Strain identifier

BacDive ID: 3901

Type strain: Yes

Species: Deinobacterium chartae

Strain Designation: K-bf-PMWA-4.1, K4.1

Strain history: <- M. Salkinoja-Salonen, Univ. Helsinki; K4.1 <- Univ. Helsinki; HAMBI 2721 <- J.V. Ekman; K-bf-PMWA-4.1

NCBI tax ID(s): 521158 (species)

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General

@ref: 15718

BacDive-ID: 3901

DSM-Number: 21458

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

description: Deinobacterium chartae K-bf-PMWA-4.1 is an aerobe, chemoorganotroph, mesophilic bacterium that was isolated from paper mill, biofim in the wire section.

NCBI tax id

  • NCBI tax id: 521158
  • Matching level: species

strain history

  • @ref: 15718
  • history: <- M. Salkinoja-Salonen, Univ. Helsinki; K4.1 <- Univ. Helsinki; HAMBI 2721 <- J.V. Ekman; K-bf-PMWA-4.1

doi: 10.13145/bacdive3901.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/deinococcota
  • domain: Bacteria
  • phylum: Deinococcota
  • class: Deinococci
  • order: Deinococcales
  • family: Deinococcaceae
  • genus: Deinobacterium
  • species: Deinobacterium chartae
  • full scientific name: Deinobacterium chartae Ekman et al. 2011

@ref: 15718

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinobacterium

species: Deinobacterium chartae

full scientific name: Deinobacterium chartae Ekman et al. 2011

strain designation: K-bf-PMWA-4.1, K4.1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23351negative1.4-2.5 µm0.8-1.3 µmrod-shapedno
69480positive94.733

colony morphology

  • @ref: 23351
  • colony color: pale-pink
  • medium used: R2A

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15718R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
23351Reasoner's 2A agar (R2A)yes

culture temp

@refgrowthtypetemperaturerange
15718positivegrowth37mesophilic
23351positiveoptimum37-45

culture pH

  • @ref: 23351
  • ability: positive
  • type: growth
  • pH: 6.0-10.3
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 23351
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 23351
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
23351no
69480no91.961

halophily

  • @ref: 23351
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: >3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2335117521(-)-quinic acid-assimilation
2335115588D-malate-assimilation
23351169971,2-propandiol-assimilation
23351288162-deoxy-d-ribose-assimilation
2335130762salicylate-assimilation
23351309162-oxoglutarate-assimilation
233512,3-butanone-assimilation
23351182404-hydroxy-L-proline-assimilation
23351178794-hydroxybenzoate-assimilation
23351158875-aminovaleric acid-assimilation
2335130089acetate-assimilation
2335115963ribitol-assimilation
2335117925alpha-D-glucose-assimilation
2335127613amygdalin-assimilation
2335140656beta-D-allose-assimilation
2335127689decanoate-assimilation
2335117057cellobiose-assimilation
2335130719citraconate-assimilation
23351citramalic acid-assimilation
2335118333D-arabitol-assimilation
2335115824D-fructose-assimilation
2335112936D-galactose-assimilation
2335115748D-glucuronate-assimilation
2335116024D-mannose-assimilation
23351D-ribono-1,4-lactone-assimilation
2335116523D-serine-assimilation
2335117924D-sorbitol-assimilation
2335116551D-trehalose-assimilation
23351DL-carnitine-assimilation
23351dl-octopamine-assimilation
2335116813galactitol-assimilation
2335117113erythritol-assimilation
2335116537galactarate-assimilation
2335116865gamma-aminobutyric acid-assimilation
2335114336glycerol 1-phosphate-assimilation
2335115428glycine-assimilation
2335115443inulin-assimilation
2335130849L-arabinose-assimilation
2335118403L-arabitol-assimilation
2335129985L-glutamate-assimilation
2335115699L-homoserine-assimilation
2335115729L-ornithine-assimilation
2335117295L-phenylalanine-assimilation
2335116857L-threonine-assimilation
2335116414L-valine-assimilation
2335124996lactate-assimilation
2335125115malate-assimilation
2335143943methyl alpha-D-mannoside-assimilation
23351methyl beta-D-glucuronic acid-assimilation
2335174863methyl beta-D-xylopyranoside-assimilation
23351n-acetyl-neuraminic acid-assimilation
23351506227N-acetylglucosamine-assimilation
2335117148putrescine-assimilation
2335115361pyruvate-assimilation
2335141865sebacic acid-assimilation
23351sec-butylamine-assimilation
2335132488sedoheptulosan-assimilation
2335135962sorbic acid-assimilation
23351143136succinamate-assimilation
2335117992sucrose-assimilation
2335162517tricarballylate-assimilation
2335153424tween 20-assimilation
2335116704uridine-assimilation
2335117151xylitol-assimilation
2335129864mannitol-builds acid from
2335133942ribose-builds acid from
2335117306maltose-oxidation
23351286442-oxopentanoate+assimilation
233513-hydroxy 2-butanone+assimilation
23351181014-hydroxyphenylacetic acid+assimilation
23351174265-dehydro-D-gluconate+assimilation
2335113705acetoacetate+assimilation
2335118305arbutin+assimilation
2335173706bromosuccinate+assimilation
2335117968butyrate+assimilation
2335137397chondroitin sulfate+assimilation
2335116947citrate+assimilation
2335117108D-arabinose+assimilation
2335129990D-aspartate+assimilation
2335115895D-galactonic acid lactone+assimilation
2335118024D-galacturonic acid+assimilation
233518391D-gluconate+assimilation
2335117315D-glucosamine+assimilation
2335117784D-glucosaminic acid+assimilation
2335114314D-glucose 6-phosphate+assimilation
2335116443D-tagatose+assimilation
2335116398D-threonine+assimilation
2335165327D-xylose+assimilation
2335123652dextrin+assimilation
2335116016dihydroxyacetone+assimilation
2335129806fumarate+assimilation
23351495056gamma-cyclodextrin+assimilation
233515291gelatin+assimilation
2335128066gentiobiose+assimilation
2335129042glucose 1-phosphate+assimilation
2335132323glucuronamide+assimilation
2335117754glycerol+assimilation
2335128087glycogen+assimilation
2335129805glycolate+assimilation
2335173804glycyl L-aspartic acid+assimilation
2335117120hexanoate+assimilation
2335116977L-alanine+assimilation
2335117196L-asparagine+assimilation
2335129991L-aspartate+assimilation
2335118287L-fucose+assimilation
2335115971L-histidine+assimilation
2335118019L-lysine+assimilation
2335175323lactitol+assimilation
2335115792malonate+assimilation
23351melibionic acid+assimilation
2335117540methyl beta-D-galactoside+assimilation
2335151850methyl pyruvate+assimilation
2335117268myo-inositol+assimilation
23351506227N-acetylglucosamine+assimilation
23351oxalomalic acid+assimilation
2335118394palatinose+assimilation
2335150048phenylethylamine+assimilation
2335117272propionate+assimilation
2335117814salicin+assimilation
2335130031succinate+assimilation
23351132950tartrate+assimilation
2335132528turanose+assimilation
2335128757fructose+builds acid from
2335117234glucose+builds acid from
2335117306maltose+builds acid from
2335117203L-proline+nitrogen source
2335117748thymidine+nitrogen source

