Strain identifier

BacDive ID: 132457

Type strain: Yes

Species: Desulfurella amilsii

Strain Designation: TR1

Strain history: A. J. M. Stams; Wageningen Univ., Netherlands; TR1.

NCBI tax ID(s): 1562698 (species)

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General

@ref: 24246

BacDive-ID: 132457

DSM-Number: 29984

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

description: Desulfurella amilsii TR1 is an obligate anaerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from acidic river sediment.

NCBI tax id

  • NCBI tax id: 1562698
  • Matching level: species

strain history

@refhistory
24246<- A. P. Florentino, Univ. Wageningen; TR1 <- A. P. Florentino {2014}
67770A. J. M. Stams; Wageningen Univ., Netherlands; TR1.

doi: 10.13145/bacdive132457.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfurellales
  • family: Desulfurellaceae
  • genus: Desulfurella
  • species: Desulfurella amilsii
  • full scientific name: Desulfurella amilsii Florentino et al. 2016

@ref: 24246

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfurellales

family: Desulfurellaceae

genus: Desulfurella

species: Desulfurella amilsii

full scientific name: Desulfurella amilsii Florentino et al. 2016

strain designation: TR1

type strain: yes

Morphology

cell morphology

  • @ref: 43712
  • gram stain: negative
  • cell length: 1.5-2 µm
  • cell width: 0.5-0.7 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43712
  • colony size: 0.5-1 mm
  • colony color: Whitish
  • colony shape: circular
  • incubation period: 30 days
  • medium used: Basal medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43712Basal mediumyes
24246DESULFURELLA MEDIUM (DSMZ Medium 480)yeshttps://mediadive.dsmz.de/medium/480Name: DESULFURELLA MEDIUM (DSMZ Medium 480) Composition: Sulfur 9.98004 g/l Na-acetate 4.99002 g/l NaHCO3 2.49501 g/l Na2S x 9 H2O 0.499002 g/l CaCl2 x 2 H2O 0.329341 g/l MgCl2 x 6 H2O 0.329341 g/l KCl 0.329341 g/l KH2PO4 0.329341 g/l NH4Cl 0.329341 g/l Yeast extract 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 MnCl2 x 4 H2O 9.98004e-05 g/l Pyridoxine hydrochloride 9.98004e-05 g/l ZnCl2 6.98603e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Nicotinic acid 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
43712positivegrowth20-52
43712positiveoptimum50thermophilic
24246positivegrowth50thermophilic
67770positivegrowth50thermophilic

culture pH

@refabilitytypepHPH range
43712positivegrowth3-7acidophile
43712positiveoptimum6-6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43712
  • oxygen tolerance: obligate anaerobe

spore formation

  • @ref: 43712
  • spore formation: no

halophily

  • @ref: 43712
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 3.8 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-7(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4371216150benzoate-assimilation
4371217968butyrate-assimilation
4371227689decanoate-assimilation
4371225115malate-assimilation
4371216236ethanol-assimilation
4371229806fumarate-assimilation
4371217234glucose-assimilation
4371215428glycine-assimilation
4371245296hexadecane-assimilation
437127896hexadecanoate-assimilation
4371248944isobutyrate-assimilation
4371225017leucine-assimilation
4371225094lysine-assimilation
4371217790methanol-assimilation
43712peptone-assimilation
4371217272propionate-assimilation
4371228017starch-assimilation
4371230031succinate-assimilation
4371217992sucrose-assimilation
4371225115malate-electron donor
4371229806fumarate-electron donor
437127896hexadecanoate-electron donor
4371217272propionate-electron donor
4371217234glucose-fermentation
4371217754glycerol-fermentation
4371229034ferric iron-reduction
4371217632nitrate-reduction
4371216189sulfate-reduction
4371217359sulfite-reduction
4371233403elemental sulfur+electron acceptor
4371216094thiosulfate+electron acceptor
4371230089acetate+electron donor
4371229016arginine+electron donor
4371218276dihydrogen+electron donor
4371224996lactate+electron donor
4371215740formate+electron donor
4371215361pyruvate+fermentation
437125291gelatin+hydrolysis
43712yeast extract+required for growth

metabolite production

  • @ref: 43712
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43712catalase-1.11.1.6
43712cytochrome oxidase+/-1.9.3.1
43712urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
24246acidic river sedimentTinto River basinSpainESPEurope
43712Sediments of the Tinto RiverTinto RiverSpainESPEurope2013-03
67770Sediments of the Tinto RiverSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#Condition#Acidic
#Environmental#Aquatic#River (Creek)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_93865.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16506;96_2874;97_3533;98_28116;99_93865&stattab=map
  • Last taxonomy: Desulfurella amilsii
  • 16S sequence: LN624414
  • Sequence Identity:
  • Total samples: 46
  • soil counts: 2
  • aquatic counts: 39
  • animal counts: 5

Safety information

risk assessment

  • @ref: 24246
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24246
  • description: Desulfurella amilsii partial 16S rRNA gene, isolate TR1
  • accession: LN624414
  • length: 1528
  • database: ena
  • NCBI tax ID: 1562698

Genome sequences

  • @ref: 67770
  • description: Desulfurella amilsii TR1
  • accession: GCA_002119425
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1562698

GC content

@refGC-contentmethod
2424634sequence analysis
6777034genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno93.566yes
gram-positiveno99.137yes
anaerobicyes98.906yes
halophileno93.674no
spore-formingno91.872yes
glucose-utilno78.906yes
aerobicno98.536yes
thermophileyes100yes
glucose-fermentno89.439yes
motileyes68.455yes

External links

@ref: 24246

culture collection no.: DSM 29984, JCM 30680

straininfo link

  • @ref: 90794
  • straininfo: 400640

literature

  • topic: Phylogeny
  • Pubmed-ID: 26704766
  • title: Desulfurella amilsii sp. nov., a novel acidotolerant sulfur-respiring bacterium isolated from acidic river sediments.
  • authors: Florentino AP, Brienza C, Stams AJM, Sanchez-Andrea I
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000866
  • year: 2015
  • mesh: Acids, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deltaproteobacteria/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Spain, Sulfur, Sulfur-Reducing Bacteria/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Enzymology

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
24246Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29984Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29984)
43712Anna P. Florentino, Claudio Brienza, Alfons J. M. Stams, Irene Sánchez-AndreaDesulfurella amilsii sp. nov., a novel acidotolerant sulfur-respiring bacterium isolated from acidic river sediments10.1099/ijsem.0.000866IJSEM 66: 1249-1253 201626704766
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/
90794Reimer, 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-ID400640.1