Archive BacDiveID:10.13145/bacdive6189.20230509.8.1

Strain identifier

BacDive ID: 6189

Type strain:

Species: Rhodoplanes elegans

Strain history: A. Hiraishi AS130.

NCBI tax ID(s): 29408 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 4535

BacDive-ID: 6189

DSM-Number: 11907

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile

description: Rhodoplanes elegans DSM 11907 is an anaerobe, mesophilic, motile bacterium that was isolated from activated sludge.

NCBI tax id

NCBI tax id: 29408
Matching level: species

strain history

@ref	history
4535	<- ATCC <- JCM <- A. Hiraishi; AS130
67770	A. Hiraishi AS130.

doi: 10.13145/bacdive6189.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Alphaproteobacteria
order: Hyphomicrobiales
family: Nitrobacteraceae
genus: Rhodoplanes
species: Rhodoplanes elegans
full scientific name: Rhodoplanes elegans Hiraishi and Ueda 1994

@ref: 4535

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Nitrobacteraceae

genus: Rhodoplanes

species: Rhodoplanes elegans

full scientific name: Rhodoplanes elegans Hiraishi and Ueda 1994

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	yes	95.377
69480		99.997	negative

Culture and growth conditions

culture medium

@ref: 4535
name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)
growth: yes
link: https://mediadive.dsmz.de/medium/27
composition: Name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27) Composition: Disodium succinate 1.0 g/l KH2PO4 0.5 g/l Ammonium acetate 0.5 g/l NaCl 0.4 g/l NH4Cl 0.4 g/l MgSO4 x 7 H2O 0.4 g/l Yeast extract 0.3 g/l L-Cysteine HCl 0.3 g/l CaCl2 x 2 H2O 0.05 g/l Fe(III) citrate 0.005 g/l Resazurin 0.005 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Vitamin B12 Distilled water

culture temp

@ref	growth	type	temperature	range
4535	positive	growth	28	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

oxygen tolerance

@ref: 4535
oxygen tolerance: anaerobe

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.975

observation

@ref: 67770
observation: quinones: Q-10, RQ-10

Isolation, sampling and environmental information

isolation

@ref	sample type	country	origin.country	continent
4535	activated sludge
67770	Activated sludge from the main purification stage of a sewage treatment plant in Tokyo	Japan	JPN	Asia

isolation source categories

Cat1: #Engineered
Cat2: #Waste
Cat3: #Activated sludge

taxonmaps

@ref: 69479
File name: preview.99_74446.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_2492;97_3043;98_16748;99_74446&stattab=map
Last taxonomy: Rhodoplanes
16S sequence: D25311
Sequence Identity:
Total samples: 108
soil counts: 15
aquatic counts: 55
animal counts: 27
plant counts: 11

Safety information

risk assessment

@ref: 4535
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 4535
description: Rhodoplanes elegans gene for 16S rRNA
accession: D25311
length: 1447
database: ena
NCBI tax ID: 29408

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Rhodoplanes elegans DSM 11907	GCA_016653355	scaffold	ncbi	29408
66792	Rhodoplanes elegans DSM 11907	GCA_003258805	scaffold	ncbi	29408
66792	Rhodoplanes elegans strain DSM 11907	29408.6	wgs	patric	29408
66792	Rhodoplanes elegans strain DSM 11907	29408.4	wgs	patric	29408
66792	Rhodoplanes elegans DSM 11907	2891191727	draft	img	29408

GC content

@ref: 67770
GC-content: 69.7
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
flagellated	yes	64.671	no
gram-positive	no	98.751	no
anaerobic	yes	70.588	yes
aerobic	no	61.337	no
halophile	no	93.794	no
spore-forming	no	94.38	no
thermophile	no	97.188	yes
glucose-util	yes	75.058	no
motile	yes	90.306	no
glucose-ferment	no	90.115	no

External links

@ref: 4535

culture collection no.: DSM 11907, ATCC 51906, JCM 9224, AS 130, CGMCC 1.5008, IFO 16660, NBRC 16660, NCIMB 13415

straininfo link

@ref: 75670
straininfo: 43237

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	22228659	Rhodoplanes piscinae sp. nov. isolated from pond water.	Chakravarthy SK, Ramaprasad EVV, Shobha E, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.037663-0	2012	Bacterial Typing Techniques, Bacteriochlorophyll A/analysis, Base Composition, Carotenoids/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Hyphomicrobiaceae/classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Ponds/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA	Genetics
Phylogeny	24695055	Rhodoplanes oryzae sp. nov., a phototrophic alphaproteobacterium isolated from the rhizosphere soil of paddy.	Srinivas A, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.063347-0	2014	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hyphomicrobiaceae/classification/genetics/isolation & purification, India, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry	Genetics
Phylogeny	26420766	Pseudorhodoplanes sinuspersici gen. nov., sp. nov., isolated from oil-contaminated soil.	Tirandaz H, Dastgheib SMM, Amoozegar MA, Shavandi M, de la Haba RR, Ventosa A	Int J Syst Evol Microbiol	10.1099/ijsem.0.000643	2015	Alphaproteobacteria/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Iran, Molecular Sequence Data, Petroleum Pollution, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, *Soil Pollutants, Ubiquinone/chemistry	Genetics

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
4535	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11907)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-11907
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	33211880
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
75670	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID43237.1	StrainInfo: A central database for resolving microbial strain identifiers