Thiobacillus thioparus | Type strain | DSM 505, ATCC 8158, CIP 104484, NCIMB 8370, JCM 3859, BCRC 11089, IAM 12101, IAM 12113, NBRC 103402 | BacDiveID:6145

Strain identifier

BacDive ID: 6145

Type strain:

Species: Thiobacillus thioparus

Culture col. no.: DSM 505, ATCC 8158, CIP 104484, NCIMB 8370, JCM 3859, BCRC 11089, IAM 12101, IAM 12113, NBRC 103402

Strain history: CIP <- 2013, DSMZ <- NCIB <- KR Butlin <- RL Starkey

NCBI tax ID(s): 1123393 (strain), 931 (species)

SI-ID 34928

ATCC 8158, CIP 104484, DSM 505, NCIMB 8370, NCIB 8370, JCM 3859, CCRC 11089, IAM 12113, IAM12101, CECT 5269, CECT 811, CCT 2951, BCRC 11089, NBRC 103402

Special Collections

Other strains from Thiobacillus thioparus

Section

Thiobacillus thioparus DSM 505 is a Gram-negative bacterium that was isolated from agricultural soil.

Gram-negative
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Nitrosomonadales*
	Family	*Thiobacillaceae*
	Genus	*Thiobacillus*
	Species	**Thiobacillus thioparus**
	Full Scientific Name (LPSN)	Thiobacillus thioparus Beijerinck 1904 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

[Ref.: #123527]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98

[Ref.: #123527]	Cell shape	rod-shaped

[Ref.: #123527]	Motility	yes

Incubation period

2-3 days

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

THIOBACILLUS MEDIUM (DSMZ Medium 36)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

[Ref.: #123527]

Culture medium

CIP Medium 249

[Ref.: #123527]

Culture medium growth

[Ref.: #123527]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #123527]

Culture medium

CIP Medium 124

[Ref.: #123527]

Culture medium growth

[Ref.: #123527]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #243]			growth	26 °C
[Ref.: #67770]			growth	30 °C
[Ref.: #123527]			growth	15-37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]	Ability of spore formation	no Confidence in %90.821
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

Name of produced compound

glutamate synthase

Observation

quinones: Q-8

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #123527]		esculin ChEBI	-	hydrolysis
[Ref.: #123527]		nitrate ChEBI	+	reduction
[Ref.: #123527]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #123527]		indole ChEBI	no

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #68382]		acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #123527]		alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]		alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]		alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]		alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]		alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]		alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]		alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #123527]		beta-galactosidase	+/-	3.2.1.23
[Ref.: #68382]		beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]		beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]		beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #123527]		catalase	-	1.11.1.6
[Ref.: #68382]		cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]		esterase (C 4)	+		* from API zym
[Ref.: #68382]		esterase lipase (C 8)	+		* from API zym
[Ref.: #123527]		gelatinase	-
[Ref.: #68382]		leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #68382]		lipase (C 14)	-		* from API zym
[Ref.: #123527]		lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]		N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]		naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #123527]		ornithine decarboxylase	-	4.1.1.17
[Ref.: #123527]		oxidase	+
[Ref.: #68382]		trypsin	-	3.4.21.4	* from API zym
[Ref.: #123527]		urease	-	3.5.1.5
[Ref.: #68382]		valine arylamidase	-		* from API zym
		Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #123527]	7985	-	-	+	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #243]	Sample type/isolated from	agricultural soil
[Ref.: #243]	Geographic location (country and/or sea, region)	Rutgers University, New Jersey
[Ref.: #243]	Country	USA
[Ref.: #243]	Country ISO 3 Code	USA
[Ref.: #243]	Continent	North America
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Engineered	#Agriculture	-

What are isolation sources categories?

