Strain identifier

BacDive ID: 141030

Type strain: Yes

Species: Pigmentiphaga aceris

Strain Designation: SAP-32

Strain history: <- Soon Dong Lee, Jeju National Univ.

NCBI tax ID(s): 1940612 (species)

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General

@ref: 64878

BacDive-ID: 141030

DSM-Number: 104039

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

description: Pigmentiphaga aceris SAP-32 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from sap drawn from the Acer pictum from Mount Halla, Jeju, Republic of Korea.

NCBI tax id

  • NCBI tax id: 1940612
  • Matching level: species

strain history

@refhistory
64878<- S. D. Lee, Faculty of Science Education, Jeju National University, Jeju, Republic of Korea; SAP-32
67771<- Soon Dong Lee, Jeju National Univ.

doi: 10.13145/bacdive141030.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Pigmentiphaga
  • species: Pigmentiphaga aceris
  • full scientific name: Pigmentiphaga aceris Lee 2017

@ref: 64878

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Pigmentiphaga

species: Pigmentiphaga aceris

full scientific name: Pigmentiphaga aceris Lee 2017

strain designation: SAP-32

type strain: yes

Morphology

cell morphology

  • @ref: 43913
  • gram stain: negative
  • cell length: 1.6-2.3 µm
  • cell width: 0.8-0.9 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: lophotrichous

colony morphology

  • @ref: 43913
  • colony size: 1-2 mm
  • colony color: cream
  • colony shape: circular
  • incubation period: 5 days
  • medium used: Nutrient agar

pigmentation

  • @ref: 43913
  • production: no
  • name: diffusible pigments

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43913ISP 2 agaryes
43913Nutrient agar (NA)yes
43913Reasoner's 2A agar (R2A)yes
43913Trypticase soy agaryes
64878NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43913positivegrowth10-30
43913positiveoptimum30mesophilic
43913nogrowth37mesophilic
64878positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

  • @ref: 43913
  • ability: positive
  • type: growth
  • pH: 7.0-8.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43913aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
43913NaClpositivegrowth0-2 %(w/v)
43913NaClpositiveoptimum1 %(w/v)
43913NaClnogrowth3 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4391317128adipate-assimilation
4391327689decanoate-assimilation
4391317108D-arabinose-assimilation
4391317634D-glucose-assimilation
4391316899D-mannitol-assimilation
4391316024D-mannose-assimilation
4391324265gluconate-assimilation
4391317306maltose-assimilation
43913506227N-acetylglucosamine-assimilation
4391318401phenylacetate-assimilation
4391317234glucose-builds acid from
439134853esculin-degradation
439135291gelatin-hydrolysis
4391317632nitrate-reduction
4391316947citrate+assimilation
4391325115malate+assimilation

metabolite production

  • @ref: 43913
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43913catalase+1.11.1.6
43913cytochrome oxidase+1.9.3.1
43913arginine dihydrolase-3.5.3.6
43913urease-3.5.1.5
43913alkaline phosphatase+3.1.3.1
43913esterase (C 4)+
43913esterase Lipase (C 8)+
43913leucine arylamidase+3.4.11.1
43913valine arylamidase+
43913alpha-chymotrypsin+3.4.21.1
43913acid phosphatase+3.1.3.2
43913naphthol-AS-BI-phosphohydrolase+
43913lipase (C 14)-
43913cystine arylamidase-3.4.11.3
43913trypsin-3.4.21.4
43913alpha-galactosidase-3.2.1.22
43913beta-galactosidase-3.2.1.23
43913beta-glucuronidase-3.2.1.31
43913alpha-glucosidase-3.2.1.20
43913beta-glucosidase-3.2.1.21
43913N-acetyl-beta-glucosaminidase-3.2.1.52
43913alpha-mannosidase-3.2.1.24
43913alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
43913sap drawn from the Acer pictum from Mount Halla, Jeju, Republic of KoreaMount Halla, JejuRepublic of KoreaKORAsia
64878tree sap from Acer pictum Thunb.Jeju, Mount HallaRepublic of KoreaKORAsia
67771From Sap of plantJejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body Product#Plant#Plant sap (Flux)

taxonmaps

  • @ref: 69479
  • File name: preview.99_83201.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_1835;97_44173;98_57769;99_83201&stattab=map
  • Last taxonomy: Pigmentiphaga aceris subclade
  • 16S sequence: LT719155
  • Sequence Identity:
  • Total samples: 3725
  • soil counts: 1139
  • aquatic counts: 772
  • animal counts: 1021
  • plant counts: 793

Safety information

risk assessment

  • @ref: 64878
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64878
  • description: Pigmentiphaga sp. SAP-32 partial 16S rRNA gene, strain SAP-32
  • accession: LT719155
  • length: 1439
  • database: ena
  • NCBI tax ID: 1940612

GC content

  • @ref: 64878
  • GC-content: 64.4
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 64878

culture collection no.: KCTC 52619, DSM 104039

straininfo link

  • @ref: 96843
  • straininfo: 398655

literature

  • topic: Phylogeny
  • Pubmed-ID: 28840799
  • title: Pigmentiphaga aceris sp. nov., isolated from tree sap.
  • authors: Lee SD
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002073
  • year: 2017
  • mesh: Acer/*microbiology, Alcaligenaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
43913Soon Dong LeePigmentiphaga aceris sp. nov., isolated from tree sap10.1099/ijsem.0.002073IJSEM 67: 3198-3202 201728840799
64878Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104039Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104039)
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/
96843Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID398655.1