Strain identifier
BacDive ID: 13879
Type strain: 
Species: Rhodoligotrophos appendicifer
Strain Designation: 120-1
Strain history: T. Imanaka 120-1.
NCBI tax ID(s): 987056 (species)
version 8.1 (current version)
General
@ref: 17233
BacDive-ID: 13879
DSM-Number: 23582
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative, coccus-shaped
description: Rhodoligotrophos appendicifer 120-1 is a microaerophile, mesophilic, Gram-negative bacterium that was isolated from freshwater lake.
NCBI tax id
- NCBI tax id: 987056
- Matching level: species
strain history
| @ref | history |
|---|---|
| 17233 | <- T. Imanaka, Ritsumeikan University, Dept. of Biotechnology, College of Life Sciences, Japan; 120-1 |
| 67770 | T. Imanaka 120-1. |
doi: 10.13145/bacdive13879.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Parvibaculaceae
- genus: Rhodoligotrophos
- species: Rhodoligotrophos appendicifer
- full scientific name: Rhodoligotrophos appendicifer Fukuda et al. 2012
@ref: 17233
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Parvibaculaceae
genus: Rhodoligotrophos
species: Rhodoligotrophos appendicifer
full scientific name: Rhodoligotrophos appendicifer Fukuda et al. 2012
strain designation: 120-1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|
| 30298 | negative | 0.7 µm | coccus-shaped | no | |
| 69480 | negative | 99.96 |
pigmentation
- @ref: 30298
- production: yes
Culture and growth conditions
culture medium
- @ref: 17233
- name: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514a
- composition: Name: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a) Composition: Agar 15.0 g/l NaCl 9.725 g/l MgCl2 2.95 g/l Bacto peptone 2.5 g/l Na2SO4 1.62 g/l CaCl2 0.9 g/l Yeast extract 0.5 g/l KCl 0.275 g/l NaHCO3 0.08 g/l Fe(III) citrate 0.05 g/l KBr 0.04 g/l SrCl2 0.017 g/l H3BO3 0.011 g/l Na2HPO4 0.004 g/l Na-silicate 0.002 g/l NaF 0.0012 g/l (NH4)NO3 0.0008 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 17233 | positive | growth | 30 | mesophilic |
| 30298 | positive | growth | 05-35 | |
| 30298 | positive | optimum | 30 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30298 | positive | growth | 06-09 | alkaliphile |
| 30298 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 30298
- oxygen tolerance: microaerophile
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30298 | no | |
| 69481 | no | 99 |
| 69480 | no | 99.956 |
observation
- @ref: 67770
- observation: quinones: Q-9, Q-10
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30298 | 17128 | adipate | + | carbon source |
| 30298 | 22599 | arabinose | + | carbon source |
| 30298 | 24265 | gluconate | + | carbon source |
| 30298 | 17234 | glucose | + | carbon source |
| 30298 | 25115 | malate | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30298 | acid phosphatase | + | 3.1.3.2 |
| 30298 | catalase | + | 1.11.1.6 |
| 30298 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | continent | country | origin.country |
|---|---|---|---|---|---|
| 17233 | freshwater lake | Skarvsnes region, Naga-ike | Australia and Oceania | ||
| 67770 | Freshwater sample containing microbial mats collected at the bottom of a freshwater lake, Naga-ike | Skarvsnes region | Antarctica | Antarctica | ATA |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Lake (large) |
taxonmaps
- @ref: 69479
- File name: preview.99_130216.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_813;96_4262;97_5205;98_6605;99_130216&stattab=map
- Last taxonomy: Rhodoligotrophos appendicifer
- 16S sequence: AB617575
- Sequence Identity:
- Total samples: 1495
- soil counts: 892
- aquatic counts: 445
- animal counts: 109
- plant counts: 49
Safety information
risk assessment
- @ref: 17233
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17233
- description: Rhodoligotrophos appendicifer gene for 16S rRNA, complete sequence, strain: ATCC BAA-2115
- accession: AB617575
- length: 1462
- database: ena
- NCBI tax ID: 987056
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodoligotrophos appendicifer 120-1 | GCA_007474605 | contig | ncbi | 987056 |
| 66792 | Rhodoligotrophos appendicifer strain 120-1 | 987056.3 | wgs | patric | 987056 |
| 66792 | Rhodoligotrophos appendicifer DSM 23582 | 2828001536 | draft | img | 987056 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 17233 | 61.1 | high performance liquid chromatography (HPLC) |
| 30298 | 61.1 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| motile | no | 85.653 | yes |
| flagellated | no | 94.785 | yes |
| gram-positive | no | 96.916 | no |
| anaerobic | no | 96.707 | yes |
| halophile | no | 71.492 | no |
| spore-forming | no | 93.993 | yes |
| thermophile | no | 95.064 | yes |
| glucose-util | yes | 88.061 | yes |
| aerobic | yes | 75.59 | yes |
| glucose-ferment | no | 93.174 | no |
External links
@ref: 17233
culture collection no.: DSM 23582, ATCC BAA 2115, JCM 16873
straininfo link
- @ref: 83054
- straininfo: 402543
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22003040 | Rhodoligotrophos appendicifer gen. nov., sp. nov., an appendaged bacterium isolated from a freshwater Antarctic lake. | Fukuda W, Yamada K, Miyoshi Y, Okuno H, Atomi H, Imanaka T | Int J Syst Evol Microbiol | 10.1099/ijs.0.032953-0 | 2011 | Alphaproteobacteria/*classification/genetics/isolation & purification, Antarctic Regions, Bacterial Typing Techniques, Base Composition, Fatty Acids/analysis, Fresh Water/*microbiology, Hydrogen-Ion Concentration, Lakes/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analysis | Genetics |
| Phylogeny | 25002364 | Rhodoligotrophos jinshengii sp. nov., isolated from activated sludge. | Deng SK, Chen GQ, Chen Q, Cai S, Yao L, He J, Li SP | Int J Syst Evol Microbiol | 10.1099/ijs.0.066050-0 | 2014 | Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/chemistry, Waste Water | Genetics |
| Phylogeny | 31502947 | Rhodoligotrophos defluvii sp. nov., isolated from activated sludge. | Liu YL, Meng D, Li RR, Gu PF, Fan XY, Huang ZS, Du ZJ, Li Q | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003691 | 2019 | Alphaproteobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/analogs & derivatives/chemistry, Waste Water/microbiology | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 17233 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23582) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23582 | |||
| 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 | |||
| 30298 | 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 | 26639 | 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) | |||
| 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 | |||
| 83054 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402543.1 | StrainInfo: A central database for resolving microbial strain identifiers |