Sphingomonas sp. (DSM 102535, Root1294)

Name: Sphingomonas sp. (DSM 102535, Root1294)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131938

Type strain

Strain Designation Root1294

Culture col. no. DSM 102535 Root1294

NCBI tax ID(s) 28214

Special Collections DSMZ Arabidopsis

History <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root1294 <- Y. Bai

Links

Root1294 is a bacterium that was isolated from roots of Arabidopsis thaliana ecotype Shakdara .

genome sequence Bacteria

Name and taxonomic classification

SI-ID 407405

DSM 102535

@ref 20215

Last LPSN update 2026-02-09 11:31:35

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomonas

Full scientific name Sphingomonas Yabuuchi et al. 1990

Synonyms (18)

Novistakelama
Parastakelama
Alteristakelama
Pseudostakelama
Parayabuuchia
Humisphingomonas
Pseudosphingomonas
Neorhizorhabdus
Alterisphingomonas
Solisphingomonas
Parasphingomonas
Flavisphingomonas
Alteriyabuuchia
Edaphosphingomonas
Alterisphingopyxis
Alterirhizorhabdus
Paraquisediminimonas
Pararhizorhabdus

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	94.969
125439	negative	98.9

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23730	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	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

Culture temp

@ref	Growth	Type	Temperature (°C)
23730	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.4

Spore formation

@ref	Spore formation	Confidence
125438		91.424
125439		97.7

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
23730	roots of Arabidopsis thaliana ecotype Shakdara (Sha)	Arabidopsis thaliana	Cologne (50.958N 6.856E)	Germany	DEU	Europe	50.958	6.856 50.958/6.856

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Root1294 assembly for Sphingomonas sp. Root1294	scaffold	GCA_001426255	1736447.3	2643221671	1736447	61.66

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingomonas sp. Root1294
NCBI: GCA_001426255

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.70	no
125439	motility	BacteriaNetⓘ	yes	60.40	no
125439	gram_stain	BacteriaNetⓘ	negative	98.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas sp. Root1294 Root1294
NCBI: GCA_001426255.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.97	no
125438	anaerobic	anaerobicⓘ	no	97.03	no
125438	aerobic	aerobicⓘ	yes	88.18	no
125438	spore-forming	spore-formingⓘ	no	91.42	no
125438	thermophilic	thermophileⓘ	no	96.74	yes
125438	flagellated	motile2+ⓘ	yes	68.84	no

Literature

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 )
#23730	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102535
#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) .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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