Strain identifier

BacDive ID: 14079

Type strain: Yes

Species: Shewanella loihica

Strain Designation: PV4

Strain history: CIP <- 2007, DSMZ <- J. Zhou, Okhlahoma Univ., Norman, USA: strain PV4

NCBI tax ID(s): 359303 (species)

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General

@ref: 7166

BacDive-ID: 14079

DSM-Number: 17748

keywords: 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped

description: Shewanella loihica PV4 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from an iron-rich microbial mat.

NCBI tax id

  • NCBI tax id: 359303
  • Matching level: species

strain history

@refhistory
7166<- J. Zhou; PV4 <- R. Stapleton
120643CIP <- 2007, DSMZ <- J. Zhou, Okhlahoma Univ., Norman, USA: strain PV4

doi: 10.13145/bacdive14079.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Shewanellaceae
  • genus: Shewanella
  • species: Shewanella loihica
  • full scientific name: Shewanella loihica Gao et al. 2006

@ref: 7166

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella loihica

full scientific name: Shewanella loihica Gao et al. 2006

strain designation: PV4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31813negative1.8 µm0.7 µmrod-shapedyes
120643negativerod-shapedyes

pigmentation

  • @ref: 31813
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7166LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
7166BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium514.pdf
39985Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120643CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
120643CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
7166positivegrowth20
31813positivegrowth0-42
31813positiveoptimum18
39985positivegrowth20

culture pH

@refabilitytypepHPH range
31813positivegrowth4.5-10alkaliphile
31813positiveoptimum06-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31813facultative anaerobe
120643obligate aerobe

spore formation

  • @ref: 31813
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31813NaClpositivegrowth0.5-5 %
31813NaClpositiveoptimum2 %

observation

  • @ref: 31813
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3181316947citrate+carbon source
3181328260galactose+carbon source
3181317234glucose+carbon source
3181324996lactate+carbon source
3181325115malate+carbon source
3181315792malonate+carbon source
3181317306maltose+carbon source
31813506227N-acetylglucosamine+carbon source
3181330031succinate+carbon source
12064317632nitrate+reduction
12064316301nitrite+reduction

metabolite production

  • @ref: 120643
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31813cytochrome oxidase+1.9.3.1
31813urease+3.5.1.5
120643oxidase+
120643catalase+1.11.1.6
120643urease+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
120643-+++-++++++++--+-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7166an iron-rich microbial matPacific Ocean near HawaiiUSAUSANorth America
120643Iron rich-microbial matLoihi Seamount, HawaiiUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Microbial community
  • Cat3: #Microbial mat

taxonmaps

  • @ref: 69479
  • File name: preview.99_1310.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_59;96_759;97_884;98_1035;99_1310&stattab=map
  • Last taxonomy: Shewanella loihica
  • 16S sequence: DQ286387
  • Sequence Identity:
  • Total samples: 1108
  • soil counts: 89
  • aquatic counts: 720
  • animal counts: 279
  • plant counts: 20

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71661Risk group (German classification)
1206431Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31813
  • description: Shewanella loihica strain PV-4 16S ribosomal RNA gene, partial sequence
  • accession: DQ286387
  • length: 1537
  • database: nuccore
  • NCBI tax ID: 323850

GC content

  • @ref: 31813
  • GC-content: 53.8

External links

@ref: 7166

culture collection no.: DSM 17748, ATCC BAA-1088, CIP 109777

straininfo link

  • @ref: 83248
  • straininfo: 286036

literature

  • topic: Phylogeny
  • Pubmed-ID: 16902030
  • title: Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean.
  • authors: Gao H, Obraztova A, Stewart N, Popa R, Fredrickson JK, Tiedje JM, Nealson KH, Zhou J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64354-0
  • year: 2006
  • mesh: Base Composition, Culture Media, Cyanoacrylates/analysis, DNA, Bacterial/chemistry, Fatty Acids/analysis, Genome, Bacterial, Iron, *Marine Biology, Molecular Sequence Data, Pacific Ocean, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Shewanella/chemistry/*classification/isolation & purification/physiology, Species Specificity, Temperature, Ubiquinone/analysis, Vitamin K 2/analogs & derivatives, *Water Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7166Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17748)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17748
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
31813Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2808128776041
39985Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7557
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
83248Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID286036.1StrainInfo: A central database for resolving microbial strain identifiers
120643Curators of the CIPCollection of Institut Pasteur (CIP 109777)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109777