Strain identifier

BacDive ID: 13102

Type strain: Yes

Species: Pseudomonas mediterranea

Strain Designation: 9.1

Strain history: CIP <- 2002, L. Sutra, INRA, Angers, France: strain CFBP 5447 <- 1994, V. Catara, Sicilia, Italy

NCBI tax ID(s): 1348058 (strain), 183795 (species)

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General

@ref: 6499

BacDive-ID: 13102

DSM-Number: 16733

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, motile, rod-shaped, plant pathogen

description: Pseudomonas mediterranea 9.1 is an obligate aerobe, mesophilic, Gram-negative plant pathogen that was isolated from pith necrosis on tomato plant.

NCBI tax id

NCBI tax idMatching level
183795species
1348058strain

strain history

@refhistory
6499<- CFBP <- V. Catara; 9.1
120875CIP <- 2002, L. Sutra, INRA, Angers, France: strain CFBP 5447 <- 1994, V. Catara, Sicilia, Italy

doi: 10.13145/bacdive13102.20230509.8.1

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 mediterranea
  • full scientific name: Pseudomonas mediterranea Catara et al. 2002

@ref: 6499

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas mediterranea

full scientific name: Pseudomonas mediterranea Catara et al. 2002

strain designation: 9.1

type strain: yes

Morphology

cell morphology

  • @ref: 120875
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 120875
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6499CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
39928MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120875CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6499positivegrowth30mesophilic
39928positivegrowth30mesophilic
120875positivegrowth5-37
120875nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120875
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
120875NaClpositivegrowth0-4 %
120875NaClnogrowth6 %
120875NaClnogrowth8 %
120875NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
12087516947citrate+carbon source
1208754853esculin-hydrolysis
12087517632nitrate+reduction
12087516301nitrite+reduction
12087517632nitrate-respiration

antibiotic resistance

  • @ref: 120875
  • 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
12087535581indoleno

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
120875oxidase+
120875beta-galactosidase-3.2.1.23
120875alcohol dehydrogenase-1.1.1.1
120875gelatinase+/-
120875amylase+
120875DNase-
120875caseinase-3.4.21.50
120875catalase+1.11.1.6
120875tween esterase-
120875lecithinase-
120875lipase-
120875lysine decarboxylase-4.1.1.18
120875ornithine decarboxylase-4.1.1.17
120875protease+
120875tryptophan deaminase-
120875urease-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
120875--+--+--+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6499+-----+-+++++-++-++-+
6499---+--+-++++--++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120875+++++--+-----------+++----+----+++-----+---++--+-+++-++++--++-+++-----++++++++-++++++-+-++++++++++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
6499pith necrosis on tomato plantItalyITAEurope
120875TomatoItalyITAEuropeSicily1994

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Stem (Branch)

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: AF386080
  • Sequence Identity:
  • Total samples: 42314
  • soil counts: 16904
  • aquatic counts: 8731
  • animal counts: 11521
  • plant counts: 5158

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
6499yes1Risk group (German classification)
1208751Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6499
  • description: Pseudomonas mediterranea strain CFBP 5447 16S ribosomal RNA gene, partial sequence
  • accession: AF386080
  • length: 1438
  • database: ena
  • NCBI tax ID: 1348058

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas mediterranea DSM 16733GCA_900106005chromosomencbi183795
66792Pseudomonas mediterranea CFBP 5447GCA_000774145scaffoldncbi1348058
66792Pseudomonas mediterranea CFBP 54471348058.4wgspatric1348058
66792Pseudomonas mediterranea strain DSM 16733183795.36completepatric183795
66792Pseudomonas mediterranea CFBP 54472627854246draftimg1348058
66792Pseudomonas mediterranea CFBP5447 (CFBP5447 re-assembly)2596583589draftimg183795
66792Pseudomonas mediterranea DSM 167332675902957draftimg183795

GC content

  • @ref: 6499
  • GC-content: 60.2
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes91.381no
gram-positiveno98.366no
anaerobicno97.544no
aerobicyes91.113no
halophileno89.368no
spore-formingno95.009no
glucose-utilyes95.751no
flagellatedyes84.95no
thermophileno99.836yes
glucose-fermentno91.563yes

External links

@ref: 6499

culture collection no.: DSM 16733, CCM 7691, CFBP 5447, ICMP 14184, CIP 107708

straininfo link

  • @ref: 82311
  • straininfo: 87880

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12361283Phenotypic and genomic evidence for the revision of Pseudomonas corrugata and proposal of Pseudomonas mediterranea sp. nov.Catara V, Sutra L, Morineau A, Achouak W, Christen R, Gardan LInt J Syst Evol Microbiol10.1099/00207713-52-5-17492002Base Composition, Base Sequence, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Genomics, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Diseases/microbiology, Pseudomonas/*classification/genetics/metabolism/pathogenicity, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
Metabolism24418340Production of filmable medium-chain-length polyhydroxyalkanoates produced from glycerol by Pseudomonas mediterranea.Pappalardo F, Fragala M, Mineo PG, Damigella A, Catara AF, Palmeri R, Rescifina AInt J Biol Macromol10.1016/j.ijbiomac.2014.01.0142014Biocompatible Materials/*chemistry/*metabolism, Chemical Phenomena, Glycerol/*metabolism, Mechanical Phenomena, Molecular Weight, Polyesters/chemistry, Polyhydroxyalkanoates/*biosynthesis/*chemistry, Pseudomonas/*metabolism, TemperatureBiotechnology
Genetics25540338Draft Genome Sequence of Pseudomonas mediterranea Strain CFBP 5447T, a Producer of Filmable Medium-Chain-Length Polyhydroxyalkanoates.Licciardello G, Bella P, Devescovi G, Strano CP, Sarris PF, Catara AF, Venturi V, Catara VGenome Announc10.1128/genomeA.01260-142014
35442049First report of tomato pith necrosis caused by Pseudomonas mediterranea in South Korea.Lee YJ, Luo H, Kim WG, Yu JMPlant Dis10.1094/PDIS-07-21-1434-PDN2022
Phylogeny35442877Pseudomonas uvaldensis sp. nov., a bacterial pathogen causing onion bulb rot.Khanal M, Timilsina S, Bhatta BP, Bophela K, Coutinho T, Cochran K, Malla SInt J Syst Evol Microbiol10.1099/ijsem.0.0053112022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Genes, Bacterial, *Onions/microbiology, Phylogeny, Pseudomonas, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
36471469First report of Pseudomonas mediterranea causing tomato pith necrosis in Croatia.Ivic D, Novak A, Plavec J, Ilicic R, Popovic Milovanovic TPlant Dis10.1094/PDIS-10-22-2371-PDN2022

Reference

@idauthorscataloguedoi/urltitle
6499Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16733)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16733
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
39928Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5174
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
82311Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87880.1StrainInfo: A central database for resolving microbial strain identifiers
120875Curators of the CIPCollection of Institut Pasteur (CIP 107708)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107708