Strain identifier

BacDive ID: 4151

Type strain: Yes

Species: Megalodesulfovibrio paquesii

Strain Designation: SB1

Strain history: A. J. M. Stams SB1.

NCBI tax ID(s): 299072 (species)

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General

@ref: 6562

BacDive-ID: 4151

DSM-Number: 16681

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, vibrio-shaped

description: Megalodesulfovibrio paquesii SB1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from sulfidogenic sludge of a full-scale synthesis-gas-fed bioreactor treating wastewater from a zinc smelter.

NCBI tax id

  • NCBI tax id: 299072
  • Matching level: species

strain history

@refhistory
6562<- BHGW van Houten, Wageningen University, Laboratory of Microbiology, Netherlands; SB1 <- BHGW van Houten {2001}
67770A. J. M. Stams SB1.

doi: 10.13145/bacdive4151.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfovibrionales
  • family: Desulfovibrionaceae
  • genus: Megalodesulfovibrio
  • species: Megalodesulfovibrio paquesii
  • full scientific name: Megalodesulfovibrio paquesii (van Houten et al. 2009) Waite et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Desulfovibrio paquesii

@ref: 6562

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfovibrionales

family: Desulfovibrionaceae

genus: Megalodesulfovibrio

species: Megalodesulfovibrio paquesii

full scientific name: Megalodesulfovibrio paquesii (van Houten et al. 2009) Waite et al. 2020

strain designation: SB1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
23213negative5.0-8.0 µm1.0 µmvibrio-shaped
23213spiral-shapedyes
28922negative5.5 µm3.75 µmspiral-shapedyes

pigmentation

  • @ref: 28922
  • production: no

Culture and growth conditions

culture medium

  • @ref: 6562
  • name: DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/63
  • composition: Name: DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63) Composition: MgSO4 x 7 H2O 2.0 g/l Na-DL-lactate 2.0 g/l NH4Cl 1.0 g/l Yeast extract 1.0 g/l Na2SO4 1.0 g/l FeSO4 x 7 H2O 0.5 g/l K2HPO4 0.5 g/l CaCl2 x 2 H2O 0.1 g/l Na-thioglycolate 0.1 g/l Ascorbic acid 0.1 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6562positivegrowth37mesophilic
23213positivegrowth10-45
28922positivegrowth04-40
28922positiveoptimum25mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
23213positivegrowth6.5-8.5alkaliphile
28922positivegrowth3.5-9.5acidophile
28922positiveoptimum5.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6562anaerobe
23213anaerobe
28922aerobe

halophily

@refsaltgrowthtested relationconcentration
28922NaClpositivegrowth0.3-10 %
28922NaClpositiveoptimum3 %

observation

  • @ref: 28922
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2321317632nitrate-electron acceptor
2321330089acetate-electron donor
2321317968butyrate-electron donor
2321315354choline-electron donor
2321315356cysteine-electron donor
2321317790methanol-electron donor
2321317272propionate-electron donor
2321315354choline-fermentation
2321325115malate-fermentation
2321316236ethanol+electron donor
2321315740formate+electron donor
2321329806fumarate+electron donor
2321317754glycerol+electron donor
2321324996lactate+electron donor
2321325115malate+electron donor
2321315361pyruvate+electron donor
2321330031succinate+electron donor
2321316189sulfate+reduction
2321317359sulfite+reduction
2321316094thiosulfate+reduction
28922370543-hydroxybutyrate+carbon source
2892230089acetate+carbon source
2892221217L-alaninamide+carbon source
2892216449alanine+carbon source
2892222653asparagine+carbon source
2892235391aspartate+carbon source
2892217234glucose+carbon source
2892217754glycerol+carbon source
2892228087glycogen+carbon source
2892227570histidine+carbon source
28922182404-hydroxy-L-proline+carbon source
2892217596inosine+carbon source
2892224996lactate+carbon source
2892225017leucine+carbon source
2892226271proline+carbon source
2892217822serine+carbon source
2892230031succinate+carbon source
2892226986threonine+carbon source
2892216704uridine+carbon source
2892227248urocanic acid+carbon source
2892217632nitrate+reduction

