Strain identifier
BacDive ID: 159876
Type strain:
Species: Xinfangfangia soli
Strain Designation: ZQBW
Strain history: <- Qiang Hu, Nanjing Agricultural Univ.
NCBI tax ID(s): 2185115 (species)
General
@ref: 66627
BacDive-ID: 159876
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped, colony-forming
description: Xinfangfangia soli ZQBW is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from diuron-polluted soil.
NCBI tax id
- NCBI tax id: 2185115
- Matching level: species
strain history
- @ref: 67771
- history: <- Qiang Hu, Nanjing Agricultural Univ.
doi: 10.13145/bacdive159876.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Xinfangfangia
- species: Xinfangfangia soli
- full scientific name: Xinfangfangia soli Hu et al. 2018
synonyms
- @ref: 20215
- synonym: Tabrizicola soli
@ref: 66627
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Xinfangfangia
species: Xinfangfangia soli
strain designation: ZQBW
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
66627 | negative | rod-shaped | no | |
69480 | negative | 99.994 |
colony morphology
- @ref: 66627
- colony color: light yellow
- colony shape: circular
- incubation period: 3 days
- medium used: R2A medium
Culture and growth conditions
culture medium
@ref | name | growth |
---|---|---|
66627 | LB (Luria-Bertani) MEDIUM | no |
66627 | marine broth | no |
66627 | Reasoner's 2A agar (R2A) | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
66627 | positive | optimum | 30 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
- @ref: 66627
- ability: positive
- type: optimum
- pH: 7
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
66627 | no | |
69480 | no | 99.98 |
halophily
- @ref: 66627
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-0.5 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
66627 | 16024 | D-mannose | - | assimilation |
66627 | 16899 | D-mannitol | - | assimilation |
66627 | 17128 | adipate | - | assimilation |
66627 | 17306 | maltose | - | assimilation |
66627 | 17634 | D-glucose | - | assimilation |
66627 | 18401 | phenylacetate | - | assimilation |
66627 | 25115 | malate | - | assimilation |
66627 | 27689 | decanoate | - | assimilation |
66627 | 30849 | L-arabinose | - | assimilation |
66627 | 32032 | potassium gluconate | - | assimilation |
66627 | 53258 | citric acid | - | assimilation |
66627 | 53258 | sodium citrate | - | assimilation |
66627 | 59640 | N-acetylglucosamine | - | assimilation |
66627 | 17634 | D-glucose | - | fermentation |
66627 | 5291 | gelatin | - | hydrolysis |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. | is resistant | resistance conc. |
---|---|---|---|---|---|---|---|
66627 | 17076 | streptomycin | yes | yes | 10 µg (disc) | ||
66627 | 6104 | kanamycin | yes | yes | 30 µg (disc) | ||
66627 | 27902 | tetracycline | yes | yes | 30 µg (disc) | ||
66627 | 17698 | chloramphenicol | yes | yes | 30 µg (disc) | ||
66627 | 59062 | polymyxin | yes | yes | 300 µg (disc) | ||
66627 | 9215 | spectinomycin | yes | yes | 100 µg (disc) | ||
66627 | 7731 | ofloxacin | yes | yes | 5 µg (disc) | ||
66627 | 100241 | ciprofloxacin | yes | yes | 5 µg (disc) | ||
66627 | 28001 | vancomycin | yes | yes | 30 µg (disc) | ||
66627 | 17334 | penicillin | yes | yes | 10 µg (disc) | ||
66627 | 28077 | rifampicin | yes | yes | 5 µg (disc) | ||
66627 | 7507 | neomycin | yes | yes | 30 µg (disc) | ||
66627 | 28368 | novobiocin | yes | yes | 30 µg (disc) | ||
66627 | 100147 | nalidixic acid | yes | yes | 30 µg (disc) | ||
66627 | 9321 | sulbactam | yes | yes | 75 µg (disc) | ||
66627 | 2637 | Amikacin | yes | yes | 30 µg (disc) | ||
66627 | 17833 | gentamicin | yes | yes | 10 µg (disc) | ||
66627 | 28669 | bacitracin | yes | yes | 0.04 µg (disc) | ||
66627 | 6472 | lincomycin | yes | yes | 2 µg (disc) |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