enzymes

  • @ref: 23351
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

  • @ref: 15718
  • sample type: paper mill, biofim in the wire section
  • country: Finland
  • origin.country: FIN
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Engineered product
#Engineered#Industrial#Plant (Factory)
#Environmental#Biofilm

taxonmaps

  • @ref: 69479
  • File name: preview.99_57019.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5644;96_25324;97_31746;98_40665;99_57019&stattab=map
  • Last taxonomy: Deinobacterium chartae subclade
  • 16S sequence: AM988777
  • Sequence Identity:
  • Total samples: 423
  • soil counts: 65
  • aquatic counts: 276
  • animal counts: 60
  • plant counts: 22

Safety information

risk assessment

  • @ref: 15718
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15718
  • description: Deinobacterium chartae partial 16S rRNA gene, type strain K4.1T
  • accession: AM988777
  • length: 1461
  • database: ena
  • NCBI tax ID: 521158

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deinobacterium chartae DSM 21458GCA_014202645scaffoldncbi521158
66792Deinobacterium chartae strain DSM 21458521158.3wgspatric521158
66792Deinobacterium chartae DSM 214582861587418draftimg521158

GC content

  • @ref: 15718
  • GC-content: 66.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno60no
flagellatedno94.008yes
gram-positiveyes69.667no
anaerobicno97.188no
aerobicyes85.442yes
halophileno89.989no
spore-formingno88.359no
glucose-utilyes81.108yes
thermophileno67.964no
motileno87.46yes
glucose-fermentno90.765no

External links

@ref: 15718

culture collection no.: DSM 21458, HAMBI 2721

straininfo link

  • @ref: 73411
  • straininfo: 401948

literature

  • topic: Phylogeny
  • Pubmed-ID: 20382794
  • title: Deinobacterium chartae gen. nov., sp. nov., an extremely radiation-resistant, biofilm-forming bacterium isolated from a Finnish paper mill.
  • authors: Ekman JV, Raulio M, Busse HJ, Fewer DP, Salkinoja-Salonen M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.017970-0
  • year: 2010
  • mesh: Bacteria/*classification/genetics/*isolation & purification/radiation effects, Bacterial Typing Techniques, Base Composition, *Biofilms, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Finland, *Industrial Microbiology, Molecular Sequence Data, Paper, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15718Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21458)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21458
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
23351Jaakko V. Ekman, Mari Raulio, Hans-Jürgen Busse, David P. Fewer, Mirja Salkinoja-Salonen10.1099/ijs.0.017970-0Deinobacterium chartae gen. nov., sp. nov., an extremely radiation-resistant, biofilm-forming bacterium isolated from a Finnish paper millIJSEM 61: 540-548 201120382794
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)
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
73411Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401948.1StrainInfo: A central database for resolving microbial strain identifiers