Rhizorhabdus dicambivorans (KACC 18661, CCTCC AB 2016143, DSM 107650)

Name: Rhizorhabdus dicambivorans (KACC 18661, CCTCC AB 2016143, DSM 107650)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140624

Type strain

Strain Designation Ndbn-20

Culture col. no. KACC 18661 CCTCC AB 2016143 DSM 107650 Ndbn-20

NCBI tax ID(s) 1850238

Special Collections DSMZ Literature strains

Links

Rhizorhabdus dicambivorans Ndbn-20 is an obligate aerobe, mesophilic, Gram-negative prokaryote that forms circular colonies and was isolated from compost.

Gram-negative rod-shaped colony-forming obligate aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 402225

DSM 107650

@ref 20215

Last LPSN update 2025-12-16 10:03:38

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Rhizorhabdus

Species Rhizorhabdus dicambivorans

Full scientific name Rhizorhabdus dicambivorans Yao et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
43148	negative	0.8-1.2 µm	0.4-0.6 µm	rod-shaped
125439	negative				97.4
125438	negative				94.969

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
43148	pale yellow	circular	7 days	R2A

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
43148	Reasoner's 2A agar (R2A)
64826	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
43148	positive	optimum	30	mesophilic
43148	positive	growth	15-40
64826	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
43148	positive	optimum	7
43148	positive	growth	5.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43148	obligate aerobe
125439	obligate aerobe	96.8

Spore formation

@ref	Type of spore	Confidence
43148	spore
125439		96
125438		90.496

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43148	NaCl	positive	growth	0-2.0 %(w/v)
43148	NaCl	positive	optimum	0.5 %

Observation

43148

Observationdegradation of dicamba

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43148	17128 ChEBI	adipate	-	assimilation
43148	22599 ChEBI	arabinose	-	assimilation
43148	65327 ChEBI	D-xylose	+	builds acid from
43148	27689 ChEBI	decanoate	-	assimilation
43148	4853 ChEBI	esculin	+	hydrolysis
43148	28757 ChEBI	fructose	+	builds acid from
43148	28260 ChEBI	galactose	-	builds acid from
43148	5291 ChEBI	gelatin	-	hydrolysis
43148	17234 ChEBI	glucose	-	fermentation
43148	25115 ChEBI	malate	-	assimilation
43148	17306 ChEBI	maltose	-	assimilation
43148	29864 ChEBI	mannitol	-	assimilation
43148	37684 ChEBI	mannose	-	assimilation
43148	28053 ChEBI	melibiose	-	builds acid from
43148	506227 ChEBI	N-acetylglucosamine	-	assimilation
43148	17632 ChEBI	nitrate	+	reduction
43148	32032 ChEBI	potassium gluconate	-	assimilation
43148	33942 ChEBI	ribose	+	builds acid from
43148	53258 ChEBI	sodium citrate	-	assimilation
43148	28017 ChEBI	starch	+	builds acid from
43148	17992 ChEBI	sucrose	-	builds acid from
43148	16199 ChEBI	urea	+	hydrolysis

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
43148	28971	ampicillin	10 µg (disc)
43148	3393	carbenicillin	100 µg (disc)
43148	17698	chloramphenicol	30 µg (disc)
43148	3745	clindamycin		30 µg (disc)
43148	17833	gentamicin	10 µg (disc)
43148	6104	kanamycin	30 µg (disc)
43148	48844	roxithromycin	15 µg (disc)
43148	17076	streptomycin		10 µg (disc)
43148	27902	tetracycline	30 µg (disc)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43148	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43148	acid phosphatase	-	3.1.3.2
43148	alkaline phosphatase	-	3.1.3.1
43148	alpha-galactosidase	+	3.2.1.22
43148	alpha-glucosidase	+	3.2.1.20
43148	alpha-mannosidase	+	3.2.1.24
43148	beta-D-fucosidase	+	3.2.1.38
43148	beta-galactosidase	+	3.2.1.23
43148	beta-glucosidase	+	3.2.1.21
43148	beta-glucuronidase	+	3.2.1.31
43148	catalase	-	1.11.1.6
43148	chymotrypsin	+	3.4.4.5
43148	cystine arylamidase	+	3.4.11.3
43148	cytochrome oxidase	-	1.9.3.1
43148	esterase (C 4)	-
43148	esterase Lipase (C 8)	-
43148	leucine arylamidase	-	3.4.11.1
43148	lipase (C 14)	+
43148	N-acetyl-glucosidase	+
43148	naphthol-AS-BI-phosphohydrolase	-
43148	trypsin	-	3.4.21.4
43148	valine arylamidase	-

