Sphingopyxis terrae (DSM 8831, ATCC 51381, IFO 15098)

Name: Sphingopyxis terrae (DSM 8831, ATCC 51381, IFO 15098)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14275

Type strain

Strain Designation E-1-A

Culture col. no. DSM 8831 ATCC 51381 IFO 15098 NBRC 15098 E-1-A 9 more

NCBI tax ID(s) 1219058 33052 2448440

Special Collections DSMZ JCM KCTC CIP Literature strains

History <- IFO <- F. Kawai, Kobe Univ. Commerce <- Kyoto Univ. IFO 15098 <-- F. Kawai E-1-A. CIP <- 1994, IFO <- F. Kawai, Kobe Univ. of Commerce, Japan: strain E-1-A

Links

Sphingopyxis terrae E-1-A is an obligate aerobe, Gram-negative, motile bacterium that was isolated from activated sludge.

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

Name and taxonomic classification

SI-ID 9371

LMG 17326,ATCC 51381,CIP 104198,DSM 8831,IFO 15098,JCM 10195,IFO 15908,KCTC 2814,NCIMB 13385,NBRC 15098,NCCB 95164,LMD 95.164,HAMBI 1834,IAM 14462,KACC 10928,BCRC 17643,CCRC 17643

@ref 20215

Last LPSN update 2026-02-09 11:21:22

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingopyxis

Species Sphingopyxis terrae

Full scientific name Sphingopyxis terrae (Takeuchi et al. 1993) Takeuchi et al. 2001

Synonyms (1)

Sphingomonas terrae

BacDive ID	Other strains from **Sphingopyxis terrae** (2)	Type strain
14284	S. terrae UI2, DSM 24316, CCM 7428, MTCC 8591 (type strain)
135453	S. terrae CIP 104253, CCUG 27293, GIFU 11456, IFO 10924, ...

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
123463	negative	rod-shaped
125438	negative		96.494
125439	negative		98.9

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3421	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
3421	GRACILIBACILLUS MEDIUM (DSMZ Medium 802)	Medium recipe at MediaDive	Name: GRACILIBACILLUS MEDIUM (DSMZ Medium 802) Composition: NaCl 100.0 g/l KH2PO4 23.4 g/l MgSO4 x 7 H2O 20.0 g/l Tris-HCl 12.0 g/l Glucose 2.0 g/l KCl 2.0 g/l Yeast extract 2.0 g/l Trypticase peptone 2.0 g/l NaBr 0.1 g/l FeCl2 x 4 H2O 0.04 g/l MnCl2 x 4 H2O 0.04 g/l HCl 0.0064 g/l CoCl2 x 6 H2O 0.00049505 g/l ZnCl2 0.000138614 g/l NiCl2 x 6 H2O 0.000138614 g/l AlCl3 x 6 H2O 0.000118812 g/l Na2MoO4 x 2 H2O 7.9208e-05 g/l Na2WO4 x 2 H2O 1.18812e-05 g/l H3BO3 1.18812e-05 g/l CuCl2 x 2 H2O 3.9604e-06 g/l Distilled water CaCl2
37376	MEDIUM 29- Brain heart agar		Distilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
123463	CIP Medium 29	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
3421	positive	growth	28
37376	positive	growth	30
67770	positive	growth	30
123463	positive	growth	30-37
123463	negative	growth	5
123463	negative	growth	41
123463	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
123463	obligate aerobe
125439	obligate aerobe	99.3

Spore formation

@ref	Spore formation	Confidence
125438		91.669
125439		95.3

Compound production

3421

Compoundpolyethyleneglycols with MW of 200-20.000

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65237	17128 ChEBI	adipate	-	assimilation
123463	16947 ChEBI	citrate	-	carbon source
65237	16899 ChEBI	D-mannitol	-	assimilation
65237	16024 ChEBI	D-mannose	-	assimilation
65237	27689 ChEBI	decanoate	-	assimilation
65237	5291 ChEBI	gelatin	-	hydrolysis
65237	17234 ChEBI	glucose	-	builds acid from
65237	17234 ChEBI	glucose	+	assimilation
65237	30849 ChEBI	L-arabinose	-	assimilation
65237	25115 ChEBI	malate	+	assimilation
65237	506227 ChEBI	N-acetylglucosamine	-	assimilation
123463	17632 ChEBI	nitrate	-	reduction
123463	16301 ChEBI	nitrite	-	reduction
65237	18401 ChEBI	phenylacetate	-	assimilation
123463	132112 ChEBI	sodium thiosulfate	-	builds gas from

