Strain identifier

BacDive ID: 11942

Type strain: Yes

Species: Rhodopirellula baltica

Strain Designation: SH 1

Strain history: <- H. Schlesner; SH 1

NCBI tax ID(s): 265606 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 3965

BacDive-ID: 11942

DSM-Number: 10527

keywords: genome sequence, Bacteria, aerobe, mesophilic, Gram-negative, ovoid-shaped

description: Rhodopirellula baltica SH 1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from brackish water.

NCBI tax id

  • NCBI tax id: 265606
  • Matching level: species

strain history

  • @ref: 3965
  • history: <- H. Schlesner; SH 1

doi: 10.13145/bacdive11942.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/planctomycetota
  • domain: Bacteria
  • phylum: Planctomycetota
  • class: Planctomycetia
  • order: Pirellulales
  • family: Pirellulaceae
  • genus: Rhodopirellula
  • species: Rhodopirellula baltica
  • full scientific name: Rhodopirellula baltica Schlesner et al. 2004

@ref: 3965

domain: Bacteria

phylum: Planctomycetes

class: Planctomycetia

order: Planctomycetales

family: Pirellulaceae

genus: Rhodopirellula

species: Rhodopirellula baltica

full scientific name: Rhodopirellula baltica Schlesner et al. 2004

strain designation: SH 1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31241negative1.75 µm1.75 µmovoid-shapedno
69480negative99.995

pigmentation

  • @ref: 31241
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 3965
  • name: M13a (PIRELLULA) MEDIUM (DSMZ Medium 600a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/600a
  • composition: Name: M13a (PIRELLULA) MEDIUM (DSMZ Medium 600a) Composition: NaCl 11.735 g/l MgCl2 x 6 H2O 2.49 g/l Na2SO4 1.96 g/l MgSO4 x 7 H2O 0.594 g/l CaCl2 0.55 g/l KCl 0.332 g/l Peptone 0.25 g/l Yeast extract 0.25 g/l Glucose 0.25 g/l Nitrilotriacetic acid 0.2 g/l NaHCO3 0.096 g/l CaCl2 x 2 H2O 0.0667 g/l KBr 0.048 g/l H3BO3 0.013 g/l SrCl2 0.012 g/l NaF 0.0015 g/l ZnSO4 x 7 H2O 0.001095 g/l FeSO4 x 7 H2O 0.0005 g/l Na-EDTA 0.00025 g/l (NH4)6Mo7O24 x 4 H2O 0.000185 g/l MnSO4 x H2O 0.000154 g/l Pyridoxine hydrochloride 0.0001 g/l p-Aminobenzoic acid 0.0001 g/l Nicotinamide 0.0001 g/l Riboflavin 0.0001 g/l Calcium pantothenate 0.0001 g/l Thiamine-HCl x 2 H2O 0.0001 g/l Biotin 4e-05 g/l CuSO4 x 5 H2O 3.92e-05 g/l Co(NO3)2 x 6 H2O 2.48e-05 g/l Na2B4O7 x 10 H2O 1.77e-05 g/l Folic acid 1e-05 g/l Vitamin B12 2e-06 g/l Tris-HCl buffer Distilled water

culture temp

@refgrowthtypetemperaturerange
3965positivegrowth25mesophilic
31241positivegrowth28-32mesophilic
31241positiveoptimum28-30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 31241
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31241no
69481no100
69480no99.98

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3124117057cellobiose+carbon source
3124123652dextrin+carbon source
3124128757fructose+carbon source
3124128260galactose+carbon source
3124124265gluconate+carbon source
3124117234glucose+carbon source
3124117754glycerol+carbon source
3124117716lactose+carbon source
3124117306maltose+carbon source
3124137684mannose+carbon source
3124128053melibiose+carbon source
31241506227N-acetylglucosamine+carbon source
3124116634raffinose+carbon source
3124126546rhamnose+carbon source
3124133942ribose+carbon source
3124117814salicin+carbon source
3124117992sucrose+carbon source
3124127082trehalose+carbon source
3124118222xylose+carbon source
312414853esculin+hydrolysis

metabolite production

  • @ref: 31241
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

  • @ref: 31241
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

  • @ref: 3965
  • sample type: brackish water
  • geographic location: Baltic Sea (Kiel Fjord)

isolation source categories

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

Safety information

risk assessment

  • @ref: 3965
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodopirellula baltica SH 1243090.15completepatric243090
66792Rhodopirellula baltica SH 1GCA_000196115completencbi243090