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	valine metabolism	100	9 of 9
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	Entner Doudoroff pathway	100	10 of 10
66794	glycogen metabolism	100	5 of 5
66794	threonine metabolism	100	10 of 10
66794	adipate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	denitrification	100	2 of 2
66794	gallate degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	butanoate fermentation	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	quinate degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	3-phenylpropionate degradation	86.67	13 of 15
66794	photosynthesis	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	propionate fermentation	80	8 of 10
66794	3-chlorocatechol degradation	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	alanine metabolism	79.31	23 of 29
66794	heme metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	methionine metabolism	76.92	20 of 26
66794	vitamin B1 metabolism	76.92	10 of 13
66794	purine metabolism	76.6	72 of 94
66794	CMP-KDO biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	toluene degradation	75	3 of 4
66794	lactate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	tryptophan metabolism	73.68	28 of 38
66794	flavin biosynthesis	73.33	11 of 15
66794	pentose phosphate pathway	72.73	8 of 11
66794	proline metabolism	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	tyrosine metabolism	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	phenol degradation	70	14 of 20
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	lipid metabolism	67.74	21 of 31
66794	octane oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	glycolysis	64.71	11 of 17
66794	glutathione metabolism	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	myo-inositol biosynthesis	60	6 of 10
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	oxidative phosphorylation	57.14	52 of 91
66794	propanol degradation	57.14	4 of 7
66794	lysine metabolism	57.14	24 of 42
66794	degradation of sugar alcohols	56.25	9 of 16
66794	d-mannose degradation	55.56	5 of 9
66794	lipid A biosynthesis	55.56	5 of 9
66794	nitrate assimilation	55.56	5 of 9
66794	alginate biosynthesis	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	ketogluconate metabolism	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	carnitine metabolism	50	4 of 8
66794	resorcinol degradation	50	1 of 2
66794	sulfate reduction	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	degradation of hexoses	44.44	8 of 18
66794	degradation of sugar acids	44	11 of 25
66794	polyamine pathway	43.48	10 of 23
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	elloramycin biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	arachidonic acid metabolism	38.89	7 of 18
66794	chlorophyll metabolism	33.33	6 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	allantoin degradation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	sulfoquinovose degradation	33.33	1 of 3
66794	carotenoid biosynthesis	31.82	7 of 22
66794	ascorbate metabolism	31.82	7 of 22
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	starch degradation	30	3 of 10
66794	d-xylose degradation	27.27	3 of 11
66794	vitamin B12 metabolism	26.47	9 of 34
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	daunorubicin biosynthesis	22.22	2 of 9

Fatty acid profile

Metadata FA analysis

@ref

43148

Fatty acid	Percentage
C18:1ω7c / C18:1ω6c	46.17
C16:1ω7c / C16:1ω6c	11.68
C17:1ω6c	10.96
C16:0	10.36
C14:0 2OH	7.56
11-methyl C18:1ω7c	2.61
C16:1ω5c	2.35
C17:1ω8c	1.67
cyclo-C19:0ω8c	1.41
C15:0 2OH	1.34
C17:0	1.18
C14:0	0.75
C18:1ω5c	0.66
C18:0	0.42
C18:1ω9c	0.19
C12:0	0.18
C13:0 2OH	0.15

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Composting

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
43148	compost	Mount Zijin, Nanjing, Jiangsu Province, PR China	China	CHN	Asia	32	118 32/118
64826	compost of plant litter		China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence KP064570 (>99% sequence identity) for Rhizorhabdus dicambivorans from Microbeatlas

Aquatic Samples	157
Soil Samples	176
Animal Samples	48
Plant Samples	9
Total Samples	390

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
64826	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM235527v1 assembly for Rhizorhabdus dicambivorans Ndbn-20	complete	GCA_002355275	1850238.3	2775506841	1850238	97.85

