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BacDive ID 13633
Type strain
Culture col. no. DSM 19331 CCBAU 33202 JCM 14381 LMG 23997 JCM 14831
NCBI tax ID(s) 573179
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.3 (current version):
version 9.3 (current version)

General

@ref: 8049

BacDive-ID: 13633

DSM-Number: 19331

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

description: Rhizobium pisi DSM 19331 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from effective nodules of Vicia faba.

NCBI tax id

  • NCBI tax id: 573179
  • Matching level: species

strain history

@refhistory
8049<- X. Sui, China Agric. Univ., College Biol. Sci., Beijing; CCBAU 33202 <- C. F. Tiang et al., China Agric. Univ., Coll. Biol. Sci., Beijing
67770C. F. Tian CCBAU 33202.

doi: 10.13145/bacdive13633.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Rhizobium
  • species: Rhizobium pisi
  • full scientific name: Rhizobium pisi Ramírez-Bahena et al. 2008

  • synonyms

    • @ref: 20215
    • synonym: Rhizobium fabae

@ref: 8049

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Rhizobium

species: Rhizobium fabae

full scientific name: Rhizobium fabae Tian et al. 2008

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31192negative2-2.5 µm0.5-0.7 µmrod-shapedyes
125439negative97.7
125438negative98.833

colony morphology

  • @ref: 8049
  • incubation period: 1-2 days

pigmentation

  • @ref: 31192
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 8049
  • name: YMA-MEDIUM (MODIFIED) (DSMZ Medium 1031a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1031a
  • composition: Name: YMA-MEDIUM (modified) (DSMZ Medium 1031a) Composition: Agar 20.0 g/l Mannitol 10.0 g/l Yeast extract 1.0 g/l K2HPO4 0.5 g/l Na glutamate 0.5 g/l MgSO4 x 7 H2O 0.1 g/l CaCl2 x 2 H2O 0.0528 g/l NaCl 0.05 g/l FeCl3 x 6 H2O 0.00666 g/l Distilled water

culture temp

@refgrowthtypetemperature
8049positivegrowth28
31192positivegrowth10-37
31192positiveoptimum28
67770positivegrowth30

culture pH

@refabilitytypepH
31192positivegrowth05-08
31192positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
31192aerobe
125439obligate aerobe97.8

spore formation

@refspore formationconfidence
31192no
125439no97.2
125438no90.486

halophily

@refsaltgrowthtested relationconcentration
31192NaClpositivegrowth0-2 %
31192NaClpositiveoptimum0-2 %

observation

  • @ref: 31192
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3119222599arabinose+carbon source
3119229016arginine+carbon source
3119235391aspartate+carbon source
3119228757fructose+carbon source
3119228260galactose+carbon source
3119217234glucose+carbon source
3119217716lactose+carbon source
3119225115malate+carbon source
3119217306maltose+carbon source
3119237684mannose+carbon source
3119226271proline+carbon source
3119215361pyruvate+carbon source
3119216634raffinose+carbon source
3119226546rhamnose+carbon source
3119217814salicin+carbon source
3119217992sucrose+carbon source
3119227082trehalose+carbon source
3119218222xylose+carbon source

enzymes

@refvalueactivityec
31192catalase+1.11.1.6
31192cytochrome oxidase+1.9.3.1
31192urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
8049effective nodules of Vicia fabaVicia fabaJiangxi province, NanchangChinaCHNAsia
67770Effective nodules of Vicia faba in NanchangVicia fabaJiangxi ProvinceChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_77.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_62;97_65;98_70;99_77&stattab=map
  • Last taxonomy: Rhizobium
  • 16S sequence: DQ835306
  • Sequence Identity:
  • Total samples: 333
  • soil counts: 50
  • aquatic counts: 32
  • animal counts: 28
  • plant counts: 223

Safety information

risk assessment

  • @ref: 8049
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhizobium fabae strain CCBAU 33202 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceFJ3928731065nuccore573179
8049Rhizobium fabae strain CCBAU 33202 16S ribosomal RNA gene, partial sequenceDQ8353061353nuccore573179

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhizobium fabae CCBAU 33202GCA_003985135scaffoldncbi573179
66792Rhizobium fabae DSM 19331GCA_014196235scaffoldncbi573179
66792Rhizobium fabae strain CCBAU 33202573179.3wgspatric573179
66792Rhizobium fabae strain DSM 19331573179.4wgspatric573179
66792Rhizobium fabae DSM 193312829836708draftimg573179

GC content

  • @ref: 8049
  • GC-content: 61.9

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.833yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.552yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.123yes
125438spore-formingspore-formingAbility to form endo- or exosporesno90.486no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99.25yes
125438motile2+flagellatedAbility to perform flagellated movementyes71.959no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno97.2
125439BacteriaNetmotilityAbility to perform movementyes57.2
125439BacteriaNetgram_stainReaction to gram-stainingnegative97.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.8

External links

@ref: 8049

culture collection no.: DSM 19331, CCBAU 33202, JCM 14381, LMG 23997, JCM 14831

literature

  • topic: Phylogeny
  • Pubmed-ID: 19060074
  • title: Rhizobium fabae sp. nov., a bacterium that nodulates Vicia faba.
  • authors: Tian CF, Wang ET, Wu LJ, Han TX, Chen WF, Gu CT, Gu JG, Chen WX
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.2008/000703-0
  • year: 2008
  • mesh: Fatty Acids/analysis, Genes, Bacterial/genetics, Molecular Sequence Data, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Rhizobium/chemistry/*classification/genetics/*physiology, Species Specificity, Vicia faba/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
8049Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19331)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19331
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
31192Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127519
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1

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