Strain identifier

BacDive ID: 133249

Type strain: Yes

Species: Pedobacter vanadiisoli

Strain Designation: XNV015

Strain history: <- Zhiyong Wang, Huzhong Agricultural Univ.

NCBI tax ID(s): 1761975 (species)

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General

@ref: 25116

BacDive-ID: 133249

keywords: 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming

description: Pedobacter vanadiisoli XNV015 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil of a vanadium mine.

NCBI tax id

  • NCBI tax id: 1761975
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Zhiyong Wang, Huzhong Agricultural Univ.

doi: 10.13145/bacdive133249.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Pedobacter
  • species: Pedobacter vanadiisoli
  • full scientific name: Pedobacter vanadiisoli Wang et al. 2016

@ref: 25116

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter vanadiisoli

strain designation: XNV015

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
25116negative1.0-1.5 µm0.5-0.6 µmrod-shapedno
67771rod-shapedno
67771negative

colony morphology

  • @ref: 25116
  • colony size: 2.0-4.0 mm
  • colony color: light pink
  • colony shape: circular
  • incubation period: 2 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

  • @ref: 25116
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
25116positivegrowth10-37
25116positiveoptimum28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
25116positivegrowth4.0-9.0alkaliphile
25116positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
25116aerobe
67771aerobe

spore formation

  • @ref: 25116
  • type of spore: endospore
  • spore formation: no

halophily

  • @ref: 25116
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2.0 %(w/v)

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25116168082-dehydro-D-gluconate-assimilation
25116161933-hydroxybenzoate-assimilation
25116178794-hydroxybenzoate-assimilation
25116174265-dehydro-D-gluconate-assimilation
2511630089acetate-assimilation
2511617128adipate-assimilation
2511617968butyrate-assimilation
2511616947citrate-assimilation
2511615824D-fructose-builds acid from
2511616899D-mannitol-assimilation
2511616988D-ribose-builds acid from
2511616988D-ribose-assimilation
2511617924D-sorbitol-builds acid from
2511617924D-sorbitol-assimilation
2511627689decanoate-assimilation
25116370543-hydroxybutyrate-assimilation
2511624265gluconate-assimilation
2511617268myo-inositol-assimilation
2511617240itaconate-assimilation
2511616977L-alanine-assimilation
2511618287L-fucose-assimilation
2511615971L-histidine-assimilation
2511617203L-proline-assimilation
2511617115L-serine-assimilation
2511624996lactate-assimilation
2511615792malonate-assimilation
2511617632nitrate-reduction
2511618401phenylacetate-assimilation
2511617272propionate-assimilation
2511630911sorbitol-builds acid from
251169300suberic acid-assimilation
2511627897tryptophan-energy source
2511631011valerate-assimilation
2511617057cellobiose+builds acid from
2511617634D-glucose+builds acid from
2511617634D-glucose+assimilation
2511616024D-mannose+assimilation
251164853esculin+hydrolysis
2511616236ethanol+builds acid from
251165291gelatin+hydrolysis
2511628087glycogen+assimilation
2511630849L-arabinose+builds acid from
2511630849L-arabinose+assimilation
2511662345L-rhamnose+assimilation
2511617716lactose+builds acid from
2511625115malate+assimilation
2511617306maltose+builds acid from
2511617306maltose+assimilation
2511628053melibiose+assimilation
25116506227N-acetylglucosamine+assimilation
2511664681phenyl beta-D-glucuronide+assimilation
2511626546rhamnose+builds acid from
2511617814salicin+assimilation
2511617992sucrose+builds acid from
2511617992sucrose+assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
2511617113erythritolyesyes
2511627902tetracyclineyesyes
251166472lincomycinyesyes
2511617833gentamicinyesyes
2511628001vancomycinyesyes
2511617698chloramphenicolyesyes
2511617076streptomycinyesyes
251167507neomycinyesyes
251163534cephalexinyesyes
251162637amikacinyesyes
251163547cephradineyesyes
2511628077rifampicinyesyes
251166104kanamycinyesyes
251163393carbenicillinyesyes
251167809oxacillinyesyes
2511617334penicillinyesyes
2511628971ampicillinyesyes
251163515cefuroximeyesyes
251168232piperacillinyesyes
251163508ceftazidimeyesyes

metabolite production

  • @ref: 25116
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 25116
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25116acid phosphatase+3.1.3.2
25116alkaline phosphatase+3.1.3.1
25116alpha-galactosidase+3.2.1.22
25116alpha-glucosidase+3.2.1.20
25116arginine dihydrolase-3.5.3.6
25116beta-galactosidase+3.2.1.23
25116beta-glucosidase+3.2.1.21
25116beta-glucuronidase-3.2.1.31
25116catalase+1.11.1.6
25116chymotrypsin-3.4.4.5
25116cytochrome oxidase+1.9.3.1
25116esterase-
25116esterase lipase (C 8)+
25116leucine arylamidase+3.4.11.1
25116N-acetyl-beta-glucosaminidase+3.2.1.52
25116naphthol-AS-BI-phosphohydrolase+
25116phenylalanine ammonia-lyase+4.3.1.24
25116phenylalanine deaminase+4.3.1.5
25116trypsin+3.4.21.4
25116tryptophan deaminase-4.1.99.1
25116urease-3.5.1.5
25116valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture temperatureisolation procedure
25116soil of a vanadium mineXianning, Hubei provinceChinaCHNAsia291141/10 TSB28dilution-plating method
67771From soil, vanadium mineXianning, Hubei provinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_11539.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_1456;97_1737;98_8645;99_11539&stattab=map
  • Last taxonomy: Pedobacter vanadiisoli
  • 16S sequence: KU179044
  • Sequence Identity:
  • Total samples: 41
  • soil counts: 6
  • aquatic counts: 7
  • plant counts: 28

Sequence information

16S sequences

  • @ref: 25116
  • description: Pedobacter sp. XNV015 16S ribosomal RNA gene, partial sequence
  • accession: KU179044
  • length: 1444
  • database: nuccore
  • NCBI tax ID: 1761975

GC content

@refGC-contentmethod
2511643.8high performance liquid chromatography (HPLC)
6777143.8

External links

@ref: 25116

culture collection no.: KCTC 42866, CCTCC AB 2015319

literature

  • topic: Phylogeny
  • Pubmed-ID: 27600161
  • title: Pedobacter vanadiisoli sp. nov., isolated from soil of a vanadium mine.
  • authors: Wang Z, Tan Y, Xu D, Wang G, Yuan J, Zheng S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001480
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Mining, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Vanadium, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
25116Z. T. Wang, Y.,Xu, D.,Wang, G.,Yuan, J.,Zheng, S.Pedobacter vanadiisoli sp. nov., isolated from soil of a vanadium mine10.1099/ijsem.0.001480IJSEM 66: 5112-5117 201627600161
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/