Name: Rhodanobacter spathiphylli B39
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17515

Type strain:

Species: Rhodanobacter spathiphylli

Strain Designation: B39

Culture col. no.: DSM 17631, LMG 23181, CIP 109139

Strain history: CIP <- 2006, D. De Clercq, KU Leuven, Herverlee-Leuven, Belgium: strain B39

NCBI tax ID(s): 347483 (species)

SI-ID 280567

LMG 23181, DSM 17631, CIP 109139

Special Collections

Section

Rhodanobacter spathiphylli B39 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from root of Spathiphyllum plants grown on a compost amended potting mix.

Gram-negative
rod-shaped
aerobe
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	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Rhodanobacteraceae*
	Genus	*Rhodanobacter*
	Species	**Rhodanobacter spathiphylli**
	Full Scientific Name (LPSN)	Rhodanobacter spathiphylli De Clercq et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #31727]	Gram stain	negative
[Ref.: #122690]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99

[Ref.: #31727]	Cell length	1.5-4 µm

[Ref.: #31727]	Cell width	0.8 µm

[Ref.: #31727]	Cell shape	rod-shaped
[Ref.: #122690]	Cell shape	rod-shaped

[Ref.: #31727]	Motility	no
[Ref.: #122690]	Motility	no

[Ref.: #31727]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7095]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #7095]

Culture medium growth

[Ref.: #7095]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7095]

Culture medium composition

expand / minimize

[Ref.: #7095]

Culture medium

LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)

[Ref.: #7095]

Culture medium growth

[Ref.: #7095]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7095]

Culture medium composition

expand / minimize

[Ref.: #40125]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #40125]

Culture medium growth

[Ref.: #40125]

Culture medium composition

expand / minimize

[Ref.: #122690]

Culture medium

CIP Medium 72

[Ref.: #122690]

Culture medium growth

[Ref.: #122690]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7095]	growth	30 °C
[Ref.: #31727]	growth	25-35 °C
[Ref.: #31727]	optimum	35 °C
[Ref.: #40125]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #31727]			optimum	7
[Ref.: #31727]			growth	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31727]	Oxygen tolerance	aerobe
[Ref.: #122690]	Oxygen tolerance	obligate aerobe

[Ref.: #31727]

Ability of spore formation

[Ref.: #31727]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31727]	citrate ChEBI	+	carbon source
[Ref.: #31727]	glycogen ChEBI	+	carbon source
[Ref.: #122690]	nitrate ChEBI	-	reduction
[Ref.: #122690]	nitrite ChEBI	-	reduction
[Ref.: #31727]	salicin ChEBI	+	carbon source
[Ref.: #31727]	sorbitol ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #122690]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #31727]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #31727]	catalase	+	1.11.1.6
[Ref.: #122690]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31727]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122690]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #122690]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #122690]	11675	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #7095]	Sample type/isolated from	root of Spathiphyllum plants grown on a compost amended potting mix
[Ref.: #7095]	Host species	Spathiphyllum
[Ref.: #7095]	Geographic location (country and/or sea, region)	Leuven
[Ref.: #7095]	Country	Belgium
[Ref.: #7095]	Country ISO 3 Code	BEL
[Ref.: #7095]	Continent	Europe

[Ref.: #122690]	Sample type/isolated from	Plant, Root of Spathiphyllum plants
[Ref.: #122690]	Country	Belgium
[Ref.: #122690]	Country ISO 3 Code	BEL
[Ref.: #122690]	Continent	Europe
[Ref.: #122690]	Isolation date	2003
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	#Composting
#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 AM087226 (>99% sequence identity) for Rhodanobacter spathiphylli from Microbeatlas

Aquatic Samples	341
Soil Samples	2015
Animal Samples	383
Plant Samples	253
Total Samples	2992

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

[Ref.: #7095]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122690]	Biosafety level	1	Risk group (French classification)

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.: #31727]	Rhodanobacter spathiphylli 16S rRNA gene, strain type strain: B39	AM087226	1497	GenBank ENA	1163407 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodanobacter spathiphylli B39	GCA_000264295	contig	GenBank ENA	1163407 tax ID	*
[Ref.: #66792]	Rhodanobacter spathiphylli B39	1163407.3	wgs	PATRIC	1163407 tax ID	*
[Ref.: #66792]	Rhodanobacter spathiphylli B39	2537561836	draft	JGI IMG/M	1163407 tax ID	*

[Ref.: #31727]

GC-content

67.6 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodanobacter spathiphylli B39 PATRIC: 1163407.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	98.402	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	87.978	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	86.467	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.339	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	60.298	yes

Availability in culture collections External links

[Ref.: #7095]

Culture collection no.

DSM 17631, LMG 23181, CIP 109139

[Ref.: #86512]

SI-ID 280567

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodanobacter ginsengisoli sp. nov. and Rhodanobacter terrae sp. nov., isolated from soil cultivated with Korean ginseng.	Weon HY, Kim BY, Hong SB, Jeon YA, Kwon SW, Go SJ, Koo BS	Int J Syst Evol Microbiol	10.1099/ijs.0.65018-0	2007	*
Phylogeny	Rhodanobacter spathiphylli sp. nov., a gammaproteobacterium isolated from the roots of Spathiphyllum plants grown in a compost-amended potting mix.	De Clercq D, Van Trappen S, Cleenwerck I, Ceustermans A, Swings J, Coosemans J, Ryckeboer J	Int J Syst Evol Microbiol	10.1099/ijs.0.64131-0	2006	*

References

#7095

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17631

#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 )

#31727

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28003 (see below)

#40125 ; Curators of the CIP;

#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) .

#68382

Automatically annotated from API zym .

#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) .

#86512

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-ID280567.1 )

#122690 Collection of Institut Pasteur ; Curators of the CIP; CIP 109139

#28003

IJSEM 1755 2006 ( DOI 10.1099/ijs.0.64131-0 , PubMed 16902003 )

* These data were automatically processed and therefore are not curated

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