Strain identifier

BacDive ID: 13106

Type strain: Yes

Species: Pseudomonas lini

Strain Designation: DLE411J, D-LE411J

Strain history: CIP <- 2002, CFBP <- P. Lemanceau, Dijon, France: strain D-LE411J

NCBI tax ID(s): 163011 (species)

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General

@ref: 6577

BacDive-ID: 13106

DSM-Number: 16768

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

description: Pseudomonas lini DLE411J is an aerobe, mesophilic, motile bacterium that was isolated from bulk and rhizospheric soil.

NCBI tax id

  • NCBI tax id: 163011
  • Matching level: species

strain history

@refhistory
6577<- CFBP <- P. Lemanceau; D-LE411J
120616CIP <- 2002, CFBP <- P. Lemanceau, Dijon, France: strain D-LE411J

doi: 10.13145/bacdive13106.20230509.8.1

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 lini
  • full scientific name: Pseudomonas lini Delorme et al. 2002

@ref: 6577

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas lini

full scientific name: Pseudomonas lini Delorme et al. 2002

strain designation: DLE411J, D-LE411J

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.186
6948099.998negative
120616yesnegativerod-shaped

pigmentation

  • @ref: 120616
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6577REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a)yeshttps://mediadive.dsmz.de/medium/220aName: REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a) Composition: Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
39896MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120616CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6577positivegrowth28mesophilic
39896positivegrowth30mesophilic
59231positivegrowth20-30
120616positivegrowth5-30
120616nogrowth37mesophilic
120616nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59231aerobe
120616obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.971

halophily

@refsaltgrowthtested relationconcentration
120616NaClpositivegrowth0-2 %
120616NaClnogrowth4 %
120616NaClnogrowth6 %
120616NaClnogrowth8 %
120616NaClnogrowth10 %

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
12061616947citrate+carbon source
1206164853esculin-hydrolysis
12061617632nitrate+reduction
12061616301nitrite+reduction
12061617632nitrate-respiration

antibiotic resistance

  • @ref: 120616
  • 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
12061635581indoleno

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
120616oxidase+
120616beta-galactosidase-3.2.1.23
120616alcohol dehydrogenase-1.1.1.1
120616gelatinase-
120616amylase-
120616DNase-
120616caseinase-3.4.21.50
120616catalase+1.11.1.6
120616tween esterase-
120616lecithinase-
120616lipase-
120616lysine decarboxylase-4.1.1.18
120616ornithine decarboxylase-4.1.1.17
120616protease-
120616tryptophan deaminase-
120616urease-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
120616--+--++-+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6577+--+----+++++-++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120616+++++--+-----------++-----+----+++--+------++----+++-+--+--++-++++-+---+++-+++-++++++-+-+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
6577bulk and rhizospheric soilFranceFRAEurope
59231Bulk and rhizospheric soilFranceFRAEurope
120616GroundFranceFRAEurope1993

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_555.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_98;99_555&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AY035996
  • Sequence Identity:
  • Total samples: 42314
  • soil counts: 16904
  • aquatic counts: 8731
  • animal counts: 11521
  • plant counts: 5158

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65771Risk group (German classification)
1206161Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6577
  • description: Pseudomonas lini strain CFBP 5737 16S ribosomal RNA gene, partial sequence
  • accession: AY035996
  • length: 1545
  • database: ena
  • NCBI tax ID: 163011

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas lini DSM 16768GCA_001042905contigncbi163011
66792Pseudomonas lini CCUG 51522GCA_008801525contigncbi163011
66792Pseudomonas lini strain CCUG 51522163011.24wgspatric163011
66792Pseudomonas lini strain DSM 16768163011.3wgspatric163011
66792Pseudomonas lini DSM 167682663763025draftimg163011
66792Pseudomonas lini DSM 167682636416176draftimg163011
66792Pseudomonas lini DSM 16768GCA_900104735chromosomencbi163011

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.855no
glucose-fermentno89.046yes
flagellatedyes74.894no
gram-positiveno98.134no
anaerobicno97.242yes
aerobicyes89.896no
halophileno89.928no
spore-formingno95.63no
thermophileno99.831yes
glucose-utilyes94.401yes

External links

@ref: 6577

culture collection no.: CCUG 51522, DSM 16768, CCM 7692, CFBP 5737, ICMP 14138, CIP 107460

straininfo link

  • @ref: 82314
  • straininfo: 87863

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11931164Pseudomonas lini sp. nov., a novel species from bulk and rhizospheric soils.Delorme S, Lemanceau P, Christen R, Corberand T, Meyer JM, Gardan LInt J Syst Evol Microbiol10.1099/00207713-52-2-5132002DNA, Bacterial/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/*classification/physiology, RNA, Ribosomal, 16S/chemistry, Siderophores/analysis, *Soil Microbiology, Species Specificity, Water MicrobiologyGenetics
Phylogeny32776868Pseudomonas viciae sp. nov., isolated from rhizosphere of broad bean.Zhao H, Ma Y, Wu X, Zhang LInt J Syst Evol Microbiol10.1099/ijsem.0.0043732020Bacterial 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, *Rhizosphere, *Soil Microbiology, Ubiquinone/chemistry, Vicia faba/*microbiologyEnzymology

Reference

@idauthorscataloguedoi/urltitle
6577Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16768)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16768
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
39896Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4898
59231Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51522)https://www.ccug.se/strain?id=51522
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)
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
82314Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87863.1StrainInfo: A central database for resolving microbial strain identifiers
120616Curators of the CIPCollection of Institut Pasteur (CIP 107460)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107460