Strain identifier

BacDive ID: 138523

Type strain: Yes

Species: Caldimonas manganoxidans

Strain history: CIP <- 2002, JCM <- 1999, M. Takeda: strain HS, Leptothrix sp.

NCBI tax ID(s): 196015 (species)

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General

@ref: 39908

BacDive-ID: 138523

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

description: Caldimonas manganoxidans CIP 107619 is a thermophilic, Gram-negative, motile bacterium of the family Comamonadaceae.

NCBI tax id

  • NCBI tax id: 196015
  • Matching level: species

strain history

@refhistory
67770M. Takeda strain HS.
39908CIP <- 2002, JCM <- 1999, M. Takeda: strain HS, Leptothrix sp.

doi: 10.13145/bacdive138523.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Caldimonas
  • species: Caldimonas manganoxidans
  • full scientific name: Caldimonas manganoxidans Takeda et al. 2002

@ref: 39908

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Caldimonas

species: Caldimonas manganoxidans

type strain: yes

Morphology

cell morphology

  • @ref: 39908
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 39908
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
39908MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
39908CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
39908positivegrowth45thermophilic
67770positivegrowth45thermophilic
39908positivegrowth25-45
39908nogrowth5psychrophilic
39908nogrowth10psychrophilic

Physiology and metabolism

compound production

  • @ref: 67770
  • compound: Thermostable poly(3-hydroxybutyrate) depolymerase

halophily

@refsaltgrowthtested relationconcentration
39908NaClnogrowth0 %
39908NaClnogrowth2 %
39908NaClnogrowth4 %
39908NaClnogrowth6 %
39908NaClnogrowth8 %
39908NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3990816947citrate+carbon source
399084853esculin-hydrolysis
3990817632nitrate+reduction
3990816301nitrite-reduction
3990817632nitrate-respiration

antibiotic resistance

  • @ref: 39908
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 39908
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
39908oxidase+
39908beta-galactosidase+3.2.1.23
39908alcohol dehydrogenase-1.1.1.1
39908gelatinase-
39908amylase+
39908DNase-
39908caseinase-3.4.21.50
39908catalase+1.11.1.6
39908tween esterase+
39908lecithinase-
39908lipase-
39908lysine decarboxylase-4.1.1.18
39908ornithine decarboxylase-4.1.1.17
39908protease+
39908tryptophan deaminase-
39908urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
39908--+--+-----+---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
39908++-------++---------------+----+-+--+-------------+--+------+-+++----------+------------+-++-+---+-

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample type
39908MatsueJapanJPNAsia
67770MatsueJapanJPNAsiaHot spring water
39908MatsueJapanJPNAsiaEnvironment, Hot spring water

taxonmaps

  • @ref: 69479
  • File name: preview.99_6648.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_3153;97_3862;98_4904;99_6648&stattab=map
  • Last taxonomy: Caldimonas
  • 16S sequence: AB008801
  • Sequence Identity:
  • Total samples: 1155
  • soil counts: 193
  • aquatic counts: 452
  • animal counts: 357
  • plant counts: 153

Safety information

risk assessment

  • @ref: 39908
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Caldimonas manganoxidans gene for 16S rRNA, partial sequence
  • accession: AB008801
  • length: 1466
  • database: ena
  • NCBI tax ID: 196015

Genome sequences

  • @ref: 67770
  • description: Caldimonas manganoxidans ATCC BAA-369
  • accession: GCA_000381125
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1265502

GC content

  • @ref: 67770
  • GC-content: 66.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.402no
flagellatedyes77.092no
gram-positiveno99.196no
anaerobicno97.865no
aerobicyes89.608no
halophileno90.753no
spore-formingno94.562no
thermophileyes87.528yes
glucose-utilyes51.104no
glucose-fermentno87.84no

External links

@ref: 39908

culture collection no.: CIP 107619, JCM 10698, ATCC BAA 369, IFO 16448, NBRC 104253, NBRC 16448

straininfo link

  • @ref: 95230
  • straininfo: 88658

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12054255Caldimonas manganoxidans gen. nov., sp. nov., a poly(3-hydroxybutyrate)-degrading, manganese-oxidizing thermophile.Takeda M, Kamagata Y, Ghiorse WC, Hanada S, Koizumi JIInt J Syst Evol Microbiol10.1099/00207713-52-3-8952002Bacterial Typing Techniques, Betaproteobacteria/chemistry/*classification/genetics/growth & development, DNA, Ribosomal/analysis, Fresh Water/*microbiology, *Hot Temperature, Hydroxybutyrates/*metabolism, Manganese/*metabolism, Molecular Sequence Data, Oxidation-Reduction, Phenotype, Phylogeny, Polyesters/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Phylogeny24122117Caldimonas meghalayensis sp. nov., a novel thermophilic betaproteobacterium isolated from a hot spring of Meghalaya in northeast India.Rakshak K, Ravinder K, Nupur, Srinivas TN, Kumar PAAntonie Van Leeuwenhoek10.1007/s10482-013-0043-x2013Bacterial Typing Techniques, Base Composition, Cluster Analysis, Comamonadaceae/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella/physiology, Hot Springs/*microbiology, India, Locomotion, Microscopy, Electron, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorstitledoi/urlcatalogue
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
39908Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107619Collection of Institut Pasteur (CIP 107619)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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/
95230Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID88658.1