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Strain identifier

BacDive ID: 2061

Type strain: Yes

Species: Pandoraea thiooxydans

Strain Designation: ATSB16

Strain history: <- LMG <- T.-M. Sa; ATSB16

NCBI tax ID(s): 445709 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 18000

BacDive-ID: 2061

DSM-Number: 25325

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

description: Pandoraea thiooxydans ATSB16 is an aerobe, chemolithoautotroph, mesophilic bacterium that was isolated from rhizosphere soils of sesame Sesamum indicum L..

NCBI tax id

  • NCBI tax id: 445709
  • Matching level: species

strain history: <- LMG <- T.-M. Sa; ATSB16

doi: 10.13145/bacdive2061.20220920.7

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Pandoraea
  • species: Pandoraea thiooxydans
  • full scientific name: Pandoraea thiooxydans Anandham et al. 2010

@ref: 18000

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Pandoraea

species: Pandoraea thiooxydans

full scientific name: Pandoraea thiooxydans Anandham et al. 2010

strain designation: ATSB16

type strain: yes

Morphology

cell morphology

  • @ref: 23162
  • gram stain: negative
  • cell length: 1.2-4.5 µm
  • cell width: 0.5-0.7 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

@refincubation periodcolony colorcolony shapemedium used
180001-2 days
231622 dayswhitecircularR2A

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18000CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://bacmedia.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
23162Reasoner's 2A agar (R2A)yes
42013MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
18000positivegrowth30mesophilic
23162positivegrowth4-42
23162positiveoptimum30mesophilic
42013positivegrowth30mesophilic

culture pH

@refabilitytypepH
23162positivegrowth4.0-10.0
23162positiveoptimum7.0

Physiology and metabolism

oxygen tolerance

  • @ref: 23162
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 23162
  • type: chemolithoautotroph

halophily

  • @ref: 23162
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23162168082-dehydro-D-gluconate-assimilation
23162161933-hydroxybenzoate-assimilation
23162178794-hydroxybenzoate-assimilation
23162174265-dehydro-D-gluconate-assimilation
2316227689decanoate-assimilation
2316216988D-ribose-assimilation
2316217268myo-inositol-assimilation
2316217240itaconate-assimilation
2316230849L-arabinose-assimilation
2316228053melibiose-assimilation
23162506227N-acetylglucosamine-assimilation
2316217814salicin-assimilation
2316217992sucrose-assimilation
2316227897tryptophan-energy source
231624853esculin-hydrolysis
231625291gelatin-hydrolysis
23162yeast extract-required for growth
23162370543-hydroxybutyrate+assimilation
2316217128adipate+assimilation
2316227442beta-D-fucose+assimilation
2316217634D-glucose+assimilation
2316216899D-mannitol+assimilation
2316216024D-mannose+assimilation
2316217924D-sorbitol+assimilation
2316228087glycogen+assimilation
2316216977L-alanine+assimilation
2316218287L-fucose+assimilation
2316217203L-proline+assimilation
2316262345L-rhamnose+assimilation
2316217115L-serine+assimilation
2316224996lactate+assimilation
2316225115malate+assimilation
2316217306maltose+assimilation
2316230860methylmalonic acid+assimilation
2316218401phenylacetate+assimilation
2316232032potassium gluconate+assimilation
2316217272propionate+assimilation
2316232954sodium acetate+assimilation
231629300suberic acid+assimilation
2316231011valerate+assimilation
2316217234glucose+fermentation
2316253426tween 80+hydrolysis
2316217632nitrate+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

