Strain identifier

BacDive ID: 13839

Type strain: Yes

Species: Wenxinia marina

Strain Designation: HY34

Strain history: S. Liu HY-34.

NCBI tax ID(s): 1123501 (strain), 390641 (species)

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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 idMatching level
1123501strain
390641species

strain history

@refhistory
17784<- JCM <- Z.-P. Liu, CAS; HY34
67770S. 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

@refgrowthtypetemperaturerange
17784positivegrowth30mesophilic
32022positivegrowth15-42
32022positiveoptimum36mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32022positivegrowth6.5-8.5alkaliphile
32022positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

  • @ref: 32022
  • oxygen tolerance: aerobe

spore formation

  • @ref: 32022
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32022NaClpositivegrowth0.5-9 %
32022NaClpositiveoptimum2 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3202230089acetate+carbon source
3202216449alanine+carbon source
3202222599arabinose+carbon source
3202228885butanol+carbon source
3202217057cellobiose+carbon source
3202215740formate+carbon source
3202228757fructose+carbon source
3202233984fucose+carbon source
3202228260galactose+carbon source
3202224265gluconate+carbon source
3202217234glucose+carbon source
3202229987glutamate+carbon source
3202217754glycerol+carbon source
3202224996lactate+carbon source
3202217716lactose+carbon source
3202225115malate+carbon source
3202217306maltose+carbon source
3202229864mannitol+carbon source
3202237684mannose+carbon source
3202228053melibiose+carbon source
3202226271proline+carbon source
3202215361pyruvate+carbon source
3202216634raffinose+carbon source
3202226546rhamnose+carbon source
3202233942ribose+carbon source
3202230911sorbitol+carbon source
3202230031succinate+carbon source
3202217992sucrose+carbon source
3202227082trehalose+carbon source
3202253424tween 20+carbon source
3202253423tween 40+carbon source
3202253426tween 80+carbon source
3202218222xylose+carbon source
320224853esculin+hydrolysis
3202217632nitrate+reduction
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
17784catalase+1.11.1.6
17784cytochrome-c oxidase+1.9.3.1
32022alkaline phosphatase+3.1.3.1
32022catalase+1.11.1.6
32022gelatinase+
32022cytochrome oxidase+1.9.3.1
32022urease+3.5.1.5
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
17784-----+-+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17784marine sedimentXijiang oilfield in the South China Sea near Fujian provinceChinaCHNAsia
67770Sediment of the Xijiang oilfield in the South China SeaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Wenxinia marina CGMCC 1.6105GCA_014645075contigncbi390641
66792Wenxinia marina DSM 248381123501.3wgspatric1123501
66792Wenxinia marina DSM 248381123501.8plasmidpatric1123501
66792Wenxinia marina strain CGMCC 1.6105390641.3wgspatric390641
66792Wenxinia marina DSM 248382806310715completeimg1123501
66792Wenxinia marina DSM 248382515154190draftimg1123501
67770Wenxinia marina DSM 24838GCA_000836695scaffoldncbi1123501
67770Wenxinia marina DSM 24838GCA_000379485scaffoldncbi1123501

GC content

@refGC-contentmethod
1778469.4thermal denaturation, midpoint method (Tm)
3202269.4

External links

@ref: 17784

culture collection no.: DSM 24838, CGMCC 1.6105, JCM 14017, CIP 109725

straininfo link

  • @ref: 83015
  • straininfo: 309515

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17684242Wenxinia 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 ZPInt J Syst Evol Microbiol10.1099/ijs.0.64825-02007China, 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/*microbiologyGenetics
Genetics25197468Genome 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 HPStand Genomic Sci10.4056/sigs.56010282014

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17784Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24838)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24838
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32022Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2827428776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
69479João 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
83015Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309515.1StrainInfo: A central database for resolving microbial strain identifiers