Strain identifier
BacDive ID: 13839
Type strain:
Species: Wenxinia marina
Strain Designation: HY34
Strain history: S. Liu HY-34.
NCBI tax ID(s): 1123501 (strain), 390641 (species)
General
@ref: 17784
BacDive-ID: 13839
DSM-Number: 24838
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, ovoid-shaped
description: Wenxinia marina HY34 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from marine sediment.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1123501 | strain |
390641 | species |
strain history
@ref | history |
---|---|
17784 | <- JCM <- Z.-P. Liu, CAS; HY34 |
67770 | S. Liu HY-34. |
doi: 10.13145/bacdive13839.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Wenxinia
- species: Wenxinia marina
- full scientific name: Wenxinia marina Ying et al. 2007
@ref: 17784
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Wenxinia
species: Wenxinia marina
full scientific name: Wenxinia marina Ying et al. 2007
strain designation: HY34
type strain: yes
Morphology
cell morphology
- @ref: 32022
- gram stain: negative
- cell length: 1.3 µm
- cell width: 0.75 µm
- cell shape: ovoid-shaped
- motility: no
colony morphology
- @ref: 17784
- incubation period: 1-2 days
pigmentation
- @ref: 32022
- production: yes
Culture and growth conditions
culture medium
- @ref: 17784
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: 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
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
17784 | positive | growth | 30 | mesophilic |
32022 | positive | growth | 15-42 | |
32022 | positive | optimum | 36 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32022 | positive | growth | 6.5-8.5 | alkaliphile |
32022 | positive | optimum | 7.75 |
Physiology and metabolism
oxygen tolerance
- @ref: 32022
- oxygen tolerance: aerobe
spore formation
- @ref: 32022
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32022 | NaCl | positive | growth | 0.5-9 % |
32022 | NaCl | positive | optimum | 2 % |
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32022 | 30089 | acetate | + | carbon source |
32022 | 16449 | alanine | + | carbon source |
32022 | 22599 | arabinose | + | carbon source |
32022 | 28885 | butanol | + | carbon source |
32022 | 17057 | cellobiose | + | carbon source |
32022 | 15740 | formate | + | carbon source |
32022 | 28757 | fructose | + | carbon source |
32022 | 33984 | fucose | + | carbon source |
32022 | 28260 | galactose | + | carbon source |
32022 | 24265 | gluconate | + | carbon source |
32022 | 17234 | glucose | + | carbon source |
32022 | 29987 | glutamate | + | carbon source |
32022 | 17754 | glycerol | + | carbon source |
32022 | 24996 | lactate | + | carbon source |
32022 | 17716 | lactose | + | carbon source |
32022 | 25115 | malate | + | carbon source |
32022 | 17306 | maltose | + | carbon source |
32022 | 29864 | mannitol | + | carbon source |
32022 | 37684 | mannose | + | carbon source |
32022 | 28053 | melibiose | + | carbon source |
32022 | 26271 | proline | + | carbon source |
32022 | 15361 | pyruvate | + | carbon source |
32022 | 16634 | raffinose | + | carbon source |
32022 | 26546 | rhamnose | + | carbon source |
32022 | 33942 | ribose | + | carbon source |
32022 | 30911 | sorbitol | + | carbon source |
32022 | 30031 | succinate | + | carbon source |
32022 | 17992 | sucrose | + | carbon source |
32022 | 27082 | trehalose | + | carbon source |
32022 | 53424 | tween 20 | + | carbon source |
32022 | 53423 | tween 40 | + | carbon source |
32022 | 53426 | tween 80 | + | carbon source |
32022 | 18222 | xylose | + | carbon source |
32022 | 4853 | esculin | + | hydrolysis |
32022 | 17632 | nitrate | + | reduction |
68369 | 25115 | malate | - | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | - | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
17784 | catalase | + | 1.11.1.6 |
17784 | cytochrome-c oxidase | + | 1.9.3.1 |
32022 | alkaline phosphatase | + | 3.1.3.1 |
32022 | catalase | + | 1.11.1.6 |
32022 | gelatinase | + | |
32022 | cytochrome oxidase | + | 1.9.3.1 |
32022 | urease | + | 3.5.1.5 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
17784 | - | - | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
17784 | marine sediment | Xijiang oilfield in the South China Sea near Fujian province | China | CHN | Asia |
67770 | Sediment of the Xijiang oilfield in the South China Sea | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_6571.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_3116;97_3817;98_4849;99_6571&stattab=map
- Last taxonomy: Wenxinia marina
- 16S sequence: DQ640643
- Sequence Identity:
- Total samples: 1234
- soil counts: 150
- aquatic counts: 935
- animal counts: 115
- plant counts: 34
Safety information
risk assessment
- @ref: 17784
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17784
- description: Wenxinia marina strain HY34 16S ribosomal RNA gene, partial sequence
- accession: DQ640643
- length: 1428
- database: ena
- NCBI tax ID: 390641
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Wenxinia marina CGMCC 1.6105 | GCA_014645075 | contig | ncbi | 390641 |
66792 | Wenxinia marina DSM 24838 | 1123501.3 | wgs | patric | 1123501 |
66792 | Wenxinia marina DSM 24838 | 1123501.8 | plasmid | patric | 1123501 |
66792 | Wenxinia marina strain CGMCC 1.6105 | 390641.3 | wgs | patric | 390641 |
66792 | Wenxinia marina DSM 24838 | 2806310715 | complete | img | 1123501 |
66792 | Wenxinia marina DSM 24838 | 2515154190 | draft | img | 1123501 |
67770 | Wenxinia marina DSM 24838 | GCA_000836695 | scaffold | ncbi | 1123501 |
67770 | Wenxinia marina DSM 24838 | GCA_000379485 | scaffold | ncbi | 1123501 |
GC content
@ref | GC-content | method |
---|---|---|
17784 | 69.4 | thermal denaturation, midpoint method (Tm) |
32022 | 69.4 |
External links
@ref: 17784
culture collection no.: DSM 24838, CGMCC 1.6105, JCM 14017, CIP 109725
straininfo link
- @ref: 83015
- straininfo: 309515
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17684242 | Wenxinia marina gen. nov., sp. nov., a novel member of the Roseobacter clade isolated from oilfield sediments of the South China Sea. | Ying JY, Wang BJ, Dai X, Yang SS, Liu SJ, Liu ZP | Int J Syst Evol Microbiol | 10.1099/ijs.0.64825-0 | 2007 | China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Petroleum/metabolism, RNA, Ribosomal, 16S/genetics, Roseobacter/chemistry/*classification/genetics/metabolism, Seawater/*microbiology | Genetics |
Genetics | 25197468 | Genome sequence of the Wenxinia marina type strain (DSM 24838(T)), a representative of the Roseobacter group isolated from oilfield sediments. | Riedel T, Fiebig A, Han J, Huntemann M, Spring S, Petersen J, Ivanova NN, Markowitz V, Woyke T, Goker M, Kyrpides NC, Klenk HP | Stand Genomic Sci | 10.4056/sigs.5601028 | 2014 |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
17784 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24838) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24838 | ||||
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 | ||||
32022 | 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 | 28274 | 28776041 | ||
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) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68369 | Automatically annotated from API 20NE | ||||||
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 | ||||
83015 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID309515.1 | StrainInfo: A central database for resolving microbial strain identifiers |