Strain identifier
BacDive ID: 6044
Type strain:
Species: Halomonas organivorans
Strain Designation: G-16.1
Strain history: CIP <- 2004, A. Ventosa, Sevilla, Spain: strain G-16.1
NCBI tax ID(s): 257772 (species)
General
@ref: 6341
BacDive-ID: 6044
DSM-Number: 16226
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Halomonas organivorans G-16.1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from saline soils.
NCBI tax id
- NCBI tax id: 257772
- Matching level: species
strain history
@ref | history |
---|---|
6341 | <- A. Ventosa, Univ. Seville, Dept. Microbiol. Parasitol., Spain; G-16.1 <- M. T. García et al. |
121433 | CIP <- 2004, A. Ventosa, Sevilla, Spain: strain G-16.1 |
doi: 10.13145/bacdive6044.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Oceanospirillales
- family: Halomonadaceae
- genus: Halomonas
- species: Halomonas organivorans
- full scientific name: Halomonas organivorans García et al. 2004
@ref: 6341
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Halomonadaceae
genus: Halomonas
species: Halomonas organivorans
full scientific name: Halomonas organivorans García et al. 2004
strain designation: G-16.1
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31242 | negative | 2.5 µm | 1.1 µm | rod-shaped | yes | |
69480 | yes | 97.929 | ||||
69480 | negative | 99.961 | ||||
121433 | negative | rod-shaped | yes |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6341 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 60.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water |
33934 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
121433 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6341 | positive | growth | 37 | mesophilic |
31242 | positive | growth | 15-45 | |
31242 | positive | optimum | 37 | mesophilic |
33934 | positive | growth | 30 | mesophilic |
121433 | positive | growth | 15-41 | |
121433 | no | growth | 5 | psychrophilic |
121433 | no | growth | 45 | thermophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31242 | positive | growth | 06-10 | alkaliphile |
31242 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31242 | aerobe |
121433 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.899 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31242 | NaCl | positive | growth | 1.5-30 % |
31242 | NaCl | positive | optimum | 8.75 % |
121433 | NaCl | positive | growth | 10 % |
121433 | NaCl | no | growth | 0 % |
121433 | NaCl | no | growth | 2 % |
121433 | NaCl | no | growth | 4 % |
121433 | NaCl | no | growth | 6 % |
121433 | NaCl | no | growth | 8 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31242 | 16000 | ethanolamine | + | carbon source |
31242 | 16449 | alanine | + | carbon source |
31242 | 18403 | L-arabitol | + | carbon source |
31242 | 22653 | asparagine | + | carbon source |
31242 | 35391 | aspartate | + | carbon source |
31242 | 28757 | fructose | + | carbon source |
31242 | 28260 | galactose | + | carbon source |
31242 | 17234 | glucose | + | carbon source |
31242 | 29987 | glutamate | + | carbon source |
31242 | 17754 | glycerol | + | carbon source |
31242 | 28087 | glycogen | + | carbon source |
31242 | 27570 | histidine | + | carbon source |
31242 | 17596 | inosine | + | carbon source |
31242 | 25017 | leucine | + | carbon source |
31242 | 29864 | mannitol | + | carbon source |
31242 | 37684 | mannose | + | carbon source |
31242 | 51850 | methyl pyruvate | + | carbon source |
31242 | 506227 | N-acetylglucosamine | + | carbon source |
31242 | 26271 | proline | + | carbon source |
31242 | 17148 | putrescine | + | carbon source |
31242 | 26546 | rhamnose | + | carbon source |
31242 | 17822 | serine | + | carbon source |
31242 | 30911 | sorbitol | + | carbon source |
31242 | 30031 | succinate | + | carbon source |
31242 | 17992 | sucrose | + | carbon source |
31242 | 26986 | threonine | + | carbon source |
31242 | 27082 | trehalose | + | carbon source |
31242 | 53423 | tween 40 | + | carbon source |
31242 | 53426 | tween 80 | + | carbon source |
31242 | 16704 | uridine | + | carbon source |
31242 | 27248 | urocanic acid | + | carbon source |
31242 | 4853 | esculin | + | hydrolysis |
121433 | 16947 | citrate | - | carbon source |
121433 | 4853 | esculin | - | hydrolysis |
121433 | 606565 | hippurate | + | hydrolysis |
121433 | 17632 | nitrate | + | reduction |
121433 | 16301 | nitrite | - | reduction |
121433 | 15792 | malonate | - | assimilation |
121433 | 17632 | nitrate | + | respiration |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
31242 | 16136 | hydrogen sulfide | yes |
121433 | 35581 | indole | no |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31242 | catalase | + | 1.11.1.6 |
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 |
121433 | oxidase | + | |
121433 | beta-galactosidase | - | 3.2.1.23 |
121433 | alcohol dehydrogenase | - | 1.1.1.1 |
121433 | gelatinase | - | |
121433 | amylase | - | |
121433 | caseinase | - | 3.4.21.50 |
121433 | catalase | + | 1.11.1.6 |
121433 | tween esterase | + | |
121433 | gamma-glutamyltransferase | + | 2.3.2.2 |
121433 | lecithinase | - | |
121433 | lipase | - | |
121433 | lysine decarboxylase | - | 4.1.1.18 |
121433 | ornithine decarboxylase | - | 4.1.1.17 |
121433 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
