Strain identifier

BacDive ID: 141125

Type strain: Yes

Species: Mesorhizobium sophorae

NCBI tax ID(s): 1300294 (species)

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General

@ref: 44033

BacDive-ID: 141125

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative, rod-shaped, colony-forming

description: Mesorhizobium sophorae ICMP 19535 is a Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from root nodules of Sophora microphylla from a river outwash fan.

NCBI tax id

  • NCBI tax id: 1300294
  • Matching level: species

doi: 10.13145/bacdive141125.20230509.8.1

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 sophorae
  • full scientific name: Mesorhizobium sophorae De Meyer et al. 2016

@ref: 44033

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Phyllobacteriaceae

genus: Mesorhizobium

species: Mesorhizobium sophorae

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
44033negative2 µm1 µmrod-shaped
69480yes94.098
69480negative99.994

colony morphology

  • @ref: 44033
  • colony size: 0.2-0.7 mm
  • colony color: light cream
  • colony shape: circular
  • medium used: YMA

Culture and growth conditions

culture medium

@refnamegrowth
44033YMAyes
44033YMByes

culture temp

@refgrowthtypetemperaturerange
44033positivegrowth15-30
44033nogrowth4psychrophilic
44033nogrowth7psychrophilic
44033nogrowth37mesophilic
44033positivegrowth28mesophilic

culture pH

  • @ref: 44033
  • ability: positive
  • type: growth
  • pH: 4.0-7.0
  • PH range: acidophile

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no99
69480no99.995

halophily

  • @ref: 44033
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 1-8 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
44033167632-oxobutanoate-respiration
44033739183-O-methyl-D-glucose-respiration
44033645522-hydroxybutyrate-respiration
4403373706bromosuccinate-respiration
4403316947citrate-respiration
4403378697D-fructose 6-phosphate-respiration
440338391D-gluconate-respiration
4403314314D-glucose 6-phosphate-respiration
4403315588D-malate-respiration
4403333801D-saccharate-respiration
4403316523D-serine-respiration
4403316537galactarate-respiration
440335291gelatin-respiration
4403332735guanidinium chloride-respiration
4403317596inosine-respiration
4403317464L-galactonic acid gamma-lactone-respiration
4403318183L-pyroglutamic acid-respiration
4403317115L-serine-respiration
4403374611methyl (R)-lactate-respiration
4403351850methyl pyruvate-respiration
4403335418n-acetylneuraminate-respiration
4403375273niaproof-respiration
44033309162-oxoglutarate-respiration
4403317309pectin-respiration
4403326490quinate-respiration
4403375229sodium bromate-respiration
4403317164stachyose-respiration
4403345735troleandomycin-respiration
4403317634D-glucose+assimilation
4403317306maltose+assimilation
4403330849L-arabinose+assimilation
44033370543-hydroxybutyrate+respiration
4403316865gamma-aminobutyric acid+respiration
4403330089acetate+respiration
4403313705acetoacetate+respiration
4403317925alpha-D-glucose+respiration
4403336219alpha-lactose+respiration
44033161680aztreonam+respiration
4403318333D-arabitol+respiration
4403317057cellobiose+respiration
4403315824D-fructose+respiration
4403328847D-fucose+respiration
4403312936D-galactose+respiration
4403317306maltose+respiration
4403316899D-mannitol+respiration
4403316024D-mannose+respiration
4403328053melibiose+respiration
4403316634raffinose+respiration
4403316551D-trehalose+respiration
4403328066gentiobiose+respiration
4403317754glycerol+respiration
4403316977L-alanine+respiration
4403316467L-arginine+respiration
4403329991L-aspartate+respiration
4403318287L-fucose+respiration
4403315589L-malate+respiration
4403362345L-rhamnose+respiration
4403324996lactate+respiration
440336472lincomycin+respiration
4403337657methyl D-glucoside+respiration
4403317268myo-inositol+respiration
4403328037N-acetylgalactosamine+respiration
44033506227N-acetylglucosamine+respiration
44033100147nalidixic acid+respiration
4403317272propionate+respiration
4403329673rifamycin sv+respiration
4403375198tetrazolium blue+respiration
440331 % sodium lactate+/-respiration
44033181014-hydroxyphenylacetic acid+/-respiration
4403329990D-aspartate+/-respiration
4403318024D-galacturonic acid+/-respiration
4403315748D-glucuronate+/-respiration
4403317924D-sorbitol+/-respiration
4403332528turanose+/-respiration
4403323652dextrin+/-respiration
4403315740formate+/-respiration
4403371321fusidate+/-respiration
4403332323glucuronamide+/-respiration
4403370744glycine-proline+/-respiration
4403329985L-glutamate+/-respiration
4403315971L-histidine+/-respiration
4403348607lithium chloride+/-respiration
4403350694minocycline+/-respiration
4403363154N-acetyl-beta-D-mannosamine+/-respiration
4403375248potassium tellurite+/-respiration
4403317814salicin+/-respiration
4403364103sodium butyrate+/-respiration
4403317992sucrose+/-respiration
4403375193tetrazolium violet+/-respiration
4403353423tween 40+/-respiration
4403328001vancomycin+/-respiration

