Sphingomonas azotifigens (DSM 18530, CCTCC AB 205007, IAM 15283)

Name: Sphingomonas azotifigens (DSM 18530, CCTCC AB 205007, IAM 15283)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14246

Type strain

Strain Designation Y-39

Culture col. no. DSM 18530 CCTCC AB 205007 IAM 15283 NBRC 15497 Y-39 3 more

NCBI tax ID(s) 1219041 330920

Special Collections DSMZ JCM Literature strains CIP

History DSMZ <- A. Yokota; IAM 15283 <- Y. Oyaizu-Masuchi and K. Komagata CIP <- 2006, IAM JCM <-- IAM 15283 <-- A. Yokota Y-39. CIP <- 2006, IAM

Links

Sphingomonas azotifigens Y-39 is an aerobe, Gram-negative, motile bacterium that was isolated from root of rice plant.

Gram-negative motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 62895

IFO 15497,NBRC 15497,IAM 15283,DSM 18530,JCM 21734,CIP 109209

@ref 20215

Last LPSN update 2026-05-29 08:28:14

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomonas

Species Sphingomonas azotifigens

Full scientific name Sphingomonas azotifigens Xie and Yokota 2006

Synonyms (1)

Alteristakelama azotifigens

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31688	negative	01-03 µm	0.5-1 µm	rod-shaped
125439	negative				94.807
125438	negative				94.214
116689	negative			rod-shaped

Colony morphology

116689

Hemolysis ability0

Pigmentation

31688

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7581	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
7581	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
37481	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116689	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7581	positive	growth	30
7581	positive	growth	28
31688	positive	growth	25-40
31688	positive	optimum	25-37
37481	positive	growth	30
67770	positive	growth	27

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31688	aerobe
116689	microaerophile
125439	obligate aerobe	99.488

Spore formation

@ref	Spore formation	Confidence
31688
125439		98.684

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31688	NaCl	positive	growth	0-2 %
31688	NaCl	positive	optimum	0-2 %

Observation

@ref	Observation
31688	aggregates in chains
67770	quinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31688	30089 ChEBI	acetate	+	carbon source
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68371	27613 ChEBI	amygdalin	+	builds acid from	from API 50CH acid
31688	22599 ChEBI	arabinose	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
31688	35391 ChEBI	aspartate	+	carbon source
31688	17057 ChEBI	cellobiose	+	carbon source
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	+	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	+	builds acid from	from API 50CH acid
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
31688	28757 ChEBI	fructose	+	carbon source
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
31688	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
31688	17234 ChEBI	glucose	+	carbon source
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
31688	17716 ChEBI	lactose	+	carbon source
68371	17716 ChEBI	lactose	+	builds acid from	from API 50CH acid
31688	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
31688	17306 ChEBI	maltose	+	carbon source
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
116689	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
116689	16301 ChEBI	nitrite	-	reduction
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
31688	16634 ChEBI	raffinose	+	carbon source
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
31688	30031 ChEBI	succinate	+	carbon source
31688	17992 ChEBI	sucrose	+	carbon source
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
31688	27082 ChEBI	trehalose	+	carbon source
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
31688	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
116689	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
31688	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	+	3.1.3.2	from API zym
116689	alcohol dehydrogenase	-	1.1.1.1
31688	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
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	+	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	+	3.2.1.31	from API zym
31688	catalase	+	1.11.1.6
116689	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
31688	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68369	gelatinase	-		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
116689	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
116689	ornithine decarboxylase	-	4.1.1.17
116689	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
116689	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
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
116689	-	+	+	+	-	+	+	+	+	-	+	+	-	+	+	+	+	+	+	+

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
7581	-	-	-	-	-	+	-	+	+	+/-	+	-	+	+	-	-	-	+	-	-	+
7581	-	-	-	-	-	+	-	+	+	+	+	-	+	+/-	-	-	-	+	-	-	+

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
116689	not determinedn.d.	-	-	-	+	-	+	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	-	+	+/-	+	+/-	+	+	+	+/-	+	+	-	+/-	-	-	-	-	+/-	+	+/-	-	+	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7581	root of rice plant	Mishima	Japan	JPN	Asia
67770	Rice plant		Japan	JPN	Asia
116689	Environment, Paddy soil and the roots of Oryza sativa		Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB217471 (>99% sequence identity) for Sphingomonas from Microbeatlas

