Variovorax terrae sp. nov. Isolated from Soil with Potential Antioxidant Activity.	Woo CY, Kim J	J Microbiol Biotechnol	10.4014/jmb.2205.05018	2022	Antioxidants/analysis, Bacterial Typing Techniques, Comamonadaceae, DNA, Bacterial/genetics, Fatty Acids/analysis, Phosphatidylethanolamines/analysis, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil Microbiology	Transcriptome

Reference

@id	authors	title	doi/url	catalogue
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	10.1099/ijsem.0.004332
21863	Curators of the DSMZ		https://www.dsmz.de/collection/catalogue/details/culture/DSM-27352	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27352)
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)	https://diaspora-project.de/progress.html#genomes
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.	MicrobeAtlas 1.0 beta	https://microbeatlas.org/
88802	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	10.60712/SI-ID407207.1