Strain identifier
BacDive ID: 11361
Type strain:
Species: Herbaspirillum frisingense
Strain history: IAM 14974 <-- DSM 13128 <-- G. Kirchhof et al. GSF30.
NCBI tax ID(s): 92645 (species)
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
@ref | history |
---|---|
4914 | <- G. Kirchhof et al.; GSF 30 |
67770 | IAM 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
@ref | name | growth | link | composition |
---|---|---|---|---|
4914 | HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) | yes | https://mediadive.dsmz.de/medium/428 | Name: 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 |
4914 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
4914 | positive | growth | 35 | mesophilic |
57691 | positive | growth | 30-37 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 57691
- oxygen tolerance: aerobe
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
4914 | Miscanthus sacchariflorus washed leaves | Miscanthus sacchariflorus | Bavaria, fields of LPG Freising | Germany | DEU | Europe |
57691 | Miscanthus sacchariflorus washed leaves | Bavaria | Germany | DEU | Europe | |
67770 | Roots and aerial parts (stems, leaves) |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Herbaspirillum frisingense 16S rRNA gene, strain GSF30 | AJ238358 | 1466 | ena | 864073 |
20218 | Herbaspirillum frisingense gene for 16S rRNA, partial sequence, strain: NBRC 102522 | AB681856 | 1458 | ena | 92645 |
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
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 91.892 | no |
flagellated | no | 53.268 | no |
gram-positive | no | 99.083 | no |
anaerobic | no | 99.034 | yes |
aerobic | yes | 88.755 | yes |
halophile | no | 95.753 | no |
spore-forming | no | 93.863 | no |
glucose-util | yes | 83.725 | no |
thermophile | no | 99.391 | yes |
glucose-ferment | no | 89.626 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 11211253 | Herbaspirillum 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 A | Int J Syst Evol Microbiol | 10.1099/00207713-51-1-157 | 2001 | Base 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, DNA | Genetics |
Metabolism | 18761671 | Endophytic root colonization of gramineous plants by Herbaspirillum frisingense. | Rothballer M, Eckert B, Schmid M, Fekete A, Schloter M, Lehner A, Pollmann S, Hartmann A | FEMS Microbiol Ecol | 10.1111/j.1574-6941.2008.00582.x | 2008 | Acyl-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 Specificity | Phylogeny |
Phylogeny | 23625231 | Paraherbaspirillum soli gen. nov., sp. nov. isolated from soil. | Anandham R, Kim SJ, Moon JY, Weon HY, Kwon SW | J Microbiol | 10.1007/s12275-013-2563-5 | 2013 | Base Composition, Fatty Acids/metabolism, Molecular Sequence Data, Oxalobacteraceae/classification/genetics/*isolation & purification/metabolism, Phylogeny, Republic of Korea, *Soil Microbiology | Metabolism |
23825472 | The 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 U | Front Microbiol | 10.3389/fmicb.2013.00168 | 2013 | |||
Pathogenicity | 24043849 | Root 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 U | J Exp Bot | 10.1093/jxb/ert276 | 2013 | Colony 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/genetics | Metabolism |
32553974 | Structural 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 YP | Int J Biol Macromol | 10.1016/j.ijbiomac.2020.06.093 | 2020 | Carbohydrate Conformation, Deoxy Sugars/*genetics, Herbaspirillum/*genetics, Hydrolysis, Lipopolysaccharides/*genetics, Magnetic Resonance Spectroscopy/methods, Methylation, O Antigens/*genetics, Operon/genetics, Polysaccharides, Bacterial/*genetics | ||
Pathogenicity | 34827347 | High 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 H | Antibiotics (Basel) | 10.3390/antibiotics10111409 | 2021 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4914 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13128) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13128 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
57691 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 47444) | https://www.ccug.se/strain?id=47444 | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69479 | João 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 | |||
80592 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49410.1 | StrainInfo: A central database for resolving microbial strain identifiers |