Aquatic Samples	50
Soil Samples	18
Animal Samples	14
Plant Samples	26
Total Samples	108

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7581	1	Risk group (German classification) According to TRBA 466
116689	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
67770	ASM209147v1 assembly for Sphingomonas azotifigens NBRC 15497	contig	GCA_002091475	1219041.3	1219041	45.35

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Sphingomonas azotifigens gene for 16S rRNA, partial sequence, strain: NBRC 15497	AB680881	1414		330920
7581	Sphingomonas azotifigens gene for 16S rRNA, partial sequence, strain: NBRC 15497	AB217471	1422		330920

GC content

@ref	GC-content (mol%)	Method
31688	68
67770	68	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: ASM209147v1 assembly for Sphingomonas azotifigens NBRC 15497
BV-BRC: 1219041.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.49	no
125439	gram_stain	BacteriaNetⓘ	negative	94.81	no
125439	motility	BacteriaNetⓘ	yes	61.03	no
125439	spore_formation	BacteriaNetⓘ	no	98.68	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas azotifigens NBRC 15497 strain NBRC 15497
PATRIC: 1219041.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.21	no
125438	anaerobic	anaerobicⓘ	no	94.40	yes
125438	spore-forming	spore-formingⓘ	no	84.88	yes
125438	aerobic	aerobicⓘ	yes	85.22	no
125438	thermophilic	thermophileⓘ	no	97.87	yes
125438	flagellated	motile2+ⓘ	yes	74.87	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Simple absolute quantification method correcting for quantitative PCR efficiency variations for microbial community samples.	Brankatschk R, Bodenhausen N, Zeyer J, Burgmann H.	Appl Environ Microbiol	10.1128/aem.07878-11	2012
	Sphingomonas sediminicola Is an Endosymbiotic Bacterium Able to Induce the Formation of Root Nodules in Pea (Pisum sativum L.) and to Enhance Plant Biomass Production.	Mazoyon C, Hirel B, Pecourt A, Catterou M, Gutierrez L, Sarazin V, Dubois F, Duclercq J.	Microorganisms	10.3390/microorganisms11010199	2023
Phylogeny	A primary assessment of the endophytic bacterial community in a xerophilous moss (Grimmia montana) using molecular method and cultivated isolates.	Liu XL, Liu SL, Liu M, Kong BH, Liu L, Li YH.	Braz J Microbiol	10.1590/s1517-83822014000100022	2014
	An Isolated Arthrobacter sp. Enhances Rice (Oryza sativa L.) Plant Growth.	Chhetri G, Kim I, Kang M, So Y, Kim J, Seo T.	Microorganisms	10.3390/microorganisms10061187	2022
Phylogeny	Sphingomonas pokkalii sp. nov., a novel plant associated rhizobacterium isolated from a saline tolerant pokkali rice and its draft genome analysis.	Menon RR, Kumari S, Kumar P, Verma A, Krishnamurthi S, Rameshkumar N	Syst Appl Microbiol	10.1016/j.syapm.2019.02.003	2019
Phylogeny	Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively.	Kim SJ, Moon JY, Lim JM, Ahn JH, Weon HY, Ahn TY, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.055269-0	2013
Phylogeny	Sphingomonas japonica sp. nov., isolated from the marine crustacean Paralithodes camtschatica.	Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.003285-0	2009
Phylogeny	Sphingomonas sanxanigenens sp. nov., isolated from soil.	Huang HD, Wang W, Ma T, Li GQ, Liang FL, Liu RL	Int J Syst Evol Microbiol	10.1099/ijs.0.000257-0	2009
Phylogeny	Sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity.	Romanenko LA, Uchino M, Frolova GM, Tanaka N, Kalinovskaya NI, Latyshev N, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.64441-0	2007
Phylogeny	Sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of Oryza sativa.	Xie CH, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.64056-0	2006

References

#7581	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18530
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#27965	IJSEM 889 2006 ( DOI 10.1099/ijs.0.64056-0 , PubMed 16585711 )
#31688	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 #27965
#37481	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#68371	Automatically annotated from API 50CH acid .
#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 .
#116689	Collection of Institut Pasteur ; Curators of the CIP; CIP 109209
#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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Sphingomonas azotifigens (DSM 18530, CCTCC AB 205007, IAM 15283)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002091475

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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