Strain identifier

BacDive ID: 140573

Type strain: Yes

Species: Siminovitchia terrae

Strain Designation: RA9

NCBI tax ID(s): 1914933 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 8.1 (current version)

General

@ref: 43172

BacDive-ID: 140573

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped

description: Siminovitchia terrae RA9 is an aerobe, spore-forming, mesophilic bacterium that was isolated from rhizosphere soil of Cistus ladanifer plants.

NCBI tax id

  • NCBI tax id: 1914933
  • Matching level: species

doi: 10.13145/bacdive140573.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Siminovitchia
  • species: Siminovitchia terrae
  • full scientific name: Siminovitchia terrae (Díez-Méndez et al. 2017) Gupta et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus terrae

@ref: 43172

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Bacillaceae

genus: Bacillus

species: Bacillus terrae

strain designation: RA9

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43172positive2.4-3.0 µm0.8-1.1 µmrod-shapedyes
69480yes92.035
69480positive100

colony morphology

  • @ref: 43172
  • colony color: white to cream
  • medium used: NA

Culture and growth conditions

culture medium

  • @ref: 43172
  • name: Nutrient agar (NA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43172positiveoptimum30mesophilic
43172positivegrowth15-45

culture pH

@refabilitytypepH
43172positivegrowth6-8
43172positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43172
  • oxygen tolerance: aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
43172Oval central or subterminalendosporeyes
69481yes100
69480yes100

halophily

  • @ref: 43172
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-7 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4317217632nitrate-reduction
431724853esculin-hydrolysis
4317225115malate+assimilation
4317218401phenylacetate+assimilation
4317217234glucose-assimilation
4317237684mannose-assimilation
4317229864mannitol-assimilation
4317217306maltose-assimilation
4317224265gluconate-assimilation
4317227689decanoate-assimilation
4317217128adipate-assimilation
4317215792malonate+assimilation
4317230089acetate+assimilation
4317216977L-alanine+assimilation
4317215971L-histidine+assimilation
4317217203L-proline+assimilation
4317262345L-rhamnose-assimilation
43172506227N-acetylglucosamine-assimilation
4317216988D-ribose-assimilation
4317217268myo-inositol-assimilation
4317217992sucrose-assimilation
4317217814salicin-assimilation
4317228053melibiose-assimilation
4317218287L-fucose-assimilation
4317217924D-sorbitol-assimilation
4317230849L-arabinose-assimilation
4317217240itaconate-assimilation
431729300suberic acid-assimilation
4317231011valerate-assimilation
4317216947citrate-assimilation
4317224996lactate-assimilation
431722-oxogluconate-assimilation
43172581435-dehydro-D-gluconate-assimilation
43172161933-hydroxybenzoate-assimilation
43172178794-hydroxybenzoate-assimilation
43172370543-hydroxybutyrate-assimilation
4317217115L-serine-assimilation
4317217272propionate+/-assimilation
4317228087glycogen+/-assimilation

metabolite production

@refChebi-IDmetaboliteproduction
4317216136hydrogen sulfideno
4317215688acetoinno
4317235581indoleno

enzymes

@refvalueactivityec
43172catalase+1.11.1.6
43172cytochrome oxidase+1.9.3.1
43172gelatinase-
43172caseinase-3.4.21.50
43172amylase-
43172beta-galactosidase-3.2.1.23
43172phenylalanine deaminase-4.3.1.5
43172urease-3.5.1.5
43172arginine dihydrolase-3.5.3.6
43172acid phosphatase+3.1.3.2
43172alkaline phosphatase+3.1.3.1
43172leucine arylamidase+3.4.11.1
43172chymotrypsin+3.4.4.5
43172phosphohydrolase+
43172esterase (C 4)-
43172esterase Lipase (C 8)-
43172lipase (C 14)-
43172cystine arylamidase-3.4.11.3
43172valine arylamidase-
43172trypsin-3.4.21.4
43172N-acetyl-beta-glucosaminidase-3.2.1.52
43172alpha-glucosidase-3.2.1.20
43172beta-glucosidase-3.2.1.21
43172alpha-galactosidase-3.2.1.22
43172alpha-fucosidase-3.2.1.51
43172alpha-mannosidase-3.2.1.24
43172glucuronidase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43172C14:01.1
    43172C16:03.1
    43172C14:0 iso9.2
    43172C15:0 iso33.3
    43172C16:0 iso10.3
    43172C17:0 iso1.9
    43172C15:0 anteiso26
    43172C17:0 anteiso3.9
    43172C16:1ω11c6.9
    43172C16:1ω7c alcohol2.9
  • type of FA analysis: whole cell analysis
  • incubation medium: TSA
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 2
  • software version: Sherlock 6.1
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 43172
  • sample type: rhizosphere soil of Cistus ladanifer plants
  • geographic location: León
  • country: Spain
  • origin.country: ESP
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Rhizosphere

Sequence information

16S sequences

  • @ref: 43172
  • description: 16S rRNA gene sequences
  • accession: KY072724
  • length: 1500
  • database: ena
  • NCBI tax ID: 1914933

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Siminovitchia terrae LMG 29736GCA_003605405scaffoldncbi1914933
66792Bacillus terrae strain LMG 297361914933.3wgspatric1914933
66792Bacillus terrae LMG 297362881644220draftimg1914933

GC content

  • @ref: 43172
  • GC-content: 43.1
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes89.156yes
motileyes89.156yes
flagellatedyes72.178no
flagellatedyes72.178no
gram-positiveyes81.271yes
gram-positiveyes81.271yes
anaerobicno98.965yes
anaerobicno98.965yes
aerobicyes91.98yes
aerobicyes91.98yes
halophileyes55.541no
halophileyes55.541no
spore-formingyes95.041yes
spore-formingyes95.041yes
thermophileno99.621yes
thermophileno99.621yes
glucose-utilyes71.062yes
glucose-utilyes71.062yes
glucose-fermentno95.096no
glucose-fermentno95.096no

External links

@ref: 43172

culture collection no.: LMG 29736, CECT 9170

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
43172Alexandra Díez-Méndez, Raúl Rivas, Pedro F. Mateos, Eustoquio Martínez-Molina, Primitivo Julio Santín, Juan Antonio Sánchez-Rodríguez and Encarna VelázquezBacillus terrae sp. nov. isolated from Cistus ladanifer rhizosphere soil10.1099/ijsem.0.001742IJSEM 67: 1478-1481 201727983469
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
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