Strain identifier

BacDive ID: 166099

Type strain: Yes

Species: Phytohalomonas tamaricis

Strain Designation: R4HLG17

NCBI tax ID(s): 2081032 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.1 (current version):
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 9.1 (current version)

General

@ref: 68256

BacDive-ID: 166099

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

description: Phytohalomonas tamaricis R4HLG17 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from roots of Tamarix ramosissima.

NCBI tax id

  • NCBI tax id: 2081032
  • Matching level: species

doi: 10.13145/bacdive166099.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Halomonadaceae
  • genus: Phytohalomonas
  • species: Phytohalomonas tamaricis
  • full scientific name: Phytohalomonas tamaricis Liu et al. 2020

@ref: 68256

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Phytohalomonas

species: Phytohalomonas tamaricis

strain designation: R4HLG17

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
68256negative0.9-1.5 µm0.3-0.4 µmrod-shapedno
69480negative99.986

colony morphology

  • @ref: 68256
  • colony color: yellow
  • colony shape: circular
  • medium used: ISP5 agar

Culture and growth conditions

culture temp

@refgrowthtypetemperature
68256positivegrowth16-45
68256positiveoptimum30

culture pH

@refabilitytypepHPH range
68256positivegrowth5-9alkaliphile
68256positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 68256
  • oxygen tolerance: aerobe

spore formation

  • @ref: 68256
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
68256NaClpositivegrowth0-16 %(w/v)
68256NaClpositiveoptimum5-6 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6825617632nitrate-reduction
6825628017starch-hydrolysis
68256casein-hydrolysis
682564853esculin+hydrolysis
682565291gelatin+hydrolysis
6825617634D-glucose+assimilation
6825616024D-mannose+assimilation
6825632032potassium gluconate+assimilation
6825630849L-arabinose+/-assimilation
6825617306maltose-assimilation
6825616899D-mannitol-assimilation
6825616947citrate-assimilation
6825618401phenylacetate-assimilation
6825617128adipate-assimilation
6825625115malate-assimilation
682562,3-butanediol-respiration
68256645522-hydroxybutyrate-respiration
68256167632-oxobutanoate+respiration
68256168102-oxoglutarate-respiration
68256286442-oxopentanoate-respiration
68256370543-hydroxybutyrate-respiration
68256167244-hydroxybutyrate+/-respiration
68256182404-hydroxy-L-proline+/-respiration
68256181014-hydroxyphenylacetic acid-respiration
6825616411acetic acid-respiration
6825615963ribitol-respiration
6825640585alpha-cyclodextrin-respiration
6825617925alpha-D-glucose+respiration
6825636219alpha-lactose+/-respiration
6825673706bromosuccinate-respiration
6825616383cis-aconitate+respiration
6825616947citrate+respiration
6825615570D-alanine+/-respiration
6825618333D-arabitol+respiration
6825617057cellobiose+/-respiration
6825623652dextrin+respiration
6825615824D-fructose+respiration
6825615895D-galactonic acid lactone+respiration
6825612936D-galactose+respiration
6825618024D-galacturonic acid-respiration
6825630612D-glucarate-respiration
682568391D-gluconate+/-respiration
6825617784D-glucosaminic acid-respiration
6825614314D-glucose 6-phosphate+/-respiration
6825615748D-glucuronate-respiration
6825617126DL-carnitine-respiration
6825624996lactate-respiration
6825616899D-mannitol+respiration
6825616024D-mannose+respiration
6825627605D-psicose-respiration
6825616523D-serine-respiration
6825617924D-sorbitol+respiration
6825617113erythritol-respiration
6825616000ethanolamine-respiration
6825615740formate-respiration
6825616865gamma-aminobutyric acid-respiration
6825628066gentiobiose+respiration
6825629042glucose 1-phosphate+/-respiration
6825632323glucuronamide-respiration
6825617754glycerol+/-respiration
6825614336glycerol 1-phosphate+respiration
6825628087glycogen+respiration
6825673804glycyl L-aspartic acid-respiration
6825617596inosine+respiration
6825617240itaconate-respiration
682566359lactulose+respiration
6825621217L-alaninamide-respiration
6825616977L-alanine+respiration
6825673786L-alanylglycine-respiration
6825630849L-arabinose+respiration
6825617196L-asparagine+/-respiration
6825629991L-aspartate+respiration
6825618287L-fucose-respiration
6825629988L-glutamate+respiration
6825615971L-histidine-respiration
6825615603L-leucine+respiration
6825615729L-ornithine-respiration
6825617295L-phenylalanine+respiration
6825617203L-proline+respiration
6825657606L-pyroglutamate+respiration
6825662345L-rhamnose+respiration
6825617115L-serine+/-respiration
6825616857L-threonine-respiration
6825615792malonate+respiration
6825617306maltose+respiration
6825628053melibiose-respiration
68256320055methyl beta-D-glucopyranoside-respiration
6825651850methyl pyruvate-respiration
6825675146monomethyl succinate-respiration
6825617268myo-inositol-respiration
6825628800N-acetylgalactosamine-respiration
6825659640N-acetylglucosamine+/-respiration
6825673784glycyl-l-glutamate+/-respiration
6825650048phenylethylamine-respiration
6825617272propionate+respiration
6825617148putrescine-respiration
6825626490quinate+/-respiration
6825616634raffinose+respiration
6825641865sebacic acid-respiration
68256143136succinamate-respiration
6825630031succinate+/-respiration
6825617992sucrose+respiration
6825617748thymidine+respiration
6825627082trehalose-respiration
6825632528turanose-respiration
6825653423tween 40+respiration
6825653426tween 80+respiration
6825616704uridine-respiration
6825627248urocanic acid-respiration
6825617151xylitol+respiration

