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, Gram-negative, motile, rod-shaped

description: Roseateles depolymerans 61A is an obligate aerobe, Gram-negative, motile 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/bacdive2992.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Sphaerotilaceae
  • 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 arrangementconfidence
23092negative2.0 µm0.5 µmrod-shapedyespolar
32233negative2 µm0.5 µmrod-shapedyes
125439negative90.4
125438negative99

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

@refgrowthtypetemperature
23092nogrowth45.0
23092positiveoptimum35.0
32233positivegrowth20-30
59470positivegrowth37
4500positivegrowth28

culture pH

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

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
23092obligate aerobe
32233aerobe
59470aerobe
125438aerobe92.462
125439obligate aerobe90.2

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 93.5

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:group2AB0036241452nuccore76731
32233Roseateles depolymerans partial 16S rRNA gene, type strain CCUG 52219TAM5014431396nuccore76731
4500Roseateles depolymerans strain 61A (DSM11813) gene for 16S rRNA, clone:group1AB0036231452nuccore76731
124043Roseateles depolymerans strain CCUG 52219 16S ribosomal RNA gene, partial sequence.OQ629324385nuccore76731

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.011yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes92.462yes
125438spore-formingspore-formingAbility to form endo- or exosporesno85.449no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99.436no
125438motile2+flagellatedAbility to perform flagellated movementyes85.061yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno93.5
125439BacteriaNetmotilityAbility to perform movementyes75.4
125439BacteriaNetgram_stainReaction to gram-stainingnegative90.4
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe90.2

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
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1