Strain identifier
BacDive ID: 6039
Type strain:
Species: Halomonas sulfidaeris
Strain Designation: Esulfide1, NZp
Strain history: CIP <- 2003, C. Marquez, Sevilla Univ., Sevilla, Spain: strain Esulfide1, N2p <- J. Kaye, Washington Univ., Washington, USA
NCBI tax ID(s): 891402 (strain), 115553 (species)
General
@ref: 6080
BacDive-ID: 6039
DSM-Number: 15722
keywords: 16S sequence, Bacteria, facultative aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Halomonas sulfidaeris Esulfide1 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from sulfide rock, Main Endearour field.
NCBI tax id
NCBI tax id | Matching level |
---|---|
891402 | strain |
115553 | species |
strain history
@ref | history |
---|---|
6080 | <- M. C. Marquez; NZp <- J. Z. Kaye |
123380 | CIP <- 2003, C. Marquez, Sevilla Univ., Sevilla, Spain: strain Esulfide1, N2p <- J. Kaye, Washington Univ., Washington, USA |
doi: 10.13145/bacdive6039.20230509.8.1
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 sulfidaeris
- full scientific name: Halomonas sulfidaeris Kaye et al. 2004
synonyms
- @ref: 20215
- synonym: Vreelandella sulfidaeris
@ref: 6080
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Halomonadaceae
genus: Halomonas
species: Halomonas sulfidaeris
full scientific name: Halomonas sulfidaeris Kaye et al. 2004
strain designation: Esulfide1, NZp
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
29992 | negative | 2.5 µm | 1 µm | rod-shaped | yes |
123380 | negative | rod-shaped | yes |
pigmentation
- @ref: 29992
- production: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6080 | 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 |
33874 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
123380 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6080 | positive | growth | 28 | mesophilic |
29992 | positive | optimum | 27.5 | mesophilic |
33874 | positive | growth | 30 | mesophilic |
123380 | positive | growth | 5-37 | |
123380 | no | growth | 41 | thermophilic |
123380 | no | growth | 45 | thermophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29992 | positive | growth | 05-10 | alkaliphile |
29992 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 29992
- oxygen tolerance: facultative aerobe
spore formation
- @ref: 29992
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29992 | NaCl | positive | growth | 0.5-24 % |
29992 | NaCl | positive | optimum | 2.5 % |
123380 | NaCl | positive | growth | 4-10 % |
123380 | NaCl | no | growth | 0 % |
123380 | NaCl | no | growth | 2 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29992 | 22599 | arabinose | + | carbon source |
29992 | 29016 | arginine | + | carbon source |
29992 | 22653 | asparagine | + | carbon source |
29992 | 16236 | ethanol | + | carbon source |
29992 | 28757 | fructose | + | carbon source |
29992 | 25115 | malate | + | carbon source |
29992 | 15792 | malonate | + | carbon source |
29992 | 29864 | mannitol | + | carbon source |
29992 | 17992 | sucrose | + | carbon source |
29992 | 27082 | trehalose | + | carbon source |
29992 | 18222 | xylose | + | carbon source |
29992 | 17632 | nitrate | + | reduction |
123380 | 16947 | citrate | - | carbon source |
123380 | 4853 | esculin | - | hydrolysis |
123380 | 606565 | hippurate | - | hydrolysis |
123380 | 17632 | nitrate | + | reduction |
123380 | 16301 | nitrite | - | reduction |
123380 | 15792 | malonate | - | assimilation |
metabolite production
- @ref: 123380
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
29992 | catalase | + | 1.11.1.6 |
29992 | cytochrome oxidase | + | 1.9.3.1 |
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 |
123380 | oxidase | + | |
123380 | beta-galactosidase | + | 3.2.1.23 |
123380 | alcohol dehydrogenase | - | 1.1.1.1 |
123380 | gelatinase | - | |
123380 | amylase | - | |
123380 | caseinase | - | 3.4.21.50 |
123380 | catalase | + | 1.11.1.6 |
123380 | tween esterase | - | |
123380 | gamma-glutamyltransferase | + | 2.3.2.2 |
123380 | lecithinase | - | |
123380 | lipase | - | |
123380 | lysine decarboxylase | - | 4.1.1.18 |
123380 | ornithine decarboxylase | - | 4.1.1.17 |
123380 | phenylalanine ammonia-lyase | + | 4.3.1.24 |
123380 | protease | - | |
123380 | tryptophan deaminase | - | |
123380 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123380 | - | + | + | + | - | + | - | - | - | - | - | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
6080 | sulfide rock, Main Endearour field | NE Pacific Ocean | Canada | CAN | North America | |
123380 | Sulfide rock | Pacific Ocean | Canada | CAN | North America | 1995 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Geologic |
#Condition | #Sulfuric |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6080 | 1 | Risk group (German classification) |
123380 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Halomonas sulfidaeris genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 874 | AB367237 | 874 | ena | 891402 |
20218 | Halomonas sulfidaeris genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1224 | AB367238 | 1224 | ena | 891402 |
6080 | Halomonas sulfidaeris strain Esulfide1 16S ribosomal RNA gene, complete sequence | AF212204 | 1430 | ena | 891402 |
GC content
- @ref: 29992
- GC-content: 56
External links
@ref: 6080
culture collection no.: DSM 15722, CIP 108041, ATCC BAA 803, CECT 5817
straininfo link
- @ref: 75526
- straininfo: 131421
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15023967 | Halomonas neptunia sp. nov., Halomonas sulfidaeris sp. nov., Halomonas axialensis sp. nov. and Halomonas hydrothermalis sp. nov.: halophilic bacteria isolated from deep-sea hydrothermal-vent environments. | Kaye JZ, Marquez MC, Ventosa A, Baross JA | Int J Syst Evol Microbiol | 10.1099/ijs.0.02799-0 | 2004 | DNA, Bacterial/genetics, Environment, Halomonas/*classification/genetics/growth & development/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Temperature | Genetics |
Phylogeny | 26431725 | Halomonas salicampi sp. nov., a halotolerant and alkalitolerant bacterium isolated from a saltern soil. | Lee JC, Kim YS, Yun BS, Whang KS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000650 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Halomonas/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Salinity, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry | Genetics |
Genetics | 31171615 | Complete Genome Sequence of Halomonas sulfidaeris Strain Esulfide1 Isolated from a Metal Sulfide Rock at a Depth of 2,200 Meters, Obtained Using Nanopore Sequencing. | Saito M, Nishigata A, Galipon J, Arakawa K | Microbiol Resour Announc | 10.1128/MRA.00327-19 | 2019 | Phylogeny | |
Phylogeny | 32816656 | Halomonas rituensis sp. nov. and Halomonas zhuhanensis sp. nov., isolated from natural salt marsh sediment on the Tibetan Plateau. | Gao P, Lu H, Xing P, Wu QL | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004395 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Halomonas/*classification/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, *Wetlands | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
6080 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15722) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15722 | ||||
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 | ||
29992 | 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 | 26358 | ||
33874 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5620 | |||||
68382 | Automatically annotated from API zym | ||||||
75526 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID131421.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
123380 | Curators of the CIP | Collection of Institut Pasteur (CIP 108041) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108041 |