Strain identifier
BacDive ID: 17658
Type strain: 
Species: Hydrocarboniphaga effusa
Strain Designation: AP103
Strain history: <- G. J. Zylstra; AP103
NCBI tax ID(s): 243629 (species)
version 8.1 (current version)
General
@ref: 6290
BacDive-ID: 17658
DSM-Number: 16095
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Hydrocarboniphaga effusa AP103 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 243629
- Matching level: species
strain history
- @ref: 6290
- history: <- G. J. Zylstra; AP103
doi: 10.13145/bacdive17658.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Nevskiales
- family: Nevskiaceae
- genus: Hydrocarboniphaga
- species: Hydrocarboniphaga effusa
- full scientific name: Hydrocarboniphaga effusa Palleroni et al. 2004
@ref: 6290
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Xanthomonadales
family: Nevskiaceae
genus: Hydrocarboniphaga
species: Hydrocarboniphaga effusa
full scientific name: Hydrocarboniphaga effusa Palleroni et al. 2004
strain designation: AP103
type strain: yes
Morphology
cell morphology
- @ref: 30166
- gram stain: negative
- cell length: 1.2 µm
- cell width: 0.8 µm
- cell shape: rod-shaped
- motility: yes
Culture and growth conditions
culture medium
- @ref: 6290
- name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)
- growth: yes
- link: https://mediadive.dsmz.de/medium/381
- composition: Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 6290 | positive | growth | 30 | mesophilic |
| 30166 | positive | optimum | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 30166
- oxygen tolerance: aerobe
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30166 | 15963 | ribitol | + | carbon source |
| 30166 | 29016 | arginine | + | carbon source |
| 30166 | 22653 | asparagine | + | carbon source |
| 30166 | 35391 | aspartate | + | carbon source |
| 30166 | 16236 | ethanol | + | carbon source |
| 30166 | 29987 | glutamate | + | carbon source |
| 30166 | 17754 | glycerol | + | carbon source |
| 30166 | 27570 | histidine | + | carbon source |
| 30166 | 24996 | lactate | + | carbon source |
| 30166 | 25017 | leucine | + | carbon source |
| 30166 | 25115 | malate | + | carbon source |
| 30166 | 29864 | mannitol | + | carbon source |
| 30166 | 37684 | mannose | + | carbon source |
| 30166 | 28044 | phenylalanine | + | carbon source |
| 30166 | 17272 | propionate | + | carbon source |
| 30166 | 15361 | pyruvate | + | carbon source |
| 30166 | 26546 | rhamnose | + | carbon source |
| 30166 | 30031 | succinate | + | carbon source |
| 30166 | 17992 | sucrose | + | carbon source |
| 30166 | 53426 | tween 80 | + | carbon source |
enzymes
- @ref: 30166
- value: gelatinase
- activity: +
Isolation, sampling and environmental information
isolation
- @ref: 6290
- sample type: soil
- geographic location: New Jersey
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_737.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_146;96_449;97_514;98_591;99_737&stattab=map
- Last taxonomy: Hydrocarboniphaga effusa subclade
- 16S sequence: AY363245
- Sequence Identity:
- Total samples: 2909
- soil counts: 488
- aquatic counts: 1243
- animal counts: 941
- plant counts: 237
Safety information
risk assessment
- @ref: 6290
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6290
- description: Hydrocarboniphaga effusa strain AP103 16S ribosomal RNA gene, partial sequence
- accession: AY363245
- length: 1477
- database: ena
- NCBI tax ID: 1172194
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Hydrocarboniphaga effusa AP103 | GCA_000271305 | contig | ncbi | 1172194 |
| 66792 | Hydrocarboniphaga effusa AP103 | 1172194.9 | wgs | patric | 1172194 |
| 66792 | Hydrocarboniphaga effusa AP103 | 2521172591 | draft | img | 1172194 |
GC content
| @ref | GC-content |
|---|---|
| 6290 | 60 |
| 30166 | 60.5 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 83.195 | yes |
| gram-positive | no | 98.868 | yes |
| anaerobic | no | 99.375 | no |
| aerobic | yes | 96.364 | yes |
| halophile | no | 92.088 | no |
| spore-forming | no | 95.629 | no |
| flagellated | no | 62.889 | no |
| thermophile | no | 96.252 | yes |
| glucose-util | yes | 77.093 | no |
| glucose-ferment | no | 93.356 | no |
External links
@ref: 6290
culture collection no.: DSM 16095, ATCC BAA 332
straininfo link
- @ref: 86649
