Strain identifier

BacDive ID: 11861

Type strain: Yes

Species: Aminobacter ciceronei

Strain Designation: IMB-1

Variant: Isotype of BacDive ID 139880

Strain history: CIP <- 2005, P. Kämpfer, Justus-Liebig Univ., Giessen, Germany <- I. Mc Donald, Waikato Univ., Hamilton, New Zealand: strain IMB-1

NCBI tax ID(s): 150723 (species)

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General

@ref: 6995

BacDive-ID: 11861

DSM-Number: 17455

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

description: Aminobacter ciceronei IMB-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from CH3Br-fumigated agricultural soil.

NCBI tax id

  • NCBI tax id: 150723
  • Matching level: species

strain history

@refhistory
6995<- P. Kämpfer <- I. R. McDonald; IMB-1
67770IAM 15301 <-- CIP 108660 <-- P. Kämpfer <-- I. McDonald IMB-1.
118277CIP <- 2005, P. Kämpfer, Justus-Liebig Univ., Giessen, Germany <- I. Mc Donald, Waikato Univ., Hamilton, New Zealand: strain IMB-1

doi: 10.13145/bacdive11861.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Phyllobacteriaceae
  • genus: Aminobacter
  • species: Aminobacter ciceronei
  • full scientific name: Aminobacter ciceronei McDonald et al. 2005

@ref: 6995

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Phyllobacteriaceae

genus: Aminobacter

species: Aminobacter ciceronei

full scientific name: Aminobacter ciceronei McDonald et al. 2005

strain designation: IMB-1

variant: Isotype of BacDive ID 139880

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31512negative1.3 µm0.6 µmrod-shapedyes
69480negative99.988
118277negativerod-shapedyes

pigmentation

@refproductionname
31512no
118277noPyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6995R2A 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
33260MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
6995positivegrowth28mesophilic
31512positivegrowth28-30mesophilic
31512positiveoptimum29mesophilic
33260positivegrowth25mesophilic
67770positivegrowth25mesophilic
118277positivegrowth25-30mesophilic
118277nogrowth5psychrophilic
118277nogrowth10psychrophilic
118277nogrowth37mesophilic
118277nogrowth41thermophilic

culture pH

@refabilitytypepH
31512positivegrowth6.5-7.5
31512positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6995aerobe
31512aerobe
118277obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
118277NaClpositivegrowth0-4 %
118277NaClnogrowth6 %
118277NaClnogrowth8 %
118277NaClnogrowth10 %

observation

  • @ref: 31512
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31512370543-hydroxybutyrate+carbon source
3151230089acetate+carbon source
3151216449alanine+carbon source
3151222599arabinose+carbon source
3151235391aspartate+carbon source
3151228757fructose+carbon source
3151228260galactose+carbon source
3151217234glucose+carbon source
3151227570histidine+carbon source
3151224996lactate+carbon source
3151225017leucine+carbon source
3151217306maltose+carbon source
3151229864mannitol+carbon source
3151237684mannose+carbon source
31512506227N-acetylglucosamine+carbon source
3151218257ornithine+carbon source
3151226271proline+carbon source
3151217272propionate+carbon source
3151215361pyruvate+carbon source
3151226546rhamnose+carbon source
3151233942ribose+carbon source
3151217822serine+carbon source
3151230911sorbitol+carbon source
3151217992sucrose+carbon source
3151227082trehalose+carbon source
3151216296D-tryptophan+carbon source
3151218222xylose+carbon source
11827716947citrate-carbon source
1182774853esculin-hydrolysis
11827717632nitrate+reduction
11827716301nitrite-reduction
11827717632nitrate-respiration