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantis sensitive
23162100147nalidixic acidyesyes
2316228971ampicillinyesyes
2316217698chloramphenicolyesyes
231626104kanamycinyesyes
2316245924trimethoprimyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2316235581indoleno
6836935581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
2316235581indole-
6836935581indole-

enzymes

@refvalueactivityec
23162acid phosphatase-3.1.3.2
23162alkaline phosphatase-3.1.3.1
23162alpha-chymotrypsin-3.4.21.1
23162alpha-fucosidase-3.2.1.51
23162alpha-galactosidase-3.2.1.22
23162alpha-glucosidase-3.2.1.20
23162alpha-mannosidase-3.2.1.24
23162arginine dihydrolase-3.5.3.6
23162beta-galactosidase-3.2.1.23
23162beta-glucosidase-3.2.1.21
23162beta-glucuronidase-3.2.1.31
23162catalase-1.11.1.6
23162cystine arylamidase-3.4.11.3
23162cytochrome oxidase+1.9.3.1
23162esterase (C 4)+
23162esterase lipase (C 8)-
23162leucine arylamidase+3.4.11.1
23162lipase (C 14)-
23162N-acetyl-beta-glucosaminidase-3.2.1.52
23162naphthol-AS-BI-phosphohydrolase+
23162trypsin-3.4.21.4
23162tryptophan deaminase-4.1.99.1
23162urease+3.5.1.5
23162valine arylamidase-
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
18000+------------------+-

Isolation, sampling and environmental information

isolation

  • @ref: 18000
  • sample type: rhizosphere soils of sesame Sesamum indicum L.
  • host species: Sesamum indicum
  • geographic location: Jung ha-dong
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

  • @ref: 18000
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18000
  • description: Pandoraea thiooxydans strain ATSB16 16S ribosomal RNA gene, partial sequence
  • accession: EF397578
  • length: 1410
  • database: ena
  • NCBI tax ID: 445709

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pandoraea thiooxydans DSM 25325GCA_001017775completencbi445709
66792Pandoraea thiooxydans ATSB16GCA_001931675completencbi445709
66792Pandoraea thiooxydans strain ATSB16445709.9completepatric445709
66792Pandoraea thiooxydans strain DSM 25325445709.3completepatric445709
66792Pandoraea thiooxydans ATSB162721755763completeimg445709
66792Pandoraea thiooxydans DSM 253252648501246completeimg445709

GC content

@refGC-contentmethod
1800064.0
2316264.0high performance liquid chromatography (HPLC)

External links

@ref: 18000

culture collection no.: DSM 25325, KACC 12757, LMG 24779

straininfo link

@refpassport
20218http://www.straininfo.net/strains/849717
20218http://www.straininfo.net/strains/849718

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19643869Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.).Anandham R, Indiragandhi P, Kwon SW, Sa TM, Jeon CO, Kim YK, Jee HJInt J Syst Evol Microbiol10.1099/ijs.0.012823-02009Burkholderiaceae/classification/genetics/*isolation & purification/*metabolism, Chemoautotrophic Growth, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Sesamum/*microbiology, *Soil Microbiology, Thiosulfates/*metabolismMetabolism
Genetics26603120Complete genome sequence of Pandoraea thiooxydans DSM 25325(T), a thiosulfate-oxidizing bacterium.Yong D, Ee R, Lim YL, Yu CY, Ang GY, How KY, Tee KK, Yin WF, Chan KGJ Biotechnol10.1016/j.jbiotec.2015.11.0092015*Base Sequence, Biodegradation, Environmental, Burkholderiaceae/enzymology/*genetics/metabolism, DNA, Bacterial/genetics, Genome, Bacterial, Molecular Sequence Data, Oxidation-Reduction, Oxidoreductases/genetics/metabolism, Rhizosphere, Sequence Analysis, DNA, Soil Microbiology, Thiosulfates/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
18000Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25325)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25325
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
23162Rangasamy Anandham, Pandiyan Indiragandhi, Soon Wo Kwon, Tong Min Sa, Che Ok Jeon, Yong Ki Kim, Hyeong Jin Jee10.1099/ijs.0.012823-0Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.)IJSEM 60: 21-26 201019643869
42013Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68369Automatically annotated from API 20NE