Strain identifier

BacDive ID: 11364

Type strain: Yes

Species: Herbaspirillum lusitanum

Strain Designation: P6-12, Strain P6-12

Strain history: CIP <- 2004, CECT <- A. Valverde: strain P6-12

NCBI tax ID(s): 213312 (species)

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General

@ref: 6795

BacDive-ID: 11364

DSM-Number: 17154

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

description: Herbaspirillum lusitanum P6-12 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from root nodules of Phaseolus vulgaris plants grown in a soil from Sierra da Peneda.

NCBI tax id

  • NCBI tax id: 213312
  • Matching level: species

strain history

@refhistory
6795<- E. Velázquez, Univ. Salamanca, Spain; P6-12 <- A. Valverde, Dept. Producción Vegetal, Inst. Recursos Naturales y Agrobiol., Consejo Superior de Investigaciones Científicas, Spain
67772Valverde, A., Consejo Superior de Investigaciones Científicas
120680CIP <- 2004, CECT <- A. Valverde: strain P6-12

doi: 10.13145/bacdive11364.20230509.8.1

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 lusitanum
  • full scientific name: Herbaspirillum lusitanum Valverde et al. 2003

@ref: 6795

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Herbaspirillum

species: Herbaspirillum lusitanum

full scientific name: Herbaspirillum lusitanum Valverde et al. 2003

strain designation: P6-12, Strain P6-12

type strain: yes

Morphology

cell morphology

  • @ref: 120680
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 120680
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6795NUTRIENT 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
33924MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120680CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
120680CIP Medium 583yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=583

culture temp

@refgrowthtypetemperaturerange
6795positivegrowth28mesophilic
33924positivegrowth30mesophilic
67772positiveoptimum28mesophilic
120680positivegrowth10-30
120680nogrowth5psychrophilic
120680nogrowth37mesophilic
120680nogrowth41thermophilic

culture pH

@refabilitytypepH
67772positivemaximum8.0
67772positiveminimum5.0

Physiology and metabolism

oxygen tolerance

  • @ref: 120680
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
120680NaClpositivegrowth0-2 %
120680NaClnogrowth4 %
120680NaClnogrowth6 %
120680NaClnogrowth8 %
120680NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12068016947citrate-carbon source
1206804853esculin-hydrolysis
12068017632nitrate-reduction
12068016301nitrite-reduction
12068017632nitrate-respiration

metabolite production

  • @ref: 120680
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
120680oxidase+
120680beta-galactosidase-3.2.1.23
120680alcohol dehydrogenase-1.1.1.1
120680gelatinase-
120680amylase-
120680DNase-
120680caseinase-3.4.21.50
120680catalase+1.11.1.6
120680tween esterase-
120680lecithinase-
120680lipase-
120680lysine decarboxylase-4.1.1.18
120680ornithine decarboxylase-4.1.1.17
120680tryptophan deaminase-
120680urease+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
120680-+++-++---++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120680+-+-+--------------+++-++-++---+-+---+-+---++++-+++-++++++-+++---++--------++--++-+----++++++++++-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentsampling dategeographic locationlatitudelongitudeisolation date
6795root nodules of Phaseolus vulgaris plants grown in a soil from Sierra da PenedaPhaseolus vulgarisPortugalPRTEurope
58368Root nodules,Phaseolus vulgarisPortugalPRTEurope2000Sierra da Penada
67772Phaseolus vulgaris, root nodulesPortugalPRTEurope2000Alto-Minho, Arcos de Valdevez41.85-8.41667
120680Plant, EndophyllousPortugalPRTEuropeArcos de Valdevez2000

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root nodule

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: AF543312
  • 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
67951Risk group (German classification)
677721
1206801Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6795
  • description: Herbaspirillum lusitanum 16S ribosomal RNA gene, complete sequence
  • accession: AF543312
  • length: 1524
  • database: ena
  • NCBI tax ID: 1161913

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Herbaspirillum lusitanum P6-121161913.3wgspatric1161913
66792Herbaspirillum lusitanum P6-122548876994draftimg1161913
67772Herbaspirillum lusitanum P6-12GCA_000256565contigncbi1161913

GC content

  • @ref: 6795
  • GC-content: 57.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes92.1no
gram-positiveno98.974no
anaerobicno98.125no
aerobicyes90.299no
halophileno96.611no
spore-formingno94.647no
flagellatedyes56.799no
thermophileno99.386yes
glucose-utilyes86.864no
glucose-fermentno90.731no

External links

@ref: 6795

culture collection no.: DSM 17154, CCUG 48869, CECT 5661, LMG 21710, UCCCB3, CIP 108242

straininfo link

  • @ref: 80595
  • straininfo: 88963

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14657133Herbaspirillum lusitanum sp. nov., a novel nitrogen-fixing bacterium associated with root nodules of Phaseolus vulgaris.Valverde A, Velazquez E, Gutierrez C, Cervantes E, Ventosa A, Igual JMInt J Syst Evol Microbiol10.1099/ijs.0.02677-02003Geography, Herbaspirillum/*classification/*genetics/isolation & purification/physiology, Molecular Sequence Data, Nitrates/metabolism, Nitrites/metabolism, Nitrogen Fixation, Phaseolus/*microbiology, *Phylogeny, Plant Roots/microbiologyGenetics
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
Genetics22815451Draft genome sequence of Herbaspirillum lusitanum P6-12, an endophyte isolated from root nodules of Phaseolus vulgaris.Weiss VA, Faoro H, Tadra-Sfeir MZ, Raittz RT, de Souza EM, Monteiro RA, Cardoso RL, Wassem R, Chubatsu LS, Huergo LF, Muller-Santos M, Steffens MB, Rigo LU, Pedrosa Fde O, Cruz LMJ Bacteriol10.1128/JB.00657-122012DNA, Bacterial/*chemistry/*genetics, Endophytes/genetics/isolation & purification, *Genome, Bacterial, Herbaspirillum/*genetics/isolation & purification, Molecular Sequence Data, Phaseolus/*microbiology, Root Nodules, Plant/*microbiology, *Sequence Analysis, DNAEnzymology
Metabolism32216024Characterization of biopolymers produced by planktonic and biofilm cells of Herbaspirillum lusitanum P6-12.Velichko NS, Grinev VS, Fedonenko YPJ Appl Microbiol10.1111/jam.146472020Bacterial Capsules/chemistry/metabolism, *Biofilms/growth & development, Biopolymers/*chemistry/metabolism, Extracellular Polymeric Substance Matrix/chemistry/metabolism, Glycoproteins/chemistry/metabolism, Herbaspirillum/*chemistry/growth & development/metabolism/*physiology, Lipopolysaccharides/chemistry/metabolism, Polysaccharides, Bacterial/chemistry/metabolism
35614280Whole-cell electric sensor for determination of sodium dodecyl sulfate.Velichko NS, Guliy OI, Kanevsky MV, Kupryashina MA, Fedonenko YPWorld J Microbiol Biotechnol10.1007/s11274-022-03309-12022*Environmental Pollution, Sodium Dodecyl Sulfate/chemistry, Sulfates, *Surface-Active Agents/chemistry

Reference

@idauthorscataloguedoi/urltitle
6795Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17154)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17154
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
33924Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5843
58368Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48869)https://www.ccug.se/strain?id=48869
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
80595Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88963.1StrainInfo: A central database for resolving microbial strain identifiers
120680Curators of the CIPCollection of Institut Pasteur (CIP 108242)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108242