Strain identifier
BacDive ID: 10420
Type strain: 
Species: Plesiocystis pacifica
Strain Designation: Sir-1
Strain history: T. Iizuka SIR-1.
NCBI tax ID(s): 191768 (species)
version 8.1 (current version)
General
@ref: 5591
BacDive-ID: 10420
DSM-Number: 14875
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Plesiocystis pacifica Sir-1 is a mesophilic bacterium that was isolated from semi-dried seagrass .
NCBI tax id
- NCBI tax id: 191768
- Matching level: species
strain history
| @ref | history |
|---|---|
| 5591 | <- T. Iizuka; SIR-1 |
| 67770 | T. Iizuka SIR-1. |
doi: 10.13145/bacdive10420.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Myxococcales
- family: Nannocystaceae
- genus: Plesiocystis
- species: Plesiocystis pacifica
- full scientific name: Plesiocystis pacifica Iizuka et al. 2003
@ref: 5591
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Myxococcales
family: Nannocystaceae
genus: Plesiocystis
species: Plesiocystis pacifica
full scientific name: Plesiocystis pacifica Iizuka et al. 2003
strain designation: Sir-1
type strain: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 5591 | CY/3 SEAWATER MEDIUM (DSMZ Medium 1602) | yes | https://mediadive.dsmz.de/medium/1602 | Name: CY/3-SEAWATER MEDIUM (DSMZ Medium 1602) Composition: NaCl 20.0 g/l MgSO4 x 7 H2O 8.0 g/l CaCl2 x 2 H2O 1.0 g/l Casitone 1.0 g/l KCl 0.5 g/l Yeast extract 0.33 g/l NaHCO3 0.16 g/l KBr 0.08 g/l SrCl2 x 6 H2O 0.03 g/l Ferric citrate 0.01 g/l Sodium beta-glycerophosphate 0.01 g/l EDTA 0.0005 g/l Cyanocobalamine 0.0005 g/l FeSO4 x 7 H2O 0.0002 g/l H3BO3 3e-05 g/l CoCl2 x 6 H2O 2e-05 g/l ZnSO4 x 7 H2O 1e-05 g/l MnCl2 x 4 H2O 3e-06 g/l Na2MoO4 x 2 H2O 3e-06 g/l NiCl2 x 6 H2O 2e-06 g/l CuCl2 x 2 H2O 1e-06 g/l Distilled water |
| 5591 | VY/4-SWS AGAR (DSMZ Medium 958) | yes | https://mediadive.dsmz.de/medium/958 | Name: VY/4-SWS AGAR (DSMZ Medium 958) Composition: NaCl 20.0 g/l Agar 15.0 g/l MgSO4 x 7 H2O 8.0 g/l Yeast cell paste 2.5 g/l CaCl2 x 2 H2O 1.0 g/l KCl 0.5 g/l NaHCO3 0.16 g/l KBr 0.08 g/l SrCl2 x 6 H2O 0.03 g/l Sodium beta-glycerophosphate 0.01 g/l Ferric citrate 0.01 g/l Cyanocobalamine 0.0005 g/l EDTA 0.0005 g/l FeSO4 x 7 H2O 0.0002 g/l H3BO3 3e-05 g/l CoCl2 x 6 H2O 2e-05 g/l ZnSO4 x 7 H2O 1e-05 g/l Na2MoO4 x 2 H2O 3e-06 g/l MnCl2 x 4 H2O 3e-06 g/l NiCl2 x 6 H2O 2e-06 g/l CuCl2 x 2 H2O 1e-06 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 5591 | positive | growth | 30 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
compound production
- @ref: 5591
- compound: haloalkane dehalogenase
observation
- @ref: 67770
- observation: quinones: MK-8(H2)
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 5591 | semi-dried seagrass (Zostera) | Zostera | Iriomote-Jima Island, Okinawa | Japan | JPN | Asia |
| 67770 | Semi-dried sample of sea grass | Iriomote-jima Island | Japan | JPN | Asia |
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Aquatic plant
taxonmaps
- @ref: 69479
- File name: preview.99_3266.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_385;96_1701;97_2036;98_2502;99_3266&stattab=map
- Last taxonomy: Plesiocystis pacifica subclade
- 16S sequence: AB083432
- Sequence Identity:
- Total samples: 3138
- soil counts: 471
- aquatic counts: 1671
- animal counts: 937
- plant counts: 59
Safety information
risk assessment
- @ref: 5591
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5591
- description: Plesiocystis pacifica gene for 16S ribosomal RNA
- accession: AB083432
- length: 1484
- database: ena
- NCBI tax ID: 391625
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Plesiocystis pacifica SIR-1 | GCA_000170895 | contig | ncbi | 391625 |
| 66792 | Plesiocystis pacifica SIR-1 | 391625.5 | wgs | patric | 391625 |
| 66792 | Plesiocystis pacifica SIR-1 | 640963030 | draft | img | 391625 |
GC content
- @ref: 5591
- GC-content: 69.3
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| gram-positive | no | 96.735 | no |
| anaerobic | no | 96.916 | no |
| halophile | yes | 54.391 | no |
| spore-forming | no | 82.277 | no |
| glucose-util | yes | 77.994 | no |
| aerobic | yes | 72.833 | no |
| motile | no | 64.814 | no |
| flagellated | no | 90.312 | no |
| thermophile | no | 97.577 | yes |
| glucose-ferment | no | 86.007 | no |
External links
@ref: 5591
culture collection no.: DSM 14875, AJ 13960, JCM 11591
straininfo link
- @ref: 79702
- straininfo: 100867
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 12656172 | Plesiocystis pacifica gen. nov., sp. nov., a marine myxobacterium that contains dihydrogenated menaquinone, isolated from the Pacific coasts of Japan. | Iizuka T, Jojima Y, Fudou R, Hiraishi A, Ahn JW, Yamanaka S | Int J Syst Evol Microbiol | 10.1099/ijs.0.02418-0 | 2003 | Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Japan, Microscopy, Electron, Scanning, Molecular Sequence Data, Myxococcales/*classification/genetics/isolation & purification/*metabolism, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Vitamin K 2/*analogs & derivatives/*metabolism | Genetics |
| Phylogeny | 30413766 | Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites. | Amiri Moghaddam J, Crusemann M, Alanjary M, Harms H, Davila-Cespedes A, Blom J, Poehlein A, Ziemert N, Konig GM, Schaberle TF | Sci Rep | 10.1038/s41598-018-34954-y | 2018 | Bacterial Proteins/*genetics, Computational Biology, *Genome, Bacterial, *Metabolome, Multigene Family, Myxococcales/classification/genetics/*metabolism, Phylogeny, Seawater/*microbiology | Genetics |
| 35049927 | New Deoxyenhygrolides from Plesiocystis pacifica Provide Insights into Butenolide Core Biosynthesis. | Hug JJ, Kjaerulff L, Garcia R, Muller R | Mar Drugs | 10.3390/md20010072 | 2022 | 4-Butyrolactone/*analogs & derivatives/biosynthesis/chemistry, Animals, Aquatic Organisms, *Myxococcales |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 5591 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14875) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14875 | |
| 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 | |
| 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) | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 69479 | João 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 | |
| 79702 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100867.1 | StrainInfo: A central database for resolving microbial strain identifiers |