Strain identifier
BacDive ID: 7176
Type strain:
Species: Methylobacterium aquaticum
Strain Designation: GR16
Strain history: CIP <- 2004, A. Ventosa, Sevilla Univ., Sevilla, Spain: strain GR16
NCBI tax ID(s): 270351 (species)
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
@ref | history |
---|---|
6408 | <- A. Ventosa <- V. Gallego; GR16 |
33945 | 2004, A. Ventosa, Sevilla Univ., Sevilla, Spain: strain GR16 |
116434 | CIP <- 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
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
31326 | negative | 6.25 µm | 1.6 µm | rod-shaped | yes |
116434 | negative | rod-shaped | yes |
pigmentation
@ref | production | name |
---|---|---|
31326 | yes | |
116434 | no | Pyocyanin |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6408 | PLATE COUNT AGAR (DSMZ Medium 464) | yes | https://mediadive.dsmz.de/medium/464 | Name: 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 |
33945 | MEDIUM 229 - for Methylobacterium aminovorans | yes | Distilled 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 | |
116434 | CIP Medium 229 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=229 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6408 | positive | growth | 28 | mesophilic |
31326 | positive | growth | 20-30 | |
31326 | positive | optimum | 28 | mesophilic |
33945 | positive | growth | 25 | mesophilic |
116434 | positive | growth | 25-30 | mesophilic |
116434 | no | growth | 5 | psychrophilic |
116434 | no | growth | 10 | psychrophilic |
116434 | no | growth | 37 | mesophilic |
116434 | no | growth | 41 | thermophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31326 | positive | growth | 5.0-7.0 |
31326 | positive | optimum | 6 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31326 | aerobe |
116434 | facultative anaerobe |
spore formation
- @ref: 31326
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31326 | NaCl | positive | growth | 0.0-1.0 % |
116434 | NaCl | positive | growth | 0 % |
116434 | NaCl | no | growth | 2 % |
116434 | NaCl | no | growth | 4 % |
116434 | NaCl | no | growth | 6 % |
116434 | NaCl | no | growth | 8 % |
116434 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31326 | 30089 | acetate | + | carbon source |
31326 | 22599 | arabinose | + | carbon source |
31326 | 22653 | asparagine | + | carbon source |
31326 | 16947 | citrate | + | carbon source |
31326 | 15740 | formate | + | carbon source |
31326 | 28757 | fructose | + | carbon source |
31326 | 33984 | fucose | + | carbon source |
31326 | 28260 | galactose | + | carbon source |
31326 | 17234 | glucose | + | carbon source |
31326 | 29987 | glutamate | + | carbon source |
31326 | 24996 | lactate | + | carbon source |
31326 | 25115 | malate | + | carbon source |
31326 | 17272 | propionate | + | carbon source |
31326 | 15361 | pyruvate | + | carbon source |
31326 | 30031 | succinate | + | carbon source |
31326 | 53423 | tween 40 | + | carbon source |
31326 | 53426 | tween 80 | + | carbon source |
31326 | 17632 | nitrate | + | reduction |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | + | builds acid from |
68371 | 18287 | L-fucose | + | builds acid from |
68371 | 28847 | D-fucose | + | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | + | builds acid from |
68371 | 32528 | turanose | - | builds acid from |
68371 | 28066 | gentiobiose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 28017 | starch | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | - | builds acid from |
68371 | 17992 | sucrose | - | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17306 | maltose | - | builds acid from |
68371 | 17057 | cellobiose | - | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 4853 | esculin | - | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 27613 | amygdalin | - | builds acid from |
68371 | 59640 | N-acetylglucosamine | - | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | - | builds acid from |
68371 | 15824 | D-fructose | + | builds acid from |
68371 | 17634 | D-glucose | - | builds acid from |
68371 | 12936 | D-galactose | + | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | + | builds acid from |
68371 | 65327 | D-xylose | + | builds acid from |
68371 | 16988 | D-ribose | + | builds acid from |
68371 | 30849 | L-arabinose | + | builds acid from |
68371 | 17108 | D-arabinose | + | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
116434 | 16947 | citrate | + | carbon source |
116434 | 4853 | esculin | - | hydrolysis |
116434 | 17632 | nitrate | - | reduction |
116434 | 16301 | nitrite | - | reduction |
116434 | 17632 | nitrate | - | respiration |
metabolite production
- @ref: 116434
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
31326 | catalase | + | 1.11.1.6 |
31326 | urease | + | 3.5.1.5 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | + | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
116434 | oxidase | - | |
116434 | beta-galactosidase | - | 3.2.1.23 |
