Strain identifier
BacDive ID: 13510
Type strain:
Species: Sciscionella marina
Strain history: <- XP Tian, Yunnan Inst., China
NCBI tax ID(s): 1123244 (strain), 508770 (species)
General
@ref: 15447
BacDive-ID: 13510
DSM-Number: 45152
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Sciscionella marina DSM 45152 is an aerobe, spore-forming, mesophilic bacterium that was isolated from marine sand sediment at a depth about 500 m.
NCBI tax id
NCBI tax id | Matching level |
---|---|
508770 | species |
1123244 | strain |
strain history
@ref | history |
---|---|
15447 | <- S.-K. Tang and W.-J. Li, YIM; SCSIO 00231 <- X.-P. Tian et al. |
67770 | KCTC 19433 <-- X.-P. Tian SCSIO 00231. |
67771 | <- XP Tian, Yunnan Inst., China |
doi: 10.13145/bacdive13510.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Pseudonocardiales
- family: Pseudonocardiaceae
- genus: Sciscionella
- species: Sciscionella marina
- full scientific name: Sciscionella marina Tian et al. 2009
@ref: 15447
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Sciscionella
species: Sciscionella marina
full scientific name: Sciscionella marina Tian et al. 2009 emend. Nouioui et al. 2018
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence |
---|---|---|
28934 | positive | |
67771 | positive | |
69480 | positive | 100 |
pigmentation
- @ref: 28934
- production: no
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
15447 | https://www.dsmz.de/microorganisms/photos/DSM_45152.jpg | Medium 65 28°C | © Leibniz-Institut DSMZ |
66793 | EM_DSM_45152_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_45152_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_45152_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_45152_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_45152_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 15447
- name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
- growth: yes
- link: https://mediadive.dsmz.de/medium/65
- composition: Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15447 | positive | growth | 28 | mesophilic |
28934 | positive | growth | 10-37 | |
28934 | positive | optimum | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
28934 | positive | growth | 6.0-8.0 |
28934 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
28934 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 98 |
69480 | yes | 98.741 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
28934 | NaCl | positive | growth | 0-13 % |
28934 | NaCl | positive | optimum | 4 % |
observation
- @ref: 67770
- observation: quinones: MK-9(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
28934 | 17057 | cellobiose | + | carbon source |
28934 | 28757 | fructose | + | carbon source |
28934 | 28260 | galactose | + | carbon source |
28934 | 17234 | glucose | + | carbon source |
28934 | 17716 | lactose | + | carbon source |
28934 | 29864 | mannitol | + | carbon source |
28934 | 37684 | mannose | + | carbon source |
28934 | 33942 | ribose | + | carbon source |
28934 | 27082 | trehalose | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
28934 | catalase | + | 1.11.1.6 |
28934 | gelatinase | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
15447 | marine sand sediment at a depth about 500 m | northern South China Sea | China | CHN | Asia |
67770 | Marine sand sediment at a depth of about 500 m | northern South China Sea | |||
67771 | From marine sediment | Northern South China Sea | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
#Environmental | #Terrestrial | #Sandy |
taxonmaps
- @ref: 69479
- File name: preview.99_3870.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1985;97_2386;98_2947;99_3870&stattab=map
- Last taxonomy: Sciscionella marina subclade
- 16S sequence: EU503139
- Sequence Identity:
- Total samples: 1082
- soil counts: 390
- aquatic counts: 101
- animal counts: 545
- plant counts: 46
Safety information
risk assessment
- @ref: 15447
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15447
- description: Sciscionella marina strain SCSIO 00231 16S ribosomal RNA gene, partial sequence
- accession: EU503139
- length: 1465
- database: ena
- NCBI tax ID: 508770
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Sciscionella marina DSM 45152 | 1123244.5 | wgs | patric | 1123244 |
66792 | Sciscionella marina DSM 45152 | 2515154143 | draft | img | 1123244 |
67770 | Sciscionella marina DSM 45152 | GCA_000379465 | scaffold | ncbi | 1123244 |
GC content
@ref | GC-content | method |
---|---|---|
28934 | 69 | |
67770 | 67.8 | genome sequence analysis |
67770 | 69 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 98 | no |
motile | no | 94.931 | no |
flagellated | no | 98.467 | no |
gram-positive | yes | 84.096 | yes |
anaerobic | no | 98.756 | yes |
aerobic | yes | 87.217 | yes |
halophile | no | 78.876 | no |
spore-forming | yes | 80.726 | no |
glucose-util | yes | 86.258 | yes |
thermophile | no | 97.635 | yes |
glucose-ferment | no | 92.477 | no |
External links
@ref: 15447
culture collection no.: DSM 45152, CCTCC AA 208009, KCTC 19433, SCSIO 00231, JCM 16222, NBRC 106527
straininfo link
- @ref: 82702
- straininfo: 408186
literature
- topic: Phylogeny
- Pubmed-ID: 19196758
- title: Sciscionella marina gen. nov., sp. nov., a marine actinomycete isolated from a sediment in the northern South China Sea.
- authors: Tian XP, Zhi XY, Qiu YQ, Zhang YQ, Tang SK, Xu LH, Zhang S, Li WJ
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.001982-0
- year: 2009
- mesh: Actinomycetales/chemistry/*classification/genetics/isolation & purification, Cell Wall/chemistry, China, Geologic Sediments/*microbiology, Molecular Sequence Data, Oceans and Seas, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
15447 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45152) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45152 | ||||
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 | ||||
28934 | 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 | 25373 | 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) | ||||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 28604660 | 35: 676-683 2017 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||||
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 | ||||
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 | ||||
82702 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID408186.1 | StrainInfo: A central database for resolving microbial strain identifiers |