Strain identifier

BacDive ID: 14149

Type strain: Yes

Species: Novosphingobium subterraneum

Strain Designation: B0478

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

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

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General

@ref: 4723

BacDive-ID: 14149

DSM-Number: 12447

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative

description: Novosphingobium subterraneum B0478 is a Gram-negative bacterium that was isolated from subsurface core at 180 m depth.

NCBI tax id

NCBI tax idMatching level
1219057strain
48936species

strain history

@refhistory
4723<- D.L. Balkwill <- J.K. Fredrickson; B0478
415321997, D. L. Balkwill, Florida State Univ., Tallahassee, FL, USA: strain SMCC B0478
123353CIP <- 1997, D. L. Balkwill, Florida State Univ., Tallahassee, FL, USA: strain SMCC B0478

doi: 10.13145/bacdive14149.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Novosphingobium
  • species: Novosphingobium subterraneum
  • full scientific name: Novosphingobium subterraneum corrig. (Balkwill et al. 1997) Takeuchi et al. 2001

  • synonyms

    @refsynonym
    20215Sphingomonas subterranea
    20215Novosphingobium subterraneae
    20215Novosphingobium suterraneae

@ref: 4723

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium subterraneum

full scientific name: Novosphingobium subterraneum (Balkwill et al. 1997) Takeuchi et al. 2001

strain designation: B0478

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
123353negativerod-shapedno
69480negative95.231

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4723PLATE COUNT AGAR (DSMZ Medium 464)yeshttps://mediadive.dsmz.de/medium/464Name: PLATE COUNT AGAR (DSMZ Medium 464) Composition: Agar 15.0 g/l Tryptone 5.0 g/l Yeast extract 2.5 g/l Dextrose 1.0 g/l Distilled water
4723MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)yeshttps://mediadive.dsmz.de/medium/457Name: MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) Composition: Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
41532MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123353CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
4723positivegrowth30
41532positivegrowth25
123353positivegrowth25-37
123353nogrowth5
123353nogrowth10
123353nogrowth41

Physiology and metabolism

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

halophily

@refsaltgrowthtested relationconcentration
123353NaClpositivegrowth0-2 %
123353NaClnogrowth4 %
123353NaClnogrowth6 %
123353NaClnogrowth8 %
123353NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
123353citrate-carbon source16947
123353esculin+hydrolysis4853
123353nitrate-reduction17632
123353nitrite-reduction16301
123353nitrate-respiration17632

antibiotic resistance

  • @ref: 123353
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 123353
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
123353oxidase+
123353beta-galactosidase+3.2.1.23
123353alcohol dehydrogenase-1.1.1.1
123353gelatinase-
123353amylase-
123353DNase-
123353caseinase-3.4.21.50
123353catalase+1.11.1.6
123353tween esterase+
123353lecithinase-
123353lipase-
123353lysine decarboxylase-4.1.1.18
123353ornithine decarboxylase-4.1.1.17
123353protease-
123353tryptophan deaminase-
123353urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123353-+++-+++--++--+++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123353----+/------+++--------++/-++++/-+--++--+/-+/-+------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123353+-+-+--++++----++++-++-+--------------+---------------+-------+++-----------------------++++-----+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4723subsurface core at 180 m depthS.C., AllendaleUSAUSANorth America
123353Environment, Atlantic coastal plain subsurface sediments (saturated)South CarolinaUnited States of AmericaUSANorth America1986

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Core sample

taxonmaps

  • @ref: 69479
  • File name: preview.99_1358.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_437;97_499;98_1073;99_1358&stattab=map
  • Last taxonomy: Novosphingobium subterraneum
  • 16S sequence: U20773
  • Sequence Identity:
  • Total samples: 4519
  • soil counts: 621
  • aquatic counts: 2580
  • animal counts: 673
  • plant counts: 645

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
47231Risk group (German classification)
1233531Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Novosphingobium subterraneum gene for 16S rRNA, complete sequenceAB0250141446nuccore48936
20218Novosphingobium subterraneum gene for 16S rRNA, partial sequence, strain: NBRC 16086AB6810461410nuccore48936
4723Sphingomonas subterraneae SMCC B0478 16S small subunit rRNA gene, partial sequenceU207731417nuccore48936
124043Novosphingobium subterraneum NBRC 16086 gene for 16S rRNA, partial sequence.LC752393562nuccore48936