66627 | 15688 | acetoin | no |
66627 | 16136 | hydrogen sulfide | no |
66627 | 35581 | indole | no |
enzymes
@ref | value | activity | ec |
---|---|---|---|
66627 | alkaline phosphatase | - | 3.1.3.1 |
66627 | alpha-chymotrypsin | - | 3.4.21.1 |
66627 | alpha-fucosidase | - | 3.2.1.51 |
66627 | alpha-galactosidase | - | 3.2.1.22 |
66627 | alpha-mannosidase | - | 3.2.1.24 |
66627 | arginine dihydrolase | - | 3.5.3.6 |
66627 | beta-galactosidase | - | 3.2.1.23 |
66627 | beta-glucosidase | - | 3.2.1.21 |
66627 | beta-glucuronidase | - | 3.2.1.31 |
66627 | cystine arylamidase | - | 3.4.11.3 |
66627 | gelatinase | - | |
66627 | lipase (C 14) | - | |
66627 | lysine decarboxylase | - | 4.1.1.18 |
66627 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
66627 | ornithine decarboxylase | - | 4.1.1.17 |
66627 | trypsin | - | 3.4.21.4 |
66627 | tryptophan deaminase | - | 4.1.99.1 |
66627 | urease | - | 3.5.1.5 |
66627 | valine arylamidase | - | |
66627 | acid phosphatase | + | 3.1.3.2 |
66627 | esterase (C 4) | + | |
66627 | esterase Lipase (C 8) | + | |
66627 | leucine arylamidase | + | 3.4.11.1 |
66627 | naphthol-AS-BI-phosphohydrolase | + | |
66627 | alpha-glucosidase | +/- | 3.2.1.20 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature | isolation procedure |
---|---|---|---|---|---|---|---|---|---|---|---|---|
66627 | diuron-polluted soil | Nanjing | China | CHN | Asia | 32.3267 | 118.836 | MSM | 1.0 g NH4NO3, 1.5 g K2HPO4, 0.5 g KH2PO4, 0.2 g MgSO4, 1.0 g NaCl per litre distilled water, pH 7.0 supplemented with 30 mg/l diuron and 1 g/l glucose | 28 days | 30 | Transferred 1:20 into fresh medium every week. The final enrichment culture was spread on R2A agar containing 30 mg/l diuron |
67771 | From polluted soil | Nanjing, Jiangsu Province | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Soil |
#Engineered | #Contamination |
Sequence information
16S sequences
- @ref: 66627
- description: Tabrizicola sp. ZQBW 16S ribosomal RNA gene, partial sequence
- accession: MG190346
- length: 1428
- database: ena
- NCBI tax ID: 2185115
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Tabrizicola soli CCTCC AB 2017177 | GCA_015999335 | scaffold | ncbi | 2185115 |
66792 | Xinfangfangia soli strain CCTCC AB 2017177 | 2185115.3 | wgs | patric | 2185115 |
GC content
- @ref: 66627
- GC-content: 67.00
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 89 | no |
motile | no | 62.794 | yes |
flagellated | no | 92.57 | no |
gram-positive | no | 97.967 | yes |
anaerobic | no | 98.262 | yes |
aerobic | yes | 88.915 | yes |
halophile | no | 84.349 | no |
spore-forming | no | 94.171 | yes |
glucose-util | yes | 71.662 | no |
thermophile | no | 96.951 | yes |
glucose-ferment | no | 89.697 | no |
External links
@ref: 66627
culture collection no.: KCTC 62102, CCTCC AB 2017177
literature
- topic: Phylogeny
- Pubmed-ID: 29947602
- title: Xinfangfangia soli gen. nov., sp. nov., isolated from a diuron-polluted soil.
- authors: Hu Q, Zhang L, Hang P, Zhou XY, Jia WB, Li SP, Jiang JD
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.002887
- year: 2018
- mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diuron, Fatty Acids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Ubiquinone/chemistry
- topic2: Transcriptome
Reference
@id | authors | title | doi/url | journal | pubmed |
---|---|---|---|---|---|
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 | ||
66627 | Qiang Hu, Long Zhang, Ping Hang, Xi-Yi Zhou, Wei-Bin Jia, Shun-Peng Li and Jian-Dong Jiang | Xinfangfangia soli gen. nov., sp. nov., isolated from a diuron-polluted soil | 10.1099/ijsem.0.002887 | IJSEM 68: 2622-2626 2018 | 29947602 |
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 | ||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||
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 |