Name: Roseomonas oryzicola YC6724
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 23504

Type strain:

Species: Roseomonas oryzicola

Strain Designation: YC6724

Culture col. no.: DSM 21423, KCTC 22478, NBRC 109439

Strain history: <- YR Chung, Kyeongsang Univ.

NCBI tax ID(s): 535904 (species)

SI-ID 405671

DSM 21423

Special Collections

DSMZ
KCTC

Section

When using BacDive for research please cite our paper

Roseomonas oryzicola YC6724 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere of rice under conventional tillage.

Gram-negative
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodospirillales*
	Family	*Acetobacteraceae*
	Genus	*Roseomonas*
	Species	**Roseomonas oryzicola**
	Full Scientific Name (LPSN)	Roseomonas oryzicola Chung et al. 2015

Synonym

Neoroseomonas oryzicola

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %98.31

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21099]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #21099]

Culture medium growth

[Ref.: #21099]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21099]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21099]			growth	28 °C
[Ref.: #67771]			growth	25-30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %97.4

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

[Ref.: #21099]	Sample type/isolated from	rhizosphere of rice (Oryza sativa L.) under conventional tillage
[Ref.: #21099]	Host species	Oryza sativa
[Ref.: #21099]	Geographic location (country and/or sea, region)	Jinju
[Ref.: #21099]	Country	Republic of Korea
[Ref.: #21099]	Country ISO 3 Code	KOR
[Ref.: #21099]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From rice field
[Ref.: #67771]	Geographic location (country and/or sea, region)	Jinju
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU707562 (>99% sequence identity) for Roseomonas oryzicola from Microbeatlas

Aquatic Samples	595
Soil Samples	258
Animal Samples	89
Plant Samples	36
Total Samples	978

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

[Ref.: #21099]

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.: #21099]	Neoroseomonas oryzicola strain YC6724 16S ribosomal RNA gene, partial sequence	EU707562	1451	GenBank ENA	535904 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Neoroseomonas oryzicola KCTC 22478	GCA_012163135	scaffold	GenBank ENA	535904 tax ID	*
[Ref.: #66792]	Roseomonas oryzicola strain KCTC 22478	535904.3	wgs	PATRIC	535904 tax ID	*
[Ref.: #66792]	Roseomonas oryzicola KCTC 22478	2894772417	draft	JGI IMG/M	535904 tax ID	*

[Ref.: #21099]	GC-content	70.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	70.47 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Roseomonas oryzicola KCTC 22478 NCBI: GCA_012163135.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.31	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	88.471	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	82.047	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	84.979	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	95.476	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	65.316	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Neoroseomonas oryzicola KCTC 22478 NCBI: GCA_012163135
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	75.1
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	55.4
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	68.2
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	97.4

Availability in culture collections External links

[Ref.: #21099]

Culture collection no.

DSM 21423, KCTC 22478, NBRC 109439

[Ref.: #87615]

SI-ID 405671

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Roseomonas rubea sp. nov., isolated from rice paddy soil.	Lee HJ, Whang KS	Int J Syst Evol Microbiol	10.1099/ijsem.0.005251	2022	*
Phylogeny	Roseomonas oryzicola sp. nov., isolated from the rhizosphere of rice (Oryza sativa L.).	Chung EJ, Yoon HS, Kim KH, Jeon CO, Chung YR	Int J Syst Evol Microbiol	10.1099/ijsem.0.000656	2015	*

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 )

#21099

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21423

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#87615

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-ID405671.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Search for species Roseomonas oryzicola in external resources:
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PANGAEA
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Roseomonas oryzicola KCTC 22478

Neoroseomonas oryzicola KCTC 22478

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