metabolite production

@refChebi-IDmetaboliteproduction
6825635581indoleno
6825615688acetoinno

metabolite tests

  • @ref: 68256
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68256catalase+1.11.1.6
68256cytochrome oxidase+1.9.3.1
68256beta-galactosidase+3.2.1.23
68256urease-3.5.1.5
68256arginine dihydrolase-3.5.3.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68256C10:02.8
    68256C12:02.6
    68256C14:00.7
    68256C16:016.9
    68256C17:0 cyclo0.9
    68256C12:0 2OH0.9
    68256C12:0 3OH8.3
    68256C19:0 cyclo w8c6.4
    68256C16:1 w7c/C16:1 w6c24.6
    68256C18:1 w7c/C18:1 w6c34
  • type of FA analysis: whole cell analysis
  • incubation medium: ISP5
  • incubation temperature: 30
  • incubation time: 2
  • library/peak naming table: TSBA 6.0
  • system: MIS MIDI
  • method/protocol: Sasser, 1990

Isolation, sampling and environmental information

isolation

  • @ref: 68256
  • sample type: roots of Tamarix ramosissima
  • geographic location: Kumtag Desert, Xinjiang province
  • country: China
  • origin.country: CHN
  • continent: Asia
  • enrichment culture: nutrient agar and R2A agar
  • enrichment culture duration: 5-7 days
  • enrichment culture temperature: 30

Sequence information

16S sequences

  • @ref: 68256
  • description: Phytohalomonas tamaricis 16S ribosomal RNA gene, partial sequence
  • accession: KU973623
  • length: 1416
  • database: nuccore
  • NCBI tax ID: 1912956

Genome sequences

  • @ref: 68256
  • description: Phytohalomonas tamaricis R4HLG17
  • accession: GCA_003012345
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2081032

GC content

  • @ref: 68256
  • GC-content: 55.1
  • method: genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno99.986yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.535yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes83.267yes
69480spore-formingspore-formingAbility to form endo- or exosporesno86.85yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.98yes
69480flagellatedmotile2+Ability to perform flagellated movementno66.781yes

External links

@ref: 68256

culture collection no.: ACCC 19929, KCTC 52415

literature

  • topic: Phylogeny
  • Pubmed-ID: 31535159
  • title: Phytohalomonas tamaricis gen. nov., sp. nov., an endophytic bacterium isolated from Tamarix ramosissima roots growing in Kumtag desert.
  • authors: Liu L, Wang SY, He CF, Zhang XX, Chi M, Liang LX, Li LB
  • journal: Arch Microbiol
  • DOI: 10.1007/s00203-019-01724-x
  • year: 2019
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Desert Climate, Fatty Acids/analysis, Halomonadaceae/chemistry/*classification/genetics, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Tamaricaceae/*microbiology
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournal
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
68256Lei Liu, Shi-yan Wang, Cong-fen He, Xiao-xia Zhang, Miao Chi, Li-xiong Liang and Lu-bin LiPhytohalomonas tamaricis gen. nov., sp. nov., an endophytic bacterium isolated from Tamarix ramosissima roots growing in Kumtag desert10.1007/s00203-019-01724-xArch Microbiol 202: 143-151 2020
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