Global distribution of 16S sequence HM173629 (>99% sequence identity) for Thiobacillus thioparus from Microbeatlas

Aquatic Samples	45
Soil Samples	14
Animal Samples	1
Plant Samples	2
Total Samples	62

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #243]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #123527]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #243]	Thiobacillus thioparus strain Starkey 16S ribosomal RNA (rrs) gene, partial sequence	HM173629	1403	GenBank ENA	931 tax ID
[Ref.: #20218]	Thiobacillus thioparus culture-collection DSM:505 16S ribosomal RNA gene, partial sequence	GU967679	1382	GenBank ENA	931 tax ID	*
[Ref.: #124043]	Thiobacillus thioparus strain NCIMB 8370 16S ribosomal RNA (rrs) gene, partial sequence.	HM173630	1403	GenBank ENA	931 tax ID	*
[Ref.: #124043]	Thiobacillus thioparus strain THI 111 16S ribosomal RNA gene, partial sequence.	HM535226	1460	GenBank ENA	931 tax ID	*
[Ref.: #20218]	Thiobacillus thioparus strain ATCC 8158 16S ribosomal RNA gene, partial sequence	M79426	1237	GenBank ENA	931 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Thiobacillus thioparus DSM 505	GCA_000373385	scaffold	GenBank ENA	1123393 tax ID
[Ref.: #66792]	Thiobacillus thioparus DSM 505	1123393.3	wgs	PATRIC	1123393 tax ID	*
[Ref.: #66792]	Thiobacillus thioparus DSM 505	2515154076	draft	JGI IMG/M	1123393 tax ID	*

[Ref.: #243]	GC-content	63.0 mol%
[Ref.: #67770]	GC-content	62 mol%	thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Thiobacillus thioparus DSM 505 DSM 505 NCBI: GCA_000373385.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Thiobacillus thioparus DSM 505 PATRIC: 1123393.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	71.781	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	90.821	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	53.542	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.16	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	82.936	no

Availability in culture collections External links

Culture collection no.

DSM 505, ATCC 8158, CIP 104484, NCIMB 8370, JCM 3859, BCRC 11089, IAM 12101, IAM 12113, NBRC 103402

SI-ID 34928

*

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Cultivation	Key internal factors leading to the variability in CO2 fixation efficiency of different sulfur-oxidizing bacteria during autotrophic cultivation.	Wang YN, Kai Y, Wang L, Tsang YF, Fu X, Hu J, Xie Y	J Environ Manage	10.1016/j.jenvman.2020.110957	2020	*
Metabolism	[Effect of Thiosulfate on the Carbon Fixation Capability of Thiobacillus thioparus and Its Mechanism].	Li H, Wang L, Wang YN	Huan Jing Ke Xue	10.13227/j.hjkx.201610043	2017	*
Cultivation	Inhibitory effect of self-generated extracellular dissolved organic carbon on carbon dioxide fixation in sulfur-oxidizing bacteria during a chemoautotrophic cultivation process and its elimination.	Wang YN, Tsang YF, Wang L, Fu X, Hu J, Li H, Le Y	Bioresour Technol	10.1016/j.biortech.2017.12.089	2017	*
Phylogeny	Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the 'Proteobacteria', and four new families within the orders Nitrosomonadales and Rhodocyclales.	Boden R, Hutt LP, Rae AW	Int J Syst Evol Microbiol	10.1099/ijsem.0.001927	2017	*
Metabolism	Response of cbb gene transcription levels of four typical sulfur-oxidizing bacteria to the CO2 concentration and its effect on their carbon fixation efficiency during sulfur oxidation.	Wang YN, Wang L, Tsang YF, Fu X, Hu J, Li H, Le Y	Enzyme Microb Technol	10.1016/j.enzmictec.2016.06.015	2016	*
Phylogeny	Phylogenetic assessment of culture collection strains of Thiobacillus thioparus, and definitive 16S rRNA gene sequences for T. thioparus, T. denitrificans, and Halothiobacillus neapolitanus.	Boden R, Cleland D, Green PN, Katayama Y, Uchino Y, Murrell JC, Kelly DP	Arch Microbiol	10.1007/s00203-011-0747-0	2011	*
	Permanent draft genome of Thiobacillus thioparus DSM 505(T), an obligately chemolithoautotrophic member of the Betaproteobacteria.	Hutt LP, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy T, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Boden R	Stand Genomic Sci	10.1186/s40793-017-0229-3	2017	*

References

#243	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 505

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68382

Automatically annotated from API zym .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#75632

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID34928.1 )

#123527 Collection of Institut Pasteur ; Curators of the CIP; CIP 104484

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

* These data were automatically processed and therefore are not curated

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