Strain identifier

BacDive ID: 12823

Type strain: Yes

Species: Pseudomonas citronellolis

Strain history: CIP <- 1995, DSM <- ATCC <- W. Seubert

NCBI tax ID(s): 1215097 (strain), 53408 (species)

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General

@ref: 12711

BacDive-ID: 12823

DSM-Number: 50332

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Pseudomonas citronellolis DSM 50332 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil under pine trees.

NCBI tax id

NCBI tax idMatching level
53408species
1215097strain

strain history

@refhistory
12711<- ATCC <- W. Seubert
67770K. Komagata <-- R. Hugh 846 <-- ATCC 13674 <-- W. Seubert.
118305CIP <- 1995, DSM <- ATCC <- W. Seubert

doi: 10.13145/bacdive12823.20250331.9.3

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 citronellolis
  • full scientific name: Pseudomonas citronellolis Seubert 1960 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Pseudomonas humi

@ref: 12711

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas citronellolis

full scientific name: Pseudomonas citronellolis Seubert 1960 emend. Lang et al. 2007

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
118305negativerod-shapedno
125438negative98.485
125439yes92.5
125439negative97.7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12711NUTRIENT 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
40147MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118305CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
118305CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
12711positivegrowth30
40147positivegrowth30
46720positivegrowth30
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
46720aerobe
118305obligate aerobe
125438aerobe91.119

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 97.3

compound production

@refcompound
12711polyhydroxyalkanoic acids
12711isoprene

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11830517632nitrate+reduction
11830516301nitrite+reduction
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

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11830535581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
118305oxidase+
118305catalase+1.11.1.6
118305urease-3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118305-+++-+--+-++---+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
12711+--+----+-----++-++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12711soil under pine treesVirginiaUSAUSANorth America
46720Soil under pine treesUSAUSANorth America
67770Soil under pine trees in northern VirginiaUSAUSANorth America
118305Environment, Soil under pine trees

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_854.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_203;97_221;98_250;99_854&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: Z76659
  • Sequence Identity:
  • Total samples: 112
  • soil counts: 16
  • aquatic counts: 31
  • animal counts: 53
  • plant counts: 12

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
127111Risk group (German classification)
1183051Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas citronellolis gene for 16S rRNA, strain: ATCC 13674AB0213961499nuccore53408
12711P.citronellolis 16S rRNA geneZ766591510nuccore53408
67770Pseudomonas citronellolis gene for 16S rRNA, partial sequence, strain: NBRC 103043AB6819231462nuccore53408

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas citronellolis NBRC 103043 strain NBRC 1030431215097.3wgspatric1215097
66792Pseudomonas citronellolis strain DSM 5033253408.24wgspatric53408
66792Pseudomonas citronellolis strain LMG 1837853408.9wgspatric53408
66792Pseudomonas citronellolis LMG 183782663762793draftimg53408
67770Pseudomonas citronellolis NBRC 103043GCA_002091555contigncbi1215097
67770Pseudomonas citronellolis LMG 18378GCA_900112375scaffoldncbi53408
67770Pseudomonas citronellolis DSM 50332GCA_004745455contigncbi53408

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe69.8
125439BacteriaNetgram_stainReaction to gram-stainingnegative97.7
125439BacteriaNetmotilityAbility to perform movementyes92.5
125439BacteriaNetspore_formationAbility to form endo- or exosporesno97.3
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.485no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.574yes
125438spore-formingspore-formingAbility to form endo- or exosporesno84.045no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes91.119yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99.5yes
125438motile2+flagellatedAbility to perform flagellated movementyes88.754no

External links

@ref: 12711

culture collection no.: DSM 50332, ATCC 13674, CIP 104381, CCUG 17933, LMG 18378, NRRL B-2504, CFBP 5585, JCM 13426, BCRC 14345, IAM 15129, JCM 21587, KACC 10776, KCTC 12148, NBRC 103043, NCIMB 12783

