Strain identifier

BacDive ID: 132680

Type strain: Yes

Species: Serpentinicella alkaliphila

Strain Designation: 3b

Strain history: M. Quemeneur; Mediterr. Inst. of Oceanogr., France; 3b.

NCBI tax ID(s): 1734049 (species)

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General

@ref: 24469

BacDive-ID: 132680

DSM-Number: 100013

keywords: genome sequence, 16S sequence, Bacteria, obligate anaerobe, spore-forming, Gram-positive, motile, rod-shaped, colony-forming

description: Serpentinicella alkaliphila 3b is an obligate anaerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from hyperalkaline spring in a serpentinite-hosted hydrothermal field, carbonate chimney.

NCBI tax id

  • NCBI tax id: 1734049
  • Matching level: species

strain history

@refhistory
24469<- M. Quemeneur, IRD, MIO; Marseille, France; 3b <- N. Mei {2014}
67770M. Quemeneur; Mediterr. Inst. of Oceanogr., France; 3b.

doi: 10.13145/bacdive132680.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Clostridiaceae
  • genus: Serpentinicella
  • species: Serpentinicella alkaliphila
  • full scientific name: Serpentinicella alkaliphila Mei et al. 2016

@ref: 24469

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Serpentinicella

species: Serpentinicella alkaliphila

full scientific name: Serpentinicella alkaliphila Mei et al. 2016

strain designation: 3b

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25025positive1.0-10.0 µm0.4-0.6 µmrod-shapedyes
69480yes96.227
69480positive100

colony morphology

  • @ref: 25025
  • colony size: 1.0-2.0 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 7 days
  • medium used: BYG medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25025BYG mediumyes
24469SERPENTINICELLA MEDIUM (DSMZ Medium 898b)yeshttps://mediadive.dsmz.de/medium/898bName: SERPENTINICELLA MEDIUM (DSMZ Medium 898b) Composition: NaHCO3 9.98004 g/l Yeast extract 4.99002 g/l Na2CO3 2.75449 g/l Na-crotonate 1.71657 g/l Na2S2O3 x 5 H2O 1.49701 g/l NaCl 0.998004 g/l NH4Cl 0.998004 g/l Na2S x 9 H2O 0.499002 g/l KCl 0.199601 g/l KH2PO4 0.199601 g/l MgCl2 x 6 H2O 0.0998004 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l Sodium resazurin 0.000499002 g/l CoCl2 x 6 H2O 0.000189621 g/l Pyridoxine hydrochloride 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l ZnCl2 6.98603e-05 g/l Thiamine HCl 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l Folic acid 1.99601e-05 g/l Biotin 1.99601e-05 g/l H3BO3 5.98802e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
25025positivegrowth30-43
25025positiveoptimum37mesophilic
24469positivegrowth37mesophilic
67770positivegrowth35mesophilic

culture pH

@refabilitytypepHPH range
25025positivegrowth7.8-10.1alkaliphile
25025positiveoptimum9.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
25025obligate anaerobe
69480anaerobe99.714

spore formation

@refspore descriptiontype of sporespore formationconfidence
25025terminal without swollen sporangia, 0.5–0.7 µm in diametersporeyes
69481yes100
69480yes99.999

