Strain identifier

BacDive ID: 140835

Type strain: Yes

Species: Haloparvum sedimenti

Strain history: H. Xiang; Inst. of Microbiol., CAS, China; DYS4.

NCBI tax ID(s): 1678448 (species)

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General

@ref: 43638

BacDive-ID: 140835

keywords: genome sequence, 16S sequence, Archaea, aerobe, chemoorganotroph, Gram-negative, pleomorphic-shaped, colony-forming

description: Haloparvum sedimenti CGMCC 1.14998 is an aerobe, chemoorganotroph, Gram-negative archaeon that forms circular colonies and was isolated from a rock salt, Jiangcheng Salt Mine.

NCBI tax id

  • NCBI tax id: 1678448
  • Matching level: species

strain history

  • @ref: 67770
  • history: H. Xiang; Inst. of Microbiol., CAS, China; DYS4.

doi: 10.13145/bacdive140835.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Haloferacales
  • family: Haloferacaceae
  • genus: Haloparvum
  • species: Haloparvum sedimenti
  • full scientific name: Haloparvum sedimenti Chen et al. 2016

@ref: 43638

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Haloferacales

family: Haloferacaceae

genus: Haloparvum

species: Haloparvum sedimenti

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43638negative0.6-0.8 µm0.3-0.4 µmpleomorphic-shapedno
69480negative99.951

colony morphology

  • @ref: 43638
  • colony size: 1 mm
  • colony color: Light-red
  • colony shape: circular
  • incubation period: 14-21 days
  • medium used: CM agar plates

Culture and growth conditions

culture medium

  • @ref: 43638
  • name: CM agar plates
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43638positivegrowth25-50
43638positiveoptimum42-45thermophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
43638positivegrowth6.5-8.5alkaliphile
43638positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43638
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 43638
  • type: chemoorganotroph

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.984

halophily

@refsaltgrowthtested relationconcentrationhalophily level
43638NaClpositivegrowth1.7-5.1 M
43638NaClpositiveoptimum3.4 Mhalophilic

observation

  • @ref: 43638
  • observation: lyse in distilled water

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4363816947citrate-carbon source
4363816899D-mannitol-carbon source
4363817754glycerol-carbon source
4363815428glycine-carbon source
4363816977L-alanine-carbon source
4363829991L-aspartate-carbon source
4363818019L-lysine-carbon source
4363817716lactose-carbon source
4363828017starch-carbon source
4363816947citrate-energy source
4363816899D-mannitol-energy source
4363817754glycerol-energy source
4363815428glycine-energy source
4363816977L-alanine-energy source
4363829991L-aspartate-energy source
4363818019L-lysine-energy source
4363817716lactose-energy source
4363828017starch-energy source
43638casein-hydrolysis
436385291gelatin-hydrolysis
4363828017starch-hydrolysis
4363853424tween 20-hydrolysis
4363853423tween 40-hydrolysis
4363853425tween 60-hydrolysis
4363853426tween 80-hydrolysis
4363815824D-fructose+carbon source
4363817634D-glucose+carbon source
4363817306maltose+carbon source
4363816024D-mannose+carbon source
4363865327D-xylose+carbon source
4363829985L-glutamate+carbon source
4363815729L-ornithine+carbon source
4363815361pyruvate+carbon source
4363817992sucrose+carbon source
4363815824D-fructose+energy source
4363817634D-glucose+energy source
4363817306maltose+energy source
4363816024D-mannose+energy source
4363865327D-xylose+energy source
4363829985L-glutamate+energy source
4363815729L-ornithine+energy source
4363815361pyruvate+energy source
4363817992sucrose+energy source
4363817632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4363828368novobiocinyesyes30 µg (disc)
4363828077rifampicinyesyes5 µg (disc)
4363828971ampicillinyesyes10 µg (disc)
4363817698chloramphenicolyesyes30 µg (disc)
43638100241ciprofloxacinyesyes5 µg (disc)
4363848923erythromycinyesyes15 µg (disc)
436386104kanamycinyesyes10 µg (disc)
436387507neomycinyesyes30 µg (disc)
43638100246norfloxacinyesyes10 µg (disc)
4363817076streptomycinyesyes10 µg (disc)
4363827902tetracyclineyesyes30 µg (disc)
4363828001vancomycinyesyes30 µg (disc)
4363828669bacitracinyesyes0.04 Unit (disc)
4363818208penicillin gyesyes10 Unit (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4363835581indoleno
4363816136hydrogen sulfideyes

enzymes

@refvalueactivityec
43638catalase+1.11.1.6
43638cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
43638a rock salt, Jiangcheng Salt MineYunnan ProvinceChinaCHNAsia22.68101.642
67770Rock salt of the Jiangcheng Salt MineYunnan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Condition#Saline
#Engineered#Other#Mine
#Environmental#Terrestrial#Geologic

Sequence information

16S sequences

@refdescriptionaccessiondatabase
4363816S rRNA (rrnA) gene, partial sequenceKP202830nuccore
4363816S rRNA (rrnB) gene, partial sequenceKP202831nuccore

Genome sequences

  • @ref: 67770
  • description: Haloparvum sedimenti DYS4
  • accession: GCA_001462205
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1678448

GC content

  • @ref: 67770
  • GC-content: 68.2
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno60no
flagellatedno96.775no
gram-positiveno97.547no
anaerobicno95.138no
aerobicyes83.201no
halophileyes91.339yes
spore-formingno95.415no
glucose-utilyes85.328no
motileno82.655yes
thermophileno83.262no
glucose-fermentno84.448no

External links

@ref: 43638

culture collection no.: CGMCC 1.14998, JCM 30891, Dys DYS4

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27001607Haloparvum sedimenti gen. nov., sp. nov., a member of the family Haloferacaceae.Chen S, Liu HC, Zhou J, Xiang HInt J Syst Evol Microbiol10.1099/ijsem.0.0010332016Base Composition, China, DNA, Archaeal/genetics, Genes, Archaeal, Glycolipids/chemistry, Halobacteriaceae/*classification/genetics/isolation & purification, Mining, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium ChlorideTranscriptome
Phylogeny27666573Haloparvum alkalitolerans sp. nov., alkali-tolerant haloarchaeon isolated from commercial salt.Kondo Y, Minegishi H, Echigo A, Shimane Y, Kamekura M, Itoh T, Ohkuma M, Tanaka A, Takahashi-Ando N, Fukushima Y, Yoshida Y, Ihara K, Usami RInt J Syst Evol Microbiol10.1099/ijsem.0.0015132016Alkalies, Base Composition, DNA, Archaeal/genetics, Genes, Archaeal, Halobacteriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Philippines, Phospholipids/chemistry, *Phylogeny, RNA Polymerase II/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Sodium ChlorideTranscriptome

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
43638Shaoxing Chen, Hong-Can Liu, Jian Zhou, Hua XiangHaloparvum sedimenti gen. nov., sp. nov., a member of the family Haloferacaceae10.1099/ijsem.0.001033IJSEM 66: 2327-2334 201627001607
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