Strain identifier

BacDive ID: 13129

Type strain: Yes

Species: Pseudomonas alcaliphila

Strain Designation: AL 15-21, AL15-21

Strain history: CIP <- 2003, I. Yumoto, AIST, Sapporo, Japan: strain AL15-21

NCBI tax ID(s): 1215093 (strain), 101564 (species)

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General

@ref: 7164

BacDive-ID: 13129

DSM-Number: 17744

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Pseudomonas alcaliphila AL 15-21 is an aerobe, mesophilic, motile bacterium that was isolated from seawater.

NCBI tax id

NCBI tax idMatching level
1215093strain
101564species

strain history

@refhistory
7164<- IAM <- I. Yumoto, Natl. Industr. Research Inst., Sapporo; AL 15-21
67770I. Yumoto AL15-21.
116207CIP <- 2003, I. Yumoto, AIST, Sapporo, Japan: strain AL15-21

doi: 10.13145/bacdive13129.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Pseudomonas
  • species: Pseudomonas alcaliphila
  • full scientific name: Pseudomonas alcaliphila Yumoto et al. 2001

@ref: 7164

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas alcaliphila

full scientific name: Pseudomonas alcaliphila Yumoto et al. 2001

strain designation: AL 15-21, AL15-21

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.745
6948099.999negative
116207nonegativerod-shaped

pigmentation

  • @ref: 116207
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7164BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
39976MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116207CIP Medium 469yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=469
116207CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7164positivegrowth28mesophilic
39976positivegrowth30mesophilic
60326positivegrowth30mesophilic
67770positivegrowth30mesophilic
116207positivegrowth10-41
116207nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60326aerobe
116207obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.882

halophily

@refsaltgrowthtested relationconcentration
116207NaClpositivegrowth0-6 %
116207NaClnogrowth8 %
116207NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine+hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
11620716947citrate+carbon source
1162074853esculin-hydrolysis
11620717632nitrate+reduction
11620716301nitrite-reduction
11620717632nitrate-respiration

antibiotic resistance

  • @ref: 116207
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11620735581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6
116207oxidase+
116207beta-galactosidase-3.2.1.23
116207alcohol dehydrogenase+1.1.1.1
116207gelatinase+/-
116207amylase-
116207DNase-
116207caseinase+3.4.21.50
116207catalase+1.11.1.6
116207tween esterase-
116207lecithinase+
116207lipase+
116207lysine decarboxylase-4.1.1.18
116207ornithine decarboxylase-4.1.1.17
116207protease+
116207tryptophan deaminase-
116207urease-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
116207-+++-+--+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7164+--+----+--+--++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116207++-----------------------------+-+---------++----+++-+++----+-+++------+++-+++++++-+---++++++++++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7164seawaterRumoi, HokkaidoJapanJPNAsia
60326SeawaterJapanJPNAsia
67770Seawatercoast of Rumoi, HokkaidoJapanJPNAsia
116207Environment, Sea waterRumoi, HokkaidoJapanJPNAsia1999

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_2828.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_64;98_1532;99_2828&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AB030583
  • Sequence Identity:
  • Total samples: 7465
  • soil counts: 769
  • aquatic counts: 2670
  • animal counts: 2451
  • plant counts: 1575

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71641Risk group (German classification)
1162071Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas alcalophila 16S ribosomal RNA, partial sequenceAB0305831489ena101564
20218Pseudomonas alcaliphila gene for 16S rRNA, partial sequence, strain: NBRC 102411AB6817671462ena101564

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas alcaliphila NBRC 102411GCA_002091495contigncbi1215093
66792Pseudomonas alcaliphila JCM 10630GCA_900101755scaffoldncbi101564
66792Pseudomonas alcaliphila NBRC 102411 strain NBRC 1024111215093.3wgspatric1215093
66792Pseudomonas alcaliphila strain JCM 10630101564.8wgspatric101564
66792Pseudomonas alcaliphila NBRC 1024112806311028draftimg1215093
66792Pseudomonas alcaliphila JCM 106302663762780draftimg101564

GC content

  • @ref: 67770
  • GC-content: 63.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.16no
gram-positiveno98.765no
anaerobicno97.53no
aerobicyes92.02yes
halophileno84.083no
spore-formingno95.661no
thermophileno99.822yes
glucose-utilyes93.904no
flagellatedyes91.92no
glucose-fermentno89.684no

