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, Gram-negative, motile, rod-shaped, colony-forming

description: Allorhizobium terrae CC-HIH110 is a Gram-negative, motile, rod-shaped 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/bacdive163970.20240916.9.1

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

@refgram stainconfidencecell lengthcell widthcell shapemotilityflagellum arrangement
69480negative97.5
69541negative1.8-2.1 µm0.7-0-9 µmrod-shapedyespolar

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

@refgrowthtypetemperature
67770positivegrowth30
69541positivegrowth15-37
69541positiveoptimum30

culture pH

@refabilitytypepH
69541positivegrowth5.0-8.0
69541positiveoptimum7

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 90.903

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).TaichungTaiwan, Province of ChinaTWNAsia

Sequence information

16S sequences

  • @ref: 67770
  • description: Allorhizobium terrae 16S ribosomal RNA gene, partial sequence
  • accession: KU248159
  • length: 1468
  • database: nuccore
  • NCBI tax ID: 1848972

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

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.5no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.716no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes81.343no
69480spore-formingspore-formingAbility to form endo- or exosporesno90.903no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.443no
69480flagellatedmotile2+Ability to perform flagellated movementyes75.495no

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/
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
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