Strain identifier

BacDive ID: 163970

Type strain: Yes

Species: Allorhizobium terrae

Strain Designation: CC-HIH110

Strain history: C.-C. Young; Coll. of Agric. & Nat. Resour., Natl. Chung Hsing Univ., Taiwan; CC-HIH110.

NCBI tax ID(s): 1848972 (species)

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General

@ref: 67770

BacDive-ID: 163970

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

description: Allorhizobium terrae CC-HIH110 is a mesophilic, Gram-negative, motile bacterium that forms circular colonies and was isolated from Paddy soil in Taiwan.

NCBI tax id

  • NCBI tax id: 1848972
  • Matching level: species

strain history

  • @ref: 67770
  • history: C.-C. Young; Coll. of Agric. & Nat. Resour., Natl. Chung Hsing Univ., Taiwan; CC-HIH110.

doi: 10.13145/bacdive163970.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Allorhizobium
  • species: Allorhizobium terrae
  • full scientific name: Allorhizobium terrae Lin et al. 2020

@ref: 67770

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Rhizobiaceae

genus: Allorhizobium

species: Allorhizobium terrae

full scientific name: Allorhizobium terrae Lin et al. 2020

strain designation: CC-HIH110

type strain: yes

Morphology

cell morphology

  • @ref: 69541
  • gram stain: negative
  • cell length: 1.8-2.1 µm
  • cell width: 0.7-0-9 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: polar

colony morphology

  • @ref: 69541
  • colony size: 2-3 mm
  • colony color: cream-white
  • colony shape: circular
  • incubation period: 2 days
  • medium used: YMA

Culture and growth conditions

culture medium

  • @ref: 69541
  • name: YMA
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
67770positivegrowth30mesophilic
69541positivegrowth15-37
69541positiveoptimum30mesophilic

culture pH

@refabilitytypepH
69541positivegrowth5.0-8.0
69541positiveoptimum7

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
69541NaClpositivegrowth2 %(w/v)
69541NaClpositiveoptimum1 %

observation

@refobservation
67770quinones: Q-10
69541Polar lipids present are DPG,PG, PE, PDE, PME, PC, three ALs, two PLs and an L.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6954116136hydrogen sulfide-assimilation
6954135581indole-assimilation
6954117634D-glucose+assimilation
6954116899D-mannitol+assimilation
6954116024D-mannose+assimilation
6954130849L-arabinose+assimilation
6954125115malate+assimilation
69541506227N-acetyl-D-glucosamine+assimilation
6954117632nitrate+assimilation
6954116004(R)-lactate+carbon source
6954116651(S)-lactate+carbon source
69541168102-oxoglutarate+carbon source
6954117925alpha-D-glucose+carbon source
695418295beta-hydroxybutyrate+carbon source
6954173706bromosuccinate+carbon source
6954117057cellobiose+carbon source
6954116383cis-aconitate+carbon source
6954116947citrate+carbon source
6954118333D-arabitol+carbon source
6954178697D-fructose 6-phosphate+carbon source
6954115895D-galactonic acid lactone+carbon source
6954112936D-galactose+carbon source
6954118024D-galacturonic acid+carbon source
6954118391D-gluconate+carbon source
6954115748D-glucuronate+carbon source
6954116899D-mannitol+carbon source
6954116024D-mannose+carbon source
6954127605D-psicose+carbon source
6954117924D-sorbitol+carbon source
6954117113erythritol+carbon source
6954115740formate+carbon source
6954128066gentiobiose+carbon source
6954117754glycerol+carbon source
6954121217L-alaninamide+carbon source
6954173786L-alanylglycine+carbon source
6954130849L-arabinose+carbon source
6954128120L-fructose+carbon source
6954115971L-histidine+carbon source
6954162345L-rhamnose+carbon source
6954117716lactose+carbon source
695416359lactulose+carbon source
6954115792malonate+carbon source
6954117306maltose+carbon source
6954128053melibiose+carbon source
69541320055methyl beta-D-glucopyranoside+carbon source
6954151850methyl pyruvate+carbon source
6954175146monomethyl succinate+carbon source
6954117268myo-inositol+carbon source
6954128037n-acetyl-D-galactosamine+carbon source
69541506227N-acetyl-D-glucosamine+carbon source
6954117272propionate+carbon source
6954126490quinate+carbon source
6954116634raffinose+carbon source
6954115963ribitol+carbon source
69541143136succinamate+carbon source
6954130031succinate+carbon source
6954117992sucrose+carbon source
6954117748thymidine+carbon source
6954127082trehalose+carbon source
6954132528turanose+carbon source
6954116704uridine+carbon source
6954127248urocanic acid+carbon source
6954117151xylitol+carbon source

