Strain identifier

BacDive ID: 11361

Type strain: Yes

Species: Herbaspirillum frisingense

Strain history: IAM 14974 <-- DSM 13128 <-- G. Kirchhof et al. GSF30.

NCBI tax ID(s): 92645 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 4914

BacDive-ID: 11361

DSM-Number: 13128

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic

description: Herbaspirillum frisingense DSM 13128 is an aerobe, mesophilic bacterium that was isolated from Miscanthus sacchariflorus washed leaves.

NCBI tax id

  • NCBI tax id: 92645
  • Matching level: species

strain history

@refhistory
4914<- G. Kirchhof et al.; GSF 30
67770IAM 14974 <-- DSM 13128 <-- G. Kirchhof et al. GSF30.

doi: 10.13145/bacdive11361.20230509.8.1

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 frisingense
  • full scientific name: Herbaspirillum frisingense Kirchhof et al. 2001

@ref: 4914

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Herbaspirillum

species: Herbaspirillum frisingense

full scientific name: Herbaspirillum frisingense Kirchhof et al. 2001

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4914HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428)yeshttps://mediadive.dsmz.de/medium/428Name: HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) Composition: Agar 19.802 g/l Na2HPO4 x 2 H2O 2.87129 g/l KH2PO4 2.27723 g/l D-Glucose 1.9802 g/l Na-lactate 0.990099 g/l Na-pyruvate 0.990099 g/l D-Mannitol 0.990099 g/l DL-Malate 0.990098 g/l Na-acetate 0.990098 g/l Yeast extract 0.990098 g/l NH4Cl 0.990098 g/l Disodium succinate 0.990098 g/l MgSO4 x 7 H2O 0.495049 g/l Ferric ammonium citrate 0.049505 g/l CaCl2 x 2 H2O 0.00990098 g/l NaVO3 x H2O 0.00495049 g/l Thiamine-HCl x 2 H2O 0.00247525 g/l Nicotinic acid 0.00247525 g/l Pyridoxine hydrochloride 0.00247525 g/l Calcium pantothenate 0.00247525 g/l H3BO3 0.00148515 g/l CoCl2 x 6 H2O 0.000990099 g/l Riboflavin 0.00049505 g/l ZnSO4 x 7 H2O 0.00049505 g/l MnCl2 x 4 H2O 0.000148515 g/l Na2MoO4 x 2 H2O 0.000148515 g/l NiCl2 x 6 H2O 9.90099e-05 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Vitamin B12 4.95049e-05 g/l Folic acid 9.90099e-06 g/l Biotin 4.9505e-06 g/l Distilled water
4914NUTRIENT 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

culture temp

@refgrowthtypetemperaturerange
4914positivegrowth35mesophilic
57691positivegrowth30-37mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 57691
  • oxygen tolerance: aerobe

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
4914Miscanthus sacchariflorus washed leavesMiscanthus sacchariflorusBavaria, fields of LPG FreisingGermanyDEUEurope
57691Miscanthus sacchariflorus washed leavesBavariaGermanyDEUEurope
67770Roots and aerial parts (stems, leaves)

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1657.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_128;97_137;98_154;99_1657&stattab=map
  • Last taxonomy: Herbaspirillum
  • 16S sequence: AB681856
  • Sequence Identity:
  • Total samples: 534
  • soil counts: 135
  • aquatic counts: 95
  • animal counts: 109
  • plant counts: 195

Safety information

risk assessment

  • @ref: 4914
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Herbaspirillum frisingense 16S rRNA gene, strain GSF30AJ2383581466ena864073
20218Herbaspirillum frisingense gene for 16S rRNA, partial sequence, strain: NBRC 102522AB6818561458ena92645

Genome sequences

  • @ref: 67770
  • description: Herbaspirillum frisingense GSF30
  • accession: GCA_000300975
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 864073

GC content

  • @ref: 67770
  • GC-content: 64
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes91.892no
flagellatedno53.268no
gram-positiveno99.083no
anaerobicno99.034yes
aerobicyes88.755yes
halophileno95.753no
spore-formingno93.863no
glucose-utilyes83.725no
thermophileno99.391yes
glucose-fermentno89.626no

