Strain identifier

BacDive ID: 5940

Type strain: Yes

Species: Halorubrum lacusprofundi

Strain history: CIP <- 1997, JCM <- ATCC <- C.A. Mancuso

NCBI tax ID(s): 416348 (strain), 2247 (species)

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General

@ref: 1912

BacDive-ID: 5940

DSM-Number: 5036

keywords: genome sequence, 16S sequence, Archaea, mesophilic, Gram-negative

description: Halorubrum lacusprofundi DSM 5036 is a mesophilic, Gram-negative archaeon that was isolated from sediment-water interface.

NCBI tax id

NCBI tax idMatching level
2247species
416348strain

strain history

@refhistory
1912<- P.D. Franzmann, ACAM 34
67770ATCC 49239 <-- C. A. Mancuso ACAM 34.
120543CIP <- 1997, JCM <- ATCC <- C.A. Mancuso

doi: 10.13145/bacdive5940.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Haloferacales
  • family: Halorubraceae
  • genus: Halorubrum
  • species: Halorubrum lacusprofundi
  • full scientific name: Halorubrum lacusprofundi (Franzmann et al. 1989) McGenity and Grant 1996

  • synonyms

    @refsynonym
    20215Halorubrobacterium lacusprofundi
    20215Halobacterium lacusprofundi

@ref: 1912

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Halorubraceae

genus: Halorubrum

species: Halorubrum lacusprofundi

full scientific name: Halorubrum lacusprofundi (Franzmann et al. 1989) McGenity and Grant 1996

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.853
120543negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1912HALOBACTERIA MEDIUM (DSMZ Medium 372)yeshttps://mediadive.dsmz.de/medium/372Name: HALOBACTERIA MEDIUM (DSMZ Medium 372) Composition: NaCl 200.0 g/l MgSO4 x 7 H2O 20.0 g/l Agar 20.0 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l Na glutamate 1.0 g/l FeCl2 x 4 H2O 0.036 g/l MnCl2 x 4 H2O 0.00036 g/l Distilled water
1912HALOBACTERIUM LACUSPROFUNDII MEDIUM (DSMZ Medium 589)yeshttps://mediadive.dsmz.de/medium/589Name: HALOBACTERIUM LACUSPROFUNDII MEDIUM (DSMZ Medium 589) Composition: NaCl 181.0 g/l MgCl2 x 6 H2O 75.0 g/l Agar 15.0 g/l Sodium succinate 10.0 g/l MgSO4 x 7 H2O 7.4 g/l KCl 7.4 g/l CaCl2 x 2 H2O 1.0 g/l Yeast extract 1.0 g/l Biotin 0.0001 g/l Thiamine-HCl x 2 H2O 0.0001 g/l Vitamin B12 0.0001 g/l Distilled water
39268MEDIUM 221 - for Halorubrum lacusprofundiyesDistilled water make up to (990.000 ml);Sodium chloride (180.000 g);Potassium chloride (7.400 g);Magnesium chloride hexahydrate (75.000 g);Magnesium sulphate heptahydrate (7.400 g);Calcium chloride dihydrate (1.000 g);Yeast extract (1.000 g);Succinic acid
120543CIP Medium 268yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=268
120543CIP Medium 221yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=221

culture temp

@refgrowthtypetemperaturerange
1912positivegrowth30mesophilic
39268positivegrowth30mesophilic
67770positivegrowth35mesophilic
120543positivegrowth15-45
120543nogrowth5psychrophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.983

observation

  • @ref: 67770
  • observation: quinones: MK-8, MK-8(H2)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120543hippurate-hydrolysis606565
120543nitrate-reduction17632
120543nitrite-reduction16301

antibiotic resistance

  • @ref: 120543
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 120543
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12054315688acetoin-
12054317234glucose-

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
120543oxidase+
120543beta-galactosidase+3.2.1.23
120543gelatinase-
120543catalase+1.11.1.6
120543gamma-glutamyltransferase-2.3.2.2
120543phenylalanine ammonia-lyase-4.3.1.24
120543tryptophan deaminase-
120543urease-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
120543--++-+---+++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120543--+/-+/-+/-+/-----------------------------------+/-+/-+/------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
1912sediment-water interfaceDeep Lake, Vestfold HillsAustralia and Oceania
67770Diphasic water-sediment sample from the Deep Lake in Antarctica
120543Environment, Diphasic water sediment sampleDeep lakeAntarcticaAntarcticaATA

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_187248.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17655;96_68889;97_89538;98_121821;99_187248&stattab=map
  • Last taxonomy: Halorubrum lacusprofundi
  • 16S sequence: X82170
  • Sequence Identity:
  • Total samples: 70
  • soil counts: 10
  • aquatic counts: 60

