Strain identifier

BacDive ID: 24437

Type strain: Yes

Species: Chryseomonas luteola

Strain Designation: BY-1

Strain history: <- KACC <- Z. Zeng et al., Key Laboratory of Microbiological Engineering of Agricultural Environment, Nanjing Agricultural University

NCBI tax ID(s): 1076620 (species)

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General

@ref: 21140

BacDive-ID: 24437

DSM-Number: 27927

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

description: Chryseomonas luteola BY-1 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from soil form agricultural field exposed to herbicide fomesafen for many years.

NCBI tax id

  • NCBI tax id: 1076620
  • Matching level: species

strain history

  • @ref: 21140
  • history: <- KACC <- Z. Zeng et al., Key Laboratory of Microbiological Engineering of Agricultural Environment, Nanjing Agricultural University

doi: 10.13145/bacdive24437.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Chryseomonas
  • species: Chryseomonas luteola
  • full scientific name: Chryseomonas luteola (Kodama et al. 1985) Holmes et al. 1987

  • synonyms

    @refsynonym
    20215Pseudomonas luteola
    20215Chryseomonas polytricha
    20215Pseudomonas zeshuii

@ref: 21140

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas zeshuii

full scientific name: Pseudomonas zeshuii Feng et al. 2012

strain designation: BY-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30513negative3 µm0.7 µmrod-shapedno
69480yes99.075
69480negative99.994

pigmentation

  • @ref: 30513
  • production: yes

multimedia

  • @ref: 21140
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27927.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21140TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
21140LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21140positivegrowth28mesophilic
30513positivegrowth20-40
30513positiveoptimum32.5mesophilic

culture pH

@refabilitytypepHPH range
30513positivegrowth05-09alkaliphile
30513positiveoptimum7

Physiology and metabolism

spore formation

@refspore formationconfidence
30513no
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
30513NaClpositivegrowth0-5 %
30513NaClpositiveoptimum0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30513370543-hydroxybutyrate+carbon source
30513178794-hydroxybenzoate+carbon source
3051321217L-alaninamide+carbon source
3051316449alanine+carbon source
30513286442-oxopentanoate+carbon source
3051322599arabinose+carbon source
3051322653asparagine+carbon source
3051335391aspartate+carbon source
3051316947citrate+carbon source
3051315740formate+carbon source
3051333984fucose+carbon source
3051324175galacturonate+carbon source
3051324265gluconate+carbon source
3051317234glucose+carbon source
3051329987glutamate+carbon source
3051317754glycerol+carbon source
3051315792malonate+carbon source
3051317306maltose+carbon source
3051329864mannitol+carbon source
3051351850methyl pyruvate+carbon source
3051326271proline+carbon source
3051326490quinate+carbon source
3051326546rhamnose+carbon source
3051317822serine+carbon source
3051330031succinate+carbon source
3051327082trehalose+carbon source
305134853esculin+hydrolysis
3051317632nitrate+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

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
30513catalase+1.11.1.6
30513gelatinase+
30513urease+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 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
21140+--+++++++++-+++-++--

Isolation, sampling and environmental information

isolation

  • @ref: 21140
  • sample type: soil form agricultural field exposed to herbicide fomesafen for many years
  • geographic location: Heilongjiang province, Qiqihar city
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1236.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_224;97_842;98_978;99_1236&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: JN411093
  • Sequence Identity:
  • Total samples: 23564
  • soil counts: 2524
  • aquatic counts: 6287
  • animal counts: 12446
  • plant counts: 2307

Safety information

risk assessment

  • @ref: 21140
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21140
  • description: Pseudomonas zeshuii strain BY-1 16S ribosomal RNA gene, partial sequence
  • accession: JN411093
  • length: 1459
  • database: ena
  • NCBI tax ID: 1076620

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas zeshuii KACC 15471GCA_900141925scaffoldncbi1076620
66792Pseudomonas zeshuii strain KACC 154711076620.3wgspatric1076620
66792Pseudomonas zeshuii DSM 279272663762797draftimg1076620

GC content

  • @ref: 21140
  • GC-content: 55.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno72no
motileyes86.59no
flagellatedno52.765yes
gram-positiveno98.438yes
anaerobicno98.498no
aerobicyes92.152no
halophileno91.232yes
spore-formingno94.438yes
thermophileno99.58yes
glucose-utilyes95.535yes
glucose-fermentno87.952yes

External links

@ref: 21140

culture collection no.: DSM 27927, ACCC 05688, KACC 15471

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22199212Pseudomonas zeshuii sp. nov., isolated from herbicide-contaminated soil.Feng Z, Zhang J, Huang X, Zhang J, Chen M, Li SInt J Syst Evol Microbiol10.1099/ijs.0.037796-02011Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Herbicides, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Ubiquinone/analysisGenetics
Metabolism22757645Microbial degradation of fomesafen by a newly isolated strain Pseudomonas zeshuii BY-1 and the biochemical degradation pathway.Feng ZZ, Li QF, Zhang J, Zhang J, Huang X, Lu P, Li SPJ Agric Food Chem10.1021/jf30113072012Benzamides/*metabolism, Biodegradation, Environmental, DNA, Bacterial/analysis, Herbicides/*metabolism, Polymerase Chain Reaction, Pseudomonas/genetics/isolation & purification/*metabolism, Soil/analysis, Soil Microbiology, Soil Pollutants/metabolismEnzymology

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
21140Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27927Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27927)
30513Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172684528776041
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
68369Automatically annotated from API 20NE
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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