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Novosphingobium subterraneum NBRC 16086GCA_001598575contigncbi1219057
66792Novosphingobium subterraneum DSM 12447GCA_000807925contigncbi48936
66792Novosphingobium subterraneum DSM 1244748936.3wgspatric48936
66792Novosphingobium subterraneum NBRC 160861219057.3wgspatric1219057
66792Novosphingobium subterraneum DSM 124472636415671draftimg48936
66792Novosphingobium subterraneum NBRC 160862675903438draftimg1219057

GC content

  • @ref: 4723
  • GC-content: 60.0

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno95.231no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no91.346no
69480spore-formingspore-formingAbility to form endo- or exosporesno88.399no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.079no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.305yes
69480flagellatedmotile2+Ability to perform flagellated movementyes68.804no

External links

@ref: 4723

culture collection no.: DSM 12447, CIP 105153, IFO 16086, NBRC 16086, SMCC B0478, ATCC 700279, CCUG 56444

straininfo link

  • @ref: 83315
  • straininfo: 362266

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism8995822Taxonomic 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 CMInt J Syst Bacteriol10.1099/00207713-47-1-1911997Alcohols/metabolism, Bacteriological Techniques, Base Composition, Catalase/metabolism, Culture Media/metabolism, DNA Fingerprinting, Disaccharides/metabolism, Fatty Acids/analysis, Fermentation, Gelatin/metabolism, Glucose/metabolism, Gram-Negative Aerobic Bacteria/*classification/genetics/metabolism, Hexoses/metabolism, Hydrolases/metabolism, Indoles/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Pentoses/metabolism, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Urease/metabolism, Water MicrobiologyPhylogeny
Phylogeny15879260Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China.Liu ZP, Wang BJ, Liu YH, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.63468-02005Bacterial Typing Techniques, Biodegradation, Environmental, China, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fresh Water/*microbiology, Genes, Bacterial, Genes, rRNA, Geologic Sediments/*microbiology, Hydrocarbons, Aromatic/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/cytology/*isolation & purification/physiology, Water MicrobiologyEnzymology
Phylogeny24737793Novosphingobium 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 SInt J Syst Evol Microbiol10.1099/ijs.0.057273-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphates/*chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryGenetics
Phylogeny24994774Novosphingobium aquiterrae sp. nov., isolated from ground water.Lee JC, Kim SG, Whang KSInt J Syst Evol Microbiol10.1099/ijs.0.060749-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Groundwater/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryGenetics
Phylogeny25320143Proposal of Novosphingobium rhizosphaerae sp. nov., isolated from the rhizosphere.Kampfer P, Martin K, McInroy JA, Glaeser SPInt J Syst Evol Microbiol10.1099/ijs.0.070375-02014Alabama, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry, Zea mays/microbiologyGenetics
Phylogeny27306976Description of Novosphingobiumflavum sp. nov., isolated from soil.Nguyen TM, Myung SW, Jang H, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0012422016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome
Phylogeny27599476Novosphingobium bradum sp. nov., isolated from a spring.Sheu SY, Liu LP, Chen WMInt J Syst Evol Microbiol10.1099/ijsem.0.0014752016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydroxybutyrates/chemistry, Natural Springs/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Polyesters/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Taiwan, Ubiquinone/chemistryTranscriptome
27635318Genome 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 MAPeerJ10.7717/peerj.23322016
Phylogeny30958256Novosphingobium 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 WJInt J Syst Evol Microbiol10.1099/ijsem.0.0033842019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hot Springs/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/isolation & purification, Ubiquinone/chemistryTranscriptome
Phylogeny33411666Novosphingobium 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 JInt J Syst Evol Microbiol10.1099/ijsem.0.0046282021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Petroleum Pollution, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Sphingomonadaceae/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4723Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12447)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12447
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
41532Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17141
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83315Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362266.1StrainInfo: A central database for resolving microbial strain identifiers
123353Curators of the CIPCollection of Institut Pasteur (CIP 105153)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105153
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy