Strain identifier

BacDive ID: 13636

Type strain: Yes

Species: Rhizobium pisi

Strain history: IAM 12609 <-- ATCC (as ATCC 10004) <-- L. W. Erdman (as strain 3HOq18).

NCBI tax ID(s): 574561 (species)

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General

@ref: 9153

BacDive-ID: 13636

DSM-Number: 30132

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Rhizobium pisi DSM 30132 is a mesophilic, Gram-negative bacterium that was isolated from effective nodules Pisum sativum.

NCBI tax id

  • NCBI tax id: 574561
  • Matching level: species

strain history

@refhistory
9153<- ATCC <- L.W. Erdman, 3HOq18
67770IAM 12609 <-- ATCC (as ATCC 10004) <-- L. W. Erdman (as strain 3HOq18).

doi: 10.13145/bacdive13636.20250331.9.3

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: 9153

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Rhizobium

species: Rhizobium pisi

full scientific name: Rhizobium pisi Ramírez-Bahena et al. 2008

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
125439negative96.5
125438negative98.333

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9153NUTRIENT 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
9153RHIZOBIUM MEDIUM (DSMZ Medium 98)yeshttps://mediadive.dsmz.de/medium/98Name: RHIZOBIUM MEDIUM (DSMZ Medium 98) Composition: air-dried garden soil 80.0 g/l Agar 15.0 g/l Mannitol 10.0 g/l Yeast extract 1.0 g/l Na2CO3 0.2 g/l Distilled water

culture temp

@refgrowthtypetemperature
9153positivegrowth26
67770positivegrowth25

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: aerobe
  • confidence: 93.4

spore formation

@refspore formationconfidence
125439no96.8
125438no90.286

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
9153----++-+++++++---++/--+
9153----++-+++++++---+--+

Isolation, sampling and environmental information

isolation

@refsample typehost species
9153effective nodules Pisum sativumPisum sativum
67770Effective nodules of Pisum sativumPisum sativum

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: AY509899
  • Sequence Identity:
  • Total samples: 333
  • soil counts: 50
  • aquatic counts: 32
  • animal counts: 28
  • plant counts: 223

Safety information

risk assessment

  • @ref: 9153
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
9153Rhizobium pisi strain DSM 30132 16S ribosomal RNA gene, partial sequenceAY5098991475nuccore574561
124043Rhizobium pisi strain DSM 30132 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequence.DQ2001741101nuccore574561

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhizobium pisi DSM 30132GCA_003938655contigncbi574561
66792Rhizobium pisi strain DSM 30132574561.3wgspatric574561
66792Rhizobium pisi DSM 301322738541312draftimg574561

GC content

  • @ref: 9153
  • GC-content: 61.5

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.333no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.54no
125438spore-formingspore-formingAbility to form endo- or exosporesno90.286no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.678no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99.25yes
125438motile2+flagellatedAbility to perform flagellated movementyes69.973no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno96.8
125439BacteriaNetmotilityAbility to perform movementyes56.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative96.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe93.4

External links

@ref: 9153

culture collection no.: DSM 30132, NCIB 11478, NCIMB 11478, JCM 20680, IAM 12609, NBRC 14778

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18984681Revision of the taxonomic status of the species Rhizobium leguminosarum (Frank 1879) Frank 1889AL, Rhizobium phaseoli Dangeard 1926AL and Rhizobium trifolii Dangeard 1926AL. R. trifolii is a later synonym of R. leguminosarum. Reclassification of the strain R. leguminosarum DSM 30132 (=NCIMB 11478) as Rhizobium pisi sp. nov.Ramirez-Bahena MH, Garcia-Fraile P, Peix A, Valverde A, Rivas R, Igual JM, Mateos PF, Martinez-Molina E, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.65621-02008Bacterial Proteins/genetics, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal Spacer/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Rhizobium/*classification/genetics/physiology, Rhizobium leguminosarum/*classification/genetics/physiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny23507586Rhizobium pisi sv. trifolii K3.22 harboring nod genes of the Rhizobium leguminosarum sv. trifolii cluster.Marek-Kozaczuk M, Leszcz A, Wielbo J, Wdowiak-Wrobel S, Skorupska ASyst Appl Microbiol10.1016/j.syapm.2013.01.0052013Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, Bacterial, Host Specificity, Medicago/microbiology, Molecular Sequence Data, Molecular Typing, Phylogeny, Plant Root Nodulation, Plasmids, RNA, Ribosomal, 16S/genetics, Rhizobium leguminosarum/*classification/*genetics/isolation & purification/physiology, Root Nodules, Plant/*microbiology, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitle
9153Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30132)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30132
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
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/
68369Automatically annotated from API 20NE
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
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
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