Strain identifier

BacDive ID: 159722

Type strain: Yes

Species: Shinella pollutisoli

Strain Designation: AH-1

Strain history: <- Qing Chen, Zaozhuang Univ.

NCBI tax ID(s): 2250594 (species)

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General

@ref: 66623

BacDive-ID: 159722

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Shinella pollutisoli AH-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from TBBPA-contaminated soil sample.

NCBI tax id

  • NCBI tax id: 2250594
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Qing Chen, Zaozhuang Univ.

doi: 10.13145/bacdive159722.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Shinella
  • species: Shinella pollutisoli
  • full scientific name: Shinella pollutisoli Mu et al. 2018

@ref: 66623

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Rhizobiaceae

genus: Shinella

species: Shinella pollutisoli

strain designation: AH-1

type strain: yes

Morphology

cell morphology

  • @ref: 66623
  • gram stain: negative
  • cell length: 1.8-2.5 µm
  • cell width: 0.3-0.6 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 66623
  • colony size: 1-2 mm
  • colony color: pale yellow
  • incubation period: 2 days
  • medium used: Tryptic Soy Agar

Culture and growth conditions

culture medium

@refnamegrowth
66623LB (Luria-Bertani) agaryes
66623Nutrient agar (NA)yes
66623Reasoner's 2A agar (R2A)yes
66623tryptic soy agar (TSA)yes

culture temp

@refgrowthtypetemperaturerange
66623positiveoptimum30mesophilic
66623positivegrowth15-37
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
66623positiveoptimum7
66623positivegrowth6.5-9alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66623aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
66623NaClpositivegrowth0-2 %(w/v)
66623NaClpositiveoptimum1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
666239300suberic acid-carbon source
6662315792malonate-carbon source
6662315971L-histidine-carbon source
66623161933-hydroxybenzoate-carbon source
6662316411acetic acid-carbon source
6662317115L-serine-carbon source
6662317128adipate-carbon source
6662317240itaconate-carbon source
6662317272propionate-carbon source
6662317814salicin-carbon source
66623178794-hydroxybenzoate-carbon source
6662318287L-fucose-carbon source
6662318401phenylacetate-carbon source
6662324265gluconate-carbon source
6662324996lactate-carbon source
6662325115malate-carbon source
6662327689decanoate-carbon source
6662328053melibiose-carbon source
6662328087glycogen-carbon source
6662330031succinate-carbon source
6662331011valerate-carbon source
6662353258citric acid-carbon source
66623potassium 2-dehydro-D-gluconate-carbon source
66623potassium 5-dehydro-D-gluconate-carbon source
6662316899D-mannitol+carbon source
6662316977L-alanine+carbon source
6662316988D-ribose+carbon source
6662317203L-proline+carbon source
6662317268myo-inositol+carbon source
6662317306maltose+carbon source
6662317634D-glucose+carbon source
6662317924D-sorbitol+carbon source
6662317992sucrose+carbon source
6662330849L-arabinose+carbon source
6662359640N-acetylglucosamine+carbon source
6662362345L-rhamnose+carbon source
6662317634D-glucose-fermentation
666234853esculin-hydrolysis
666235291gelatin-hydrolysis
6662328017starch-hydrolysis
6662317632nitrate-reduction

metabolite production

  • @ref: 66623
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
66623acid phosphatase-3.1.3.2
66623alkaline phosphatase-3.1.3.1
66623alpha-glucosidase-3.2.1.20
66623arginine dihydrolase-3.5.3.6
66623beta-glucuronidase-3.2.1.31
66623cystine aminopeptidase-3.4.11.3
66623esterase (C 4)-
66623esterase Lipase (C 8)-
66623leucine aminopeptidase-3.4.1.1
66623naphthol-AS-BI-phosphohydrolase-
66623urease-3.5.1.5
66623valine aminopeptidase-
66623alpha-chymotrypsin+3.4.21.1
66623alpha-fucosidase+3.2.1.51
66623alpha-galactosidase+3.2.1.22
66623alpha-mannosidase+3.2.1.24
66623beta-galactosidase+3.2.1.23
66623beta-glucosidase+3.2.1.21
66623catalase+1.11.1.6
66623cytochrome oxidase+1.9.3.1
66623lipase (C 14)+
66623N-acetyl-beta-glucosaminidase+3.2.1.52

