Strain identifier

BacDive ID: 11892

Type strain: Yes

Species: Mesorhizobium plurifarium

Strain history: CIP <- 1999, LMG <- 1991, de Lajudie, ORSTOM, West Africa: strain ORS 1032

NCBI tax ID(s): 69974 (species)

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General

@ref: 16018

BacDive-ID: 11892

DSM-Number: 21884

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

description: Mesorhizobium plurifarium DSM 21884 is a mesophilic, Gram-negative, motile bacterium that was isolated from Acacia senegal.

NCBI tax id

  • NCBI tax id: 69974
  • Matching level: species

strain history

@refhistory
16018<- CIP <- LMG <- P. De Lajudie, ORSTOM, Dakar, Senegal (Rhizobium sp.) <- M. Neyra
67770IAM 15105 <-- LMG 11892 <-- P. de Lajudie ORS 1032 (Rhizobium sp.) <-- M. Neyra.
121874CIP <- 1999, LMG <- 1991, de Lajudie, ORSTOM, West Africa: strain ORS 1032

doi: 10.13145/bacdive11892.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Phyllobacteriaceae
  • genus: Mesorhizobium
  • species: Mesorhizobium plurifarium
  • full scientific name: Mesorhizobium plurifarium de Lajudie et al. 1998

@ref: 16018

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Phyllobacteriaceae

genus: Mesorhizobium

species: Mesorhizobium plurifarium

full scientific name: Mesorhizobium plurifarium de Lajudie et al. 1998

type strain: yes

Morphology

cell morphology

  • @ref: 121874
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16018YMA-MEDIUM (DSMZ Medium 1031)yeshttps://mediadive.dsmz.de/medium/1031Name: YMA-MEDIUM (DSMZ Medium 1031) Composition: Agar 20.0 g/l Mannitol 10.0 g/l Yeast extract 0.3 g/l MgSO4 0.2 g/l K2HPO4 0.2 g/l NaCl 0.05 g/l Distilled water
39379MEDIUM 304 - for Allorhizobium undicolayesDistilled water make up to (987.000 ml);Sodium chloride (0.050 g);Agar (20.000 g);Yeast extract (1.000 g);Potassium di-hydrogen phosphate (0.500 g);Sodium glutamate (0.500 g);Mannitol (10.000 g);Solution A - M0556 (10.000 ml);Solution B - M0557 (1.000 ml)
121874CIP Medium 296yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=296

culture temp

@refgrowthtypetemperaturerange
16018positivegrowth30mesophilic
39379positivegrowth30mesophilic
67770positivegrowth28mesophilic
121874positivegrowth25-37mesophilic
121874nogrowth10psychrophilic
121874nogrowth41thermophilic
121874nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
121874NaClpositivegrowth0 %
121874NaClnogrowth2 %
121874NaClnogrowth4 %
121874NaClnogrowth6 %
121874NaClnogrowth8 %
121874NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
121874citrate+carbon source16947
121874esculin+hydrolysis4853
121874hippurate-hydrolysis606565
121874nitrate-reduction17632
121874nitrite-reduction16301
121874nitrate-respiration17632

antibiotic resistance

  • @ref: 121874
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 121874
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12187415688acetoin-
12187417234glucose-

enzymes

@refvalueactivityec
121874oxidase-
121874beta-galactosidase-3.2.1.23
121874alcohol dehydrogenase-1.1.1.1
121874gelatinase-
121874amylase-
121874DNase-
121874caseinase-3.4.21.50
121874catalase-1.11.1.6
121874tween esterase-
121874gamma-glutamyltransferase-2.3.2.2
121874lecithinase-
121874lipase-
121874lysine decarboxylase-4.1.1.18
121874ornithine decarboxylase-4.1.1.17
121874phenylalanine ammonia-lyase-4.3.1.24
121874protease-
121874tryptophan deaminase-
121874urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121874--++-+--+-++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121874----+-----+++--------++/-++++/-+/----+---++--+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121874++++++++--++---+++++++-++-+-+--+++++++-+--+-----+++--+----++--+--------+-+-+--+++-+---+-+-++-+-++++

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
16018Acacia senegalAcacia senegalSenegalSENAfrica
67770Root nodule harvested on young seedling of Acacia senegalAcacia senegalSenegalSENAfrica
121874AcaciaSenegalSENAfrica

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_315.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_220;97_239;98_268;99_315&stattab=map
  • Last taxonomy: Mesorhizobium
  • 16S sequence: Y14158
  • Sequence Identity:
  • Total samples: 49047
  • soil counts: 28701
  • aquatic counts: 8865
  • animal counts: 7451
  • plant counts: 4030

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
160181Risk group (German classification)
1218741Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mesorhizobium plurifarium gene for 16S rRNA, partial sequence, strain: NBRC 102498AB6818351410ena69974
20218Mesorhizobium plurifarium strain LMG 11892 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequenceAF345263962ena69974
16018Mesorhizobium plurifarium 16S rRNA gene, strain LMG 11892Y141581437ena69974

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mesorhizobium plurifarium LMG 11892GCA_003024595contigncbi69974
66792Mesorhizobium plurifarium strain LMG 1189269974.15wgspatric69974

GC content

@refGC-contentmethod
1601864.4
6777064.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.091no
anaerobicno98.454no
halophileno84.979no
spore-formingno95.39no
glucose-utilyes89.181no
thermophileno98.612no
flagellatedno69.697no
motileyes85.644no
aerobicyes89.593no
glucose-fermentno87.028no

External links

@ref: 16018

culture collection no.: DSM 21884, CIP 105884, JCM 21566, LMG 11892, NBRC 102498, ORS 1032, HAMBI 208, IAM 15105

straininfo link

  • @ref: 81109
  • straininfo: 265432

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9731275Characterization of tropical tree rhizobia and description of Mesorhizobium plurifarium sp. nov.de Lajudie P, Willems A, Nick G, Moreira F, Molouba F, Hoste B, Torck U, Neyra M, Collins MD, Lindstrom K, Dreyfus B, Gillis MInt J Syst Bacteriol10.1099/00207713-48-2-3691998Acacia/microbiology, Bacterial Proteins/analysis, Base Composition, Base Sequence, DNA, Bacterial, Electrophoresis, Polyacrylamide Gel, Gene Amplification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Rhizobiaceae/chemistry/classification/*genetics, Sequence Analysis, RNA, Sodium Dodecyl SulfateEnzymology
Phylogeny22058324Mesorhizobium silamurunense sp. nov., isolated from root nodules of Astragalus species.Zhao CT, Wang ET, Zhang YM, Chen WF, Sui XH, Chen WX, Liu HC, Zhang XXInt J Syst Evol Microbiol10.1099/ijs.0.031229-02011Astragalus Plant/*microbiology, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, Mesorhizobium/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, Plant Root Nodulation, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny26296667Mesorhizobium acaciae sp. nov., isolated from root nodules of Acacia melanoxylon R. Br.Zhu YJ, Lu JK, Chen YL, Wang SK, Sui XH, Kang LHInt J Syst Evol Microbiol10.1099/ijsem.0.0004552015Acacia/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Mesorhizobium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*metabolism, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16018Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21884)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21884
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
39379Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17952
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/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
81109Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265432.1StrainInfo: A central database for resolving microbial strain identifiers
121874Curators of the CIPCollection of Institut Pasteur (CIP 105884)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105884