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
64826	Rhizorhabdus dicambivorans strain Ndbn-20 16S ribosomal RNA gene, partial sequence	KP064570	1447		1850238

GC content

@ref	GC-content (mol%)	Method
43148	65.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhizorhabdus dicambivorans Ndbn-20
IMG: 2775506841

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.00	no
125439	motility	BacteriaNetⓘ	yes	57.20	no
125439	gram_stain	BacteriaNetⓘ	negative	97.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhizorhabdus dicambivorans Ndbn-20
NCBI: GCA_002355275.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.97	no
125438	anaerobic	anaerobicⓘ	no	95.50	yes
125438	aerobic	aerobicⓘ	yes	89.71	yes
125438	spore-forming	spore-formingⓘ	no	90.50	yes
125438	thermophilic	thermophileⓘ	no	97.58	yes
125438	flagellated	motile2+ⓘ	yes	67.94	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Roles of Two Glutathione-Dependent 3,6-Dichlorogentisate Dehalogenases in Rhizorhabdus dicambivorans Ndbn-20 in the Catabolism of the Herbicide Dicamba.	Li N, Tong RL, Yao L, Chen Q, Yan X, Ding DR, Qiu JG, He J, Jiang JD	Appl Environ Microbiol	10.1128/AEM.00623-18	2018
Metabolism	3,6-Dichlorosalicylate Catabolism Is Initiated by the DsmABC Cytochrome P450 Monooxygenase System in Rhizorhabdus dicambivorans Ndbn-20.	Li N, Yao L, He Q, Qiu J, Cheng D, Ding D, Tao Q, He J, Jiang J	Appl Environ Microbiol	10.1128/AEM.02133-17	2018
Metabolism	Roles of the Gentisate 1,2-Dioxygenases DsmD and GtdA in the Catabolism of the Herbicide Dicamba in Rhizorhabdus dicambivorans Ndbn-20.	Li N, Peng Q, Yao L, He Q, Qiu J, Cao H, He J, Niu Q, Lu Y, Hui F	J Agric Food Chem	10.1021/acs.jafc.0c01523	2020
Metabolism	The Properties of 5-Methyltetrahydrofolate Dehydrogenase (MetF1) and Its Role in the Tetrahydrofolate-Dependent Dicamba Demethylation System in Rhizorhabdus dicambivorans Ndbn-20.	Yao S, Chen L, Yang Z, Yao L, Zhu J, Qiu J, Wang G, He J	J Bacteriol	10.1128/JB.00096-19	2019
Metabolism	Coexpression of Methyltransferase Gene dmt50 and Methylene Tetrahydrofolate Reductase Gene Increases Arabidopsis thaliana Dicamba Resistance.	Chen L, Yao S, Chen T, Tao Q, Xie X, Xiao X, Ding D, He Q, He J	J Agric Food Chem	10.1021/acs.jafc.8b04944	2019
Enzymology	Cloning of a novel tetrahydrofolate-dependent dicamba demethylase gene from dicamba-degrading consortium and characterization of the gene product.	Li N, Chen L, Chen E, Yuan C, Zhang H, He J	Front Microbiol	10.3389/fmicb.2022.978577	2022
Phylogeny	Rhizorhabdus dicambivorans sp. nov., a dicamba-degrading bacterium isolated from compost.	Yao L, Zhang JJ, Yu LL, Chen Q, Zhu JC, He J, Ding DR	Int J Syst Evol Microbiol	10.1099/ijsem.0.001194	2016

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 )
#43148	Li Yao, Jun-Jie Zhang, Lin-Lu Yu, Qin Chen, Jian-Chun Zhu, Jian He and De-Rong Ding: Rhizorhabdus dicambivorans sp. nov., a dicamba-degrading bacterium isolated from compost. IJSEM 66: 3317 - 3323 2016 ( DOI 10.1099/ijsem.0.001194 , PubMed 27255344 )
#64826	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 107650
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 .
#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 )

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Rhizorhabdus dicambivorans (KACC 18661, CCTCC AB 2016143, DSM 107650)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

Pathway annotation

Fatty acid profile?

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002355275

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media

Fatty acid profile