Strain identifier

BacDive ID: 2992

Type strain: Yes

Species: Roseateles depolymerans

Strain Designation: 61A

Strain history: <- T. Suyama; 61A

NCBI tax ID(s): 76731 (species)

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General

@ref: 4500

BacDive-ID: 2992

DSM-Number: 11813

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

description: Roseateles depolymerans 61A is an obligate aerobe, thermophilic, Gram-negative bacterium that was isolated from fresh water.

NCBI tax id

  • NCBI tax id: 76731
  • Matching level: species

strain history

  • @ref: 4500
  • history: <- T. Suyama; 61A

doi: 10.13145/bacdive2992.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Roseateles
  • species: Roseateles depolymerans
  • full scientific name: Roseateles depolymerans Suyama et al. 1999

@ref: 4500

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Roseateles

species: Roseateles depolymerans

full scientific name: Roseateles depolymerans Suyama et al. 1999

strain designation: 61A

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
23092negative2.0 µm0.5 µmrod-shapedyespolar
32233negative2 µm0.5 µmrod-shapedyes

colony morphology

  • @ref: 23092
  • colony color: pink
  • incubation period: 3 days
  • medium used: PHC agar plate medium

pigmentation

@refproductionname
23092yescarotenoids
23092yesBacteriochlorophyll c
32233no

Culture and growth conditions

culture medium

@refnamegrowthlink
23092PHC agar plate mediumyes
4500NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf

culture temp

@refgrowthtypetemperaturerange
23092nogrowth45.0thermophilic
23092positiveoptimum35.0mesophilic
32233positivegrowth20-30
59470positivegrowth37mesophilic
4500positivegrowth28mesophilic

culture pH

  • @ref: 23092
  • ability: positive
  • type: optimum
  • pH: 6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23092obligate aerobe
32233aerobe
59470aerobe

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
23092casamino acids+carbon source
23092citrate+carbon source16947
23092D-fructose+carbon source15824
23092D-galactose+carbon source12936
23092D-glucose+carbon source17634
23092L-malate+carbon source15589
23092lactate+carbon source24996
23092mannitol+carbon source29864
23092pyruvate+carbon source15361
23092succinate+carbon source30031
23092yeast extract+carbon source
23092poly(caprolactone)+degradation53200
23092poly(hexamethylene carbonate)+degradation
23092poly(tetramethylene carbonate)+degradation
23092casamino acids+growth
23092citrate+growth16947
23092D-fructose+growth15824
23092D-galactose+growth12936
23092D-glucose+growth17634
23092L-malate+growth15589
23092lactate+growth24996
23092mannitol+growth29864
23092pyruvate+growth15361
23092succinate+growth30031
23092yeast extract+growth
32233gluconate+carbon source24265
32233glucose+carbon source17234
32233malate+carbon source25115
32233maltose+carbon source17306

metabolite production

  • @ref: 23092
  • Chebi-ID: 53388
  • metabolite: polyhydroxybutyrate
  • production: yes

enzymes

@refvalueactivityec
23092catalase-1.11.1.6
23092cytochrome oxidase+1.9.3.1
23092gelatinase+
32233gelatinase+
32233cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment culture composition
4500fresh waterHanamuro river, Ibaraki prefectureJapanJPNAsia
23092rivercontaining emulsified poly(hexamethylene carbonate)
59470Fresh waterHanamuro riverJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #River (Creek)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5856.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_1238;97_1469;98_4356;99_5856&stattab=map
  • Last taxonomy: Roseateles
  • 16S sequence: AM501443
  • Sequence Identity:
  • Total samples: 1380
  • soil counts: 360
  • aquatic counts: 489
  • animal counts: 216
  • plant counts: 315

Safety information

risk assessment

  • @ref: 4500
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Roseateles depolymerans strain 61A (DSM11813) gene for 16S rRNA, clone:group2AB0036241452ena76731
32233Roseateles depolymerans partial 16S rRNA gene, type strain CCUG 52219TAM5014431396nuccore76731
4500Roseateles depolymerans strain 61A (DSM11813) gene for 16S rRNA, clone:group1AB0036231452ena76731

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Roseateles depolymerans DSM 11813GCA_003387155scaffoldncbi76731
66792Roseateles depolymerans strain DSM 1181376731.7wgspatric76731
66792Roseateles depolymerans DSM 118132770939641draftimg76731

GC content

  • @ref: 23092
  • GC-content: 66.2-66.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.45yes
flagellatedyes79.321yes
gram-positiveno99.02yes
anaerobicno97.367yes
aerobicyes92.924no
halophileno98.375no
spore-formingno93.813no
glucose-utilyes90.591yes
thermophileno99.075no
glucose-fermentno89.409no

External links

@ref: 4500

culture collection no.: DSM 11813, CCUG 52219

straininfo link

  • @ref: 72514
  • straininfo: 49185

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10319464Roseateles depolymerans gen. nov., sp. nov., a new bacteriochlorophyll a-containing obligate aerobe belonging to the beta-subclass of the Proteobacteria.Suyama T, Shigematsu T, Takaichi S, Nodasaka Y, Fujikawa S, Hosoya H, Tokiwa Y, Kanagawa T, Hanada SInt J Syst Bacteriol10.1099/00207713-49-2-4491999Bacteria, Aerobic/*classification/physiology/ultrastructure, Bacteriochlorophylls/*metabolism, Carotenoids/metabolism, DNA, Ribosomal/genetics, Genes, rRNA, Light-Harvesting Protein Complexes, Molecular Sequence Data, Photosynthesis, Photosynthetic Reaction Center Complex Proteins, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny17978231Description of Pelomonas aquatica sp. nov. and Pelomonas puraquae sp. nov., isolated from industrial and haemodialysis water.Gomila M, Bowien B, Falsen E, Moore ERB, Lalucat JInt J Syst Evol Microbiol10.1099/ijs.0.65149-02007Bacterial Proteins/genetics, Bacterial Typing Techniques, Betaproteobacteria/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, DNA, Ribosomal Spacer/analysis, Fatty Acids/analysis, Genotype, *Industry, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Renal Dialysis, Sequence Analysis, DNA, *Water MicrobiologyGenetics
Genetics26784990Complete genome of biodegradable plastics-decomposing Roseateles depolymerans KCTC 42856(T) (=61A(T)).Lee SH, Choe H, Kim SG, Park DS, Nasir A, Kim BK, Kim KMJ Biotechnol10.1016/j.jbiotec.2016.01.0122016Bacterial Typing Techniques, Base Composition, Base Sequence, Biodegradable Plastics, Burkholderia/*genetics/isolation & purification/metabolism, Chromosome Mapping, *Chromosomes, Bacterial, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fresh Water/microbiology, Genome Size, *Genome, Bacterial, Japan, RNA, Bacterial/genetics, Water MicrobiologyEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
4500Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11813)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11813
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
23092Tetsushi Suyama,Toru Shigematsu,Shinichi Takaichi,Yoshinobu Nodasaka,Seizo Fujikawa,Hiroyuki Hosoya,Yutaka Tokiwa,Takahiro Kanagawa,Satoshi Hanada10.1099/00207713-49-2-449Roseateles depolymerans gen. nov., sp. nov., a new bacteriochlorophyll a-containing obligate aerobe belonging to the beta-subclass of the ProteobacteriaIJSEM 49: 449-457 199910319464
32233Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128475
59470Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52219)https://www.ccug.se/strain?id=52219
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
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
72514Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49185.1StrainInfo: A central database for resolving microbial strain identifiers