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
123463	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
123463	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
65237	acid phosphatase	+	3.1.3.2
123463	alcohol dehydrogenase	-	1.1.1.1
65237	alkaline phosphatase	+	3.1.3.1
65237	alpha-chymotrypsin	+	3.4.21.1
65237	alpha-fucosidase	-	3.2.1.51
65237	alpha-galactosidase	-	3.2.1.22
65237	alpha-glucosidase	+	3.2.1.20
65237	alpha-mannosidase	-	3.2.1.24
65237	arginine dihydrolase	-	3.5.3.6
123463	beta-galactosidase	-	3.2.1.23
65237	beta-glucosidase	-	3.2.1.21
65237	beta-glucuronidase	-	3.2.1.31
123463	catalase	+	1.11.1.6
65237	cystine arylamidase	+	3.4.11.3
123463	DNase	+
65237	esterase (C 4)	+
65237	esterase Lipase (C 8)	+
123463	gelatinase	-
65237	leucine arylamidase	+	3.4.11.1
65237	lipase (C 14)	+
123463	lysine decarboxylase	-	4.1.1.18
65237	N-acetyl-beta-glucosaminidase	-	3.2.1.52
65237	naphthol-AS-BI-phosphohydrolase	+
123463	ornithine decarboxylase	-	4.1.1.17
123463	oxidase	+
123463	phenylalanine ammonia-lyase	-	4.3.1.24
65237	trypsin	+	3.4.21.4
123463	urease	-	3.5.1.5
65237	valine arylamidase	+

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
123463	not determinedn.d.	-	+	-	+	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	-	+	+	-	-	-	-	-	-	-	+	+	+	+	+	+	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Activated sludge

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
3421	activated sludge	Nagoya	Japan	JPN	Asia
67770	Activated sludge
123463	Environment, Activated sludge	Nagoya	Japan	JPN	Asia	1974

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3421	1	Risk group (German classification) According to TRBA 466
123463	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	ASM161097v1 assembly for Sphingopyxis terrae subsp. terrae NBRC 15098 203-1	complete	GCA_001610975		2684623122	1219058	90.13
67770	ASM159881v1 assembly for Sphingopyxis terrae subsp. terrae NBRC 15098	contig	GCA_001598815	1219058.3	2731957716	1219058	61.81

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Sphingopyxis terrae 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	GQ907184	579	33052
20218	Sphingopyxis terrae gene for 16S rRNA, partial sequence	D13727	1417	33052
20218	Sphingopyxis terrae gene for 16S ribosomal RNA	D84531	1386	33052
20218	Sphingopyxis terrae gene for 16S rRNA, partial sequence, strain: NBRC 15098	AB680765	1414	33052
3421	Sphingopyxis terrae strain JCM 10195 16S ribosomal RNA gene, partial sequence	MF618306	1432	33052

GC content

@ref	GC-content (mol%)	Method
3421	64.95	sequence analysis
65237	65.2	genome sequence analysis
67770	63	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: Sphingopyxis terrae NBRC 15098
PATRIC: 1219058.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.30	no
125439	gram_stain	BacteriaNetⓘ	negative	98.90	no
125439	motility	BacteriaNetⓘ	yes	57.70	no
125439	spore_formation	BacteriaNetⓘ	no	95.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingopyxis terrae subsp. terrae NBRC 15098 203-1
NCBI: GCA_001610975.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.49	no
125438	anaerobic	anaerobicⓘ	no	95.07	yes
125438	aerobic	aerobicⓘ	yes	89.02	yes
125438	spore-forming	spore-formingⓘ	no	91.67	no
125438	thermophilic	thermophileⓘ	no	96.33	yes
125438	flagellated	motile2+ⓘ	yes	65.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	16S-23S rRNA Gene Intergenic Spacer Region Variability Helps Resolve Closely Related Sphingomonads.	Tokajian S, Issa N, Salloum T, Ibrahim J, Farah M.	Front Microbiol	10.3389/fmicb.2016.00149	2016
	Complete Genome Sequence of Sphingopyxis terrae Strain 203-1 (NBRC 111660), a Polyethylene Glycol Degrader.	Ohtsubo Y, Nonoyama S, Nagata Y, Numata M, Tsuchikane K, Hosoyama A, Yamazoe A, Tsuda M, Fujita N, Kawai F.	Genome Announc	10.1128/genomea.00530-16	2016
Metabolism	Isolation and Characterization of a Bacterial Strain Capable of Efficient Berberine Degradation.	Liu S, Zhang Y, Zeng P, Wang H, Song Y, Li J.	Int J Environ Res Public Health	10.3390/ijerph16040646	2019
	Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales.	Viswanathan V, Narjala A, Ravichandran A, Jayaprasad S, Siddaramappa S.	Genome Biol Evol	10.1093/gbe/evx024	2017
Genetics	MALDI-TOF MS analysis of ribosomal proteins coded in S10 and spc operons rapidly classified the Sphingomonadaceae as alkylphenol polyethoxylate-degrading bacteria from the environment.	Hotta Y, Sato H, Hosoda A, Tamura H	FEMS Microbiol Lett	10.1111/j.1574-6968.2012.02525.x	2012
Phylogeny	Genome-based reclassification of Sphingopyxis ummariensis as a later heterotypic synonym of Sphingopyxis terrae, with the descriptions of Sphingopyxis terrae subsp. terrae subsp. nov. and Sphingopyxis terrae subsp. ummariensis subsp. nov.	Feng GD, Wang DD, Yang SZ, Li HP, Zhu HH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002465	2017
Phylogeny	Sphingopyxis ummariensis sp. nov., isolated from a hexachlorocyclohexane dump site.	Sharma P, Verma M, Bala K, Nigam A, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.008805-0	2009
Phylogeny	Sphingopyxis chilensis sp. nov., a chlorophenol-degrading bacterium that accumulates polyhydroxyalkanoate, and transfer of Sphingomonas alaskensis to Sphingopyxis alaskensis comb. nov.	Godoy F, Vancanneyt M, Martinez M, Steinbuchel A, Swings J, Rehm BHA	Int J Syst Evol Microbiol	10.1099/ijs.0.02375-0	2003
Phylogeny	Sphingopyxis witflariensis sp. nov., isolated from activated sludge.	Kampfer P, Witzenberger R, Denner EB, Busse HJ, Neef A	Int J Syst Evol Microbiol	10.1099/00207713-52-6-2029	2002
Phylogeny	Sphingopyxis yananensis sp. nov., a novel 2-nitropropane degrading bacterium isolated from a microbial fermentation bed substrate.	Zheng CC, Jiang YY, Yu TF, Li J, Ai JM, Li MP, Liu XD, Deng ZS	Arch Microbiol	10.1007/s00203-022-03132-0	2022

References

#3421	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 8831
#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 )
#37376	; Curators of the CIP;
#65237	Guang-Da Feng, Dong-Dong Wang, Song-Zhen Yang, Hua-Ping Li, Hong-Hui Zhu: Genome-based reclassification of Sphingopyxis ummariensis as a later heterotypic synonym of Sphingopyxis terrae, with the descriptions of Sphingopyxis terrae subsp. terrae subsp. nov. and Sphingopyxis terrae subsp. ummariensis subsp. nov.. IJSEM 67: 5279 - 5283 2017 ( DOI 10.1099/ijsem.0.002465 , PubMed 29087277 )
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#123463	Collection of Institut Pasteur ; Curators of the CIP; CIP 104198
#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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Sphingopyxis terrae (DSM 8831, ATCC 51381, IFO 15098)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001610975

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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