Strain identifier

BacDive ID: 7176

Type strain: Yes

Species: Methylobacterium aquaticum

Strain Designation: GR16

Strain history: CIP <- 2004, A. Ventosa, Sevilla Univ., Sevilla, Spain: strain GR16

NCBI tax ID(s): 270351 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6408

BacDive-ID: 7176

DSM-Number: 16371

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

description: Methylobacterium aquaticum GR16 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from drinking water.

NCBI tax id

  • NCBI tax id: 270351
  • Matching level: species

strain history

@refhistory
6408<- A. Ventosa <- V. Gallego; GR16
339452004, A. Ventosa, Sevilla Univ., Sevilla, Spain: strain GR16
116434CIP <- 2004, A. Ventosa, Sevilla Univ., Sevilla, Spain: strain GR16

doi: 10.13145/bacdive7176.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Methylobacteriaceae
  • genus: Methylobacterium
  • species: Methylobacterium aquaticum
  • full scientific name: Methylobacterium aquaticum Gallego et al. 2005

@ref: 6408

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Methylobacteriaceae

genus: Methylobacterium

species: Methylobacterium aquaticum

full scientific name: Methylobacterium aquaticum Gallego et al. 2005

strain designation: GR16

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31326negative6.25 µm1.6 µmrod-shapedyes
116434negativerod-shapedyes

pigmentation

@refproductionname
31326yes
116434noPyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6408PLATE COUNT AGAR (DSMZ Medium 464)yeshttps://mediadive.dsmz.de/medium/464Name: PLATE COUNT AGAR (DSMZ Medium 464) Composition: Agar 15.0 g/l Tryptone 5.0 g/l Yeast extract 2.5 g/l Dextrose 1.0 g/l Distilled water
33945MEDIUM 229 - for Methylobacterium aminovoransyesDistilled water make up to (990.000 ml);Zinc sulphate heptahydrate (5.000 mg);ManganeseII chloride tetrahydrate (5.000 mg);Magnesium sulphate heptahydrate (0.200 g);Calcium chloride dihydrate (30.000 mg);Agar (18.000 g);Yeast extract (0.200 g);Ammoniumsul
116434CIP Medium 229yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=229

culture temp

@refgrowthtypetemperaturerange
6408positivegrowth28mesophilic
31326positivegrowth20-30
31326positiveoptimum28mesophilic
33945positivegrowth25mesophilic
116434positivegrowth25-30mesophilic
116434nogrowth5psychrophilic
116434nogrowth10psychrophilic
116434nogrowth37mesophilic
116434nogrowth41thermophilic

culture pH

@refabilitytypepH
31326positivegrowth5.0-7.0
31326positiveoptimum6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31326aerobe
116434facultative anaerobe

spore formation

  • @ref: 31326
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31326NaClpositivegrowth0.0-1.0 %
116434NaClpositivegrowth0 %
116434NaClnogrowth2 %
116434NaClnogrowth4 %
116434NaClnogrowth6 %
116434NaClnogrowth8 %
116434NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3132630089acetate+carbon source
3132622599arabinose+carbon source
3132622653asparagine+carbon source
3132616947citrate+carbon source
3132615740formate+carbon source
3132628757fructose+carbon source
3132633984fucose+carbon source
3132628260galactose+carbon source
3132617234glucose+carbon source
3132629987glutamate+carbon source
3132624996lactate+carbon source
3132625115malate+carbon source
3132617272propionate+carbon source
3132615361pyruvate+carbon source
3132630031succinate+carbon source
3132653423tween 40+carbon source
3132653426tween 80+carbon source
3132617632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol+builds acid from
6837118287L-fucose+builds acid from
6837128847D-fucose+builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose+builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose+builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose+builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11643416947citrate+carbon source
1164344853esculin-hydrolysis
11643417632nitrate-reduction
11643416301nitrite-reduction
11643417632nitrate-respiration

metabolite production

  • @ref: 116434
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31326catalase+1.11.1.6
31326urease+3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
116434oxidase-
116434beta-galactosidase-3.2.1.23
116434alcohol dehydrogenase-1.1.1.1
116434gelatinase-
116434amylase+
116434DNase-
116434caseinase-3.4.21.50
116434catalase+1.11.1.6
116434tween esterase+
116434lecithinase-
116434lipase-
116434lysine decarboxylase-4.1.1.18
116434ornithine decarboxylase-4.1.1.17
116434protease-
116434tryptophan deaminase-
116434urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116434-+++-+--+-++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116434--+++++--+-+----------------------------+-+++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116434+++-----------------++-+-------+------+++--+------+--+----+-+-+----------+-+--+---+++--+++++------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6408drinking waterSevilleSpainESPEurope
116434Environment, Drinking waterSevillaSpainESPEurope2003

