Acidithiobacillus ferridurans (DSM 29468, ATCC 33020, JCM 18981)

Name: Acidithiobacillus ferridurans (DSM 29468, ATCC 33020, JCM 18981)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130138

Type strain

Strain Designation 11Fe

Culture col. no. DSM 29468 ATCC 33020 JCM 18981 11Fe

NCBI tax ID(s) 1232575

Special Collections DSMZ JCM Literature strains

Links

Acidithiobacillus ferridurans 11Fe is a facultative anaerobe, mesophilic, Gram-negative prokaryote that was isolated from ore, uranium mine.

Gram-negative rod-shaped facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 40282

ATCC 33020,CECT 830,CCRC 13823,BCRC 13823,JCM 18981,DSM 29468

@ref 20215

Last LPSN update 2025-12-16 10:00:55

Domain Pseudomonadati

Phylum Pseudomonadota

Class Acidithiobacillia

Order Acidithiobacillales

Family Acidithiobacillaceae

Genus Acidithiobacillus

Species Acidithiobacillus ferridurans

Full scientific name Acidithiobacillus ferridurans Hedrich and Johnson 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
31013	negative	1.5 µm	1.5 µm	rod-shaped
125439	negative
125438	negative

Colony morphology

21446

Incubation period3-7 days

Pigmentation

31013

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21446	LEPTOSPIRILLUM (HH) MEDIUM (DSMZ Medium 882)		Medium recipe at MediaDive	Name: LEPTOSPIRILLUM (HH) MEDIUM (DSMZ Medium 882) Composition: FeSO4 x 7 H2O 19.98 g/l CaCl2 x 2 H2O 0.146853 g/l (NH4)2SO4 0.131868 g/l MgCl2 x 6 H2O 0.0529471 g/l KH2PO4 0.0269731 g/l MnCl2 x 4 H2O 7.59241e-05 g/l ZnCl2 6.79321e-05 g/l CuCl2 x 2 H2O 6.69331e-05 g/l CoCl2 x 6 H2O 6.39361e-05 g/l H3BO3 3.0969e-05 g/l Na2MoO4 9.99001e-06 g/l H2SO4 Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
21446	positive	growth	30	mesophilic
31013	positive	optimum	29	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
31013	positive	optimum	2.1	acidophile

Physiology and metabolism

Oxygen tolerance

31013

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation
31013
125439
125438

Observation

67770

Observationquinones: Q-8

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Environmental	#Terrestrial	#Geologic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
21446	ore, uranium mine	Okayama prefecture, Ningyo-toge mine	Japan	JPN	Asia
67770	Ore from Ningyo-toge mine	Okayama	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence FN686779 (>99% sequence identity) for Acidithiobacillus from Microbeatlas

Aquatic Samples	68
Soil Samples	4
Animal Samples	1
Plant Samples
Total Samples	73

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21446	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM396665v1 assembly for Acidithiobacillus ferridurans JCM 18981	complete	GCA_003966655	1232575.7	2824077352	1232575	95.67
66792	AFD33020_v8 assembly for Acidithiobacillus ferridurans ATCC 33020	complete	GCA_018854555	1232575.20		1232575	92.83

Genome browser: GCA_003966655

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
31013	Acidithiobacillus ferrooxidans partial 16S rRNA gene, strain ATCC33020	FN686779	1407	1232575
21446	Acidithiobacillus ferrooxidans 16S partial 16S rRNA gene, strain ATCC33020	AJ278719	1408	1232575
124043	Acidithiobacillus ferridurans gene, 16S-23S rDNA region, strain: ATCC 33020.	AB189136	441	1232575
124043	Acidithiobacillus ferrooxidans 16S rRNA gene (partial), 23S rRNA gene and internal transcribed spacer 1 (ITS1), strain ATCC33020	AJ278724	634	1232575
124043	Acidithiobacillus ferridurans strain ATCC 33020 arsenate reductase (arsC), ArsR-like protein, arsenical membrane pump (arsB), ArsH-like protein, signal recognition particle protein-like protein, 30S ribosomal protein S16-like protein, and 16S ribosomal RNA processing protein RIMM-like protein genes, complete cds and unknown genes.	AF173880	6835	1232575
124043	Acidithiobacillus ferridurans strain ATCC 33020 16S ribosomal RNA gene, partial sequence.	MN746438	1102	1232575

GC content

@ref	GC-content (mol%)
31013	58
21446	58

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Acidithiobacillus ferridurans strain JCM 18981
PATRIC: 1232575.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	70.30	no
125439	gram_stain	BacteriaNetⓘ	negative	96.00	no
125439	motility	BacteriaNetⓘ	yes	77.00	no
125439	spore_formation	BacteriaNetⓘ	no	97.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acidithiobacillus ferridurans JCM 18981
NCBI: GCA_003966655.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.05	yes
125438	anaerobic	anaerobicⓘ	no	78.17	yes
125438	aerobic	aerobicⓘ	no	53.35	yes
125438	spore-forming	spore-formingⓘ	no	91.21	yes
125438	thermophilic	thermophileⓘ	no	93.31	yes
125438	flagellated	motile2+ⓘ	no	70.13	no

Literature

Title	Authors	Journal	DOI	Year
Electrochemical and structural characterization of recombinant respiratory proteins of the acidophilic iron oxidizer Ferrovum sp. PN-J47-F6 suggests adaptations to the acidic pH at protein level.	Ullrich SR, Fuchs H, Ashworth-Guth C.	Front Microbiol	10.3389/fmicb.2024.1357152	2024
Diffusible signal factor signaling controls bioleaching activity and niche protection in the acidophilic, mineral-oxidizing leptospirilli.	Bellenberg S, Salas B, Ganji S, Jorquera-Roman C, Valenzuela ML, Buetti-Dinh A, Unelius CR, Dopson M, Vera M.	Sci Rep	10.1038/s41598-021-95324-9	2021
Molecular Systematics of the Genus Acidithiobacillus: Insights into the Phylogenetic Structure and Diversification of the Taxon.	Nunez H, Moya-Beltran A, Covarrubias PC, Issotta F, Cardenas JP, Gonzalez M, Atavales J, Acuna LG, Johnson DB, Quatrini R.	Front Microbiol	10.3389/fmicb.2017.00030	2017
Proteomic Insights into the Adaptation of Acidithiobacillus ferridurans to Municipal Solid Waste Incineration Residues for Enhanced Bioleaching Efficiency.	Kucera J, Kremser K, Bouchal P, Potesil D, Vaculovic T, Vsiansky D, Guebitz GM, Mandl M.	J Proteome Res	10.1021/acs.jproteome.4c00527	2025
Genetic Engineering of Acidithiobacillus ferridurans Using CRISPR Systems To Mitigate Toxic Release in Biomining.	Chen J, Liu Y, Mahadevan R.	Environ Sci Technol	10.1021/acs.est.3c02492	2023
Complete Genome Sequence of Acidithiobacillus ferridurans JAGS, Isolated from Acidic Mine Drainage.	Chen J, Liu Y, Diep P, Jo A, Nesbo C, Edwards E, Papangelakis V, Mahadevan R.	Microbiol Resour Announc	10.1128/mra.00033-20	2020
Pangenome-level analysis of nucleoid-associated proteins in the Acidithiobacillia class: insights into their functional roles in mobile genetic elements biology.	Beard S, Moya-Beltran A, Silva-Garcia D, Valenzuela C, Perez-Acle T, Loyola A, Quatrini R.	Front Microbiol	10.3389/fmicb.2023.1271138	2023
A single-plasmid-based, easily curable CRISPR/Cas9 system for rapid, iterative genome editing in Pseudomonas putida KT2440.	Wen Q, Chen J, Li J, Dharmasiddhi IPW, Yang M, Xing J, Liu Y.	Microb Cell Fact	10.1186/s12934-024-02634-4	2024
Harnessing synthetic biology for sustainable biomining with Fe/S-oxidizing microbes.	Chen J, Liu Y, Diep P, Mahadevan R.	Front Bioeng Biotechnol	10.3389/fbioe.2022.920639	2022
Insights into Adaptive Mechanisms of Extreme Acidophiles Based on Quorum Sensing/Quenching-Related Proteins.	Huang S, Liu X, Yang W, Ma L, Li H, Liu R, Qiu J, Li Y.	mSystems	10.1128/msystems.01491-21	2022
Salt Stress-Induced Loss of Iron Oxidoreduction Activities and Reacquisition of That Phenotype Depend on rus Operon Transcription in Acidithiobacillus ferridurans.	Bonnefoy V, Grail BM, Johnson DB.	Appl Environ Microbiol	10.1128/aem.02795-17	2018
