Strain identifier

BacDive ID: 11369

Type strain: Yes

Species: Herbaspirillum aquaticum

Strain history: <- A.P. Dobritsa, Inst. Environmental Health, Lake Forest Park; IEH 4430 <- A. Scotti

NCBI tax ID(s): 568783 (species)

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General

@ref: 15436

BacDive-ID: 11369

DSM-Number: 21191

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

description: Herbaspirillum aquaticum DSM 21191 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from deionized water.

NCBI tax id

  • NCBI tax id: 568783
  • Matching level: species

strain history

  • @ref: 15436
  • history: <- A.P. Dobritsa, Inst. Environmental Health, Lake Forest Park; IEH 4430 <- A. Scotti

doi: 10.13145/bacdive11369.20230509.8.1

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 aquaticum
  • full scientific name: Herbaspirillum aquaticum Dobritsa et al. 2010

@ref: 15436

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Herbaspirillum

species: Herbaspirillum aquaticum

full scientific name: Herbaspirillum aquaticum Dobritsa et al. 2010

type strain: yes

Morphology

cell morphology

  • @ref: 29246
  • gram stain: negative
  • cell length: 2 µm
  • cell width: 0.5 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 29246
  • production: no

Culture and growth conditions

culture medium

  • @ref: 15436
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15436positivegrowth28mesophilic
29246positivegrowth10-35
29246positiveoptimum27.5mesophilic

culture pH

@refabilitytypepH
29246positivegrowth05-08
29246positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 29246
  • oxygen tolerance: aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2924630089acetate+carbon source
2924617128adipate+carbon source
2924615963ribitol+carbon source
2924616449alanine+carbon source
2924622599arabinose+carbon source
2924618403L-arabitol+carbon source
2924622653asparagine+carbon source
2924635391aspartate+carbon source
2924627689decanoate+carbon source
2924616947citrate+carbon source
2924628757fructose+carbon source
2924633984fucose+carbon source
2924628260galactose+carbon source
2924624175galacturonate+carbon source
2924624265gluconate+carbon source
2924617234glucose+carbon source
2924629987glutamate+carbon source
2924617754glycerol+carbon source
2924617240itaconate+carbon source
2924624996lactate+carbon source
2924617716lactose+carbon source
2924629864mannitol+carbon source
2924637684mannose+carbon source
29246506227N-acetylglucosamine+carbon source
2924626271proline+carbon source
2924617272propionate+carbon source
2924651850methyl pyruvate+carbon source
2924626490quinate+carbon source
2924633942ribose+carbon source
2924630911sorbitol+carbon source
292469300suberic acid+carbon source
2924630031succinate+carbon source
2924617151xylitol+carbon source
2924618222xylose+carbon source

enzymes

@refvalueactivityec
29246catalase+1.11.1.6
29246cytochrome oxidase+1.9.3.1
29246urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 15436
  • sample type: deionized water
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Engineered product
#Environmental#Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_3619.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_128;97_137;98_154;99_3619&stattab=map
  • Last taxonomy: Herbaspirillum
  • 16S sequence: FJ267649
  • Sequence Identity:
  • Total samples: 1693
  • soil counts: 197
  • aquatic counts: 342
  • animal counts: 743
  • plant counts: 411

Safety information

risk assessment

  • @ref: 15436
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15436
  • description: Herbaspirillum aquaticum strain IEH 4430 16S ribosomal RNA gene, partial sequence
  • accession: FJ267649
  • length: 1455
  • database: ena
  • NCBI tax ID: 568783

GC content

@refGC-contentmethod
1543662.1high performance liquid chromatography (HPLC)
2924662.1

External links

@ref: 15436

culture collection no.: DSM 21191, ATCC BAA 1628, KCTC 32019, IEH 4430

straininfo link

  • @ref: 80599
  • straininfo: 405192

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19671717Reclassification of Herbaspirillum putei as a later heterotypic synonym of Herbaspirillum huttiense, with the description of H. huttiense subsp. huttiense subsp. nov. and H. huttiense subsp. putei subsp. nov., comb. nov., and description of Herbaspirillum aquaticum sp. nov.Dobritsa AP, Reddy MCS, Samadpour MInt J Syst Evol Microbiol10.1099/ijs.0.009381-02009Base Composition, Base Sequence, DNA Primers, DNA, Bacterial/genetics, Fatty Acids/analysis, Genome, Herbaspirillum/*classification/*genetics/metabolism, Molecular Sequence Data, Peptide Fragments/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny29485397Herbaspirillum robiniae sp. nov., isolated from root nodules of Robinia pseudoacacia in a lead-zinc mine.Fan MC, Guo YQ, Zhang LP, Zhu YM, Chen WM, Lin YB, Wei GHInt J Syst Evol Microbiol10.1099/ijsem.0.0026662018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Herbaspirillum/*cytology/genetics/isolation & purification, Lead, Mining, *Phylogeny, RNA, Ribosomal, 16S/genetics, Robinia/*microbiology, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, ZincTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15436Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21191)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21191
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
29246Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2566628776041
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
80599Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405192.1StrainInfo: A central database for resolving microbial strain identifiers