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Freshwater

taxonmaps

  • @ref: 69479
  • File name: preview.99_5594.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15368;96_262;97_289;98_1400;99_5594&stattab=map
  • Last taxonomy: Methylobacterium aquaticum
  • 16S sequence: AJ635303
  • Sequence Identity:
  • Total samples: 3074
  • soil counts: 319
  • aquatic counts: 656
  • animal counts: 1502
  • plant counts: 597

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64081Risk group (German classification)
1164341Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Methylobacterium aquaticum gene for 16S rRNA, partial sequence, strain: DSM 16371AB2521971434ena270351
6408Methylobacterium aquaticum 16S rRNA gene, strain type strain GR16TAJ6353031406ena270351

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methylobacterium aquaticum DSM 16371GCA_001043915contigncbi270351
66792Methylobacterium aquaticum strain DSM 16371270351.6wgspatric270351
66792Methylobacterium aquaticum DSM 163712634166393draftimg270351

GC content

@refGC-contentmethod
640867.3thermal denaturation, midpoint method (Tm)
3132667.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes84.094no
gram-positiveno97.684no
anaerobicno98.523no
halophileno91.339yes
spore-formingno90.942yes
glucose-utilyes93.357yes
aerobicyes91.918yes
flagellatedno66.638no
thermophileno98.988no
glucose-fermentno88.657no

External links

@ref: 6408

culture collection no.: DSM 16371, CCM 7218, CECT 5998, CIP 108333

straininfo link

  • @ref: 76629
  • straininfo: 135123

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653888Methylobacterium hispanicum sp. nov. and Methylobacterium aquaticum sp. nov., isolated from drinking water.Gallego V, Garcia MT, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.63319-02005Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fresh Water/*microbiology, Genotype, Methylobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, *Water SupplyGenetics
Phylogeny18048737Methylobacterium platani sp. nov., isolated from a leaf of the tree Platanus orientalis.Kang YS, Kim J, Shin HD, Nam YD, Bae JW, Jeon CO, Park WInt J Syst Evol Microbiol10.1099/ijs.0.65262-02007Aerobiosis, Bacterial Typing Techniques, Catalase/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Hydrogen-Ion Concentration, Locomotion, Magnoliopsida/*microbiology, Methylobacterium/chemistry/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/analysis, Phylogeny, Pigments, Biological/metabolism, Plant Leaves/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, TemperatureEnzymology
Phylogeny23315404Methylobacterium tarhaniae sp. nov., isolated from arid soil.Veyisoglu A, Camas M, Tatar D, Guven K, Sazak A, Sahin NInt J Syst Evol Microbiol10.1099/ijs.0.049551-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Methylobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nigeria, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/analysisGenetics
Phylogeny31463788Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil.Kim J, Chhetri G, Kim I, Kim H, Kim MK, Seo TJ Microbiol10.1007/s12275-019-9007-92019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gamma Rays, Genotype, Lipids/chemistry, Methylobacterium/*classification/genetics/*isolation & purification/radiation effects, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Radiation Tolerance, Republic of Korea, Sequence Analysis, DNA, Soil, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry, Whole Genome SequencingGenetics
Phylogeny32100693Methylobacterium terricola sp. nov., a gamma radiation-resistant bacterium isolated from gamma ray-irradiated soil.Kim J, Chhetri G, Kim I, Lee B, Jang W, Kim MK, Seo TInt J Syst Evol Microbiol10.1099/ijsem.0.0040542020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gamma Rays, Methylobacterium/*classification/isolation & purification/radiation effects, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6408Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16371)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16371
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
31326Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127640
33945Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5944
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)
68371Automatically annotated from API 50CH acid
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
76629Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID135123.1StrainInfo: A central database for resolving microbial strain identifiers
116434Curators of the CIPCollection of Institut Pasteur (CIP 108333)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108333