GC content

  • @ref: 3965
  • GC-content: 55

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes82.258yes
gram-positiveno96.546no
anaerobicno98.148yes
aerobicyes90.821yes
halophileno57.962no
spore-formingno90.116yes
glucose-utilyes88.412yes
flagellatedno79.977yes
thermophileno99.215no
glucose-fermentno86.385no

External links

@ref: 3965

culture collection no.: DSM 10527, NCIMB 13988, IFAM 1310

straininfo link

  • @ref: 81155
  • straininfo: 134306

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143026Evaluation of the phylogenetic position of the planctomycete 'Rhodopirellula baltica' SH 1 by means of concatenated ribosomal protein sequences, DNA-directed RNA polymerase subunit sequences and whole genome trees.Teeling H, Lombardot T, Bauer M, Ludwig W, Glockner FOInt J Syst Evol Microbiol10.1099/ijs.0.02913-02004Bacteria/*classification/*genetics, Bacterial Proteins/genetics, Chlamydiaceae/classification/genetics, DNA-Directed RNA Polymerases/chemistry/genetics, Genome, Bacterial, Phylogeny, Protein Subunits, Ribosomal Proteins/geneticsGenetics
Phylogeny15388712Taxonomic heterogeneity within the Planctomycetales as derived by DNA-DNA hybridization, description of Rhodopirellula baltica gen. nov., sp. nov., transfer of Pirellula marina to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov. and emended description of the genus Pirellula.Schlesner H, Rensmann C, Tindall BJ, Gade D, Rabus R, Pfeiffer S, Hirsch PInt J Syst Evol Microbiol10.1099/ijs.0.63113-02004Bacteria/*classification/cytology/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics/isolation & purification, Fatty Acids/analysis/isolation & purification, Movement, Nucleic Acid Hybridization, Pigments, Biological/biosynthesis, Water MicrobiologyEnzymology
Phylogeny15621430The transcriptional regulator pool of the marine bacterium Rhodopirellula baltica SH 1T as revealed by whole genome comparisons.Lombardot T, Bauer M, Teeling H, Amann R, Glockner FOFEMS Microbiol Lett10.1016/j.femsle.2004.10.0492005Adaptation, Physiological, Bacillus subtilis/genetics, Bacteria/classification/*genetics, *Gene Expression Regulation, Bacterial, Genes, Bacterial, *Genes, Regulator, *Genome, Bacterial, Phylogeny, Sigma Factor/genetics, Signal Transduction/genetics, Transcription Factors/*genetics, Transcription, GeneticGenetics
Biotechnology16545098Biocatalytic approaches for the quantitative production of single stereoisomers from racemates.Gadler P, Glueck SM, Kroutil W, Nestl BM, Larissegger-Schnell B, Ueberbacher BT, Wallner SR, Faber KBiochem Soc Trans10.1042/BST200602962006Animals, Biotechnology/*methods, Catalysis, Stereoisomerism, Substrate Specificity, Sulfatases/metabolismMetabolism
Metabolism21255355Life cycle analysis of the model organism Rhodopirellula baltica SH 1(T) by transcriptome studies.Wecker P, Klockow C, Schuler M, Dabin J, Michel G, Glockner FOMicrob Biotechnol10.1111/j.1751-7915.2010.00183.x2010Bacteria/*genetics/*growth & development/metabolism, Bacterial Proteins/genetics/metabolism, Cell Cycle, *Gene Expression Profiling, Gene Expression Regulation, Bacterial, Models, BiologicalGenetics
23766281Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of environmental organisms: the Planctomycetes paradigm.Cayrou C, Raoult D, Drancourt MEnviron Microbiol Rep10.1111/j.1758-2229.2010.00176.x2010
27594849Developing Techniques for the Utilization of Planctomycetes As Producers of Bioactive Molecules.Jeske O, Surup F, Ketteniss M, Rast P, Forster B, Jogler M, Wink J, Jogler CFront Microbiol10.3389/fmicb.2016.012422016
Enzymology32809107Homology Modeling and Probable Active Site Cavity Prediction of Uncharacterized Arsenate Reductase in Bacterial spp.Rahman MS, Hossain MS, Saha SK, Rahman S, Sonne C, Kim KHAppl Biochem Biotechnol10.1007/s12010-020-03392-w2020Amino Acid Sequence, Arsenate Reductases/*chemistry, Bacteria/*enzymology, Bacterial Proteins/*chemistry, Catalytic Domain, *Molecular Dynamics Simulation

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
3965Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10527)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10527
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
31241Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2756528776041
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)
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
81155Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134306.1StrainInfo: A central database for resolving microbial strain identifiers