Strain identifier

BacDive ID: 131560

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
418832015, 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
119715CIP <- 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

@refgram staincell lengthcell widthcell shapemotilityconfidence
23102negative1.5-3.0 µm0.3-0.5 µmrod-shapedyes
69480yes96.748
69480negative99.962
119715negativerod-shapedno

colony morphology

  • @ref: 23102
  • colony color: beige
  • colony shape: circular
  • medium used: nutrient agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22787NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf
22787R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf
23102Nutrient agar (NA)yes
23102Reasoner's 2A agar (R2A)yes
23102trypticase soy agaryes
41883MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
22787TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
119715CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
23102positivegrowth11.0-36.0
23102nogrowth<4.0psychrophilic
23102nogrowth>45.0thermophilic
41883positivegrowth30mesophilic
22787positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 23102
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
23102no
69481no100
69480no99.97

halophily

  • @ref: 23102
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 1.0-3.0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2310217057cellobiose-builds acid from
2310218333D-arabitol-builds acid from
2310217924D-sorbitol-builds acid from
2310265327D-xylose-builds acid from
2310216813galactitol-builds acid from
2310217113erythritol-builds acid from
2310217268myo-inositol-builds acid from
2310262345L-rhamnose-builds acid from
2310217716lactose-builds acid from
2310217306maltose-builds acid from
2310228053melibiose-builds acid from
23102320061methyl alpha-D-glucopyranoside-builds acid from
2310216634raffinose-builds acid from
2310217814salicin-builds acid from
2310217992sucrose-builds acid from
2310227082trehalose-builds acid from
23102161933-hydroxybenzoate-carbon source
23102178794-hydroxybenzoate-carbon source
2310215963ribitol-carbon source
2310218305arbutin-carbon source
2310217057cellobiose-carbon source
2310216383cis-aconitate-carbon source
2310216947citrate-carbon source
2310212936D-galactose-carbon source
2310217754glycerol-carbon source
2310217268myo-inositol-carbon source
2310217240itaconate-carbon source
2310217295L-phenylalanine-carbon source
2310262345L-rhamnose-carbon source
2310268428maltitol-carbon source
2310217306maltose-carbon source
2310236986mesaconate-carbon source
2310228037N-acetylgalactosamine-carbon source
2310218401phenylacetate-carbon source
2310217148putrescine-carbon source
2310217814salicin-carbon source
231029300suberic acid-carbon source
2310217992sucrose-carbon source
2310215708trans-aconitate-carbon source
2310227082trehalose-carbon source
2310215963ribitol+builds acid from
2310217634D-glucose+builds acid from
2310216899D-mannitol+builds acid from
2310230849L-arabinose+builds acid from
2310229991L-aspartate+carbon source
23102309162-oxoglutarate+carbon source
2310216865gamma-aminobutyric acid+carbon source
2310230089acetate+carbon source
2310217128adipate+carbon source
2310278208azelaate+carbon source
2310216958beta-alanine+carbon source
2310215824D-fructose+carbon source
2310217634D-glucose+carbon source
2310216899D-mannitol+carbon source
2310216024D-mannose+carbon source
2310216988D-ribose+carbon source
2310217924D-sorbitol+carbon source
2310265327D-xylose+carbon source
23102370543-hydroxybutyrate+carbon source
2310229806fumarate+carbon source
2310224265gluconate+carbon source
2310217859glutaric acid+carbon source
2310216977L-alanine+carbon source
2310230849L-arabinose+carbon source
2310215971L-histidine+carbon source
2310215603L-leucine+carbon source
2310215729L-ornithine+carbon source
2310217203L-proline+carbon source
2310217115L-serine+carbon source
2310216828L-tryptophan+carbon source
2310228053melibiose+carbon source
23102506227N-acetylglucosamine+carbon source
2310217272propionate+carbon source
2310215361pyruvate+carbon source
231024853esculin+hydrolysis

enzymes

@refvalueactivityec
23102alpha-glucosidase-3.2.1.20
23102beta-galactosidase-3.2.1.23
23102catalase+1.11.1.6
23102cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture temperatureisolation date
22787healthy internal root tissue of 4-week-old cotton (Gossypium hirsutum, cultivar 'DES-119')Gossypium hirsutumAlabama, Macon county, TallasseeUSAUSANorth America
23102endophyte from the healthy internal root tissue of 4-week-old cotton (Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit facilitytrypticase soy agar (TSA; Oxoid)28.0
119715Plant, Internal root tissue, cottonUnited States of AmericaUSANorth America1990-01-02

isolation source categories

Cat1Cat2Cat3
#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

@refbiosafety levelbiosafety level comment
227871Risk group (German classification)
1197151Risk 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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Variovorax gossypii DSM 100435GCA_003965815contigncbi1679495
66792Variovorax gossypii strain DSM 1004351679495.4wgspatric1679495
66792Variovorax gossypii DSM 1004352831272406draftimg1679495

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes83.751no
gram-positiveno98.007yes
anaerobicno98.229no
aerobicyes93.587yes
halophileno95.706no
spore-formingno93.893yes
glucose-utilyes79.115yes
flagellatedno64.827no
thermophileno99.525no
glucose-fermentno89.399no

External links

@ref: 22787

culture collection no.: DSM 100435, CCM 8614, CIP 110912, LMG 28869

straininfo link

  • @ref: 89974
  • straininfo: 406461

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26341669Variovorax gossypii sp. nov., isolated from Gossypium hirsutum.Kampfer P, Busse HJ, McInroy JA, Glaeser SPInt J Syst Evol Microbiol10.1099/ijsem.0.0005812015Alabama, 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/chemistryGenetics
Stress35448819Improved 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 IDPlants (Basel)10.3390/plants110810912022
Phylogeny35791077Variovorax terrae sp. nov. Isolated from Soil with Potential Antioxidant Activity.Woo CY, Kim JJ Microbiol Biotechnol10.4014/jmb.2205.050182022Antioxidants/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 MicrobiologyTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
22787Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100435Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100435)
23102Peter Kämpfer,Hans-Jürgen Busse,John A. McInroy,Stefanie P. GlaeserVariovorax gossypii sp. nov., isolated from Gossypium hirsutum10.1099/ijsem.0.000581IJSEM 65: 4335-4340 201526341669
41883Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/34519
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
89974Reimer, 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 identifiers10.60712/SI-ID406461.1
119715Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110912Collection of Institut Pasteur (CIP 110912)