Strain identifier
BacDive ID: 131560
Type strain:
Species: Variovorax gossypii
Strain Designation: JM-310, JM 310
Strain history: CIP <- 2015, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM 310
NCBI tax ID(s): 1679495 (species)
General
@ref: 22787
BacDive-ID: 131560
DSM-Number: 100435
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped, colony-forming
description: Variovorax gossypii JM-310 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from healthy internal root tissue of 4-week-old cotton .
NCBI tax id
- NCBI tax id: 1679495
- Matching level: species
strain history
@ref | history |
---|---|
41883 | 2015, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM 310 |
22787 | <- P. Kämpfer, Institut für Angewandte Mikrobiologie, Universität Giessen, Germany; JM-310 <- J. McInroy, Department of Entomology and Plant Pathology, Auburn University, Alabama, USA |
119715 | CIP <- 2015, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM 310 |
doi: 10.13145/bacdive131560.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Variovorax
- species: Variovorax gossypii
- full scientific name: Variovorax gossypii Kämpfer et al. 2015
@ref: 22787
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Variovorax
species: Variovorax gossypii
full scientific name: Variovorax gossypii Kämpfer et al. 2015
strain designation: JM-310, JM 310
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
23102 | negative | 1.5-3.0 µm | 0.3-0.5 µm | rod-shaped | yes | |
69480 | yes | 96.748 | ||||
69480 | negative | 99.962 | ||||
119715 | negative | rod-shaped | no |
colony morphology
- @ref: 23102
- colony color: beige
- colony shape: circular
- medium used: nutrient agar
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
22787 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf | |
22787 | R2A MEDIUM (DSMZ Medium 830) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf | |
23102 | Nutrient agar (NA) | yes | ||
23102 | Reasoner's 2A agar (R2A) | yes | ||
23102 | trypticase soy agar | yes | ||
41883 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
22787 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
119715 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
23102 | positive | growth | 11.0-36.0 | |
23102 | no | growth | <4.0 | psychrophilic |
23102 | no | growth | >45.0 | thermophilic |
41883 | positive | growth | 30 | mesophilic |
22787 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 23102
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
23102 | no | |
69481 | no | 100 |
69480 | no | 99.97 |
halophily
- @ref: 23102
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 1.0-3.0 %(w/v)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
23102 | 17057 | cellobiose | - | builds acid from |
23102 | 18333 | D-arabitol | - | builds acid from |
23102 | 17924 | D-sorbitol | - | builds acid from |
23102 | 65327 | D-xylose | - | builds acid from |
23102 | 16813 | galactitol | - | builds acid from |
23102 | 17113 | erythritol | - | builds acid from |
23102 | 17268 | myo-inositol | - | builds acid from |
23102 | 62345 | L-rhamnose | - | builds acid from |
23102 | 17716 | lactose | - | builds acid from |
23102 | 17306 | maltose | - | builds acid from |
23102 | 28053 | melibiose | - | builds acid from |
23102 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
23102 | 16634 | raffinose | - | builds acid from |
23102 | 17814 | salicin | - | builds acid from |
23102 | 17992 | sucrose | - | builds acid from |
23102 | 27082 | trehalose | - | builds acid from |
23102 | 16193 | 3-hydroxybenzoate | - | carbon source |
23102 | 17879 | 4-hydroxybenzoate | - | carbon source |
23102 | 15963 | ribitol | - | carbon source |
23102 | 18305 | arbutin | - | carbon source |
23102 | 17057 | cellobiose | - | carbon source |
23102 | 16383 | cis-aconitate | - | carbon source |
23102 | 16947 | citrate | - | carbon source |
23102 | 12936 | D-galactose | - | carbon source |
23102 | 17754 | glycerol | - | carbon source |
23102 | 17268 | myo-inositol | - | carbon source |
23102 | 17240 | itaconate | - | carbon source |
23102 | 17295 | L-phenylalanine | - | carbon source |
23102 | 62345 | L-rhamnose | - | carbon source |
23102 | 68428 | maltitol | - | carbon source |
23102 | 17306 | maltose | - | carbon source |
23102 | 36986 | mesaconate | - | carbon source |
23102 | 28037 | N-acetylgalactosamine | - | carbon source |
23102 | 18401 | phenylacetate | - | carbon source |
23102 | 17148 | putrescine | - | carbon source |
23102 | 17814 | salicin | - | carbon source |
23102 | 9300 | suberic acid | - | carbon source |
23102 | 17992 | sucrose | - | carbon source |
23102 | 15708 | trans-aconitate | - | carbon source |
23102 | 27082 | trehalose | - | carbon source |
23102 | 15963 | ribitol | + | builds acid from |
23102 | 17634 | D-glucose | + | builds acid from |
23102 | 16899 | D-mannitol | + | builds acid from |
23102 | 30849 | L-arabinose | + | builds acid from |
23102 | 29991 | L-aspartate | + | carbon source |
23102 | 30916 | 2-oxoglutarate | + | carbon source |
23102 | 16865 | gamma-aminobutyric acid | + | carbon source |
23102 | 30089 | acetate | + | carbon source |
23102 | 17128 | adipate | + | carbon source |
23102 | 78208 | azelaate | + | carbon source |
23102 | 16958 | beta-alanine | + | carbon source |
23102 | 15824 | D-fructose | + | carbon source |
23102 | 17634 | D-glucose | + | carbon source |
23102 | 16899 | D-mannitol | + | carbon source |
