Strain identifier

BacDive ID: 11365

Type strain: Yes

Species: Herbaspirillum hiltneri

Strain Designation: N3

Strain history: CIP <- 2008, DSMZ <- M. Rothballer, GSF, Neuherberg, Germany: strain N3

NCBI tax ID(s): 341045 (species)

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General

@ref: 7022

BacDive-ID: 11365

DSM-Number: 17495

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

description: Herbaspirillum hiltneri N3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface-sterilized wheat roots .

NCBI tax id

  • NCBI tax id: 341045
  • Matching level: species

strain history

@refhistory
7022<- M. Rothballer, GSF - Dept. Rhizosphere Biol., Inst. Soil Ecol., Germany; N3 <- I. Klein
67772M. Rothballer, GSF - Deptartment of Rhizosphere Biology, Inst. Soil Ecol., Germany; N3 < Klein, I. Department of Rhizosphere Biology, GSF - National Research Centre for Environment and Health
119899CIP <- 2008, DSMZ <- M. Rothballer, GSF, Neuherberg, Germany: strain N3

doi: 10.13145/bacdive11365.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Herbaspirillum
  • species: Herbaspirillum hiltneri
  • full scientific name: Herbaspirillum hiltneri Rothballer et al. 2006

@ref: 7022

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Herbaspirillum

species: Herbaspirillum hiltneri

full scientific name: Herbaspirillum hiltneri Rothballer et al. 2006

strain designation: N3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31675negative1.6-2 µm0.5-0.6 µmrod-shapedyes
119899negativerod-shapedyes

pigmentation

  • @ref: 31675
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7022NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33337MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
119899CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
7022positivegrowth30mesophilic
31675positivegrowth26-34mesophilic
31675positiveoptimum26-34mesophilic
33337positivegrowth30mesophilic
67772positiveoptimum26-34mesophilic

culture pH

@refabilitytypepH
31675positivegrowth06-08
31675positiveoptimum06-08
67772positiveoptimum6.0-8.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31675aerobe
119899obligate aerobe

spore formation

  • @ref: 31675
  • spore formation: no

observation

  • @ref: 31675
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3167522599arabinose+carbon source
3167518403L-arabitol+carbon source
3167533984fucose+carbon source
3167528260galactose+carbon source
3167517234glucose+carbon source
3167517754glycerol+carbon source
3167528087glycogen+carbon source
3167529864mannitol+carbon source
31675506227N-acetylglucosamine+carbon source
3167528044phenylalanine+carbon source
3167526986threonine+carbon source
11989917632nitrate-reduction
11989916301nitrite-reduction

metabolite production

  • @ref: 119899
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31675catalase+1.11.1.6
31675cytochrome oxidase+1.9.3.1
119899oxidase+
119899catalase+1.11.1.6
119899urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119899-+---+--------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentsampling datelatitudelongitude
7022surface-sterilized wheat roots (Triticum aestivum)Triticum aestivumOberpfalz, NeumarktGermanyDEUEurope
67772Surface-sterilized wheat rootsBaviera, Neumarkt in der OberpfalzGermanyDEUEurope200549.283311.4667
119899Environment, Soil, surface-sterilized wheat roots, Triticum aestivumOberpfalzGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_6898.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_128;97_137;98_2888;99_6898&stattab=map
  • Last taxonomy: Herbaspirillum
  • 16S sequence: DQ150563
  • Sequence Identity:
  • Total samples: 21
  • soil counts: 3
  • aquatic counts: 4
  • animal counts: 11
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70221Risk group (German classification)
677721
1198991Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7022
  • description: Herbaspirillum hiltneri strain N3 16S ribosomal RNA gene, partial sequence
  • accession: DQ150563
  • length: 1478
  • database: ena
  • NCBI tax ID: 1262470

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Herbaspirillum hiltneri N3GCA_001267925completencbi1262470
66792Herbaspirillum hiltneri N31262470.4completepatric1262470
66792Herbaspirillum hiltneri N32645728026completeimg1262470

GC content

@refGC-content
702260.9
3167560.9-61.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes90.461yes
flagellatedyes57.4no
gram-positiveno98.871no
anaerobicno98.363yes
halophileno96.369no
spore-formingno95.26yes
thermophileno99.209yes
glucose-utilyes82.251yes
aerobicyes92.373yes
glucose-fermentno90.134no

External links

@ref: 7022

culture collection no.: DSM 17495, CIP 109904, LMG 23131, UCCCB12

straininfo link

  • @ref: 80596
  • straininfo: 297228

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16738112Herbaspirillum hiltneri sp. nov., isolated from surface-sterilized wheat roots.Rothballer M, Schmid M, Klein I, Gattinger A, Grundmann S, Hartmann AInt J Syst Evol Microbiol10.1099/ijs.0.64031-02006DNA, Bacterial/genetics, Herbaspirillum/*classification/isolation & purification/ultrastructure, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, Plant Roots/*microbiology, Triticum/*microbiologyGenetics
Genetics26514770Complete Genome Sequence of Herbaspirillum hiltneri N3 (DSM 17495), Isolated from Surface-Sterilized Wheat Roots.Guizelini D, Saizaki PM, Coimbra NA, Weiss VA, Faoro H, Sfeir MZ, Baura VA, Monteiro RA, Chubatsu LS, Souza EM, Cruz LM, Pedrosa FO, Raittz RT, Marchaukoski JN, Steffens MBGenome Announc10.1128/genomeA.01288-152015Phylogeny

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7022Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17495)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17495
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31675Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2795328776041
33337Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7700
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67772Curators of the UCCCBhttps://ucccb.uc.pt/
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
80596Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297228.1StrainInfo: A central database for resolving microbial strain identifiers
119899Curators of the CIPCollection of Institut Pasteur (CIP 109904)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109904