Strain identifier

BacDive ID: 11910

Type strain: Yes

Species: Thiomicrospira aerophila

Strain Designation: AL3

Strain history: <- D. Y. Sorokin; AL3

NCBI tax ID(s): 92245 (species)

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General

@ref: 5137

BacDive-ID: 11910

DSM-Number: 13739

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, chemolithoautotroph, thermophilic, motile, pleomorphic-shaped

description: Thiomicrospira aerophila AL3 is an obligate aerobe, chemolithoautotroph, thermophilic bacterium that was isolated from soda lake.

NCBI tax id

  • NCBI tax id: 92245
  • Matching level: species

strain history

  • @ref: 5137
  • history: <- D. Y. Sorokin; AL3

doi: 10.13145/bacdive11910.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Beggiatoales
  • family: Piscirickettsiaceae
  • genus: Thiomicrospira
  • species: Thiomicrospira aerophila
  • full scientific name: Thiomicrospira aerophila (Sorokin et al. 2001) Boden et al. 2017

  • synonyms

    @refsynonym
    20215Thioalkalimicrobium aerophilum
    20215Thialkalimicrobium aerophilum

@ref: 5137

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Thiotrichales

family: Piscirickettsiaceae

genus: Thiomicrospira

species: Thiomicrospira aerophila

full scientific name: Thiomicrospira aerophila (Sorokin et al. 2001) Boden et al. 2017

strain designation: AL3

type strain: yes

Morphology

cell morphology

  • @ref: 43182
  • cell length: 0.8-1.5 µm
  • cell width: 0.4-0.5 µm
  • cell shape: pleomorphic-shaped
  • motility: yes

colony morphology

  • @ref: 43182
  • colony color: pink
  • medium used: Thiosulfate agar

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_13739_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_13739_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_13739_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_13739_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_13739_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 5137
  • name: ALKALIPHILIC SULPHUR RESPIRING STRAINS MEDIUM (DSMZ Medium 925)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/925
  • composition: Name: ALKALIPHILIC SULPHUR RESPIRING STRAINS MEDIUM (DSMZ Medium 925) Composition: Na2CO3 20.0 g/l NaHCO3 10.0 g/l NaCl 5.0 g/l K2HPO4 1.0 g/l MgCl2 x 6 H2O 0.2 g/l H3BO3 0.0006 g/l CoCl2 x 6 H2O 0.0004 g/l ZnSO4 x 7 H2O 0.0002 g/l Na2MoO4 x 2 H2O 6e-05 g/l MnCl2 x 4 H2O 6e-05 g/l NiCl2 x 6 H2O 4e-05 g/l CuCl2 x 2 H2O 2e-05 g/l EDTA 1e-05 g/l FeSO4 x 7 H2O 4e-06 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43182positivemaximum41thermophilic
5137positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
43182positiveoptimum9.8-10.0alkaliphile
43182positiveminimum7.5
43182positivemaximum10.6

Physiology and metabolism

oxygen tolerance

  • @ref: 43182
  • oxygen tolerance: obligate aerobe

nutrition type

  • @ref: 43182
  • type: chemolithoautotroph

halophily

  • @ref: 43182
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 1.2 M

observation

  • @ref: 43182
  • observation: produce carboxysomes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4318215226tetrathionate+energy source
4318216094thiosulfate+electron donor
4318233403elemental sulfur+electron donor
4318215226tetrathionate+electron donor
4318215987trithionate+electron donor
4318215138sulfide+electron donor
4318218022thiocyanate-electron donor
4318217359sulfite-electron donor
4318218248iron-electron donor
4318218291manganese-electron donor
4318218276dihydrogen-electron donor

metabolite production

@refChebi-IDmetaboliteproduction
4318230411cobalaminyes
4318233403elemental sulfurno

enzymes

  • @ref: 43182
  • value: cytochrome oxidase
  • activity: +
  • ec: 1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5137soda lakeSiberiaRussiaRUSAsia
43182Soda lakeSoda lake in Hadyn, RussiaRussiaRUS

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Condition#Alkaline

taxonmaps

  • @ref: 69479
  • File name: preview.99_2516.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_118;96_1357;97_1611;98_1958;99_2516&stattab=map
  • Last taxonomy: Thiomicrospira aerophila
  • 16S sequence: MT022029
  • Sequence Identity:
  • Total samples: 143
  • soil counts: 11
  • aquatic counts: 109
  • animal counts: 15
  • plant counts: 8

Safety information

risk assessment

  • @ref: 5137
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
5137Thioalcalomicrobium aerophilum 16S ribosomal RNA, partial sequenceAF1265481434ena717772
5137Thiomicrospira aerophila strain AL3, DSM 13739 16S ribosomal RNA gene, partial sequenceMT0220291535ena92245

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thiomicrospira aerophila AL3GCA_000227665contigncbi717772
66792Thiomicrospira aerophila AL3717772.5completepatric717772

GC content

@refGC-content
513764.9
4318245.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.358yes
flagellatedyes83.212no
gram-positiveno99.149no
anaerobicno96.738yes
aerobicno75.292no
halophileno58.263no
spore-formingno96.294no
glucose-utilyes55.893no
thermophileno85.82no
glucose-fermentno86.823no

External links

@ref: 5137

culture collection no.: DSM 13739, CBS 100465

straininfo link

  • @ref: 81124
  • straininfo: 101018

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5137Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13739)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13739
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
43182Rich Boden, Kathleen M. Scott, John Williams, Sydney Russel, Kirsten Antonen, Alex W. Rae and Lee P. Hutt10.1099/ijsem.0.001855An evaluation of Thiomicrospira, Hydrogenovibrio and Thioalkalimicrobium: reclassification of four species of Thiomicrospira to each Thiomicrorhabdus gen. nov. and Hydrogenovibrio, and reclassification of all four species of Thioalkalimicrobium to ThiomicrospiraIJSEM 67: 1140-1151 201728581925
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
81124Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID101018.1StrainInfo: A central database for resolving microbial strain identifiers