23102 | 16024 | D-mannose | + | carbon source |
23102 | 16988 | D-ribose | + | carbon source |
23102 | 17924 | D-sorbitol | + | carbon source |
23102 | 65327 | D-xylose | + | carbon source |
23102 | 37054 | 3-hydroxybutyrate | + | carbon source |
23102 | 29806 | fumarate | + | carbon source |
23102 | 24265 | gluconate | + | carbon source |
23102 | 17859 | glutaric acid | + | carbon source |
23102 | 16977 | L-alanine | + | carbon source |
23102 | 30849 | L-arabinose | + | carbon source |
23102 | 15971 | L-histidine | + | carbon source |
23102 | 15603 | L-leucine | + | carbon source |
23102 | 15729 | L-ornithine | + | carbon source |
23102 | 17203 | L-proline | + | carbon source |
23102 | 17115 | L-serine | + | carbon source |
23102 | 16828 | L-tryptophan | + | carbon source |
23102 | 28053 | melibiose | + | carbon source |
23102 | 506227 | N-acetylglucosamine | + | carbon source |
23102 | 17272 | propionate | + | carbon source |
23102 | 15361 | pyruvate | + | carbon source |
23102 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
23102 | alpha-glucosidase | - | 3.2.1.20 |
23102 | beta-galactosidase | - | 3.2.1.23 |
23102 | catalase | + | 1.11.1.6 |
23102 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent | enrichment culture | enrichment culture temperature | isolation date |
---|---|---|---|---|---|---|---|---|---|
22787 | healthy internal root tissue of 4-week-old cotton (Gossypium hirsutum, cultivar 'DES-119') | Gossypium hirsutum | Alabama, Macon county, Tallassee | USA | USA | North America | |||
23102 | endophyte from the healthy internal root tissue of 4-week-old cotton (Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit facility | trypticase soy agar (TSA; Oxoid) | 28.0 | ||||||
119715 | Plant, Internal root tissue, cotton | United States of America | USA | North America | 1990-01-02 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Agriculture | #Plantation |
#Host | #Other | #Endosymbiont |
#Host | #Plants | #Shrub (Scrub) |
#Host | #Plants | #Tree |
#Host Body-Site | #Plant | #Root (Rhizome) |
taxonmaps
- @ref: 69479
- File name: preview.99_2305.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_308;97_342;98_387;99_2305&stattab=map
- Last taxonomy: Variovorax
- 16S sequence: KR349468
- Sequence Identity:
- Total samples: 9717
- soil counts: 3106
- aquatic counts: 2157
- animal counts: 2122
- plant counts: 2332
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
22787 | 1 | Risk group (German classification) |
119715 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 22787
- description: Variovorax gossypii strain JM-310 16S ribosomal RNA gene, partial sequence
- accession: KR349468
- length: 1437
- database: ena
- NCBI tax ID: 1679495
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Variovorax gossypii DSM 100435 | GCA_003965815 | contig | ncbi | 1679495 |
66792 | Variovorax gossypii strain DSM 100435 | 1679495.4 | wgs | patric | 1679495 |
66792 | Variovorax gossypii DSM 100435 | 2831272406 | draft | img | 1679495 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 83.751 | no |
gram-positive | no | 98.007 | yes |
anaerobic | no | 98.229 | no |
aerobic | yes | 93.587 | yes |
halophile | no | 95.706 | no |
spore-forming | no | 93.893 | yes |
glucose-util | yes | 79.115 | yes |
flagellated | no | 64.827 | no |
thermophile | no | 99.525 | no |
glucose-ferment | no | 89.399 | no |
External links
@ref: 22787
culture collection no.: DSM 100435, CCM 8614, CIP 110912, LMG 28869
straininfo link
- @ref: 89974
- straininfo: 406461
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 26341669 | Variovorax gossypii sp. nov., isolated from Gossypium hirsutum. | Kampfer P, Busse HJ, McInroy JA, Glaeser SP | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000581 | 2015 | Alabama, Bacterial Typing Techniques, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gossypium/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, Putrescine/analogs & derivatives/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry | Genetics |
Stress | 35448819 | Improved Medicago sativa Nodulation under Stress Assisted by Variovorax sp. Endophytes. | Flores-Duarte NJ, Perez-Perez J, Navarro-Torre S, Mateos-Naranjo E, Redondo-Gomez S, Pajuelo E, Rodriguez-Llorente ID | Plants (Basel) | 10.3390/plants11081091 | 2022 | ||
Phylogeny | 35791077 | Variovorax terrae sp. nov. Isolated from Soil with Potential Antioxidant Activity. | Woo CY, Kim J | J Microbiol Biotechnol | 10.4014/jmb.2205.05018 | 2022 | Antioxidants/analysis, Bacterial Typing Techniques, *Comamonadaceae, DNA, Bacterial/genetics, Fatty Acids/analysis, *Phosphatidylethanolamines/analysis, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil Microbiology | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
22787 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100435 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100435) | |||
23102 | Peter Kämpfer,Hans-Jürgen Busse,John A. McInroy,Stefanie P. Glaeser | Variovorax gossypii sp. nov., isolated from Gossypium hirsutum | 10.1099/ijsem.0.000581 | IJSEM 65: 4335-4340 2015 | 26341669 | |
41883 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/34519 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
89974 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID406461.1 | |||
119715 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110912 | Collection of Institut Pasteur (CIP 110912) |