Strain identifier

BacDive ID: 6032

Type strain: Yes

Species: Halomonas muralis

Strain Designation: R-5058

Strain history: CIP <- 2005, DSMZ <- J. Heyrman, Ghent Univ., Ghent, Belgium: strain R-5058

NCBI tax ID(s): 119000 (species)

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General

@ref: 5542

BacDive-ID: 6032

DSM-Number: 14789

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile

description: Halomonas muralis R-5058 is an obligate aerobe, mesophilic, motile bacterium that was isolated from mural painting.

NCBI tax id

  • NCBI tax id: 119000
  • Matching level: species

strain history

@refhistory
5542<- J. Heyrman, Univ. Ghent, Belgium; R-5058
121190CIP <- 2005, DSMZ <- J. Heyrman, Ghent Univ., Ghent, Belgium: strain R-5058

doi: 10.13145/bacdive6032.20230509.8.1

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 muralis
  • full scientific name: Halomonas muralis Heyrman et al. 2002

  • synonyms

    • @ref: 20215
    • synonym: Modicisalibacter muralis

@ref: 5542

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas muralis

full scientific name: Halomonas muralis Heyrman et al. 2002

strain designation: R-5058

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.705
6948099.978negative
121190yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5542BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
37452Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121190CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5542positivegrowth28mesophilic
37452positivegrowth30mesophilic
121190positivegrowth5-37
121190nogrowth41thermophilic
121190nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121190
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.919

halophily

@refsaltgrowthtested relationconcentration
121190NaClpositivegrowth6-10 %
121190NaClnogrowth0 %
121190NaClnogrowth2 %
121190NaClnogrowth4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12119017108D-arabinose-degradation
12119015824D-fructose+degradation
12119017634D-glucose+degradation
12119065327D-xylose-degradation
12119017057cellobiose-degradation
12119017716lactose-degradation
12119017306maltose+degradation
12119017814salicin-degradation
12119017992sucrose+degradation
12119016947citrate-carbon source
1211904853esculin-hydrolysis
121190606565hippurate+hydrolysis
12119017632nitrate+reduction
12119016301nitrite-reduction
12119015792malonate-assimilation

metabolite production

  • @ref: 121190
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121190oxidase+
121190beta-galactosidase-3.2.1.23
121190alcohol dehydrogenase-1.1.1.1
121190gelatinase-
121190amylase-
121190DNase-
121190caseinase-3.4.21.50
121190catalase+1.11.1.6
121190tween esterase+
121190gamma-glutamyltransferase+2.3.2.2
121190lecithinase-
121190lipase-
121190lysine decarboxylase-4.1.1.18
121190ornithine decarboxylase-4.1.1.17
121190phenylalanine ammonia-lyase+4.3.1.24
121190tryptophan deaminase-
121190urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121190-++--+----+----+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5542mural paintingHerberstein, St. Catherine chapelAustriaAUTEurope
121190Mural paintingAustriaAUTEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Engineered#Other#Painting

taxonmaps

  • @ref: 69479
  • File name: preview.99_68531.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_10021;97_12090;98_42900;99_68531&stattab=map
  • Last taxonomy: Halomonas muralis subclade
  • 16S sequence: AJ320530
  • Sequence Identity:
  • Total samples: 221
  • soil counts: 53
  • aquatic counts: 32
  • animal counts: 112
  • plant counts: 24

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
55421Risk group (German classification)
1211901Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5542
  • description: Halomonas muralis partial 16S rRNA gene, type strain LMG 20969T
  • accession: AJ320530
  • length: 1493
  • database: ena
  • NCBI tax ID: 119000

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas muralis DSM 14789GCA_900102945scaffoldncbi119000
66792Halomonas muralis strain DSM 14789119000.3wgspatric119000
66792Halomonas muralis DSM 147892599185144draftimg119000

GC content

  • @ref: 5542
  • GC-content: 62.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.537no
flagellatedno56.195no
gram-positiveno98.926no
anaerobicno99.025no
aerobicyes94.667no
halophileyes90.882no
spore-formingno95.767no
glucose-fermentno74.049no
thermophileno98.643yes
glucose-utilyes94.41no

External links

@ref: 5542

culture collection no.: DSM 14789, CIP 108825, LMG 20969

straininfo link

  • @ref: 75518
  • straininfo: 19243

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12508867Halomonas muralis sp. nov., isolated from microbial biofilms colonizing the walls and murals of the Saint-Catherine chapel (Castle Herberstein, Austria).Heyrman J, Balcaen A, De Vos P, Swings JInt J Syst Evol Microbiol10.1099/00207713-52-6-20492002Austria, Base Composition, Biofilms, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Environmental Microbiology, Fatty Acids/analysis, Genes, Bacterial, Halomonas/*classification/genetics/*isolation & purification/metabolism, Housing, Molecular Sequence Data, Paintings, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
Phylogeny19244445Halomonas ilicicola sp. nov., a moderately halophilic bacterium isolated from a saltern.Arenas M, Banon PI, Copa-Patino JL, Sanchez-Porro C, Ventosa A, Soliveri JInt J Syst Evol Microbiol10.1099/ijs.0.003509-02009Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/chemistry/*microbiology, Genes, rRNA, Geologic Sediments/chemistry/*microbiology, Halomonas/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Spain, Species Specificity, *SunlightGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5542Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14789)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14789
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
37452Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6497
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
68382Automatically annotated from API zym
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75518Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID19243.1StrainInfo: A central database for resolving microbial strain identifiers
121190Curators of the CIPCollection of Institut Pasteur (CIP 108825)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108825