Strain identifier

BacDive ID: 159876

Type strain: Yes

Species: Xinfangfangia soli

Strain Designation: ZQBW

Strain history: <- Qiang Hu, Nanjing Agricultural Univ.

NCBI tax ID(s): 2185115 (species)

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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/bacdive159876.20250331.9.3

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

@refgram staincell shapemotilityconfidence
66627negativerod-shapedno
125439negative93.7
125438negative97.5

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

@refnamegrowth
66627LB (Luria-Bertani) MEDIUMno
66627marine brothno
66627Reasoner's 2A agar (R2A)yes

culture temp

@refgrowthtypetemperature
66627positiveoptimum30
67771positivegrowth30

culture pH

  • @ref: 66627
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

  • @ref: 66627
  • spore formation: no

halophily

  • @ref: 66627
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6662716024D-mannose-assimilation
6662716899D-mannitol-assimilation
6662717128adipate-assimilation
6662717306maltose-assimilation
6662717634D-glucose-assimilation
6662718401phenylacetate-assimilation
6662725115malate-assimilation
6662727689decanoate-assimilation
6662730849L-arabinose-assimilation
6662732032potassium gluconate-assimilation
6662753258citric acid-assimilation
6662753258sodium citrate-assimilation
6662759640N-acetylglucosamine-assimilation
6662717634D-glucose-fermentation
666275291gelatin-hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
6662717076streptomycinyesyes10 µg (disc)
666276104kanamycinyesyes30 µg (disc)
6662727902tetracyclineyesyes30 µg (disc)
6662717698chloramphenicolyesyes30 µg (disc)
6662759062polymyxinyesyes300 µg (disc)
666279215spectinomycinyesyes100 µg (disc)
666277731ofloxacinyesyes5 µg (disc)
66627100241ciprofloxacinyesyes5 µg (disc)
6662728001vancomycinyesyes30 µg (disc)
6662717334penicillinyesyes10 µg (disc)
6662728077rifampicinyesyes5 µg (disc)
666277507neomycinyesyes30 µg (disc)
6662728368novobiocinyesyes30 µg (disc)
66627100147nalidixic acidyesyes30 µg (disc)
666279321sulbactamyesyes75 µg (disc)
666272637Amikacinyesyes30 µg (disc)
6662717833gentamicinyesyes10 µg (disc)
6662728669bacitracinyesyes0.04 µg (disc)
666276472lincomycinyesyes2 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
6662715688acetoinno
6662716136hydrogen sulfideno
6662735581indoleno

enzymes

@refvalueactivityec
66627alkaline phosphatase-3.1.3.1
66627alpha-chymotrypsin-3.4.21.1
66627alpha-fucosidase-3.2.1.51
66627alpha-galactosidase-3.2.1.22
66627alpha-mannosidase-3.2.1.24
66627arginine dihydrolase-3.5.3.6
66627beta-galactosidase-3.2.1.23
66627beta-glucosidase-3.2.1.21
66627beta-glucuronidase-3.2.1.31
66627cystine arylamidase-3.4.11.3
66627gelatinase-
66627lipase (C 14)-
66627lysine decarboxylase-4.1.1.18
66627N-acetyl-beta-glucosaminidase-3.2.1.52
66627ornithine decarboxylase-4.1.1.17
66627trypsin-3.4.21.4
66627tryptophan deaminase-4.1.99.1
66627urease-3.5.1.5
66627valine arylamidase-
66627acid phosphatase+3.1.3.2
66627esterase (C 4)+
66627esterase Lipase (C 8)+
66627leucine arylamidase+3.4.11.1
66627naphthol-AS-BI-phosphohydrolase+
66627alpha-glucosidase+/-3.2.1.20

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
66627diuron-polluted soilNanjingChinaCHNAsia32.3267118.836MSM1.0 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 glucose28 days30Transferred 1:20 into fresh medium every week. The final enrichment culture was spread on R2A agar containing 30 mg/l diuron
67771From polluted soilNanjing, Jiangsu ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Contamination

Sequence information

16S sequences

  • @ref: 66627
  • description: Tabrizicola soli strain ZQBW 16S ribosomal RNA gene, partial sequence
  • accession: MG190346
  • length: 1428
  • database: nuccore
  • NCBI tax ID: 2185115

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tabrizicola soli CCTCC AB 2017177GCA_015999335scaffoldncbi2185115
66792Xinfangfangia soli strain CCTCC AB 20171772185115.3wgspatric2185115

GC content

  • @ref: 66627
  • GC-content: 67.00
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno97.5yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.729yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes81.639yes
125438spore-formingspore-formingAbility to form endo- or exosporesno84.244yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.718no
125438motile2+flagellatedAbility to perform flagellated movementno56.628no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno82.9
125439BacteriaNetmotilityAbility to perform movementyes50.8
125439BacteriaNetgram_stainReaction to gram-stainingnegative93.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe86.8

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

@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
66627Qiang Hu, Long Zhang, Ping Hang, Xi-Yi Zhou, Wei-Bin Jia, Shun-Peng Li and Jian-Dong JiangXinfangfangia soli gen. nov., sp. nov., isolated from a diuron-polluted soil10.1099/ijsem.0.002887IJSEM 68: 2622-2626 201829947602
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG