Strain identifier

BacDive ID: 158437

Type strain: Yes

Species: Kyrpidia spormannii

Strain Designation: EA-1

Strain history: <- J. Gescher, Karlsruher Institut für Technologie, Germany; EA-1 <- J.E. Reiner

NCBI tax ID(s): 2055160 (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 8.1 (current version)

General

@ref: 65113

BacDive-ID: 158437

DSM-Number: 106492

keywords: genome sequence, Bacteria, aerobe, spore-forming, thermophilic, Gram-positive, rod-shaped

description: Kyrpidia spormannii EA-1 is an aerobe, spore-forming, thermophilic bacterium that was isolated from sediment from hydrothermal systems.

NCBI tax id

  • NCBI tax id: 2055160
  • Matching level: species

strain history

  • @ref: 65113
  • history: <- J. Gescher, Karlsruher Institut für Technologie, Germany; EA-1 <- J.E. Reiner

doi: 10.13145/bacdive158437.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Alicyclobacillaceae
  • genus: Kyrpidia
  • species: Kyrpidia spormannii
  • full scientific name: Kyrpidia spormannii Reiner et al. 2018

@ref: 65113

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Alicyclobacillaceae

genus: Kyrpidia

species: Kyrpidia spormannii

full scientific name: Kyrpidia spormannii Reiner et al. 2018

strain designation: EA-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
66748positive4-8 µm0.7-1.2 µmrod-shapedno
69480positive100

colony morphology

  • @ref: 66748
  • colony color: pale cream
  • incubation period: 2-5 days
  • medium used: Reasoner's 2A agar (R2A)

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
65113R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
66748Lysogeny broth mediumno
66748Reasoner's 2A agar (R2A)yes

culture temp

@refgrowthtypetemperaturerangeconfidence
65113positivegrowth55thermophilic
66748nogrowth37mesophilic
66748positiveoptimum55thermophilic
66748nogrowth70thermophilic
66748positivegrowth45-65thermophilic
69480thermophilic100

culture pH

@refabilitytypepH
66748positiveoptimum5.5
66748nogrowth<4.5
66748nogrowth>7
66748positivegrowth4.5-7

Physiology and metabolism

oxygen tolerance

  • @ref: 66748
  • oxygen tolerance: aerobe

spore formation

@reftype of sporespore formationconfidence
66748endosporeyes
69480yes98.315
69481yes100

halophily

@refsaltgrowthtested relationconcentration
66748NaClpositivegrowth0-1 %(w/v)
66748NaClnogrowth1.5 %(w/v)

observation

@refobservation
66748The strain is capable of autotrophic growth with carbon dioxide as the sole carbon source using hydrogen as electron donor and oxygen as the terminal electron acceptor.
66748Nile red stains intracellular granules.
66748Neither nitrate, DMSO, sulfate nor fumarate serves as electron acceptor under anaerobic growth conditions.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6674812936D-galactose+carbon source
6674813705acetoacetate+carbon source
6674815361pyruvate+carbon source
6674815570D-alanine+carbon source
6674815824D-fructose+carbon source
6674816024D-mannose+carbon source
6674816411acetic acid+carbon source
6674816526carbon dioxide+carbon source
6674816988D-ribose+carbon source
6674817634D-glucose+carbon source
6674818024D-galacturonic acid+carbon source
6674818287L-fucose+carbon source
6674827605D-psicose+carbon source
6674830031succinate+carbon source
6674830796(R)-malic acid+carbon source
6674830797(S)-malic acid+carbon source
6674830849L-arabinose+carbon source
6674832323glucuronamide+carbon source
6674862320L-lyxose+carbon source
6674862345L-rhamnose+carbon source
6674865327D-xylose+carbon source
6674875146monomethyl succinate+carbon source
66748168102-oxoglutarate+carbon source
6674815379dioxygen+electron acceptor
6674818276dihydrogen+electron donor
6674817234glucose-fermentation
6674822653asparagine+nitrogen source
6674831206ammonium chloride+nitrogen source

enzymes

  • @ref: 66748
  • value: cytochrome oxidase
  • activity: +
  • ec: 1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
65113sediment from hydrothermal systemsAzores, Sao MiguelPortugalPRTEurope
66748hydrothermal sediment samplesSao Miguel Island, AzoresPortugalPRTEurope37.7733-25.3036R2A agarpH 62-5 days60Sediment samples of hydrothermal systems served as inoculum. The working electrode potential was set to 594 mV versus saturated calomel electrode and the ES medium (pH 3.5; 10 mM NH4Cl, 2.5 mM NaCl, 0.3 mM KH2PO4, 0.12 mM MgSO4, 0.1 mM CaCl2, 1 ml l-1 Wolfe's mineral elixir) was constantly sparged with a gas mix consisting of 80 % N2 and 20 % CO2 (v/v). The final enrichment was performed at 60°C under autotrophic conditions in ES medium with 0.25 cm^2 of the cathodic graphite felt as inoculum. The gas phase consisted of 20 % CO2, 75 % H2 and 5 % O2 (v/v/v). After serial dilutions in ES medium, single colonies were obtained by plating the culture on Reasoner's 2A agar at 60°C and 2-5 days.

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Hydrothermal vent
#Environmental#Aquatic#Sediment

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kyrpidia spormannii EA-1GCA_002804065completencbi2055160
66792Kyrpidia spormannii EA-12775506848completeimg2055160

GC content

@refGC-contentmethod
6511358.7
6674858.7genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno84.24yes
gram-positiveyes61.852no
anaerobicno92.112yes
halophileno97.532yes
spore-formingyes90.398no
glucose-utilyes80.973no
aerobicyes79.385yes
thermophileyes99.998no
motileyes76.372yes
glucose-fermentno91.821yes

External links

@ref: 65113

culture collection no.: DSM 106492, CCOS 1194

straininfo link

  • @ref: 111238
  • straininfo: 397149

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny30234478Kyrpidia spormannii sp. nov., a thermophilic, hydrogen-oxidizing, facultative autotroph, isolated from hydrothermal systems at Sao Miguel Island, and emended description of the genus Kyrpidia.Reiner JE, Jung T, Lapp CJ, Siedler M, Bunk B, Overmann J, Gescher JInt J Syst Evol Microbiol10.1099/ijsem.0.0030372018Azores, Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Hydrothermal Vents/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
33396703Improving the Cathodic Biofilm Growth Capabilities of Kyrpidia spormannii EA-1 by Undirected Mutagenesis.Jung T, Hackbarth M, Horn H, Gescher JMicroorganisms10.3390/microorganisms90100772020

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
65113Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-106492Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 106492)
66748Johannes Eberhard Reiner, Tobias Jung, Christian Jonas Lapp, Marvin Siedler, Boyke Bunk, Jörg Overmann, Johannes GescherKyrpidia spormannii sp. nov., a thermophilic, hydrogen-oxidizing, facultative autotroph, isolated from hydrothermal systems at Sao Miguel Island, and emended description of the genus Kyrpidia10.1099/ijsem.0.003037IJSEM 68: 3735-3740 201830234478
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
111238Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID397149.1