Strain identifier

BacDive ID: 140852

Type strain: Yes

Species: Sphingomonas metalli

Strain Designation: 9O-5

NCBI tax ID(s): 1779358 (species)

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General

@ref: 43663

BacDive-ID: 140852

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming

description: Sphingomonas metalli 9O-5 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from lead-zinc ore sampled from an abondened lead-zinc mine.

NCBI tax id

  • NCBI tax id: 1779358
  • Matching level: species

doi: 10.13145/bacdive140852.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas metalli
  • full scientific name: Sphingomonas metalli Feng et al. 2016

@ref: 43663

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas metalli

strain designation: 9O-5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43663negative1-1.5 µm0.7-0.9 µmrod-shapedno
69480negative99.963

colony morphology

  • @ref: 43663
  • colony size: 1-2 mm
  • colony color: Orange
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

  • @ref: 43663
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43663positivegrowth15-37
43663positiveoptimum25-30mesophilic

culture pH

@refabilitytypepHPH range
43663positivegrowth6-9alkaliphile
43663positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43663
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
43663no
69481no98
69480no99.996

halophily

@refsaltgrowthtested relationconcentrationhalophily level
43663NaClpositivegrowth0-1 %(w/v)
43663NaClpositiveoptimum0 %(w/v)non-halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43663167632-oxobutanoate-assimilation
43663181014-hydroxyphenylacetic acid-assimilation
4366330089acetate-assimilation
4366313705acetoacetate-assimilation
4366317128adipate-assimilation
43663645522-hydroxybutyrate-assimilation
4366373706bromosuccinate-assimilation
4366327689decanoate-assimilation
4366316947citrate-assimilation
4366318024D-galacturonic acid-assimilation
4366316899D-mannitol-assimilation
4366316523D-serine-assimilation
4366317924D-sorbitol-assimilation
4366316865gamma-aminobutyric acid-assimilation
4366316467L-arginine-assimilation
4366315971L-histidine-assimilation
4366351850methyl pyruvate-assimilation
43663506227N-acetylglucosamine-assimilation
4366317309pectin-assimilation
4366318401phenylacetate-assimilation
4366317272propionate-assimilation
4366316634raffinose-assimilation
4366317164stachyose-assimilation
4366317234glucose-builds acid from
4366328017starch-hydrolysis
4366353423tween 40-hydrolysis
4366317632nitrate-reduction
4366315588D-malate+assimilation
4366315589L-malate+assimilation
43663645522-hydroxybutyrate+assimilation
43663309162-oxoglutarate+assimilation
4366317057cellobiose+assimilation
4366315824D-fructose+assimilation
4366378697D-fructose 6-phosphate+assimilation
4366328847D-fucose+assimilation
4366312936D-galactose+assimilation
436638391D-gluconate+assimilation
4366317634D-glucose+assimilation
4366314314D-glucose 6-phosphate+assimilation
4366315748D-glucuronate+assimilation
4366316024D-mannose+assimilation
4366333801D-saccharate+assimilation
4366323652dextrin+assimilation
4366315740formate+assimilation
4366316537galactarate+assimilation
4366328066gentiobiose+assimilation
4366370744glycine-proline+assimilation
4366317596inosine+assimilation
4366330849L-arabinose+assimilation
4366318287L-fucose+assimilation
4366317115L-serine+assimilation
4366317306maltose+assimilation
4366332032potassium gluconate+assimilation
4366326490quinate+assimilation
4366317814salicin+assimilation
4366327082trehalose+assimilation
436634853esculin+hydrolysis
436635291gelatin+hydrolysis

metabolite production

  • @ref: 43663
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43663cytochrome oxidase+1.9.3.1
43663catalase+1.11.1.6
43663beta-galactosidase+3.2.1.23
43663arginine dihydrolase-3.5.3.6
43663urease-3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 43663
  • sample type: lead-zinc ore sampled from an abondened lead-zinc mine
  • geographic location: Meizhou, Guangdong Province
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 24.362
  • longitude: 116.276

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Terrestrial#Geologic

Sequence information

16S sequences

  • @ref: 43663
  • description: 16S rRNA gene sequence
  • accession: KU053645
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas metalli CGMCC 1.15330GCA_014641735contigncbi1779358
66792Sphingomonas metalli strain CGMCC 1.153301779358.3wgspatric1779358

GC content

  • @ref: 43663
  • GC-content: 69.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileyes66.957yes
gram-positiveno96.829yes
anaerobicno99.48yes
aerobicyes96.034yes
halophileno94.295yes
spore-formingno95.909no
thermophileno97.461no
glucose-utilyes88.407yes
flagellatedno89.365no
glucose-fermentno91.278no

External links

@ref: 43663

culture collection no.: CGMCC 1.15330, KCTC 42759

literature

  • topic: Phylogeny
  • Pubmed-ID: 26908362
  • title: Sphingomonas metalli sp. nov., isolated from an abandoned lead-zinc mine.
  • authors: Feng GD, Yang SZ, Xiong X, Li HP, Zhu HH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000989
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lead, *Mining, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/chemistry, Zinc
  • 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
43663Guang-Da Feng, Song-Zhen Yang, Xiong Xiong, Hua-Ping Li, Hong-Hui ZhuSphingomonas metalli sp. nov., isolated from an abandoned lead–zinc mine10.1099/ijsem.0.000989IJSEM 66: 2046-2051 201626908362
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1