Name: Novosphingobium subterraneum B0478
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14149

Type strain:

Species: Novosphingobium subterraneum

Strain Designation: B0478

Culture col. no.: DSM 12447, CIP 105153, IFO 16086, NBRC 16086, SMCC B0478

Strain history: 1997, D. L. Balkwill, Florida State Univ., Tallahassee, FL, USA: strain SMCC B0478

NCBI tax ID(s): 1219057 (strain), 48936 (species)

Section

Novosphingobium subterraneum B0478 is a mesophilic bacterium that was isolated from subsurface core at 180 m depth.

mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Erythrobacteraceae*
	Genus	*Novosphingobium*
	Species	**Novosphingobium subterraneum**
	Full Scientific Name (PNU)	Novosphingobium subterraneum corrig. (Balkwill et al. 1997) Takeuchi et al. 2001

	Synonym	Sphingomonas subterranea
	Synonym	Novosphingobium subterraneae
	Synonym	Novosphingobium suterraneae

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4723]

Culture medium

PLATE COUNT AGAR (DSMZ Medium 464)

[Ref.: #4723]

Culture medium growth

[Ref.: #4723]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #4723]

Culture medium composition

expand / minimize

[Ref.: #4723]

Culture medium

MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)

[Ref.: #4723]

Culture medium growth

[Ref.: #4723]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #4723]

Culture medium composition

expand / minimize

[Ref.: #41532]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #41532]

Culture medium growth

[Ref.: #41532]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4723]			growth	30 °C
[Ref.: #41532]			growth	25 °C

[Ref.: #4723]	Temperature range	mesophilic
[Ref.: #41532]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	3-chlorocatechol degradation	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	ethylmalonyl-CoA pathway	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	phenol degradation	95	19 of 20
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	3-phenylpropionate degradation	86.67	13 of 15
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	chlorophyll metabolism	72.22	13 of 18
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	androgen and estrogen metabolism	68.75	11 of 16
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	66.67	6 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	polyamine pathway	65.22	15 of 23
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	degradation of sugar acids	64	16 of 25
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	60	6 of 10
[Ref.: #66794]	carotenoid biosynthesis	59.09	13 of 22
[Ref.: #66794]	benzoyl-CoA degradation	57.14	4 of 7
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	54.55	6 of 11
[Ref.: #66794]	cholesterol biosynthesis	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	oxidative phosphorylation	42.86	39 of 91
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	41.18	7 of 17
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	ginsenoside metabolism	31.25	5 of 16
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #4723]	Sample type/isolated from	subsurface core at 180 m depth
[Ref.: #4723]	Geographic location (country and/or sea, region)	S.C., Allendale
[Ref.: #4723]	Country	USA
[Ref.: #4723]	Country ISO 3 Code	USA
[Ref.: #4723]	Continent	North America
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Core sample

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence U20773 (>99% sequence identity) for Novosphingobium subterraneum from Microbeatlas

Aquatic Samples	2580
Soil Samples	621
Animal Samples	673
Plant Samples	645
Total Samples	4519

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

[Ref.: #4723]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #20218]	Novosphingobium subterraneum gene for 16S rRNA, complete sequence	AB025014	1446	ENA	48936 tax ID	*
[Ref.: #20218]	Novosphingobium subterraneum gene for 16S rRNA, partial sequence, strain: NBRC 16086	AB681046	1410	ENA	48936 tax ID	*
[Ref.: #4723]	Sphingomonas subterraneae SMCC B0478 16S small subunit rRNA gene, partial sequence	U20773	1417	ENA	48936 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Novosphingobium subterraneum NBRC 16086 NBRC 16086	GCA_001598575	contig	GenBank	1219057 tax ID	*
[Ref.: #66792]	Novosphingobium subterraneum DSM 12447	GCA_000807925	contig	GenBank	48936 tax ID	*
[Ref.: #66792]	Novosphingobium subterraneum DSM 12447	48936.3	wgs	PATRIC	48936 tax ID	*
[Ref.: #66792]	Novosphingobium subterraneum NBRC 16086	1219057.3	wgs	PATRIC	1219057 tax ID	*
[Ref.: #66792]	Novosphingobium subterraneum DSM 12447	2636415671	draft	JGI IMG/M	48936 tax ID	*
[Ref.: #66792]	Novosphingobium subterraneum NBRC 16086	2675903438	draft	JGI IMG/M	1219057 tax ID	*

[Ref.: #4723]

GC-content

60.0 mol%

Availability in culture collections External links

[Ref.: #4723]

Culture collection no.

DSM 12447, CIP 105153, IFO 16086, NBRC 16086, SMCC B0478

[Ref.: #20218]

Associated Passport(s) in StrainInfo

44790, 44789, 211479, 487345, 117784

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov.	Balkwill DL, Drake GR, Reeves RH, Fredrickson JK, White DC, Ringelberg DB, Chandler DP, Romine MF, Kennedy DW, Spadoni CM	Int J Syst Bacteriol	10.1099/00207713-47-1-191	1997	*
Phylogeny	Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China.	Liu ZP, Wang BJ, Liu YH, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.63468-0	2005	*
Phylogeny	Novosphingobium kunmingense sp. nov., isolated from a phosphate mine.	Xie F, Quan S, Liu D, He W, Wang Y, Ma H, Chen G, Chao Y, Qian S	Int J Syst Evol Microbiol	10.1099/ijs.0.057273-0	2014	*
Phylogeny	Novosphingobium aquiterrae sp. nov., isolated from ground water.	Lee JC, Kim SG, Whang KS	Int J Syst Evol Microbiol	10.1099/ijs.0.060749-0	2014	*
Phylogeny	Proposal of Novosphingobium rhizosphaerae sp. nov., isolated from the rhizosphere.	Kampfer P, Martin K, McInroy JA, Glaeser SP	Int J Syst Evol Microbiol	10.1099/ijs.0.070375-0	2014	*
Phylogeny	Description of Novosphingobiumflavum sp. nov., isolated from soil.	Nguyen TM, Myung SW, Jang H, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001242	2016	*
Phylogeny	Novosphingobium bradum sp. nov., isolated from a spring.	Sheu SY, Liu LP, Chen WM	Int J Syst Evol Microbiol	10.1099/ijsem.0.001475	2016	*
Phylogeny	Novosphingobium meiothermophilum sp. nov., isolated from a hot spring.	Xian WD, Li MM, Salam N, Ding YP, Zhou EM, Yin YR, Liu L, Xiao M, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003384	2019	*
Phylogeny	Novosphingobium olei sp. nov., with the ability to degrade diesel oil, isolated from oil-contaminated soil and proposal to reclassify Novosphingobium stygium as a later heterotypic synonym of Novosphingobium aromaticivorans.	Chaudhary DK, Dahal RH, Kim DU, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004628	2021	*
	Genome sequencing-assisted identification and the first functional validation of N-acyl-homoserine-lactone synthases from the Sphingomonadaceae family.	Gan HM, Dailey LK, Halliday N, Williams P, Hudson AO, Savka MA	PeerJ	10.7717/peerj.2332	2016	*

References

#4723

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12447

#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 )

#41532 ; 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) .

#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 .

#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) .

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Novosphingobium subterraneum in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF