Pseudomonas sp. (DSM 102504, Root562)

Name: Pseudomonas sp. (DSM 102504, Root562)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131898

Type strain

Strain Designation Root562

Culture col. no. DSM 102504 Root562

NCBI tax ID(s) 306

Special Collections DSMZ Arabidopsis

History DSMZ <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root562 <- Y. Bai

Links

Root562 is a bacterium that was isolated from roots of Arabidopsis thaliana ecotype Columbia-0 .

genome sequence Bacteria

Name and taxonomic classification

SI-ID 406869

DSM 102504

@ref 20215

Last LPSN update 2026-05-29 08:37:43

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pseudomonadales

Family Pseudomonadaceae

Genus Pseudomonas

Full scientific name Pseudomonas Migula 1894 (Approved Lists 1980)

Synonyms (9)

Metapseudomonas
Zestomonas
"Caenipseudomonas"
Phytopseudomonas
Ectopseudomonas
Aquipseudomonas
Geopseudomonas
Flavimonas
Chryseomonas

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	93.829
125438		92.103
125438	negative	98.5

Multimedia

@ref:	23690
multimedia content:	DSM_102504.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_102504.jpg
caption:	cells of DSM 102504 on medium 1 at 28 °C
intellectual property rights:	Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23690	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	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
23690	PSEUDOMONAS AGAR F (DSMZ Medium 907)		Medium recipe at MediaDive	Name: PSEUDOMONAS AGAR F (DSMZ Medium 907) Composition: Agar 15.0 g/l Glycerol 10.0 g/l Proteose peptone 10.0 g/l Tryptone 10.0 g/l MgSO4 1.5 g/l K2HPO4 1.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
23690	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	90.849
125439	obligate aerobe	97.404

Spore formation

@ref	Spore formation	Confidence
125439		99.257

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
23690	roots of Arabidopsis thaliana ecotype Columbia-0 (Col-0)	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	Root562 assembly for Pseudomonas sp. Root562	scaffold	GCA_001427125	1736561.3	2643221565	1736561	71.61

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Root562 assembly for Pseudomonas sp. Root562
BV-BRC: 1736561.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.40	no
125439	gram_stain	BacteriaNetⓘ	negative	93.83	no
125439	spore_formation	BacteriaNetⓘ	no	99.26	no
125439	motility	BacteriaNetⓘ	yes	78.49	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudomonas sp. Root562 Root562
NCBI: GCA_001427125.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	98.43	no
125438	aerobic	aerobicⓘ	yes	90.85	no
125438	spore-forming	spore-formingⓘ	no	83.87	no
125438	thermophilic	thermophileⓘ	no	98.00	no
125438	flagellated	motile2+ⓘ	yes	92.10	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 )
#23690	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102504
#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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