Strain identifier

BacDive ID: 140482

Type strain: Yes

Species: Noviherbaspirillum denitrificans

Strain history: <- S. Ishii, Univ. Minnesota; TSA40 {2016}

NCBI tax ID(s): 1968433 (species)

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General

@ref: 43245

BacDive-ID: 140482

DSM-Number: 113107

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

description: Noviherbaspirillum denitrificans JCM 17722 is a facultative anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from rice paddy soil under denitrification-inducing conditions.

NCBI tax id

  • NCBI tax id: 1968433
  • Matching level: species

strain history

@refhistory
67770S. Ishii TSA40.
68999<- S. Ishii, Univ. Minnesota; TSA40 {2016}

doi: 10.13145/bacdive140482.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Noviherbaspirillum
  • species: Noviherbaspirillum denitrificans
  • full scientific name: Noviherbaspirillum denitrificans corrig. Ishii et al. 2017

  • synonyms

    • @ref: 20215
    • synonym: Herbaspirillum denitrificans

@ref: 43245

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Noviherbaspirillum

species: Noviherbaspirillum denitrificans

full scientific name: Noviherbaspirillum denitrificans Ishii et al. 2017

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43245negative1.4-2.2 µm0.4-0.6 µmrod-shapedyespolar
69480yes97.191
69480negative99.999

colony morphology

  • @ref: 43245
  • colony color: white
  • colony shape: circular
  • medium used: R2A

multimedia

  • @ref: 68999
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_113107.jpg
  • caption: Micrograph of DSM 113107. Scale bar represents 2 um.
  • intellectual property rights: Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
68999R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf
43245Reasoner's 2A agar (R2A)yes
43245DNBNS mediumyes100-fold diluted nutrient broth (DNB; Difco) supplemented with 3 mM nitrate and 4.4 mM succinate
43245nutritient agaryes
43245trypticase soy broth (TSB)no

culture temp

@refgrowthtypetemperaturerange
43245positiveoptimum30mesophilic
43245positivegrowth10-42
67770positivegrowth30mesophilic
68999positivegrowth30mesophilic

culture pH

  • @ref: 43245
  • ability: positive
  • type: growth
  • pH: 5.5-9.0
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 43245
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

  • @ref: 43245
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4324517632nitrate+electron donor
4324530089acetate+electron donor
4324517968butyrate+electron donor
4324524996lactate+electron donor
4324515361pyruvate+electron donor
4324530031succinate+electron donor
4324531011valerate+electron donor
4324553423tween 40+growth
4324553426tween 80+growth
4324528757fructose-growth
4324528260galactose-growth
4324517234glucose-growth
4324517716lactose-growth
4324517306maltose-growth
4324537684mannose-growth
4324530911sorbitol-growth
4324518222xylose-growth
4324524265gluconate-growth
43245526821,2-butandiol-growth
4324516236ethanol-growth
4324562968cellulose-growth
4324528017starch-growth
4324516301nitrite+electron acceptor
4324517045dinitrogen oxide+electron acceptor
4324517754glycerol+electron donor

enzymes

@refvalueactivityec
43245catalase+1.11.1.6
43245cytochrome oxidase+1.9.3.1
43245urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation procedure
43245rice paddy soil under denitrification-inducing conditionsTokyoJapanJPNAsiafunctional single cell isolation method
67770Rice paddy soil under denitrification-inducing conditionsTokyoJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_62766.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_3405;97_4180;98_6850;99_62766&stattab=map
  • Last taxonomy: Noviherbaspirillum denitrificans
  • 16S sequence: AB542397
  • Sequence Identity:
  • Total samples: 2888
  • soil counts: 2079
  • aquatic counts: 168
  • animal counts: 245
  • plant counts: 396

Safety information

risk assessment

  • @ref: 68999
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 43245
  • description: Herbaspirillum sp. TSA40 gene for 16S ribosomal RNA, partial sequence, strain: TSA40
  • accession: AB542397
  • length: 1458
  • database: nuccore
  • NCBI tax ID: 1968433

Genome sequences

  • @ref: 67770
  • description: Noviherbaspirillum denitrificans TSA40
  • accession: GCA_002211445
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1968433

GC content

@refGC-contentmethod
6777061.8genome sequence analysis
6899961.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes83.229yes
gram-positiveno98.453yes
anaerobicno96.399yes
aerobicno50yes
halophileno96.765no
spore-formingno94.281no
glucose-utilno56.799no
thermophileno97.956yes
motileyes89.368no
glucose-fermentno88.468no

External links

@ref: 43245

culture collection no.: JCM 17722, ATCC TSD-69, TSA 40, DSM 113107

straininfo link

  • @ref: 96729
  • straininfo: 400773

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28629495Noviherbaspirillum denitrificans sp. nov., a denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov., a denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil and proposal to reclassify Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov.Ishii S, Ashida N, Ohno H, Segawa T, Yabe S, Otsuka S, Yokota A, Senoo KInt J Syst Evol Microbiol10.1099/ijsem.0.0018752017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Denitrification, Fatty Acids/chemistry, Herbaspirillum/*classification/genetics/isolation & purification, *Oryza, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny33956597Massilia horti sp. nov. and Noviherbaspirillum arenae sp. nov., two novel soil bacteria of the Oxalobacteraceae.Peta V, Raths R, Bucking HInt J Syst Evol Microbiol10.1099/ijsem.0.0047652021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Oxalobacteraceae/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/chemistry, *Soil MicrobiologyMetabolism

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
43245Satoshi Ishii, Naoaki Ashida, Hiroki Ohno, Takahiro Segawa, Shuhei Yabe, Shigeto Otsuka, Akira Yokota, Keishi SenooNoviherbaspirillum denitrificans sp. nov., a denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov., a denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil and proposal to reclassify Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov.10.1099/ijsem.0.001875IJSEM 67: 1841-1848 201728629495
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68999Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-113107Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 113107)
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/
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
96729Reimer, 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-ID400773.1