Strain identifier
BacDive ID: 17916
Type strain:
Species: Arenicella xantha
Strain Designation: Sd2-39
Strain history: N. Tanaka <-- L. A. Romanenko Sd2-39 (=KMM 3895).
NCBI tax ID(s): 644221 (species)
General
@ref: 17481
BacDive-ID: 17916
DSM-Number: 24032
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Arenicella xantha Sd2-39 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from offshore marine sandy sample.
NCBI tax id
- NCBI tax id: 644221
- Matching level: species
strain history
@ref | history |
---|---|
17481 | <- N. Tanaka, NRIC <- L. A. Romanenko, KMM; Sd2-39 |
67770 | N. Tanaka <-- L. A. Romanenko Sd2-39 (=KMM 3895). |
doi: 10.13145/bacdive17916.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Arenicellales
- family: Arenicellaceae
- genus: Arenicella
- species: Arenicella xantha
- full scientific name: Arenicella xantha Romanenko et al. 2010
@ref: 17481
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Arenicellales
family: Arenicellaceae
genus: Arenicella
species: Arenicella xantha
full scientific name: Arenicella xantha Romanenko et al. 2010
strain designation: Sd2-39
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29623 | negative | 3.5 µm | 0.55 µm | rod-shaped | no | |
69480 | negative | 99.986 |
pigmentation
- @ref: 29623
- production: yes
Culture and growth conditions
culture medium
- @ref: 17481
- name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514c
- composition: Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l Na2CO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
17481 | positive | growth | 28 | mesophilic |
29623 | positive | growth | 05-35 | |
29623 | positive | optimum | 26.5 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29623 | positive | growth | 06-11 | alkaliphile |
29623 | positive | optimum | 9 |
Physiology and metabolism
oxygen tolerance
- @ref: 29623
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.997 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29623 | NaCl | positive | growth | 01-05 % |
29623 | NaCl | positive | optimum | 2.5 % |
observation
- @ref: 67770
- observation: quinones: Q-8
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29623 | 16449 | alanine | + | carbon source |
29623 | 22599 | arabinose | + | carbon source |
29623 | 17234 | glucose | + | carbon source |
29623 | 28053 | melibiose | + | carbon source |
29623 | 33942 | ribose | + | carbon source |
29623 | 18222 | xylose | + | carbon source |
29623 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29623 | alkaline phosphatase | + | 3.1.3.1 |
29623 | catalase | + | 1.11.1.6 |
29623 | gelatinase | + | |
29623 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
17481 | offshore marine sandy sample | Sea of Japan, offshore | Russia | RUS | Asia |
67770 | Sandy sediment sample collected offshore from the Sea of Japan | Russia | RUS |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Terrestrial | #Sandy |
taxonmaps
- @ref: 69479
- File name: preview.99_129721.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1076;96_13111;97_24205;98_86865;99_129721&stattab=map
- Last taxonomy: Arenicella xantha subclade
- 16S sequence: AB500096
- Sequence Identity:
- Total samples: 997
- soil counts: 12
- aquatic counts: 965
- animal counts: 15
- plant counts: 5
Safety information
risk assessment
- @ref: 17481
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17481
- description: Arenicella xantha gene for 16S ribosomal RNA, partial sequence
- accession: AB500096
- length: 1506
- database: ena
- NCBI tax ID: 644221
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Arenicella xantha strain DSM 24032 | 644221.3 | wgs | patric | 644221 |
66792 | Arenicella xantha DSM 24032 | 2770939506 | draft | img | 644221 |
67770 | Arenicella xantha DSM 24032 | GCA_003315245 | scaffold | ncbi | 644221 |
GC content
@ref | GC-content | method |
---|---|---|
17481 | 48.1 | thermal denaturation, midpoint method (Tm) |
29623 | 48.1 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.758 | yes |
anaerobic | no | 99.264 | yes |
halophile | no | 56.226 | no |
spore-forming | no | 96.815 | no |
glucose-util | yes | 87.471 | yes |
thermophile | no | 99.537 | yes |
flagellated | no | 92.652 | yes |
aerobic | yes | 97.025 | yes |
motile | no | 87.25 | no |
glucose-ferment | no | 91.747 | no |
External links
@ref: 17481
culture collection no.: DSM 24032, KMM 3895, NRIC 0759, JCM 16153
straininfo link
- @ref: 86905
- straininfo: 403893
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19767361 | Arenicella xantha gen. nov., sp. nov., a gammaproteobacterium isolated from a marine sandy sediment. | Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV | Int J Syst Evol Microbiol | 10.1099/ijs.0.017194-0 | 2009 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Gammaproteobacteria/*classification/genetics/*isolation & purification/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics | Metabolism |
Phylogeny | 23771619 | Arenicella chitinivorans sp. nov., a gammaproteobacterium isolated from the sea urchin Strongylocentrotus intermedius. | Nedashkovskaya OI, Cleenwerck I, Zhukova NV, Kim SB, de Vos P | Int J Syst Evol Microbiol | 10.1099/ijs.0.051599-0 | 2013 | Animals, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Japan, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Strongylocentrotus/*microbiology, Ubiquinone/chemistry | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
17481 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24032) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24032 | ||||
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 | ||||
29623 | 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 | 26013 | 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) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
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 | ||||
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 | ||||
86905 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID403893.1 | StrainInfo: A central database for resolving microbial strain identifiers |