Strain identifier
BacDive ID: 11942
Type strain:
Species: Rhodopirellula baltica
Strain Designation: SH 1
Strain history: <- H. Schlesner; SH 1
NCBI tax ID(s): 265606 (species)
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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31241 | negative | 1.75 µm | 1.75 µm | ovoid-shaped | no | |
69480 | negative | 99.995 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
3965 | positive | growth | 25 | mesophilic |
31241 | positive | growth | 28-32 | mesophilic |
31241 | positive | optimum | 28-30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 31241
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
31241 | no | |
69481 | no | 100 |
69480 | no | 99.98 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31241 | 17057 | cellobiose | + | carbon source |
31241 | 23652 | dextrin | + | carbon source |
31241 | 28757 | fructose | + | carbon source |
31241 | 28260 | galactose | + | carbon source |
31241 | 24265 | gluconate | + | carbon source |
31241 | 17234 | glucose | + | carbon source |
31241 | 17754 | glycerol | + | carbon source |
31241 | 17716 | lactose | + | carbon source |
31241 | 17306 | maltose | + | carbon source |
31241 | 37684 | mannose | + | carbon source |
31241 | 28053 | melibiose | + | carbon source |
31241 | 506227 | N-acetylglucosamine | + | carbon source |
31241 | 16634 | raffinose | + | carbon source |
31241 | 26546 | rhamnose | + | carbon source |
31241 | 33942 | ribose | + | carbon source |
31241 | 17814 | salicin | + | carbon source |
31241 | 17992 | sucrose | + | carbon source |
31241 | 27082 | trehalose | + | carbon source |
31241 | 18222 | xylose | + | carbon source |
31241 | 4853 | esculin | + | 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rhodopirellula baltica SH 1 | 243090.15 | complete | patric | 243090 |
66792 | Rhodopirellula baltica SH 1 | GCA_000196115 | complete | ncbi | 243090 |
GC content
- @ref: 3965
- GC-content: 55
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 82.258 | yes |
gram-positive | no | 96.546 | no |
anaerobic | no | 98.148 | yes |
aerobic | yes | 90.821 | yes |
halophile | no | 57.962 | no |
spore-forming | no | 90.116 | yes |
glucose-util | yes | 88.412 | yes |
flagellated | no | 79.977 | yes |
thermophile | no | 99.215 | no |
glucose-ferment | no | 86.385 | no |
External links
@ref: 3965
culture collection no.: DSM 10527, NCIMB 13988, IFAM 1310
straininfo link
- @ref: 81155
- straininfo: 134306
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15143026 | Evaluation 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 FO | Int J Syst Evol Microbiol | 10.1099/ijs.0.02913-0 | 2004 | Bacteria/*classification/*genetics, Bacterial Proteins/genetics, Chlamydiaceae/classification/genetics, DNA-Directed RNA Polymerases/chemistry/genetics, Genome, Bacterial, Phylogeny, Protein Subunits, Ribosomal Proteins/genetics | Genetics |
Phylogeny | 15388712 | Taxonomic 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 P | Int J Syst Evol Microbiol | 10.1099/ijs.0.63113-0 | 2004 | Bacteria/*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 Microbiology | Enzymology |
Phylogeny | 15621430 | The 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 FO | FEMS Microbiol Lett | 10.1016/j.femsle.2004.10.049 | 2005 | Adaptation, 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, Genetic | Genetics |
Biotechnology | 16545098 | Biocatalytic 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 K | Biochem Soc Trans | 10.1042/BST20060296 | 2006 | Animals, Biotechnology/*methods, Catalysis, Stereoisomerism, Substrate Specificity, Sulfatases/metabolism | Metabolism |
Metabolism | 21255355 | Life 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 FO | Microb Biotechnol | 10.1111/j.1751-7915.2010.00183.x | 2010 | Bacteria/*genetics/*growth & development/metabolism, Bacterial Proteins/genetics/metabolism, Cell Cycle, *Gene Expression Profiling, Gene Expression Regulation, Bacterial, Models, Biological | Genetics |
23766281 | Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of environmental organisms: the Planctomycetes paradigm. | Cayrou C, Raoult D, Drancourt M | Environ Microbiol Rep | 10.1111/j.1758-2229.2010.00176.x | 2010 | |||
27594849 | Developing 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 C | Front Microbiol | 10.3389/fmicb.2016.01242 | 2016 | |||
Enzymology | 32809107 | Homology 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 KH | Appl Biochem Biotechnol | 10.1007/s12010-020-03392-w | 2020 | Amino Acid Sequence, Arsenate Reductases/*chemistry, Bacteria/*enzymology, Bacterial Proteins/*chemistry, Catalytic Domain, *Molecular Dynamics Simulation |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
3965 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10527) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10527 | |||
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 | |||
31241 | 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 | 27565 | 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) | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
81155 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID134306.1 | StrainInfo: A central database for resolving microbial strain identifiers |