Strain identifier
BacDive ID: 6020
Type strain: 
Species: Halomonas meridiana
Strain history: CIP <- 1994, ACAM <- St James <- R. Garrick and J. Gibson: strain UQM 3352
NCBI tax ID(s): 29570 (species)
version 8.1 (current version)
General
@ref: 2162
BacDive-ID: 6020
DSM-Number: 5425
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Halomonas meridiana DSM 5425 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from organic lake.
NCBI tax id
- NCBI tax id: 29570
- Matching level: species
strain history
| @ref | history |
|---|---|
| 2162 | <- P.D. Franzmann <- S.R. James <- R. Garrick |
| 67771 | <- DSM <- PD Franzmann <- SR James <- R Garrick |
| 120897 | CIP <- 1994, ACAM <- St James <- R. Garrick and J. Gibson: strain UQM 3352 |
doi: 10.13145/bacdive6020.20230509.8.1
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 meridiana
- full scientific name: Halomonas meridiana James et al. 1990
@ref: 2162
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Halomonadaceae
genus: Halomonas
species: Halomonas meridiana
full scientific name: Halomonas meridiana James et al. 1990
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell shape | motility |
|---|---|---|---|
| 67771 | negative | ||
| 120897 | negative | rod-shaped | yes |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 2162 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 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 |
| 34491 | MEDIUM 110 - for Halomonas meridiana | yes | Distilled water make up to (960.000 ml);Sodium chloride (30.000 g);Potassium chloride (5.000 g);Magnesium chloride hexahydrate (5.000 g);Magnesium sulphate heptahydrate (9.500 g);Calcium chloride dihydrate (0.200 g);Agar (15.000 g);Yeast extract (1.000g); | |
| 120897 | CIP Medium 255 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=255 | |
| 120897 | CIP Medium 110 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=110 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 2162 | positive | growth | 28 | mesophilic |
| 34491 | positive | growth | 25 | mesophilic |
| 67771 | positive | growth | 28 | mesophilic |
| 120897 | positive | growth | 10-37 | |
| 120897 | no | growth | 5 | psychrophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 67771 | aerobe |
| 120897 | obligate aerobe |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 120897 | 17632 | nitrate | + | reduction |
| 120897 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 120897
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 120897 | oxidase | + | |
| 120897 | beta-galactosidase | - | 3.2.1.23 |
| 120897 | alcohol dehydrogenase | - | 1.1.1.1 |
| 120897 | catalase | + | 1.11.1.6 |
| 120897 | lysine decarboxylase | - | 4.1.1.18 |
| 120897 | ornithine decarboxylase | - | 4.1.1.17 |
| 120897 | urease | - | 3.5.1.5 |
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 120897 | + | + | - | + | - | - | - | + | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | + | - | + | - | + | + | - | - | - | + | - | - | - | - | + | - | + | + | + | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + | - | + | - | - | - | + | + | - | + | - | - | - | - | - | + | + | + | + | - | + | - | - | + | - | - |
Isolation, sampling and environmental information
isolation
| @ref | sample type | continent | country | origin.country | geographic location |
|---|---|---|---|---|---|
| 2162 | organic lake | Australia and Oceania | |||
| 67771 | From organic lake | Australia and Oceania | Antarctica | ATA | |
| 120897 | Environment, Water | Antarctica | Antarctica | ATA | Burch lake |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Lake (large)
taxonmaps
- @ref: 69479
- File name: preview.99_137.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_104;97_111;98_121;99_137&stattab=map
- Last taxonomy: Halomonas
- 16S sequence: AJ306891
- Sequence Identity:
- Total samples: 10165
- soil counts: 435
- aquatic counts: 5177
- animal counts: 4415
- plant counts: 138
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 2162 | 1 | Risk group (German classification) |
| 120897 | 1 | Risk group (French classification) |
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Halomonas meridiana genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 920 | AB367234 | 920 | ena | 29570 |
| 20218 | Halomonas meridiana genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1204 | AB367235 | 1204 | ena | 29570 |