enzymes

@refvalueactivityec
69541catalase+1.11.1.6
69541cytochrome oxidase+1.9.3.1
69541alkaline phosphatase+3.1.3.1
69541acid phosphatase+3.1.3.2
69541esterase (C 4)+
69541esterase Lipase (C 8)+
69541leucine arylamidase+3.4.11.1
69541trypsin+3.4.21.4
69541naphthol-AS-BI-phosphohydrolase+
69541alpha-galactosidase+3.2.1.22
69541beta-galactosidase+3.2.1.23
69541alpha-glucosidase+3.2.1.20

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    69541C14:0 3OH/C16:1 ISO I8.9
    69541C16:01.8
    69541C16:0 3OH7.5
    69541C16:1 w6c/C16:1 w7c2.5
    69541C18:0 3OH1.7
    69541C18:1 2OH5.1
    69541C18:1 w6c / C18:1 w7c64.5
    69541C19:0 cyclo w8c2.6
  • type of FA analysis: whole cell analysis
  • incubation medium: Nutrient agar
  • incubation temperature: 30
  • incubation time: 2
  • incubation pH: 7
  • software version: Sherlock 6.0
  • library/peak naming table: RTSBA6.00
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
67770Paddy soil in Taiwan
69541paddy soil in Taiwan(Paddy soil was sampled plot located at Taiwan Agricultural Research Institute Council of Agriculture, Taichung, Taiwan).TaichungTaiwanTWNAsia

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Allorhizobium terrae 16S ribosomal RNA gene, partial sequenceKU2481591468ena1848972
6954116S rRNA gene sequencePRJNA531785ena

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
67770Allorhizobium terrae CC-HIH110GCA_004801395contigncbi1848972
69541genome sequenceSSOA00000000ncbi1848972

GC content

  • @ref: 67770
  • GC-content: 55
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes82.754no
flagellatedno63.187no
gram-positiveno98.243no
anaerobicno98.389no
aerobicyes91.158no
halophileno83.028no
spore-formingno95.915no
glucose-utilyes93.283no
thermophileno97.031yes
glucose-fermentno86.956no

External links

@ref: 67770

culture collection no.: JCM 31228, BCRC 80932

literature

  • topic: Phylogeny
  • Pubmed-ID: 31626583
  • title: Allorhizobium terrae sp. nov., isolated from paddy soil, and reclassification of Rhizobium oryziradicis (Zhao et al. 2017) as Allorhizobium oryziradicis comb. nov.
  • authors: Lin SY, Hameed A, Huang HI, Young CC
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003770
  • year: 2020
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Oryza, Phospholipids/chemistry, *Phylogeny, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/*classification/isolation & purification, Rhizobium, Sequence Analysis, DNA, *Soil Microbiology, Taiwan, Ubiquinone/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/url
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69541Shih-Yao Lin, Asif Hameed, Hsin-I Huang and Chiu-Chung YoungAllorhizobium terrae sp. nov., isolated from paddy soil, and reclassification of Rhizobium oryziradicis (Zhao et al. 2017) as Allorhizobium oryziradicis comb. nov.10.1099/ijsem.0.003770