Name: Rhizomicrobium palustre A48
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17877

Type strain:

Species: Rhizomicrobium palustre

Strain Designation: A48

Culture col. no.: DSM 19867, JCM 14971

Strain history: A. Ueki A48.

NCBI tax ID(s): 189966 (species)

SI-ID 407092

DSM 19867

Special Collections

DSMZ
JCM

Other strains from Rhizomicrobium palustre

Section

Rhizomicrobium palustre A48 is a Gram-negative bacterium that was isolated from roots of rice plants from irrigated rice field soil.

Gram-negative
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Micropepsales*
	Family	*Micropepsaceae*
	Genus	*Rhizomicrobium*
	Species	**Rhizomicrobium palustre**
	Full Scientific Name (LPSN)	Rhizomicrobium palustre Ueki et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %97.328

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8362]

Culture medium

RHIZOMICROBIUM MEDIUM (DSMZ Medium 1288)

[Ref.: #8362]

Culture medium growth

[Ref.: #8362]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8362]

Culture medium composition

expand / minimize

[Ref.: #8362]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #8362]

Culture medium growth

[Ref.: #8362]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #8362]			growth	28 °C
[Ref.: #67770]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

[Ref.: #67770]

Observation

quinones: Q-10

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #8362]	Sample type/isolated from	roots of rice plants (Oryza sativa cv. Haenuki, type japonica) from irrigated rice field soil
[Ref.: #8362]	Host species	Oryza sativa
[Ref.: #8362]	Geographic location (country and/or sea, region)	Yamagata, Tsuruoka, Shonai Branch of the Yamagata Agricultural Research Center
[Ref.: #8362]	Country	Japan
[Ref.: #8362]	Country ISO 3 Code	JPN
[Ref.: #8362]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Roots of living rice plants (Oryza sativa cv. Haenuki, type japonica)
[Ref.: #67770]	Host species	Oryza sativa
[Ref.: #67770]	Geographic location (country and/or sea, region)	Tsuruoka, Yamagata
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB081581 (>99% sequence identity) for Rhizomicrobium palustre subclade from Microbeatlas

Aquatic Samples	367
Soil Samples	312
Animal Samples	27
Plant Samples	416
Total Samples	1122

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #8362]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #8362]	Rhizomicrobium palustre gene for 16S ribosomal RNA, partial sequence, strain: A48	AB081581	1406	GenBank ENA	189966 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Rhizomicrobium palustre DSM 19867	GCA_011761565	scaffold	GenBank ENA	189966 tax ID
[Ref.: #66792]	Rhizomicrobium palustre strain DSM 19867	189966.3	wgs	PATRIC	189966 tax ID	*
[Ref.: #66792]	Rhizomicrobium palustre DSM 19867	2828006917	draft	JGI IMG/M	189966 tax ID	*

[Ref.: #8362]

GC-content

55.4 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rhizomicrobium palustre DSM 19867 NCBI: GCA_011761565.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhizomicrobium palustre strain DSM 19867 PATRIC: 189966.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.328	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	74.247	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	85.654	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	54.735	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.192	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	70.362	no

Availability in culture collections External links

[Ref.: #8362]

Culture collection no.

DSM 19867, JCM 14971

[Ref.: #86866]

SI-ID 407092

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhizomicrobium palustre gen. nov., sp. nov., a facultatively anaerobic, fermentative stalked bacterium in the class Alphaproteobacteria isolated from rice plant roots.	Ueki A, Kodama Y, Kaku N, Shiromura T, Satoh A, Watanabe K, Ueki K	J Gen Appl Microbiol	10.2323/jgam.56.193	2010	*

References

#8362

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19867

#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 )

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86866

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-ID407092.1 )

* These data were automatically processed and therefore are not curated

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Rhizomicrobium palustre DSM 19867

Rhizomicrobium palustre strain DSM 19867

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