Rhodanobacter spathiphylli (DSM 17631, LMG 23181, B39)

Name: Rhodanobacter spathiphylli (DSM 17631, LMG 23181, B39)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17515

Type strain

Strain Designation B39

Culture col. no. DSM 17631 LMG 23181 B39 CIP 109139

NCBI tax ID(s) 347483

Special Collections DSMZ Literature strains CIP

Links

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

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 280567

LMG 23181,DSM 17631,CIP 109139

@ref 20215

Last LPSN update 2025-12-16 09:51:06

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Rhodanobacteraceae

Genus Rhodanobacter

Species Rhodanobacter spathiphylli

Full scientific name Rhodanobacter spathiphylli De Clercq et al. 2006

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31727	negative	1.5-4 µm	0.8 µm	rod-shaped
125438	negative				99
125439	negative				98.6
122690	negative			rod-shaped

Pigmentation

31727

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7095	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
7095	LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)	Medium recipe at MediaDive	Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
40125	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122690	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7095	positive	growth	30	mesophilic
31727	positive	growth	25-35	mesophilic
31727	positive	optimum	35	mesophilic
40125	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
31727	positive	optimum	7
31727	positive	growth	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31727	aerobe
122690	obligate aerobe
125439	obligate aerobe	99.7

Spore formation

@ref	Spore formation	Confidence
31727
125439		97.9

Observation

31727

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31727	16947 ChEBI	citrate	+	carbon source
31727	28087 ChEBI	glycogen	+	carbon source
122690	17632 ChEBI	nitrate	-	reduction
122690	16301 ChEBI	nitrite	-	reduction
31727	17814 ChEBI	salicin	+	carbon source
31727	30911 ChEBI	sorbitol	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122690	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
31727	alkaline phosphatase	+	3.1.3.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31727	catalase	+	1.11.1.6
122690	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31727	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122690	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
122690	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
122690	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Composting
#Environmental	#Terrestrial	#Soil
#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	Isolation date
7095	root of Spathiphyllum plants grown on a compost amended potting mix	Spathiphyllum	Leuven	Belgium	BEL	Europe
122690	Plant, Root of Spathiphyllum plants			Belgium	BEL	Europe	2003

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7095	1	Risk group (German classification) According to TRBA 466
122690	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Rh17631 assembly for Rhodanobacter spathiphylli B39	contig	GCA_000264295	1163407.3	2537561836	1163407	31.12

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31727	Rhodanobacter spathiphylli 16S rRNA gene, strain type strain: B39	AM087226	1497		1163407

GC content

31727

GC-content (mol%)67.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodanobacter spathiphylli B39
NCBI: GCA_000264295

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.70	no
125439	gram_stain	BacteriaNetⓘ	negative	98.60	no
125439	motility	BacteriaNetⓘ	yes	87.60	no
125439	spore_formation	BacteriaNetⓘ	no	97.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodanobacter spathiphylli B39
PATRIC: 1163407.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	yes
125438	anaerobic	anaerobicⓘ	no	98.40	yes
125438	spore-forming	spore-formingⓘ	no	87.98	yes
125438	aerobic	aerobicⓘ	yes	86.47	yes
125438	thermophilic	thermophileⓘ	no	97.34	yes
125438	flagellated	motile2+ⓘ	no	60.30	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Genome sequences for six Rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities.	Kostka JE, Green SJ, Rishishwar L, Prakash O, Katz LS, Marino-Ramirez L, Jordan IK, Munk C, Ivanova N, Mikhailova N, Watson DB, Brown SD, Palumbo AV, Brooks SC.	J Bacteriol	10.1128/jb.00871-12	2012
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 .
#122690	Collection of Institut Pasteur ; Curators of the CIP; CIP 109139
#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 )

Rate our new design

Content

About us

Rhodanobacter spathiphylli (DSM 17631, LMG 23181, B39)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000264295

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media