Strain identifier
BacDive ID: 132017
Type strain: 
Species: Acuticoccus yangtzensis
Strain Designation: JL1095
Strain history: <- L. Hou, Xiamen Univ., State Key Lab. of Marine Env. Science, China; JL1095
NCBI tax ID(s): 1443441 (species)
version 8.1 (current version)
General
@ref: 23808
BacDive-ID: 132017
DSM-Number: 28604
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Acuticoccus yangtzensis JL1095 is a mesophilic, Gram-negative bacterium that was isolated from surface seawater from river estuary.
NCBI tax id
- NCBI tax id: 1443441
- Matching level: species
strain history
- @ref: 23808
- history: <- L. Hou, Xiamen Univ., State Key Lab. of Marine Env. Science, China; JL1095
doi: 10.13145/bacdive132017.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Amorphaceae
- genus: Acuticoccus
- species: Acuticoccus yangtzensis
- full scientific name: Acuticoccus yangtzensis Hou et al. 2017
@ref: 23808
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Hyphomicrobiales
family: Amorphaceae
genus: Acuticoccus
species: Acuticoccus yangtzensis
full scientific name: Acuticoccus yangtzensis Hou et al. 2017 emend. Yin et al. 2018
strain designation: JL1095
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.975
Culture and growth conditions
culture medium
- @ref: 23808
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 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 NaHCO3 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: 23808
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.996 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68369 | 17128 | adipate | - | assimilation |
| 68369 | 27689 | decanoate | - | assimilation |
| 68369 | 17306 | maltose | - | assimilation |
| 68369 | 59640 | N-acetylglucosamine | - | assimilation |
| 68369 | 16899 | D-mannitol | - | assimilation |
| 68369 | 16024 | D-mannose | - | assimilation |
| 68369 | 30849 | L-arabinose | + | assimilation |
| 68369 | 17634 | D-glucose | - | assimilation |
| 68369 | 5291 | gelatin | + | hydrolysis |
| 68369 | 4853 | esculin | - | hydrolysis |
| 68369 | 16199 | urea | + | hydrolysis |
| 68369 | 29016 | arginine | - | hydrolysis |
| 68369 | 17634 | D-glucose | - | fermentation |
| 68369 | 27897 | tryptophan | - | energy source |
| 68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 68369 | gelatinase | + | |
| 68369 | beta-glucosidase | - | 3.2.1.21 |
| 68369 | urease | + | 3.5.1.5 |
| 68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 23808 | - | - | - | - | + | - | + | - | - | + | - | - | - | - | +/- | - | - | +/- | +/- | - |
Isolation, sampling and environmental information
isolation
- @ref: 23808
- sample type: surface seawater from river estuary
- geographic location: Yangtze Estuary (31° N, 122° E)
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Estuary |
| #Environmental | #Aquatic | #Surface water |
taxonmaps
- @ref: 69479
- File name: preview.99_3727.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_419;96_1918;97_2308;98_2846;99_3727&stattab=map
- Last taxonomy: Acuticoccus yangtzensis subclade
- 16S sequence: KF741873
- Sequence Identity:
- Total samples: 1497
- soil counts: 229
- aquatic counts: 1030
- animal counts: 215
- plant counts: 23
Safety information
risk assessment
- @ref: 23808
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 23808
- description: Acuticoccus yangtzensis strain JL1095 16S ribosomal RNA gene, partial sequence
- accession: KF741873
- length: 1397
- database: ena
- NCBI tax ID: 1443441
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Acuticoccus yangtzensis JL1095 | GCA_001927245 | contig | ncbi | 1443441 |
| 66792 | Acuticoccus yangtzensis JL1095 | GCA_003073145 | contig | ncbi | 1443441 |
| 66792 | Acuticoccus yangtzensis strain JL1095 | 1443441.5 | wgs | patric | 1443441 |
GC content
- @ref: 23808
- GC-content: 51.5
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 78.296 | no |
| gram-positive | no | 98.311 | no |
| anaerobic | no | 97.116 | no |
| halophile | no | 66.94 | no |
| spore-forming | no | 95.337 | no |
| thermophile | no | 91.97 | yes |
| glucose-util | yes | 79.279 | yes |
| aerobic | yes | 90.638 | no |
| flagellated | no | 72.29 | no |
| glucose-ferment | no | 91.893 | yes |
External links
@ref: 23808
culture collection no.: DSM 28604, CGMCC 1.12795
straininfo link
- @ref: 90397
- straininfo: 406376
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25265882 | Acuticoccus yangtzensis gen. nov., sp. nov., a novel member in the family Rhodobacteraceae, isolated from the surface water of the Yangtze Estuary. | Hou L, Zhang Y, Sun J, Xie X | Curr Microbiol | 10.1007/s00284-014-0698-1 | 2014 | Base Composition, China, DNA, Bacterial, Phylogeny, RNA, Ribosomal, 16S, Rhodobacteraceae/chemistry/*classification/physiology/ultrastructure, *Water Microbiology | |
| Genetics | 29299111 | Genome sequence of Acuticoccus yangtzensis JL1095T (DSM 28604T) isolated from the Yangtze Estuary. | Hou L, Sun J, Xie X, Jiao N, Zhang Y | Stand Genomic Sci | 10.1186/s40793-017-0295-6 | 2017 | ||
| Phylogeny | 30141770 | Acuticoccus kandeliae sp. nov., isolated from rhizosphere soil of the mangrove plant Kandelia, and emended description of Acuticoccus yangtzensis. | Yin Q, Liang J, Zhang L, Ma K, Hu ZL, Zhang Y, Xu Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002990 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hong Kong, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, *Rhizosphere, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 30810521 | Acuticoccus sediminis sp. nov., isolated from deep-sea sediment of the Indian Ocean and proposal of Acuticoccaceae fam. nov. | Lai Q, Liu X, Sun F, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003289 | 2019 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Indian Ocean, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
| Genetics | 36096632 | Complete genome sequencing and analysis revealed the nitrogen utilization strategy of a novel Acuticoccus species isolated from surface water of the Indian Ocean. | Shi J, Zeng Y, Wang H, Niu Y, He P, Chen H | Mar Genomics | 10.1016/j.margen.2022.100971 | 2022 | Base Composition, Indian Ocean, *Nitrogen/metabolism, *Water, Whole Genome Sequencing | Transcriptome |
| Phylogeny | 36251750 | Acuticoccus kalidii sp. nov., a 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing endophyte from a root of Kalidium cuspidatum. | Tian J, Xu L, Zhang X, Sun JQ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005521 | 2022 | Bacterial Typing Techniques, Base Composition, Cardiolipins, Catalase/genetics, *Chenopodiaceae/microbiology, DNA, Bacterial/genetics, *Endophytes/genetics, Fatty Acids/chemistry, Glycolipids, Nucleotides, Phosphatidylethanolamines, Phospholipids/chemistry, Phylogeny, Quinones, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 23808 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28604 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28604) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 68369 | Automatically annotated from API 20NE | |||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 90397 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID406376.1 |