Strain identifier
BacDive ID: 11364
Type strain:
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)
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
@ref | history |
---|---|
6795 | <- E. Velázquez, Univ. Salamanca, Spain; P6-12 <- A. Valverde, Dept. Producción Vegetal, Inst. Recursos Naturales y Agrobiol., Consejo Superior de Investigaciones Científicas, Spain |
67772 | Valverde, A., Consejo Superior de Investigaciones Científicas |
120680 | CIP <- 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
@ref | name | growth | link | composition |
---|---|---|---|---|
6795 | 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 |
33924 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
120680 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
120680 | CIP Medium 583 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=583 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6795 | positive | growth | 28 | mesophilic |
33924 | positive | growth | 30 | mesophilic |
67772 | positive | optimum | 28 | mesophilic |
120680 | positive | growth | 10-30 | |
120680 | no | growth | 5 | psychrophilic |
120680 | no | growth | 37 | mesophilic |
120680 | no | growth | 41 | thermophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
67772 | positive | maximum | 8.0 |
67772 | positive | minimum | 5.0 |
Physiology and metabolism
oxygen tolerance
- @ref: 120680
- oxygen tolerance: obligate aerobe
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
120680 | NaCl | positive | growth | 0-2 % |
120680 | NaCl | no | growth | 4 % |
120680 | NaCl | no | growth | 6 % |
120680 | NaCl | no | growth | 8 % |
120680 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
120680 | 16947 | citrate | - | carbon source |
120680 | 4853 | esculin | - | hydrolysis |
120680 | 17632 | nitrate | - | reduction |
120680 | 16301 | nitrite | - | reduction |
120680 | 17632 | nitrate | - | respiration |
metabolite production
- @ref: 120680
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
120680 | oxidase | + | |
120680 | beta-galactosidase | - | 3.2.1.23 |
120680 | alcohol dehydrogenase | - | 1.1.1.1 |
120680 | gelatinase | - | |
120680 | amylase | - | |
120680 | DNase | - | |
120680 | caseinase | - | 3.4.21.50 |
120680 | catalase | + | 1.11.1.6 |
120680 | tween esterase | - | |
120680 | lecithinase | - | |
120680 | lipase | - | |
120680 | lysine decarboxylase | - | 4.1.1.18 |
120680 | ornithine decarboxylase | - | 4.1.1.17 |
120680 | tryptophan deaminase | - | |
120680 | urease | + | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120680 | - | + | + | + | - | + | + | - | - | - | + | + | - | - | - | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120680 | + | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | + | - | + | + | - | + | + | - | - | - | + | - | + | - | - | - | + | - | + | - | - | - | + | + | + | + | - | + | + | + | - | + | + | + | + | + | + | - | + | + | + | - | - | - | + | + | - | - | - | - | - | - | - | - | + | + | - | - | + | + | - | + | - | - | - | - | + | + | + | + | + | + | + | + | + | + | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent | sampling date | geographic location | latitude | longitude | isolation date |
---|---|---|---|---|---|---|---|---|---|---|
6795 | root nodules of Phaseolus vulgaris plants grown in a soil from Sierra da Peneda | Phaseolus vulgaris | Portugal | PRT | Europe | |||||
58368 | Root nodules,Phaseolus vulgaris | Portugal | PRT | Europe | 2000 | Sierra da Penada | ||||
67772 | Phaseolus vulgaris, root nodules | Portugal | PRT | Europe | 2000 | Alto-Minho, Arcos de Valdevez | 41.85 | -8.41667 | ||
120680 | Plant, Endophyllous | Portugal | PRT | Europe | Arcos de Valdevez | 2000 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
6795 | 1 | Risk group (German classification) |
67772 | 1 | |
120680 | 1 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Herbaspirillum lusitanum P6-12 | 1161913.3 | wgs | patric | 1161913 |
66792 | Herbaspirillum lusitanum P6-12 | 2548876994 | draft | img | 1161913 |
67772 | Herbaspirillum lusitanum P6-12 | GCA_000256565 | contig | ncbi | 1161913 |
GC content
- @ref: 6795
- GC-content: 57.9
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 92.1 | no |
gram-positive | no | 98.974 | no |
anaerobic | no | 98.125 | no |
aerobic | yes | 90.299 | no |
halophile | no | 96.611 | no |
spore-forming | no | 94.647 | no |
flagellated | yes | 56.799 | no |
thermophile | no | 99.386 | yes |
glucose-util | yes | 86.864 | no |
glucose-ferment | no | 90.731 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 14657133 | Herbaspirillum 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 JM | Int J Syst Evol Microbiol | 10.1099/ijs.0.02677-0 | 2003 | Geography, Herbaspirillum/*classification/*genetics/isolation & purification/physiology, Molecular Sequence Data, Nitrates/metabolism, Nitrites/metabolism, Nitrogen Fixation, Phaseolus/*microbiology, *Phylogeny, Plant Roots/microbiology | Genetics |
Phylogeny | 16738112 | Herbaspirillum hiltneri sp. nov., isolated from surface-sterilized wheat roots. | Rothballer M, Schmid M, Klein I, Gattinger A, Grundmann S, Hartmann A | Int J Syst Evol Microbiol | 10.1099/ijs.0.64031-0 | 2006 | DNA, Bacterial/genetics, Herbaspirillum/*classification/isolation & purification/ultrastructure, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, Plant Roots/*microbiology, Triticum/*microbiology | Genetics |
Genetics | 22815451 | Draft 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 LM | J Bacteriol | 10.1128/JB.00657-12 | 2012 | DNA, Bacterial/*chemistry/*genetics, Endophytes/genetics/isolation & purification, *Genome, Bacterial, Herbaspirillum/*genetics/isolation & purification, Molecular Sequence Data, Phaseolus/*microbiology, Root Nodules, Plant/*microbiology, *Sequence Analysis, DNA | Enzymology |
Metabolism | 32216024 | Characterization of biopolymers produced by planktonic and biofilm cells of Herbaspirillum lusitanum P6-12. | Velichko NS, Grinev VS, Fedonenko YP | J Appl Microbiol | 10.1111/jam.14647 | 2020 | Bacterial 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 | |
35614280 | Whole-cell electric sensor for determination of sodium dodecyl sulfate. | Velichko NS, Guliy OI, Kanevsky MV, Kupryashina MA, Fedonenko YP | World J Microbiol Biotechnol | 10.1007/s11274-022-03309-1 | 2022 | *Environmental Pollution, Sodium Dodecyl Sulfate/chemistry, Sulfates, *Surface-Active Agents/chemistry |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
6795 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17154) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17154 | |
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 | |
33924 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5843 | ||
58368 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 48869) | https://www.ccug.se/strain?id=48869 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
67772 | Curators of the UCCCB | https://ucccb.uc.pt/ | ||
68382 | Automatically annotated from API zym | |||
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 | |
80595 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID88963.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
120680 | Curators of the CIP | Collection of Institut Pasteur (CIP 108242) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108242 |