Thiomicrospira aerophila (DSM 13739, CBS 100465, AL3)

Name: Thiomicrospira aerophila (DSM 13739, CBS 100465, AL3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11910

Type strain

Strain Designation AL3

Culture col. no. DSM 13739 CBS 100465 AL3

NCBI tax ID(s) 92245

Special Collections DSMZ Literature strains

History DSMZ <- D. Y. Sorokin; AL3

Links

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

motile pleomorphic-shaped obligate aerobe chemolithoautotroph genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 101018

CBS 100465,DSM 13739,NCCB 95063,LMD 95.63

@ref 20215

Last LPSN update 2026-05-29 08:27:40

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 (2)

Thialkalimicrobium aerophilum
Thioalkalimicrobium aerophilum

Morphology

Cell morphology

@ref	Cell length	Cell width	Cell shape	Gram stain	Confidence
43182	0.8-1.5 µm	0.4-0.5 µm	pleomorphic-shaped
125439				negative	90.852
125438				negative	98.833

Colony morphology

@ref	Colony color	Medium used
43182	pink	Thiosulfate agar

Multimedia

@ref:	66793
multimedia content:	EM_DSM_13739_1.jpg
multimedia.multimedia content:	EM_DSM_13739_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_13739_2.jpg
multimedia.multimedia content:	EM_DSM_13739_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_13739_3.jpg
multimedia.multimedia content:	EM_DSM_13739_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_13739_4.jpg
multimedia.multimedia content:	EM_DSM_13739_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_13739_5.jpg
multimedia.multimedia content:	EM_DSM_13739_5.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5137	ALKALIPHILIC SULPHUR RESPIRING STRAINS MEDIUM (DSMZ Medium 925)		Medium recipe at MediaDive	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

@ref	Growth	Type	Temperature (°C)
5137	positive	growth	30
43182	positive	maximum	41

Culture pH

@ref	Ability	Type	PH	PH range
43182	positive	maximum	10.6
43182	positive	minimum	7.5
43182	positive	optimum	9.8-10.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43182	obligate aerobe
125439	obligate aerobe	96.406

Nutrition type

43182

Typechemolithoautotroph

Spore formation

@ref	Spore formation	Confidence
125438		91.844
125439		99.904

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43182	NaCl	positive	maximum	1.2 M

Observation

43182

Observationproduce carboxysomes

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43182	18276 ChEBI	dihydrogen	-	electron donor
43182	33403 ChEBI	elemental sulfur	+	electron donor
43182	18248 ChEBI	iron	-	electron donor
43182	18291 ChEBI	manganese	-	electron donor
43182	15138 ChEBI	sulfide	+	electron donor
43182	17359 ChEBI	sulfite	-	electron donor
43182	15226 ChEBI	tetrathionate	+	energy source
43182	15226 ChEBI	tetrathionate	+	electron donor
43182	18022 ChEBI	thiocyanate	-	electron donor
43182	16094 ChEBI	thiosulfate	+	electron donor
43182	15987 ChEBI	trithionate	+	electron donor

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43182	30411 ChEBI	cobalamin
43182	33403 ChEBI	elemental sulfur

Enzymes

@ref	Value	Activity	Ec
43182	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Condition	#Alkaline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5137	soda lake	Siberia	Russia	RUS	Asia
43182	Soda lake	Soda lake in Hadyn, Russia	Russia	RUS

Taxonmaps

69479

Global distribution of 16S sequence MT022029 (>99% sequence identity) for Thiomicrospira aerophila from Microbeatlas

Aquatic Samples	109
Soil Samples	11
Animal Samples	15
Plant Samples	8
Total Samples	143

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5137	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM22766v3 assembly for Thiomicrospira aerophila AL3	complete	GCA_000227665	717772.5	2506783063	717772	96.28

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5137	Thioalcalomicrobium aerophilum 16S ribosomal RNA, partial sequence	AF126548	1434		717772
5137	Thiomicrospira aerophila strain AL3, DSM 13739 16S ribosomal RNA gene, partial sequence	MT022029	1535		92245

GC content

@ref	GC-content (mol%)
5137	64.9
43182	45.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM22766v3 assembly for Thiomicrospira aerophila AL3
BV-BRC: 717772.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.41	no
125439	gram_stain	BacteriaNetⓘ	negative	90.85	no
125439	motility	BacteriaNetⓘ	yes	49.61	no
125439	spore_formation	BacteriaNetⓘ	no	99.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thiomicrospira aerophila AL3 AL3
NCBI: GCA_000227665.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.83	no
125438	anaerobic	anaerobicⓘ	no	87.90	no
125438	aerobic	aerobicⓘ	yes	64.14	yes
125438	spore-forming	spore-formingⓘ	no	91.84	no
125438	thermophilic	thermophileⓘ	no	91.97	yes
125438	flagellated	motile2+ⓘ	yes	75.58	no

Literature

References

#5137	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13739
#20215	Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#43182	Rich Boden, Kathleen M. Scott, John Williams, Sydney Russel, Kirsten Antonen, Alex W. Rae and Lee P. Hutt: An 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 Thiomicrospira. IJSEM 67: 1140 - 1151 2017 ( DOI 10.1099/ijsem.0.001855 , PubMed 28581925 )
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#69479	João 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 beta .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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