Strain identifier

BacDive ID: 158761

Type strain: Yes

Species: Pseudomonas floridensis

Strain Designation: GEV388

Strain history: CIP <- 2017, S. Timilsina, Florida Univ., Gainesville, Florida, USA: strain GEV388

NCBI tax ID(s): 1958950 (species)

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General

@ref: 65513

BacDive-ID: 158761

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, Gram-negative, motile, rod-shaped, colony-forming

description: Pseudomonas floridensis GEV388 is an obligate aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from symptomatic leaf spots in tomato field.

NCBI tax id

  • NCBI tax id: 1958950
  • Matching level: species

strain history

  • @ref: 119402
  • history: CIP <- 2017, S. Timilsina, Florida Univ., Gainesville, Florida, USA: strain GEV388

doi: 10.13145/bacdive158761.20230509.8.1

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 floridensis
  • full scientific name: Pseudomonas floridensis Timilsina et al. 2018

@ref: 65513

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas floridensis

strain designation: GEV388

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
65513negative1.75-3.6 µm0.75 µmrod-shapedyespolar
69480yes97.043
69480negative99.988
119402negativerod-shapedyes

colony morphology

  • @ref: 65513
  • colony size: 0.5-1.0 mm
  • colony shape: circular
  • incubation period: 1 day
  • medium used: NA

Culture and growth conditions

culture medium

@refnamegrowthlink
65513Nutrient agar (NA)yes
65513King's medium Byes
119402CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
65513positivegrowth4-37
65513positiveoptimum26-29mesophilic

culture pH

  • @ref: 65513
  • ability: positive
  • type: growth
  • pH: 5-8

Physiology and metabolism

oxygen tolerance

  • @ref: 65513
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
65513no
69480no99.757
69481no100

halophily

  • @ref: 65513
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 4 %(w/v)

observation

@refobservation
65513fluorescent cells in King's B agar
65513yellowish, mucoid biofilm on NA with 5 % sucrose
65513induces hypersensitive reaction on tobacco

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6551316651(S)-lactate+assimilation
65513309162-oxoglutarate+assimilation
6551330089acetate+assimilation
6551317925alpha-D-glucose+assimilation
6551316947citrate+assimilation
6551318333D-arabitol+assimilation
6551315824D-fructose+assimilation
6551312936D-galactose+assimilation
6551318024D-galacturonic acid+assimilation
655138391D-gluconate+assimilation
6551315748D-glucuronate+assimilation
6551315588D-malate+assimilation
6551316899D-mannitol+assimilation
6551316024D-mannose+assimilation
6551333801D-saccharate+assimilation
6551317924D-sorbitol+assimilation
6551316537galactarate+assimilation
6551316865gamma-aminobutyric acid+assimilation
6551317754glycerol+assimilation
6551316977L-alanine+assimilation
6551329991L-aspartate+assimilation
6551317464L-galactonic acid gamma-lactone+assimilation
6551329985L-glutamate+assimilation
6551315589L-malate+assimilation
6551318183L-pyroglutamic acid+assimilation
6551317115L-serine+assimilation
6551317268myo-inositol+assimilation
6551317309pectin+hydrolysis
6551326490quinate+assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis resistant
6551345735troleandomycinyesyes
655136472lincomycinyesyes
6551329673rifamycin svyesyes
6551375273niaproofyesyes
6551328001vancomycinyesyes
6551375193tetrazolium violetyesyes
6551375198tetrazolium blueyesyes

enzymes

@refvalueactivityec
65513catalase+1.11.1.6
65513cytochrome oxidase-1.9.3.1
65513arginine dihydrolase-3.5.3.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
65513symptomatic leaf spots in tomato fieldFloridaUSAUSANorth America
119402Environment, TomatoFloridaUnited States of AmericaUSANorth America2011

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)
#Infection#Plant infections#Spot (Leaf,Stem)

Safety information

risk assessment

  • @ref: 119402
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessiondatabase
6551316S rRNA gene sequenceKY614190nuccore
6551316S rRNA gene sequenceKY614191nuccore
6551316S rRNA gene sequenceKY614192nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas floridensis GEV388GCA_002087235scaffoldncbi1958950
66792Pseudomonas floridensis GEV3882791355582draftimg1958950

GC content

  • @ref: 65513
  • GC-content: 59.17
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes72.769no
gram-positiveno98.411yes
anaerobicno98.375yes
aerobicyes93.936yes
halophileno92.027no
spore-formingno94.222yes
glucose-utilyes94.925yes
thermophileno99.778yes
motileyes89.436yes
glucose-fermentno91.031no

External links

@ref: 65513

culture collection no.: LMG 30013, ATCC TSD-90, CIP 111601

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29148362Pseudomonas floridensis sp. nov., a bacterial pathogen isolated from tomato.Timilsina S, Minsavage GV, Preston J, Newberry EA, Paret ML, Goss EM, Jones JB, Vallad GEInt J Syst Evol Microbiol10.1099/ijsem.0.0024452017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Lycopersicon esculentum/*microbiology, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, Plant Diseases/microbiology, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Solanum tuberosum/microbiology, Tobacco/microbiologyTranscriptome
Phylogeny31263923Pseudomonas ovata sp. nov., Isolated from the Skin of the Tail of Farmed Murray cod (Maccullochella peelii peelii) with a Profound Ulceration.Rao Q, Liu Y, Chen C, Lin Q, Ren L, Huang M, Tu J, Luo TCurr Microbiol10.1007/s00284-019-01729-12019Animals, Aquaculture, Base Composition, China, DNA, Bacterial/genetics, Fish Diseases/*microbiology, Genes, Bacterial/genetics, Genome, Bacterial/genetics, Lipids/chemistry, Nucleic Acid Hybridization, Perciformes/*microbiology, *Phylogeny, Pseudomonas/chemistry/*classification/genetics/*physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
65513Sujan Timilsina, Gerald V. Minsavage, James Preston, Eric A. Newberry, Matthews L. Paret, Erica M. Goss, Jeffrey B. Jones and Gary E. ValladPseudomonas floridensis sp. nov., a bacterial pathogen isolated from tomato10.1099/ijsem.0.002445IJSEM 68: 64-70 201829148362
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
119402Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111601Collection of Institut Pasteur (CIP 111601)