Sphingomonas sp. (DSM 102539, Root720)

Name: Sphingomonas sp. (DSM 102539, Root720)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131937

Type strain

Strain Designation Root720

Culture col. no. DSM 102539 Root720

NCBI tax ID(s) 28214

Special Collections DSMZ Arabidopsis

History <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root720 <- Y. Bai

Links

Root720 is a bacterium that was isolated from roots of Arabidopsis thaliana ecotype Shakdara .

genome sequence Bacteria

Name and taxonomic classification

SI-ID 404620

DSM 102539

@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
125439	negative	97
125438	negative	95.369

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23729	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)
23729	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99

Spore formation

@ref	Spore formation	Confidence
125439		95.9
125438		91.424

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
23729	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	Root720 assembly for Sphingomonas sp. Root720	scaffold	GCA_001428605	1736595.3	2643221606	1736595	73.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingomonas sp. Root720
NCBI: GCA_001428605

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.90	no
125439	motility	BacteriaNetⓘ	yes	53.60	no
125439	gram_stain	BacteriaNetⓘ	negative	97.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas sp. Root720 Root720
NCBI: GCA_001428605.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.37	no
125438	anaerobic	anaerobicⓘ	no	98.03	no
125438	aerobic	aerobicⓘ	yes	88.40	no
125438	spore-forming	spore-formingⓘ	no	91.42	no
125438	thermophilic	thermophileⓘ	no	95.74	yes
125438	flagellated	motile2+ⓘ	yes	66.84	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 )
#23729	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102539
#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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