- straininfo: 101323
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15280292 | Hydrocarboniphaga effusa gen. nov., sp. nov., a novel member of the gamma-Proteobacteria active in alkane and aromatic hydrocarbon degradation. | Palleroni NJ, Port AM, Chang HK, Zylstra GJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.03016-0 | 2004 | Alkanes/*metabolism, Bacterial Typing Techniques, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry, Genes, rRNA, Hydrocarbons, Aromatic/*metabolism, Molecular Sequence Data, New Jersey, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Soil Microbiology, Soil Pollutants/metabolism, Xanthomonadaceae/*classification/cytology/isolation & purification/*physiology | Metabolism |
| Metabolism | 17317570 | Profiling mechanisms of alkane hydroxylase activity in vivo using the diagnostic substrate norcarane. | Rozhkova-Novosad EA, Chae JC, Zylstra GJ, Bertrand EM, Alexander-Ozinskas M, Deng D, Moe LA, van Beilen JB, Danahy M, Groves JT, Austin RN | Chem Biol | 10.1016/j.chembiol.2006.12.007 | 2007 | Burkholderia cepacia/*enzymology/metabolism, Cytochrome P-450 CYP4A/*metabolism, Pseudomonas putida/*enzymology/metabolism, Rhodococcus/*enzymology/metabolism, Terpenes/*metabolism | Enzymology |
| Phylogeny | 17978223 | Solimonas soli gen. nov., sp. nov., isolated from soil of a ginseng field. | Kim MK, Kim YJ, Cho DH, Yi TH, Soung NK, Yang DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.64938-0 | 2007 | Bacterial Typing Techniques, DNA, Ribosomal/analysis, Gammaproteobacteria/*classification/genetics/*isolation & purification/physiology, Genes, rRNA, Molecular Sequence Data, *Panax/growth & development, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity | Genetics |
| Phylogeny | 20348325 | Hydrocarboniphaga daqingensis sp. nov., isolated from a freshwater lake. | Liu Y, Song XF, Jiang JT, Liu YH, Xu CJ, Li H, Liu ZP | Int J Syst Evol Microbiol | 10.1099/ijs.0.019380-0 | 2010 | Alkanes/metabolism, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Gammaproteobacteria/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Water Microbiology | Genetics |
| Phylogeny | 20437162 | Panacagrimonas perspica gen. nov., sp. nov., a novel member of Gammaproteobacteria isolated from soil of a ginseng field. | Im WT, Liu QM, Yang JE, Kim MS, Kim SY, Lee ST, Yi TH | J Microbiol | 10.1007/s12275-010-0067-0 | 2010 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Microscopy, Electron, Transmission, Molecular Sequence Data, Panax/*growth & development, Phospholipids/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analysis, Xanthomonadaceae/*classification/genetics/*isolation & purification/physiology | Genetics |
| Phylogeny | 22407788 | Fontimonas thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a freshwater hot spring, and proposal of Solimonadaceae fam. nov. to replace Sinobacteraceae Zhou et al. 2008. | Losey NA, Stevenson BS, Verbarg S, Rudd S, Moore ERB, Lawson PA | Int J Syst Evol Microbiol | 10.1099/ijs.0.037127-0 | 2012 | Arkansas, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Gammaproteobacteria/*classification/genetics/isolation & purification, Hot Springs/*microbiology, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
| Genetics | 22933753 | Genome sequence of n-alkane-degrading Hydrocarboniphaga effusa strain AP103T (ATCC BAA-332T). | Chang HK, Zylstra GJ, Chae JC | J Bacteriol | 10.1128/JB.01017-12 | 2012 | Alkanes/metabolism, Base Composition, Biotransformation, Carbon/metabolism, DNA, Bacterial/*chemistry/*genetics, Gammaproteobacteria/*genetics/isolation & purification/metabolism, *Genome, Bacterial, Molecular Sequence Data, *Sequence Analysis, DNA | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 6290 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16095) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16095 | |||
| 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 | |||
| 30166 | 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 | 26516 | 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) | |||
| 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 | |||
| 86649 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID101323.1 | StrainInfo: A central database for resolving microbial strain identifiers |