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66623C19:0 10-methyl2
    66623C16:05
    66623C16:0 3OH0.6
    66623C16:1 w6c and/or C16:1 w7c0.8
    66623C19:0 cyclo w8c2.3
    66623C18:0 3OH2.5
    66623C18:03.1
    66623C12:0 aldehyde4.5
    66623C18:1 w6c and/or C18:1 w7c78.9
  • type of FA analysis: whole cell analysis
  • incubation medium: tryptic soy broth
  • agar/liquid: liquid
  • incubation temperature: 30
  • incubation time: 2
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
66623TBBPA-contaminated soil sampleSuqian City, Jiangsu ProvinceChinaCHNAsiatryptic soy agar3 days30A tetrabro-mobisphenol A (TBBPA)-contaminated soil sample (5.0 g) was added to a 250 ml flask containing 100 ml minimal medium (1.0 g NH4NO3, 1.6 g K2HPO4, 0.5 g KH2PO4, 0.2 g MgSO4 and 1.0 g NaCl per litre water at pH 7.0) supplemented with 0.1 mM TBBPA (TMM). The culture was incubated at 30°C at 150 r.p.m. for 5 days. A 5 ml aliquot of the enriched culture was subsequently transferred into 100 ml of fresh TMM. After three rounds of enrichment, the mixture was diluted in a tenfold series, and a 100 µl sample of each dilution was spread onto trypticase soy agar plates. The plates were incubated at 30°C for 3 days, and then all colonies were isolated.
67771From halogenated aromatics-contaminated soilCity of Zaozhuang, Shandong ProvinceChinaCHNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_58729.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_1474;97_1759;98_23614;99_58729&stattab=map
  • Last taxonomy: Shinella
  • 16S sequence: KY054581
  • Sequence Identity:
  • Total samples: 75
  • soil counts: 6
  • aquatic counts: 58
  • animal counts: 6
  • plant counts: 5

Sequence information

16S sequences

  • @ref: 66623
  • description: Shinella sp. strain AH-1 16S ribosomal RNA gene, partial sequence
  • accession: KY054581
  • length: 1441
  • database: ena
  • NCBI tax ID: 2250594

Genome sequences

  • @ref: 66792
  • description: Shinella pollutisoli KCTC 52677
  • accession: GCA_024609765
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 2250594

GC content

  • @ref: 66623
  • GC-content: 68.2
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno79.318no
gram-positiveno97.885yes
anaerobicno97.657yes
aerobicyes85.963no
halophileno89.325yes
spore-formingno95.684no
motileyes84.562yes
glucose-fermentno91.856no
thermophileno98.773no
glucose-utilyes87.983yes

External links

@ref: 66623

culture collection no.: KCTC 52677, CCTCC AB 2017242

literature

  • topic: Phylogeny
  • Pubmed-ID: 29949500
  • title: Shinella pollutisoli sp. nov., isolated from tetrabromobisphenol A-contaminated soil.
  • authors: Mu Y, Jia WB, Ke Z, Zhuang W, Wang HM, Jiang JD, Chen K, Chen Q
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002883
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, Polybrominated Biphenyls, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Ubiquinone/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
66623Yang Mu, Wei-Bin Jia, Zhuang Ke, Wen Zhuang, Hong-Mei Wang, Jian-Dong Jiang, Kai Chen, Qing ChenShinella pollutisoli sp. nov., isolated from tetrabromobisphenol A-contaminated soil10.1099/ijsem.0.002883IJSEM 68: 2602-2606 201829949500
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69479João 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 betahttps://microbeatlas.org/