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
19121Risk group (German classification)
1205431Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218H.lacusprofundi 16S rRNA geneX821701464ena416348
20218Halorubrum lacusprofundi gene for 16S rRNA, complete sequence, strain: JCM 8891AB6634141470ena416348
20218Halobacterium lacusprofundi 16S ribosomal RNA gene, partial sequenceU173651469ena416348

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halorubrum lacusprofundi ATCC 49239GCA_000022205completencbi416348
66792Halorubrum lacusprofundi ATCC 49239643692025completeimg416348
66792Halorubrum lacusprofundi ATCC 49239416348.21completepatric416348
66792Halorubrum lacusprofundi ATCC 49239416348.31plasmidpatric416348

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno72.496no
flagellatedno95.428no
gram-positiveno97.287no
anaerobicno97.908no
aerobicyes85.803no
halophileyes88.304no
spore-formingno94.04no
glucose-utilyes90.87no
thermophileno96.372no
glucose-fermentno78.555no

External links

@ref: 1912

culture collection no.: DSM 5036, ACAM 34, ATCC 49239, JCM 8891, UQM 3107, ACM 3107, CGMCC 1.2925, CGMCC 1.3490, CIP 105334, NCIMB 12997, VKM B-1753

straininfo link

@refstraininfo
7542542375
75426312080
75427312177

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16825640Halorubrum lipolyticum sp. nov. and Halorubrum aidingense sp. nov., isolated from two salt lakes in Xin-Jiang, China.Cui HL, Tohty D, Zhou PJ, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.64305-02006Bacterial Typing Techniques, Base Composition, China, DNA, Archaeal/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA, Halobacteriaceae/*classification/genetics/*isolation & purification/physiology, Lipids/analysis/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Archaeal/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Water MicrobiologyEnzymology
Phylogeny17082390Halorubrum orientale sp. nov., a halophilic archaeon isolated from Lake Ejinor, Inner Mongolia, China.Castillo AM, Gutierrez MC, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.64420-02006Base Composition, China, DNA, Archaeal/chemistry/genetics/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA, Halobacteriaceae/*classification/cytology/*isolation & purification/physiology, Lipids/analysis/chemistry, Magnesium/metabolism, Molecular Sequence Data, Movement, Phylogeny, Pigments, Biological/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/analysis/metabolism, Temperature, *Water MicrobiologyEnzymology
Phylogeny18768599Halorubrum kocurii sp. nov., an archaeon isolated from a saline lake.Gutierrez MC, Castillo AM, Pagaling E, Heaphy S, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.65840-02008Base Composition, Carbohydrate Metabolism, China, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Halobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Hydrogen-Ion Concentration, Hypotonic Solutions/toxicity, Lipids/analysis, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Archaeal/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Temperature, *Water MicrobiologyMetabolism
23100763An evidence of laccases in archaea.Sharma KK, Kuhad RCIndian J Microbiol10.1007/s12088-009-0039-42009
Genetics27617060Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34.Anderson IJ, DasSarma P, Lucas S, Copeland A, Lapidus A, Del Rio TG, Tice H, Dalin E, Bruce DC, Goodwin L, Pitluck S, Sims D, Brettin TS, Detter JC, Han CS, Larimer F, Hauser L, Land M, Ivanova N, Richardson P, Cavicchioli R, DasSarma S, Woese CR, Kyrpides NCStand Genomic Sci10.1186/s40793-016-0194-22016
Phylogeny28819743Halorubrum salsamenti sp. nov., a Novel Halophilic Archaeon Isolated from a Brine of Salt Mine.Chen S, He J, Zhang J, Xu Y, Huang J, Ke LXCurr Microbiol10.1007/s00284-017-1325-82017Base Composition, DNA, Archaeal, Halorubrum/chemistry/*classification/genetics/isolation & purification, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *SaltsPhenotype
Enzymology34940913Extremophile enzyme optimization for low temperature and high salinity are fundamentally incompatible.Piszkin L, Bowman JExtremophiles10.1007/s00792-021-01254-92021Cold Temperature, *Extremophiles, *Halorubrum, Salinity, Temperature

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1912Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5036)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5036
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
39268Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17342
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
75425Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42375.1StrainInfo: A central database for resolving microbial strain identifiers
75426Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID312080.1StrainInfo: A central database for resolving microbial strain identifiers
75427Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID312177.1StrainInfo: A central database for resolving microbial strain identifiers
120543Curators of the CIPCollection of Institut Pasteur (CIP 105334)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105334