antibiotic resistance

  • @ref: 118277
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 118277
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
118277oxidase+
118277beta-galactosidase-3.2.1.23
118277alcohol dehydrogenase-1.1.1.1
118277gelatinase-
118277amylase-
118277DNase-
118277caseinase-3.4.21.50
118277catalase+1.11.1.6
118277tween esterase-
118277lecithinase-
118277lipase-
118277lysine decarboxylase-4.1.1.18
118277ornithine decarboxylase-4.1.1.17
118277protease-
118277tryptophan deaminase-
118277urease+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
118277--+--+--+-+----+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118277+++++--+--+----++-++++-++-+----+++-++----------------------+-----------+-+-+--+-------+---++-++-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6995CH3Br-fumigated agricultural soilCA, IrvineUSAUSANorth America
67770Fumigated soilIrvine, CAUSAUSANorth America
118277Environment, Fumigated soilIrvine, CaliforniaUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
69951Risk group (German classification)
1182771Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6995
  • description: Aminobacter ciceronei strain IMB-1 16S ribosomal RNA gene, complete sequence
  • accession: AF034798
  • length: 1407
  • database: ena
  • NCBI tax ID: 150723

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aminobacter ciceronei DSM 17455GCA_014138635scaffoldncbi150723
66792Aminobacter ciceronei DSM 15910GCA_014138625scaffoldncbi150723
66792Aminobacter ciceronei strain DSM 15910150723.3wgspatric150723
66792Aminobacter ciceronei strain DSM 17455150723.4wgspatric150723
66792Aminobacter ciceronei DSM 159102861405929draftimg150723
66792Aminobacter ciceronei DSM 174552861419262draftimg150723

GC content

  • @ref: 31512
  • GC-content: 62.85

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.023yes
flagellatedno59.361no
gram-positiveno98.108yes
anaerobicno98.73no
aerobicyes93.509no
halophileno90.854no
spore-formingno94.475no
glucose-utilyes92.718yes
thermophileno98.804yes
glucose-fermentno91.244no

External links

@ref: 6995

culture collection no.: DSM 17455, ATCC 202197, CCUG 50580, CIP 108660, JCM 21751, DSM 15910, IAM 15301

straininfo link

  • @ref: 81079
  • straininfo: 265590

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism16102909Analysis of genes involved in methyl halide degradation in Aminobacter lissarensis CC495.Warner KL, Larkin MJ, Harper DB, Murrell JC, McDonald IRFEMS Microbiol Lett10.1016/j.femsle.2005.07.0212005Alphaproteobacteria/enzymology/*genetics/*metabolism, Amino Acid Sequence, Bacterial Proteins/chemistry/*genetics, Biodegradation, Environmental, Cloning, Molecular, Conserved Sequence, DNA, Bacterial/chemistry/genetics, Gene Order, *Genes, Bacterial, Hydrocarbons, Brominated/*metabolism, Hyphomicrobium/genetics, Methyl Chloride/*metabolism, Molecular Sequence Data, Multigene Family, Sequence Analysis, DNA, Sequence Homology, Amino Acid, SyntenyEnzymology
Phylogeny16166673Aminobacter ciceronei sp. nov. and Aminobacter lissarensis sp. nov., isolated from various terrestrial environments.McDonald IR, Kampfer P, Topp E, Warner KL, Cox MJ, Hancock TLC, Miller LG, Larkin MJ, Ducrocq V, Coulter C, Harper DB, Murrell JC, Oremland RSInt J Syst Evol Microbiol10.1099/ijs.0.63716-02005*Agriculture, Alphaproteobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Biodegradation, Environmental, California, Canada, Carbamates/metabolism, Culture Media, DNA, Bacterial/analysis, Fagus, Genes, rRNA, Herbicides/metabolism, Hydrocarbons, Brominated/metabolism, Methyl Chloride/metabolism, Molecular Sequence Data, Northern Ireland, Pesticides/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, *Trees, Triazines/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6995Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17455)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17455
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
31512Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2780828776041
33260Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6313
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
81079Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265590.1StrainInfo: A central database for resolving microbial strain identifiers
118277Curators of the CIPCollection of Institut Pasteur (CIP 108660)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108660