straininfo link

  • @ref: 82035
  • straininfo: 11919

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism8526489Microbial degradation of monoterpenes in the absence of molecular oxygen.Harder J, Probian CAppl Environ Microbiol10.1128/aem.61.11.3804-3808.19951995Anaerobiosis, Bacteria, Anaerobic/isolation & purification/metabolism, Biodegradation, Environmental, Environmental Pollutants/metabolism, Molecular Structure, Nitric Acid/metabolism, Oxidation-Reduction, Pseudomonas/growth & development/metabolism, Terpenes/chemistry/*metabolismEnzymology
Metabolism11718820Intracellular degradation of two structurally different polyhydroxyalkanoic acids accumulated in Pseudomonas putida and Pseudomonas citronellolis from mixtures of octanoic acid and 5-phenylvaleric acid.Chung DM, Choi MH, Song JJ, Yoon SC, Kang IK, Huh NEInt J Biol Macromol10.1016/s0141-8130(01)00172-62001Calorimetry, Differential Scanning, Caprylates/*chemistry, Carbon/metabolism, Carboxylic Acids/*metabolism, Culture Media, Kinetics, Pentanoic Acids/*chemistry, Polyesters/chemistry, Protein Binding, Pseudomonas/*metabolism, Pseudomonas putida/*metabolism, Temperature, Time FactorsCultivation
Phylogeny12656147Pseudomonas koreensis sp. nov., Pseudomonas umsongensis sp. nov. and Pseudomonas jinjuensis sp. nov., novel species from farm soils in Korea.Kwon SW, Kim JS, Park IC, Yoon SH, Park DH, Lim CK, Go SJInt J Syst Evol Microbiol10.1099/ijs.0.02326-02003Agriculture, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species SpecificityGenetics
Enzymology14499938Molecular cloning of the carboxylesterase gene and biochemical characterization of the encoded protein from Pseudomonas citronellolis ATCC 13674.Chao YP, Fu H, Wang YL, Huang WB, Wang JYRes Microbiol10.1016/S0923-2508(03)00144-X2003Amino Acid Sequence, Base Sequence, Carboxylesterase/*genetics/*metabolism, *Cloning, Molecular, Escherichia coli/enzymology/genetics, Gene Expression Regulation, Bacterial, Genomic Library, Molecular Sequence Data, Protein Folding, Pseudomonas/*enzymology/genetics, Sequence Analysis, DNA, TemperatureGenetics
Metabolism15284892Pyrimidine nucleotide synthesis in Pseudomonas citronellolis.West TPCan J Microbiol10.1139/w04-0282004Aspartate Carbamoyltransferase/metabolism, Enzyme Repression, Gene Expression Regulation, Bacterial, Pseudomonas/enzymology/genetics/*metabolism, Pyrimidine Nucleotides/*biosynthesisEnzymology
16349378Polyester Biosynthesis Characteristics of Pseudomonas citronellolis Grown on Various Carbon Sources, Including 3-Methyl-Branched Substrates.Choi MH, Yoon SCAppl Environ Microbiol10.1128/aem.60.9.3245-3254.19941994
Phylogeny17329778Pseudomonas delhiensis sp. nov., from a fly ash dumping site of a thermal power plant.Prakash O, Kumari K, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.64456-02007Acyclic Monoterpenes, *Carbon, Coal Ash, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, India, Molecular Sequence Data, Monoterpenes/metabolism, *Particulate Matter, Phenanthrenes/metabolism, Phylogeny, *Power Plants, Pseudomonas/*classification/genetics/isolation & purification/metabolism, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny17329787Pseudomonas knackmussii sp. nov.Stolz A, Busse HJ, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.64761-02007DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Pseudomonas/chemistry/*classification/genetics/physiology, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny18523175Pseudomonas panipatensis sp. nov., isolated from an oil-contaminated site.Gupta SK, Kumari R, Prakash O, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.65401-02008Bacterial Typing Techniques, Base Sequence, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Petroleum, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Species SpecificityGenetics
Metabolism29040817Potential for mcl-PHA production from nonanoic and azelaic acids.Gillis J, Ko K, Ramsay JA, Ramsay BACan J Microbiol10.1139/cjm-2017-05542017Acyltransferases/metabolism, Biomass, Caprylates/*metabolism, Carbon/metabolism, Dicarboxylic Acids/*metabolism, Fatty Acids/*metabolism, Polyhydroxyalkanoates/*biosynthesis, Pseudomonas/growth & development/*metabolismBiotechnology
Phylogeny30478729Pseudomonas humi sp. nov., isolated from leaf soil.Akita H, Kimura ZI, Hoshino TArch Microbiol10.1007/s00203-018-1588-x2018Fatty Acids/chemistry, Japan, Multilocus Sequence Typing, Phylogeny, Plant Leaves, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Ubiquinone/analysisEnzymology
32260526Preparation and Characterization of Films Based on a Natural P(3HB)/mcl-PHA Blend Obtained through the Co-culture of Cupriavidus Necator and Pseudomonas Citronellolis in Apple Pulp Waste.Rebocho AT, Pereira JR, Neves LA, Alves VD, Sevrin C, Grandfils C, Freitas F, Reis MAMBioengineering (Basel)10.3390/bioengineering70200342020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12711Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 50332)https://www.dsmz.de/collection/catalogue/details/culture/DSM-50332
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
40147Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16283
46720Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 17933)https://www.ccug.se/strain?id=17933
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
82035Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID11919.1StrainInfo: A central database for resolving microbial strain identifiers
118305Curators of the CIPCollection of Institut Pasteur (CIP 104381)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104381
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1