121433 | protease | - | |
121433 | tryptophan deaminase | - | |
121433 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121433 | - | + | + | - | - | + | + | + | - | - | + | + | - | - | - | + | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121433 | + | + | + | + | + | - | - | + | - | + | + | - | - | - | - | - | - | - | + | - | + | - | + | + | - | - | + | - | - | - | - | - | + | - | - | + | - | - | - | - | - | + | - | - | - | - | - | - | + | + | - | - | - | - | + | + | + | - | - | + | - | - | + | + | - | - | - | - | - | + | - | - | + | - | + | + | - | - | - | + | + | - | - | - | - | - | - | - | + | + | + | - | - | - | + | + | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
6341 | saline soils | Huelva, Isla Cristina | Spain | ESP | Europe | |
121433 | Environment, Saline soil in Isla Cristina | Spain | ESP | Europe | 2003 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Soil |
#Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_56260.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_1361;97_3720;98_15343;99_56260&stattab=map
- Last taxonomy: Halomonas
- 16S sequence: AJ616910
- Sequence Identity:
- Total samples: 47
- soil counts: 7
- aquatic counts: 34
- animal counts: 5
- plant counts: 1
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6341 | 1 | Risk group (German classification) |
121433 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 6341
- description: Halomonas organivorans partial 16S rRNA gene, type strain G-16.1T
- accession: AJ616910
- length: 1472
- database: ena
- NCBI tax ID: 257772
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Halomonas organivorans CECT 5995 | GCA_014192055 | scaffold | ncbi | 257772 |
66792 | Halomonas organivorans strain CECT 5995 | 257772.3 | wgs | patric | 257772 |
66792 | Halomonas organivorans CECT 5995 | 2824377609 | draft | img | 257772 |
GC content
@ref | GC-content |
---|---|
6341 | 61.0 |
31242 | 61.95 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | yes | 69.152 | no |
gram-positive | no | 98.406 | yes |
anaerobic | no | 98.443 | yes |
aerobic | yes | 86.648 | no |
halophile | yes | 91.158 | yes |
spore-forming | no | 95.421 | no |
glucose-util | yes | 95.314 | yes |
thermophile | no | 99.216 | yes |
motile | yes | 91.601 | yes |
glucose-ferment | no | 66.284 | no |
External links
@ref: 6341
culture collection no.: DSM 16226, CCM 7142, CECT 5995, CIP 108269
straininfo link
- @ref: 75531
- straininfo: 134288
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15388735 | Halomonas organivorans sp. nov., a moderate halophile able to degrade aromatic compounds. | Garcia MT, Mellado E, Ostos JC, Ventosa A | Int J Syst Evol Microbiol | 10.1099/ijs.0.63114-0 | 2004 | Aminosalicylic Acid/metabolism, Bacterial Typing Techniques, Base Composition, Benzoic Acid/metabolism, Biodegradation, Environmental, Cinnamates/metabolism, Coumaric Acids/metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA/genetics, Halomonas/*classification/genetics/isolation & purification/*metabolism, Hydrocarbons, Aromatic/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Parabens/metabolism, Phenol/metabolism, Phenylacetates/metabolism, Phylogeny, Propionates, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Salicylic Acid/metabolism, Sequence Analysis, DNA, Soil Microbiology, Spain | Metabolism |
Metabolism | 21695219 | Cloning, characterization and analysis of cat and ben genes from the phenol degrading halophilic bacterium Halomonas organivorans. | de Lourdes Moreno M, Sanchez-Porro C, Piubeli F, Frias L, Garcia MT, Mellado E | PLoS One | 10.1371/journal.pone.0021049 | 2011 | Amino Acid Sequence, Bacterial Proteins/chemistry/*genetics/*metabolism, Benzoates/*metabolism, Catechol 1,2-Dioxygenase/metabolism, Cloning, Molecular, DNA, Intergenic/genetics, Halomonas/enzymology/*genetics/*metabolism, Industrial Waste, Molecular Sequence Data, Phenol/*metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Alignment | Enzymology |
Phylogeny | 22328606 | Halomonas smyrnensis sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium. | Poli A, Nicolaus B, Denizci AA, Yavuzturk B, Kazan D | Int J Syst Evol Microbiol | 10.1099/ijs.0.037036-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Halomonas/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Polysaccharides, Bacterial/*biosynthesis, Ponds, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Turkey, Ubiquinone/analysis | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
6341 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16226) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16226 | |||
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 | |||
31242 | 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 | 27566 | 28776041 | |
33934 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5872 | ||||
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) | |||
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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
75531 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID134288.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121433 | Curators of the CIP | Collection of Institut Pasteur (CIP 108269) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108269 |