Strain identifier

BacDive ID: 24486

Type strain: Yes

Species: Ciceribacter lividus

Strain Designation: MSSRFBL1

Strain history: <- R. Kathiravan, M.S. Swaminathan Research Foundation, Taramani, India; MSSRFBL

NCBI tax ID(s): 1197950 (species)

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General

@ref: 21294

BacDive-ID: 24486

DSM-Number: 25528

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

description: Ciceribacter lividus MSSRFBL1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere soil of chick pea .

NCBI tax id

  • NCBI tax id: 1197950
  • Matching level: species

strain history

  • @ref: 21294
  • history: <- R. Kathiravan, M.S. Swaminathan Research Foundation, Taramani, India; MSSRFBL

doi: 10.13145/bacdive24486.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Ciceribacter
  • species: Ciceribacter lividus
  • full scientific name: Ciceribacter lividus Kathiravan et al. 2013

@ref: 21294

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Ciceribacter

species: Ciceribacter lividus

full scientific name: Ciceribacter lividus Kathiravan et al. 2013

strain designation: MSSRFBL1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31010negative1.5 µm0.4 µmrod-shapedyes
69480negative99.994

pigmentation

  • @ref: 31010
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
31010positivegrowth25-37mesophilic
31010positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
31010positivegrowth6.0-8.5alkaliphile
31010positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31010
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.983

halophily

  • @ref: 31010
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3101022599arabinose+carbon source
3101016947citrate+carbon source
3101028757fructose+carbon source
3101017306maltose+carbon source
3101037684mannose+carbon source
3101033942ribose+carbon source
3101017992sucrose+carbon source

enzymes

@refvalueactivityec
31010catalase+1.11.1.6
31010urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 21294
  • sample type: rhizosphere soil of chick pea (Cicer arietinum L.)
  • host species: Cicer arietinum
  • geographic location: Tamil Nadu, Kannivadi (10° 22' 44.40'' N 77° 49' 48.0'' E)
  • country: India
  • origin.country: IND
  • continent: Asia
  • latitude: 10.379
  • longitude: 77.83

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_24988.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_3308;97_4057;98_18553;99_24988&stattab=map
  • Last taxonomy: Rhizobiaceae
  • 16S sequence: JQ230000
  • Sequence Identity:
  • Total samples: 683
  • soil counts: 122
  • aquatic counts: 149
  • animal counts: 38
  • plant counts: 374

Safety information

risk assessment

  • @ref: 21294
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21294
  • description: Ciceribacter lividus strain MSSRFBL1 16S ribosomal RNA gene, partial sequence
  • accession: JQ230000
  • length: 1392
  • database: ena
  • NCBI tax ID: 1197950

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ciceribacter lividus DSM 25528GCA_003337715scaffoldncbi1197950
66792Ciceribacter lividus strain DSM 255281197950.4wgspatric1197950
66792Ciceribacter lividus DSM 255282770939508draftimg1197950

GC content

@refGC-contentmethod
2129471high performance liquid chromatography (HPLC)
3101071

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.722yes
flagellatedno51.643no
gram-positiveno98.502yes
anaerobicno97.296yes
aerobicyes87.276yes
halophileno85.338no
spore-formingno95.722no
glucose-utilyes91.283no
thermophileno94.963no
glucose-fermentno90.625no

External links

@ref: 21294

culture collection no.: DSM 25528, KCTC 32403

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23907221Ciceribacter lividus gen. nov., sp. nov., isolated from rhizosphere soil of chick pea (Cicer arietinum L.).Kathiravan R, Jegan S, Ganga V, Prabavathy VR, Tushar L, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijs.0.049726-02013Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cicer/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Glycolipids/chemistry, India, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Triterpenes/chemistry, Ubiquinone/chemistryGenetics
Phylogeny28984561Ciceribacter thiooxidans sp. nov., a novel nitrate-reducing thiosulfate-oxidizing bacterium isolated from sulfide-rich anoxic sediment.Deng T, Chen X, Zhang Q, Zhong Y, Guo J, Sun G, Xu MInt J Syst Evol Microbiol10.1099/ijsem.0.0023672017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/*classification/genetics/isolation & purification, Rivers/*microbiology, Sequence Analysis, DNA, Thiosulfates/metabolism, Ubiquinone/chemistryTranscriptome
Phylogeny29297848Ciceribacter azotifigens sp. nov., a nitrogen-fixing bacterium isolated from activated sludge.Siddiqi MZ, Choi GM, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0024382018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ginsenosides, *Nitrogen Fixation, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizobiaceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
21294Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25528Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25528)
31010Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172734028776041
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