116434 | alcohol dehydrogenase | - | 1.1.1.1 |
116434 | gelatinase | - | |
116434 | amylase | + | |
116434 | DNase | - | |
116434 | caseinase | - | 3.4.21.50 |
116434 | catalase | + | 1.11.1.6 |
116434 | tween esterase | + | |
116434 | lecithinase | - | |
116434 | lipase | - | |
116434 | lysine decarboxylase | - | 4.1.1.18 |
116434 | ornithine decarboxylase | - | 4.1.1.17 |
116434 | protease | - | |
116434 | tryptophan deaminase | - | |
116434 | urease | + | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116434 | - | + | + | + | - | + | - | - | + | - | + | + | - | - | - | - | - | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116434 | - | - | + | + | + | + | + | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | + | + | + | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116434 | + | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | + | - | - | - | - | - | - | - | + | - | - | - | - | - | - | + | + | + | - | - | + | - | - | - | - | - | - | + | - | - | + | - | - | - | - | + | - | + | - | + | - | - | - | - | - | - | - | - | - | - | + | - | + | - | - | + | - | - | - | + | + | + | - | - | + | + | + | + | + | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
6408 | drinking water | Seville | Spain | ESP | Europe | |
116434 | Environment, Drinking water | Sevilla | Spain | ESP | Europe | 2003 |
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
@ref | biosafety level | biosafety level comment |
---|---|---|
6408 | 1 | Risk group (German classification) |
116434 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Methylobacterium aquaticum gene for 16S rRNA, partial sequence, strain: DSM 16371 | AB252197 | 1434 | ena | 270351 |
6408 | Methylobacterium aquaticum 16S rRNA gene, strain type strain GR16T | AJ635303 | 1406 | ena | 270351 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Methylobacterium aquaticum DSM 16371 | GCA_001043915 | contig | ncbi | 270351 |
66792 | Methylobacterium aquaticum strain DSM 16371 | 270351.6 | wgs | patric | 270351 |
66792 | Methylobacterium aquaticum DSM 16371 | 2634166393 | draft | img | 270351 |
GC content
@ref | GC-content | method |
---|---|---|
6408 | 67.3 | thermal denaturation, midpoint method (Tm) |
31326 | 67.5 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 84.094 | no |
gram-positive | no | 97.684 | no |
anaerobic | no | 98.523 | no |
halophile | no | 91.339 | yes |
spore-forming | no | 90.942 | yes |
glucose-util | yes | 93.357 | yes |
aerobic | yes | 91.918 | yes |
flagellated | no | 66.638 | no |
thermophile | no | 98.988 | no |
glucose-ferment | no | 88.657 | no |
External links
@ref: 6408
culture collection no.: DSM 16371, CCM 7218, CECT 5998, CIP 108333
straininfo link
- @ref: 76629
- straininfo: 135123
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15653888 | Methylobacterium hispanicum sp. nov. and Methylobacterium aquaticum sp. nov., isolated from drinking water. | Gallego V, Garcia MT, Ventosa A | Int J Syst Evol Microbiol | 10.1099/ijs.0.63319-0 | 2005 | Bacterial 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 Supply | Genetics |
Phylogeny | 18048737 | Methylobacterium 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 W | Int J Syst Evol Microbiol | 10.1099/ijs.0.65262-0 | 2007 | Aerobiosis, 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, Temperature | Enzymology |
Phylogeny | 23315404 | Methylobacterium tarhaniae sp. nov., isolated from arid soil. | Veyisoglu A, Camas M, Tatar D, Guven K, Sazak A, Sahin N | Int J Syst Evol Microbiol | 10.1099/ijs.0.049551-0 | 2013 | Bacterial 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/analysis | Genetics |
Phylogeny | 31463788 | Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil. | Kim J, Chhetri G, Kim I, Kim H, Kim MK, Seo T | J Microbiol | 10.1007/s12275-019-9007-9 | 2019 | Bacterial 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 Sequencing | Genetics |
Phylogeny | 32100693 | Methylobacterium 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 T | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004054 | 2020 | Bacterial 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/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
6408 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16371) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16371 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
31326 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 27640 | ||
33945 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5944 | |||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
68371 | Automatically annotated from API 50CH acid | ||||||
68382 | Automatically annotated from API zym | ||||||
69479 | João 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 | ||||
76629 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID135123.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
116434 | Curators of the CIP | Collection of Institut Pasteur (CIP 108333) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108333 |