External links

@ref: 7164

culture collection no.: CCUG 54778, KCTC 12910, DSM 17744, IAM 14884, JCM 10630, CGMCC 1.6415, LMG 23134, MTCC 7934, NBRC 102411, CIP 108031

straininfo link

  • @ref: 82337
  • straininfo: 100883

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11321079Pseudomonas alcaliphila sp. nov., a novel facultatively psychrophilic alkaliphile isolated from seawater.Yumoto I, Yamazaki K, Hishinuma M, Nodasaka Y, Suemori A, Nakajima K, Inoue N, Kawasaki KInt J Syst Evol Microbiol10.1099/00207713-51-2-3492001Alkalies, Bacterial Typing Techniques, Carbohydrates, DNA, Ribosomal, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Pseudomonas/*classification/cytology/genetics/isolation & purification, RNA, Ribosomal, 16S, Seawater, Terminology as Topic, *Water MicrobiologyGenetics
Phylogeny23178721Pseudomonas sagittaria sp. nov., a siderophore-producing bacterium isolated from oil-contaminated soil.Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA, Chen WM, Shen FT, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.045567-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Petroleum Pollution, Phospholipids/analysis, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Taiwan, Ubiquinone/analysisGenetics
Phylogeny23918786Pseudomonas guguanensis sp. nov., a gammaproteobacterium isolated from a hot spring.Liu YC, Young LS, Lin SY, Hameed A, Hsu YH, Lai WA, Shen FT, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.047712-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Hot Springs/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistryGenetics
Phylogeny25574037Pseudomonas zhaodongensis sp. nov., isolated from saline and alkaline soils.Zhang L, Pan Y, Wang K, Zhang X, Zhang C, Zhang S, Fu X, Jiang JInt J Syst Evol Microbiol10.1099/ijs.0.0000572015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny29948825Taxonomic description and draft genome of Pseudomonas sediminis sp. nov., isolated from the rhizospheric sediment of Phragmites karka.Behera P, Mahapatra M, Seuylemezian A, Vaishampayan P, Ramana VV, Joseph N, Joshi A, Shouche Y, Suar M, Pattnaik AK, Rastogi GJ Microbiol10.1007/s12275-018-7549-x2018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, *Genome, Bacterial, India, Lakes, Phospholipids/analysis, Phylogeny, Pseudomonas/chemistry/*classification/*genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Rhizosphere, Saline Waters, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny30601113Pseudomonas mangrovi sp. nov., isolated from mangrove soil.Ye Y, Chen C, Ren Y, Wang R, Zhang C, Han S, Ju Z, Zhao Z, Sun C, Wu MInt J Syst Evol Microbiol10.1099/ijsem.0.0031412019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32242797Pseudomonas hydrolytica sp. nov., multiple polymer-degrading bacteria isolated from soil in China.Zhou S, Wang Y, Xia H, Liu D, Chen S, Li FInt J Syst Evol Microbiol10.1099/ijsem.0.0041292020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Genes, Bacterial, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Polymers, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny35364354Toxoflavin secreted by Pseudomonas alcaliphila inhibits the growth of Legionella pneumophila and Vermamoeba vermiformis.Faucher SP, Matthews S, Nickzad A, Vounba P, Shetty D, Bedard E, Prevost M, Deziel E, Paranjape KWater Res10.1016/j.watres.2022.1183282022Humans, *Legionella/genetics, *Legionella pneumophila/genetics, Phylogeny, Pseudomonas/genetics, Pyrimidinones, RNA, Ribosomal, 16S/genetics, Triazines, Water, Water MicrobiologyPathogenicity
Phylogeny36204622Isolation of Pseudomonas aromaticivorans sp. nov from a hydrocarbon-contaminated groundwater capable of degrading benzene-, toluene-, m- and p-xylene under microaerobic conditions.Banerjee S, Bedics A, Toth E, Kriszt B, Soares AR, Boka K, Tancsics AFront Microbiol10.3389/fmicb.2022.9291282022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7164Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17744)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17744
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
39976Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5609
60326Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54778)https://www.ccug.se/strain?id=54778
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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
82337Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100883.1StrainInfo: A central database for resolving microbial strain identifiers
116207Curators of the CIPCollection of Institut Pasteur (CIP 108031)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108031