Strain identifier

BacDive ID: 141101

Type strain: Yes

Species: Nitrincola schmidtii

Strain Designation: R4-8

Strain history: <- T. Felföldi, Eötvös Loránd Univ. Budapest, Hungary; R4-8 <- K. Korponai and T. Felföldi

NCBI tax ID(s): 1730894 (species)

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General

@ref: 64980

BacDive-ID: 141101

DSM-Number: 100788

keywords: 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped, colony-forming

description: Nitrincola schmidtii R4-8 is a facultative anaerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from a thin layer of a purple bacterial bloom occurring in a soda pan.

NCBI tax id

  • NCBI tax id: 1730894
  • Matching level: species

strain history

  • @ref: 64980
  • history: <- T. Felföldi, Eötvös Loránd Univ. Budapest, Hungary; R4-8 <- K. Korponai and T. Felföldi

doi: 10.13145/bacdive141101.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Oceanospirillaceae
  • genus: Nitrincola
  • species: Nitrincola schmidtii
  • full scientific name: Nitrincola schmidtii Borsodi et al. 2017

@ref: 64980

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Oceanospirillaceae

genus: Nitrincola

species: Nitrincola schmidtii

full scientific name: Nitrincola schmidtii Borsodi et al. 2017

strain designation: R4-8

type strain: yes

Morphology

cell morphology

  • @ref: 44009
  • gram stain: negative
  • cell length: 1.4-1.8 µm
  • cell width: 0.5-0.6 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 44009
  • colony color: beige
  • colony shape: circular
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

  • @ref: 64980
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperature
44009positivegrowth10-28
44009positiveoptimum15-20
64980positivegrowth25

culture pH

@refabilitytypepHPH range
44009positivegrowth7.0-11.0alkaliphile
44009positiveoptimum8.0-9.0

Physiology and metabolism

oxygen tolerance

  • @ref: 44009
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
44009NaClpositivegrowth0-10 %
44009NaClpositiveoptimum0-7 %

observation

@refobservation
44009smooth and convex colonies
44009the predominant quinone is Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4400916947citrate-assimilation
4400917634D-glucose-builds acid from
4400917634D-glucose-builds gas from
44009casein-hydrolysis
44009esculin ferric citrate-hydrolysis
440095291gelatin-hydrolysis
4400928017starch-hydrolysis
4400953426tween 80-hydrolysis
4400916199urea-hydrolysis
4400928044phenylalanine+assimilation
4400917632nitrate+reduction

metabolite production

@refChebi-IDmetaboliteproduction
4400935581indoleno
4400915138sulfideno

enzymes

@refvalueactivityec
44009catalase+1.11.1.6
44009cytochrome oxidase+1.9.3.1
44009phosphatase+
44009alkaline phosphatase+3.1.3.1
44009esterase (C 4)+
44009esterase Lipase (C 8)+
44009leucine arylamidase+3.4.11.1
44009acid phosphatase+3.1.3.2
44009naphthol-AS-BI-phosphohydrolase+
44009trypsin+/-3.4.21.4
44009beta-galactosidase+/-3.2.1.23
44009alpha-fucosidase+/-3.2.1.51
44009lipase (C 14)-
44009valine arylamidase-
44009cystine arylamidase-3.4.11.3
44009alpha-chymotrypsin-3.4.21.1
44009alpha-galactosidase-3.2.1.22
44009beta-glucuronidase-3.2.1.31
44009alpha-glucosidase-3.2.1.20
44009beta-glucosidase-3.2.1.21
44009N-acetyl-beta-glucosaminidase-3.2.1.52
44009alpha-mannosidase-3.2.1.24

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    44009C10:03.1
    44009C10:0 3OH5.4
    44009C12:13.3
    44009C16:013.4
    44009C16:1ω7c22.7
    44009C18:1ω7c50.9
  • type of FA analysis: whole cell analysis
  • incubation medium: Horikoshi alkaline medium
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 2
  • system: MIS MIDI
  • method/protocol: Stead & Sellwood, 1992
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
44009a thin layer of a purple bacterial bloom occurring in a soda panKiskunsag National ParkHungaryHUNEurope
64980purple bacterial bloom occurring in a soda panKiskunság National Park near Soltszentimre (46° 45.818' N 19° 10.828' E)HungaryHUNEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Lake (large)

taxonmaps

  • @ref: 69479
  • File name: preview.99_23562.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_240;96_2070;97_2495;98_17742;99_23562&stattab=map
  • Last taxonomy: Nitrincola schmidtii subclade
  • 16S sequence: KR233209
  • Sequence Identity:
  • Total samples: 189
  • soil counts: 13
  • aquatic counts: 119
  • animal counts: 57

Safety information

risk assessment

  • @ref: 64980
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64980
  • description: Nitrincola schmidtii strain R4-8 16S ribosomal RNA gene, partial sequence
  • accession: KR233209
  • length: 1459
  • database: nuccore
  • NCBI tax ID: 1730894

GC content

@refGC-contentmethod
4400945.8sequence analysis
6498045.8high performance liquid chromatography (HPLC)

External links

@ref: 64980

culture collection no.: DSM 100788, NCAIM B.02626

straininfo link

  • @ref: 96855
  • straininfo: 398460

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29056114Nitrincola alkalilacustris sp. nov. and Nitrincola schmidtii sp. nov., alkaliphilic bacteria isolated from soda pans, and emended description of the genus Nitrincola.Borsodi AK, Korponai K, Schumann P, Sproer C, Felfoldi T, Marialigeti K, Szili-Kovacs T, Toth EInt J Syst Evol Microbiol10.1099/ijsem.0.0024372017Alkalies/*chemistry, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hungary, Nucleic Acid Hybridization, Oceanospirillaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water MicrobiologyTranscriptome
Phylogeny32735211Nitrincola iocasae sp. nov., a bacterium isolated from sediment collected at a cold seep field in the South China Sea.Zhang H, Wang H, Chen H, Sun Q, Zhong Z, Wang M, Cao L, Lian C, Zhou L, Li CInt J Syst Evol Microbiol10.1099/ijsem.0.0043522020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Oceanospirillaceae/*classification/isolation & purification, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
44009Andrea K. Borsodi, Kristóf Korponai, Peter Schumann, Cathrin Spröer, Tamás Felföldi, Károly Márialigeti, Tibor Szili-Kovács, Erika TóthNitrincola alkalilacustris sp. nov. and Nitrincola schmidtii sp. nov., alkaliphilic bacteria isolated from soda pans, and emended description of the genus Nitrincola10.1099/ijsem.0.002437IJSEM 67: 5159-5164 201729056114
64980Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100788Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100788)
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/
96855Reimer, 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 identifiers10.60712/SI-ID398460.1