enzymes

@refvalueactivityec
28922acid phosphatase+3.1.3.2
28922alkaline phosphatase+3.1.3.1
28922catalase+1.11.1.6
28922cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6562sulfidogenic sludge of a full-scale synthesis-gas-fed bioreactor treating wastewater from a zinc smelterBudeldorpleinNetherlandsNLDEurope
23213sulfidogenic synthesis-gas-fed bioreactor used for remediation of wastewater from a zinc smelter
67770Sulfidogenic synthesis-gas-fed bioreactor for remediation of wastewater from a zinc smelter in Budel-DorpleinNetherlandsNLDEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Engineered#Bioremediation
#Engineered#Waste#Wastewater
#Condition#Sulfuric

taxonmaps

  • @ref: 69479
  • File name: preview.99_68533.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17519;96_78;97_37249;98_48245;99_68533&stattab=map
  • Last taxonomy: Desulfovibrio paquesii subclade
  • 16S sequence: DQ447183
  • Sequence Identity:
  • Total samples: 910
  • soil counts: 100
  • aquatic counts: 706
  • animal counts: 67
  • plant counts: 37

Safety information

risk assessment

  • @ref: 6562
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6562
  • description: Desulfovibrio paquesii strain SB1 16S ribosomal RNA gene, partial sequence
  • accession: DQ447183
  • length: 1509
  • database: ena
  • NCBI tax ID: 299072

Genome sequences

  • @ref: 66792
  • description: Desulfovibrio paquesii DSM 16681
  • accession: 2571042346
  • assembly level: draft
  • database: img
  • NCBI tax ID: 1121460

GC content

@refGC-contentmethod
656262.2high performance liquid chromatography (HPLC)
2321362.2
2892251.1

External links

@ref: 6562

culture collection no.: DSM 16681, JCM 14635

straininfo link

  • @ref: 73652
  • straininfo: 402065

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19196759Desulfovibrio paquesii sp. nov., a hydrogenotrophic sulfate-reducing bacterium isolated from a synthesis-gas-fed bioreactor treating zinc- and sulfate-rich wastewater.van Houten BH, Meulepas RJ, van Doesburg W, Smidt H, Muyzer G, Stams AJInt J Syst Evol Microbiol10.1099/ijs.0.65616-02009Bioreactors/*microbiology, Desulfovibrio/*classification/genetics/growth & development/isolation & purification, Gases/metabolism, Hydrogen/*metabolism, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Sulfates/*metabolism, Water Purification, Zinc/metabolismMetabolism
Metabolism33199799Bacteria coated cathodes as an in-situ hydrogen evolving platform for microbial electrosynthesis.Perona-Vico E, Feliu-Paradeda L, Puig S, Baneras LSci Rep10.1038/s41598-020-76694-y2020Bacteria/genetics/*growth & development/metabolism, Bacterial Physiological Phenomena, Bioelectric Energy Sources/*microbiology, Biofilms, Biosensing Techniques/instrumentation, Electrochemical Techniques, Hydrogen/*analysis, RNA, Ribosomal, 16S/genetics, Stress, PhysiologicalPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6562Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16681)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16681
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
23213Bernd H. G. W. van Houten, Roel J. W. Meulepas, Wim van Doesburg, Hauke Smidt, Gerard Muyzer, Alfons J. M. Stams10.1099/ijs.0.65616-0Desulfovibrio paquesii sp. nov., a hydrogenotrophic sulfate-reducing bacterium isolated from a synthesis-gas-fed bioreactor treating zinc- and sulfate-rich wastewaterIJSEM 59: 229-233 200919196759
28922Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125361
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
73652Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402065.1StrainInfo: A central database for resolving microbial strain identifiers