| 20218 | Halomonas meridiana (DSM 5425) 16S ribosomal RNA (16S rRNA) gene | M93356 | 1475 | ena | 29570 |
| 20218 | Halomonas meridiana gene for 16S rRNA, partial sequence, strain: NBRC 15608 | AB680914 | 1460 | ena | 29570 |
| 2162 | Halomonas meridiana partial 16S rRNA gene, strain DSM 5425 | AJ306891 | 1528 | ena | 29570 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Halomonas meridiana ACAM 246 | GCA_900129255 | contig | ncbi | 29570 |
| 66792 | Halomonas meridiana strain ACAM 246 | 29570.7 | wgs | patric | 29570 |
| 66792 | Halomonas meridiana ACAM 246 | 2698536813 | draft | img | 29570 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| gram-positive | no | 98.605 | yes |
| anaerobic | no | 98.878 | yes |
| halophile | yes | 90.104 | no |
| spore-forming | no | 95.735 | no |
| glucose-util | yes | 84.109 | no |
| motile | yes | 91.135 | no |
| flagellated | yes | 70.166 | no |
| aerobic | yes | 92.386 | yes |
| thermophile | no | 98.56 | yes |
| glucose-ferment | no | 76.156 | no |
External links
@ref: 2162
culture collection no.: DSM 5425, ACAM 246, ATCC 49692, KCTC 22196, UQM 3352, CIP 104043, IFO (now NBRC) 15608
straininfo link
- @ref: 75506
- straininfo: 34618
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 10784044 | The alpha-amylase gene amyH of the moderate halophile Halomonas meridiana: cloning and molecular characterization. | Coronado MA, Vargas C, Mellado E, Tegos G, Drainas C, Nieto JNJ, Ventosa A | Microbiology (Reading) | 10.1099/00221287-146-4-861 | 2000 | Amino Acid Sequence, Cloning, Molecular, *Genes, Bacterial, Halomonas/*genetics, Molecular Sequence Data, Mutation, Sequence Alignment, alpha-Amylases/*genetics | Genetics |
| Phylogeny | 15143014 | Halomonas boliviensis sp. nov., an alkalitolerant, moderate halophile isolated from soil around a Bolivian hypersaline lake. | Quillaguaman J, Hatti-Kaul R, Mattiasson B, Alvarez MT, Delgado O | Int J Syst Evol Microbiol | 10.1099/ijs.0.02800-0 | 2004 | Base Composition, Base Sequence, Bolivia, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fresh Water/microbiology, Halomonas/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Soil Microbiology | Metabolism |
| Phylogeny | 19656933 | Halomonas andesensis sp. nov., a moderate halophile isolated from the saline lake Laguna Colorada in Bolivia. | Guzman D, Quillaguaman J, Munoz M, Hatti-Kaul R | Int J Syst Evol Microbiol | 10.1099/ijs.0.014522-0 | 2009 | Bacterial Typing Techniques, Base Composition, Bolivia, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Fresh Water/chemistry/*microbiology, Genes, rRNA, Halomonas/chemistry/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species Specificity | Genetics |
| Phylogeny | 24510978 | Halomonas songnenensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soils. | Jiang J, Pan Y, Hu S, Zhang X, Hu B, Huang H, Hong S, Meng J, Li C, Wang K | Int J Syst Evol Microbiol | 10.1099/ijs.0.056499-0 | 2014 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Halomonas/*classification/genetics/isolation & purification, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, Ubiquinone/chemistry | Genetics |
| Phylogeny | 32129736 | Halomonas piezotolerans sp. nov., a multiple-stress-tolerant bacterium isolated from a deep-sea sediment sample of the New Britain Trench. | Yan F, Fang J, Cao J, Wei Y, Liu R, Wang L, Xie Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004069 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Halomonas/*classification/isolation & purification, Nucleic Acid Hybridization, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 2162 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5425) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5425 | |||
| 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 | |
| 34491 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15907 | ||||
| 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) | |||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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 | |||
| 75506 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID34618.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 120897 | Curators of the CIP | Collection of Institut Pasteur (CIP 104043) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104043 |