External links

@ref: 4914

culture collection no.: DSM 13128, CCUG 47444, GSF 30, JCM 21445, IAM 14974, NBRC 102522

straininfo link

  • @ref: 80592
  • straininfo: 49410

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11211253Herbaspirillum frisingense sp. nov., a new nitrogen-fixing bacterial species that occurs in C4-fibre plants.Kirchhof G, Eckert B, Stoffels M, Baldani JI, Reis VM, Hartmann AInt J Syst Evol Microbiol10.1099/00207713-51-1-1572001Base Composition, Betaproteobacteria/*classification/genetics/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Molecular Sequence Data, *Nitrogen Fixation/genetics/physiology, Nucleic Acid Hybridization/methods, Phylogeny, Plant Roots/microbiology, Poaceae/*microbiology, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Metabolism18761671Endophytic root colonization of gramineous plants by Herbaspirillum frisingense.Rothballer M, Eckert B, Schmid M, Fekete A, Schloter M, Lehner A, Pollmann S, Hartmann AFEMS Microbiol Ecol10.1111/j.1574-6941.2008.00582.x2008Acyl-Butyrolactones/metabolism, Amino Acids, Cyclic/metabolism, Genes, Reporter, Green Fluorescent Proteins/genetics, Herbaspirillum/genetics/*growth & development/metabolism, Immunohistochemistry, Indoleacetic Acids/metabolism, Microscopy, Confocal, Nitrogen Fixation, Plant Growth Regulators/metabolism, Plant Roots/cytology/*microbiology, Poaceae/cytology/*microbiology, Seedlings/cytology/microbiology, Species SpecificityPhylogeny
Phylogeny23625231Paraherbaspirillum soli gen. nov., sp. nov. isolated from soil.Anandham R, Kim SJ, Moon JY, Weon HY, Kwon SWJ Microbiol10.1007/s12275-013-2563-52013Base Composition, Fatty Acids/metabolism, Molecular Sequence Data, Oxalobacteraceae/classification/genetics/*isolation & purification/metabolism, Phylogeny, Republic of Korea, *Soil MicrobiologyMetabolism
23825472The genome of the endophytic bacterium H. frisingense GSF30(T) identifies diverse strategies in the Herbaspirillum genus to interact with plants.Straub D, Rothballer M, Hartmann A, Ludewig UFront Microbiol10.3389/fmicb.2013.001682013
Pathogenicity24043849Root ethylene signalling is involved in Miscanthus sinensis growth promotion by the bacterial endophyte Herbaspirillum frisingense GSF30(T).Straub D, Yang H, Liu Y, Tsap T, Ludewig UJ Exp Bot10.1093/jxb/ert2762013Colony Count, Microbial, Endophytes/growth & development/*physiology, Ethylenes/*metabolism/pharmacology, Gene Expression Profiling, Gene Expression Regulation, Plant/drug effects, Green Fluorescent Proteins/metabolism, Herbaspirillum/drug effects/growth & development/*physiology, Plant Proteins/genetics/metabolism, Plant Roots/anatomy & histology/drug effects/*metabolism/microbiology, Plant Shoots/drug effects/microbiology, Poaceae/drug effects/genetics/*growth & development/*microbiology, Proteomics, RNA, Messenger/genetics/metabolism, *Signal Transduction/drug effects/genetics, Transcriptome/drug effects/geneticsMetabolism
32553974Structural and genetic characterization of the colitose-containing O-specific polysaccharide from the lipopolysaccharide of Herbaspirillum frisingense GSF30(T).Velichko NS, Kokoulin MS, Sigida EN, Kuchur PD, Komissarov AS, Kovtunov EA, Fedonenko YPInt J Biol Macromol10.1016/j.ijbiomac.2020.06.0932020Carbohydrate Conformation, Deoxy Sugars/*genetics, Herbaspirillum/*genetics, Hydrolysis, Lipopolysaccharides/*genetics, Magnetic Resonance Spectroscopy/methods, Methylation, O Antigens/*genetics, Operon/genetics, Polysaccharides, Bacterial/*genetics
Pathogenicity34827347High Genomic Identity between Clinical and Environmental Strains of Herbaspirillum frisingense Suggests Pre-Adaptation to Different Hosts and Intrinsic Resistance to Multiple Drugs.Oliveira WK, Avila HL, Tadra MZ, Cardoso RL, Fadel-Pichet CMT, de Souza EM, de Oliveira Pedrosa F, Faoro HAntibiotics (Basel)10.3390/antibiotics101114092021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4914Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13128)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13128
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
57691Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47444)https://www.ccug.se/strain?id=47444
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
80592Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49410.1StrainInfo: A central database for resolving microbial strain identifiers