Strain identifier

BacDive ID: 11353

Type strain: Yes

Species: Herbaspirillum seropedicae

Strain Designation: Z 67

Strain history: IAM 14977 <-- DSM 6445 <-- ATCC 35892 <-- J. Döbereiner Z 67 <-- J. I. Baldani.

NCBI tax ID(s): 964 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 2670

BacDive-ID: 11353

DSM-Number: 6445

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

description: Herbaspirillum seropedicae Z 67 is a mesophilic bacterium that was isolated from rice roots.

NCBI tax id

  • NCBI tax id: 964
  • Matching level: species

strain history

@refhistory
2670<- ATCC <- J. Döbereiner, Z 67 <- J.I. Baldani
67770IAM 14977 <-- DSM 6445 <-- ATCC 35892 <-- J. Döbereiner Z 67 <-- J. I. Baldani.

doi: 10.13145/bacdive11353.20230509.8.1

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 seropedicae
  • full scientific name: Herbaspirillum seropedicae Baldani et al. 1986

@ref: 2670

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Herbaspirillum

species: Herbaspirillum seropedicae

full scientific name: Herbaspirillum seropedicae Baldani et al. 1986 emend. Baldani et al. 1996 emend. Lin et al. 2013

strain designation: Z 67

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2670HERBASPIRILLUM MEDIUM (DSMZ Medium 538)yeshttps://mediadive.dsmz.de/medium/538Name: HERBASPIRILLUM MEDIUM (DSMZ Medium 538) Composition: Agar 15.0 g/l Na-malate 5.0 g/l KH2PO4 0.4 g/l MgSO4 x 7 H2O 0.2 g/l K2HPO4 0.1 g/l NaCl 0.1 g/l Yeast extract 0.05 g/l CaCl2 0.02 g/l FeCl2 x 6 H2O 0.01 g/l Na2MoO4 x 2 H2O 0.002 g/l Distilled water
2670HETEROTROPHIC 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

culture temp

@refgrowthtypetemperaturerange
2670positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine+hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase+3.5.3.6
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    47973C14:04.214
    47973C16:02516
    47973C18:00.918
    47973C10:0 3OH1.111.423
    47973C12:0 2OH1.613.178
    47973C12:0 3OH2.713.455
    47973C14:0 2OH1.215.205
    47973C16:1 ω7c4215.819
    47973C17:0 CYCLO2.216.888
    47973C18:1 ω7c /12t/9t19.217.824
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
47973-+++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
47973+--++--++++++-++-++++

Isolation, sampling and environmental information

isolation

@refsample typehost species
2670rice roots
47973Roots
67770Oryza sativa rootOryza sativa

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_632.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_128;97_137;98_154;99_632&stattab=map
  • Last taxonomy: Herbaspirillum
  • 16S sequence: Y10146
  • Sequence Identity:
  • Total samples: 5208
  • soil counts: 646
  • aquatic counts: 1120
  • animal counts: 1886
  • plant counts: 1556

Safety information

risk assessment

  • @ref: 2670
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Herbaspirillum seropedicae gene for 16S rRNA, partial sequence, strain: NBRC 102524AB6818581458ena964
20218Herbaspirillum seropedicae 16S rRNA gene, strain Z67AJ2383611479ena964
2670H.seropedicae 16S rRNA geneY101461526ena964

Genome sequences

  • @ref: 67770
  • description: Herbaspirillum seropedicae Z67
  • accession: GCA_001040945
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 964

GC content

@refGC-contentmethod
267066.7high performance liquid chromatography (HPLC)
6777064.4high performance liquid chromatography (HPLC)

External links

@ref: 2670

culture collection no.: DSM 6445, ATCC 35892, NCIB 12540, CCUG 24564, LMG 6513, JCM 21448, IAM 14977, NCIMB 12540

straininfo link

  • @ref: 80585
  • straininfo: 3005

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17406771Effects of the inoculation of Burkholderia vietnamensis and related endophytic diazotrophic bacteria on grain yield of rice.Govindarajan M, Balandreau J, Kwon SW, Weon HY, Lakshminarasimhan CMicrob Ecol10.1007/s00248-007-9247-92007Burkholderia/classification/genetics/*growth & development/isolation & purification, Colony Count, Microbial, Crops, Agricultural, Culture Media, Genes, rRNA, Gram-Negative Bacteria/classification/genetics/*growth & development/isolation & purification, India, Molecular Sequence Data, *Nitrogen Fixation, Oryza/*growth & development/*microbiology, Phylogeny, Plant Roots/microbiology, Plant Shoots/microbiology, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Sequence Analysis, DNAEnzymology
Phylogeny21788228Herbaspirillum canariense sp. nov., Herbaspirillum aurantiacum sp. nov. and Herbaspirillum soli sp. nov., isolated from volcanic mountain soil, and emended description of the genus Herbaspirillum.Carro L, Rivas R, Leon-Barrios M, Gonzalez-Tirante M, Velazquez E, Valverde AInt J Syst Evol Microbiol10.1099/ijs.0.031336-02011DNA, Bacterial/genetics, Fatty Acids/metabolism, Herbaspirillum/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Volcanic Eruptions/*analysisMetabolism
Metabolism24682480Heterologous expression of pyrroloquinoline quinone (pqq) gene cluster confers mineral phosphate solubilization ability to Herbaspirillum seropedicae Z67.Wagh J, Shah S, Bhandari P, Archana G, Kumar GNAppl Microbiol Biotechnol10.1007/s00253-014-5610-12014Acinetobacter calcoaceticus/enzymology/genetics, Biosynthetic Pathways/*genetics, Erwinia/enzymology/genetics, *Gene Expression, Herbaspirillum/enzymology/*genetics/*metabolism, Metabolic Engineering, Minerals/*metabolism, Multigene Family, PQQ Cofactor/*metabolism, Phosphates/*metabolism, Pseudomonas fluorescens/enzymology/genetics, Recombinant Proteins/genetics/metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2670Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6445)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6445
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
47973Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 24564)https://www.ccug.se/strain?id=24564
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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
80585Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3005.1StrainInfo: A central database for resolving microbial strain identifiers