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4403317833gentamicinyesyes10 µg (disc)
4403317076streptomycinyesyes25 µg (disc)
440336104kanamycinyesyes30 µg (disc)
4403348923erythromycinyesyes15 µg (disc)
4403317698chloramphenicolyesyes30 µg (disc)

enzymes

@refvalueactivityec
44033catalase-1.11.1.6
44033cytochrome oxidase+1.9.3.1
44033arginine dihydrolase+/-3.5.3.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    4403311-methyl-C18:1ω7c12
    44033C16:021.4
    44033C16:1ω7c / C15:0iso2-OH2.4
    44033C18:1ω7c48.8
    44033C19:0cycloω8c10.1
    44033C17:0 iso5.3
  • type of FA analysis: whole cell analysis
  • incubation medium: YMA
  • incubation temperature: 28
  • incubation time: 1
  • library/peak naming table: TSBA 5.0
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

  • @ref: 44033
  • sample type: root nodules of Sophora microphylla from a river outwash fan
  • geographic location: Pororari River, Westland
  • country: New Zealand
  • origin.country: NZL
  • continent: Australia and Oceania

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Root nodule

taxonmaps

  • @ref: 69479
  • File name: preview.99_809.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_220;97_239;98_643;99_809&stattab=map
  • Last taxonomy: Mesorhizobium
  • 16S sequence: KC237424
  • Sequence Identity:
  • Total samples: 30688
  • soil counts: 18576
  • aquatic counts: 5652
  • animal counts: 4689
  • plant counts: 1771

Sequence information

16S sequences

  • @ref: 44033
  • description: 16S rRNA gene sequence
  • accession: KC237424
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mesorhizobium sophorae ICMP 19535GCA_002270415contigncbi1300294
66792Mesorhizobium sophorae strain ICMP 195351300294.3wgspatric1300294
66792Mesorhizobium sophorae ICMP 195352791355123draftimg1300294

GC content

  • @ref: 44033
  • GC-content: 62.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes87.15no
gram-positiveno98.101no
anaerobicno98.915no
halophileno94.031no
spore-formingno93.96no
thermophileno99.344yes
glucose-utilyes91.533no
flagellatedno84.687no
aerobicyes90.593no
glucose-fermentno91.219no

External links

@ref: 44033

culture collection no.: ICMP 19535, LMG 28223, HAMBI 3606

straininfo link

  • @ref: 96865
  • straininfo: 393610

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26610329Mesorhizobium calcicola sp. nov., Mesorhizobium waitakense sp. nov., Mesorhizobium sophorae sp. nov., Mesorhizobium newzealandense sp. nov. and Mesorhizobium kowhaii sp. nov. isolated from Sophora root nodules.De Meyer SE, Tan HW, Andrews M, Heenan PB, Willems AInt J Syst Evol Microbiol10.1099/ijsem.0.0007962015
Genetics29074646Complete Genome Sequence of Mesorhizobium sophorae ICMP 19535(T), a Highly Specific, Nitrogen-Fixing Symbiont of New Zealand Endemic Sophora spp.De Meyer SE, Nguyen DT, Wang P, Andrews MGenome Announc10.1128/genomeA.00958-172017
Phylogeny32564274Mesorhizobium terrae sp. nov., a novel species isolated from soil in Jangsu, Korea.Jung YJ, Kim HJ, Hur MAntonie Van Leeuwenhoek10.1007/s10482-020-01435-02020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, High-Throughput Nucleotide Sequencing, Mesorhizobium/*classification/isolation & purification/*physiology, Molecular Typing, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
44033Soe E. De Meyer, Heng Wee Tan, Mitchell Andrews, Peter B. Heenan and Anne WillemsMesorhizobium calcicola sp. nov., Mesorhizobium waitakense sp. nov., Mesorhizobium sophorae sp. nov., Mesorhizobium newzealandense sp. nov. and Mesorhizobium kowhaii sp. nov. isolated from Sophora root nodules10.1099/ijsem.0.000796IJSEM 66: 786-795 201626610329
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
96865Reimer, 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-ID393610.1