halophily

@refsaltgrowthtested relationconcentration
25025NaClpositivegrowth0-4.0 %(w/v)
25025NaCloptimum0-0.2 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2502513705acetoacetate-electron donor
2502522599arabinose-electron donor
2502529125arsenate-electron acceptor
25025casamino acids-electron donor
2502517057cellobiose-electron donor
2502535404chromate-electron acceptor
2502528262dimethyl sulfoxide-electron acceptor
2502533403elemental sulfur-electron acceptor
2502516236ethanol-electron donor
2502530729ethylenediaminetetraacetatoferrate-electron acceptor
2502531605ferric citrate-electron acceptor
2502529034ferric iron-electron acceptor
2502515740formate-electron donor
2502528757fructose-electron donor
2502529806fumarate-electron donor
2502528260galactose-electron donor
2502517234glucose-electron donor
2502517754glycerol-electron donor
2502530808iron trichloride-electron acceptor
2502517716lactose-electron donor
2502517306maltose-electron donor
2502537684mannose-electron donor
2502517632nitrate-electron acceptor
2502516301nitrite-electron acceptor
25025peptone-electron donor
2502516634raffinose-electron donor
2502526546rhamnose-electron donor
2502533942ribose-electron donor
2502518212selenite-electron acceptor
2502526710sodium chloride-required for growth
2502517992sucrose-electron donor
2502516189sulfate-electron acceptor
2502517359sulfite-electron acceptor
2502516094thiosulfate-electron acceptor
2502518222xylose-electron donor
2502535899crotonate+electron donor
2502529806fumarate+electron acceptor
2502524996lactate+electron donor
2502515361pyruvate+electron donor
25025yeast extract+required for growth

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
24469hyperalkaline spring in a serpentinite-hosted hydrothermal field, carbonate chimneyNew Caledonia, Prony Bay, Rivière des KaorisFranceFRAEurope-22.2995166.862
67770Carbonaceous hydrothermal chimney in Prony BayNew CaledoniaFrench OverseasFRA

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Hydrothermal vent
#Environmental#Aquatic#Thermal spring
#Condition#Alkaline
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_24172.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_191;96_12134;97_14712;98_18195;99_24172&stattab=map
  • Last taxonomy: Serpentinicella alkaliphila subclade
  • 16S sequence: KR349722
  • Sequence Identity:
  • Total samples: 70
  • soil counts: 9
  • aquatic counts: 55
  • animal counts: 2
  • plant counts: 4

Safety information

risk assessment

  • @ref: 24469
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24469
  • description: Serpentinicella alkaliphila strain 3b 16S ribosomal RNA gene, partial sequence
  • accession: KR349722
  • length: 1417
  • database: ena
  • NCBI tax ID: 1734049

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Serpentinicella alkaliphila 3BGCA_018141405chromosomencbi1734049
66792Serpentinicella alkaliphila strain DSM 1000131734049.3wgspatric1734049
66792Serpentinicella alkaliphila DSM 1000132795386145draftimg1734049
67770Serpentinicella alkaliphila DSM 100013GCA_004345905scaffoldncbi1734049

GC content

  • @ref: 24469
  • GC-content: 33.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedyes50.946no
gram-positiveno62.773no
anaerobicyes98.999yes
aerobicno97.787yes
halophileno87.316no
spore-formingyes95.846yes
thermophileno97.273yes
glucose-utilyes82.9no
motileyes87.25yes
glucose-fermentno68.072no

External links

@ref: 24469

culture collection no.: DSM 100013, JCM 30645

straininfo link

  • @ref: 90988
  • straininfo: 406320

literature

  • topic: Phylogeny
  • Pubmed-ID: 27499124
  • title: Serpentinicella alkaliphila gen. nov., sp. nov., a novel alkaliphilic anaerobic bacterium isolated from the serpentinite-hosted Prony hydrothermal field, New Caledonia.
  • authors: Mei N, Postec A, Erauso G, Joseph M, Pelletier B, Payri C, Ollivier B, Quemeneur M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001375
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, Bays, Clostridiales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Hydrothermal Vents/*microbiology, New Caledonia, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Transcriptome

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
24469Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100013Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100013)
25025N. P. Mei, A.,Erauso, G.,Joseph, M.,Pelletier, B.,Payri, C.,Ollivier, B.,Quéméneur, M.Serpentinicella alkaliphila gen. nov., sp. nov., a novel alkaliphilic anaerobic bacterium isolated from the serpentinite-hosted Prony hydrothermal field, New Caledonia10.1099/ijsem.0.001375IJSEM 66: 4464-4470 201627499124
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
90988Reimer, 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-ID406320.1