Comparative Genomic Analysis Reveals the Distribution, Organization, and Evolution of Metal Resistance Genes in the Genus Acidithiobacillus.	Li L, Liu Z, Meng D, Liu X, Li X, Zhang M, Tao J, Gu Y, Zhong S, Yin H.	Appl Environ Microbiol	10.1128/aem.02153-18	2019
Insights into the pathways of iron- and sulfur-oxidation, and biofilm formation from the chemolithotrophic acidophile Acidithiobacillus ferrivorans CF27.	Talla E, Hedrich S, Mangenot S, Ji B, Johnson DB, Barbe V, Bonnefoy V.	Res Microbiol	10.1016/j.resmic.2014.08.002	2014
Mining of novel secondary metabolite biosynthetic gene clusters from acid mine drainage.	Wang L, Liu W, Liang J, Zhao L, Li Q, Zhou C, Cen H, Weng Q, Zhang G.	Sci Data	10.1038/s41597-022-01866-6	2022
Insights into Systems for Iron-Sulfur Cluster Biosynthesis in Acidophilic Microorganisms.	Myriam P, Braulio P, Javiera RA, Claudia MV, Omar O, Renato C, Gloria L.	J Microbiol Biotechnol	10.4014/jmb.2206.06045	2022
Molecular Identification and Acid Stress Response of an Acidithiobacillus thiooxidans Strain Isolated from Rio Tinto (Spain).	Ibanez A, Barreiro C, Diez-Galan A, Cobos R, Calvo-Pena C, Coque JJR.	Int J Mol Sci	10.3390/ijms241713391	2023
Genome sequencing and metabolic network reconstruction of a novel sulfur-oxidizing bacterium Acidithiobacillus Ameehan.	Wu P, Yuan Q, Cheng T, Han Y, Zhao W, Liao X, Wang L, Cai J, He Q, Guo Y, Zhang X, Lu F, Wang J, Ma H, Huang Z.	Front Microbiol	10.3389/fmicb.2023.1277847	2023
Bioleaching of Transition Metals From Limonitic Laterite Deposits and Reassessment of the Multiple Roles of Sulfur-Oxidizing Acidophiles in the Process.	Johnson DB, Smith SL, Santos AL.	Front Microbiol	10.3389/fmicb.2021.703177	2021
From Genes to Bioleaching: Unraveling Sulfur Metabolism in Acidithiobacillus Genus.	Ibanez A, Garrido-Chamorro S, Coque JJR, Barreiro C.	Genes (Basel)	10.3390/genes14091772	2023
Growth of Leptospirillum ferriphilum in sulfur medium in co-culture with Acidithiobacillus caldus.	Smith SL, Johnson DB.	Extremophiles	10.1007/s00792-018-1001-3	2018
Sulfur Oxidation in the Acidophilic Autotrophic Acidithiobacillus spp.	Wang R, Lin JQ, Liu XM, Pang X, Zhang CJ, Yang CL, Gao XY, Lin CM, Li YQ, Li Y, Lin JQ, Chen LX.	Front Microbiol	10.3389/fmicb.2018.03290	2018
Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions.	Moya-Beltran A, Beard S, Rojas-Villalobos C, Issotta F, Gallardo Y, Ulloa R, Giaveno A, Degli Esposti M, Johnson DB, Quatrini R.	ISME J	10.1038/s41396-021-00995-x	2021
Phylogeny, Divergent Evolution, and Speciation of Sulfur-Oxidizing Acidithiobacillus Populations.	Zhang X, Liu X, Li L, Wei G, Zhang D, Liang Y, Miao B.	BMC Genomics	10.1186/s12864-019-5827-6	2019
In Silico Genome-Wide Analysis Reveals the Potential Links Between Core Genome of Acidithiobacillus thiooxidans and Its Autotrophic Lifestyle.	Zhang X, Liu Z, Wei G, Yang F, Liu X.	Front Microbiol	10.3389/fmicb.2018.01255	2018
Complete Genome Sequence of Acidithiobacillus ferridurans JCM 18981.	Miyauchi T, Kouzuma A, Abe T, Watanabe K	Microbiol Resour Announc	10.1128/MRA.01028-18	2018
Acidithiobacillus ferridurans sp. nov., an acidophilic iron-, sulfur- and hydrogen-metabolizing chemolithotrophic gammaproteobacterium.	Hedrich S, Johnson DB	Int J Syst Evol Microbiol	10.1099/ijs.0.049759-0	2013

References

#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 )
#21446	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29468
#31013	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27343 (see below)
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Acidithiobacillus ferridurans (DSM 29468, ATCC 33020, JCM 18981)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003966655

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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