Cite this strain

(DSM 102555, Root318D1)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132038

Type strain

Strain Designation Root318D1

Culture col. no. DSM 102555 Root318D1

NCBI tax ID(s) 1871043

Special Collections DSMZ Arabidopsis

Links

Name and taxonomic classification

Root318D1 is a mesophilic, Gram-negative bacterium that was isolated from roots of wild-type Arabidopsis thaliana plants.

Gram-negative mesophilic genome sequence Bacteria

SI-ID 407845

DSM 102555

Last LPSN update 2024-12-09 10:49:07

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Variovorax

Full scientific name Variovorax Willems et al. 1991

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	97.2
125438	negative	97.8

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23829	FLOUR MEDIUM (DSMZ Medium 1613)		Medium recipe at MediaDive	Name: FLOUR MEDIUM (DSMZ Medium 1613) Composition: Agar 16.0 g/l Plain flour 4.0 g/l CaCO3 0.4 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
23829	positive	growth	28	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		94.1

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.3

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
23829	roots of wild-type Arabidopsis thaliana plants	Arabidopsis thaliana	Cologne, Widdersdorf district (50.982N 6.827E)	Germany	DEU	Europe	50.982	6.827 50.982/6.827

Safety information

Sequence information

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Variovorax sp. Root318D1	GCA_001424835	scaffold		1736513
66792	Variovorax sp. Root318D1	1736513.3	wgs	PATRIC	1736513
66792	Variovorax sp. Root318D1	2643221628	draft	JGI IMG/M	1736513

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Variovorax sp. Root318D1
NCBI: GCA_001424835

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.10	no
125439	motility	BacteriaNetⓘ	yes	76.10	no
125439	gram_stain	BacteriaNetⓘ	negative	97.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.30	no

Predictions from Diaspora project based on:
Variovorax sp. Root318D1 Root318D1
NCBI: GCA_001424835.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.80	no
125438	anaerobic	anaerobicⓘ	no	96.59	no
125438	aerobic	aerobicⓘ	yes	89.91	no
125438	spore-forming	spore-formingⓘ	no	88.31	no
125438	thermophilic	thermophileⓘ	no	99.39	yes
125438	flagellated	motile2+ⓘ	yes	56.21	no

External links

Straininfo Link

@ref	Straininfo	Culture collections
90402	407845	DSM 102555

Culture collection no.

Culture collection no.
DSM 102555
Root318D1

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 )
#23829	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102555
#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) .
#90402	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 . ( DOI 10.60712/SI-ID407845.1 )
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

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