Acidihalobacter prosperus (DSM 5130, JCM 30709, LM3)

Name: Acidihalobacter prosperus (DSM 5130, JCM 30709, LM3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6148

Type strain

Strain Designation LM3

Culture col. no. DSM 5130 JCM 30709 LM3

NCBI tax ID(s) 160660

Special Collections DSMZ JCM

History <- K. O. Stetter and H. Huber, Univ. Regensburg, Germany; LM3 {1983} DSM 5130 <-- K. O. Stetter LM3.

Links

Acidihalobacter prosperus LM3 is a bacterium that was isolated from geothermally heated sea sediment.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 47898

JCM 30709,DSM 5130

@ref 20215

Last LPSN update 2026-02-09 11:19:08

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Chromatiales

Family Ectothiorhodospiraceae

Genus Acidihalobacter

Species Acidihalobacter prosperus

Full scientific name Acidihalobacter prosperus Cárdenas et al. 2015

Synonyms (1)

"Thiobacillus prosperus"

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.494
125439	negative	95.2

Colony morphology

1930

Incubation period3-7 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1930	ACIDIHALOBACTER PROSPERUS MEDIUM (DSMZ Medium 477)		Medium recipe at MediaDive	Name: ACIDIHALOBACTER PROSPERUS MEDIUM (DSMZ Medium 477) Composition: FeSO4 x 7 H2O 19.9601 g/l MgCl2 x 6 H2O 2.74451 g/l NH4Cl 1.2475 g/l KCl 0.329341 g/l K2HPO4 0.139721 g/l KH2PO4 0.139721 g/l MgSO4 x 7 H2O 0.0299401 g/l Nitrilotriacetic acid 0.0149701 g/l NaCl 0.00998004 g/l MnSO4 x H2O 0.00499002 g/l NiCl2 x 6 H2O 0.00199601 g/l CoSO4 x 7 H2O 0.00179641 g/l ZnSO4 x 7 H2O 0.00179641 g/l CaCl2 x 2 H2O 0.000998004 g/l AlK(SO4)2 x 12 H2O 0.000199601 g/l CuSO4 x 5 H2O 9.98004e-05 g/l H3BO3 9.98004e-05 g/l Na2MoO4 x 2 H2O 9.98004e-05 g/l Na2WO4 x 2 H2O 3.99202e-06 g/l Na2SeO3 x 5 H2O 2.99401e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
1930	positive	growth	35
67770	positive	growth	35

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125438		91.185
125439		93.2

Observation

67770

Observationquinones: Q-8

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	suberin monomers biosynthesis	100	2 of 2
66794	photosynthesis	100	14 of 14
66794	formaldehyde oxidation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	methylglyoxal degradation	100	5 of 5
66794	hydrogen production	100	5 of 5
66794	glycogen metabolism	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	acetate fermentation	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	tetrahydrofolate metabolism	100	14 of 14
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	lipoate biosynthesis	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	flavin biosynthesis	93.33	14 of 15
66794	threonine metabolism	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	pentose phosphate pathway	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	purine metabolism	79.79	75 of 94
66794	heme metabolism	78.57	11 of 14
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	vitamin B1 metabolism	76.92	10 of 13
66794	CMP-KDO biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	coenzyme A metabolism	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	methionine metabolism	73.08	19 of 26
66794	proline metabolism	72.73	8 of 11
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	glutathione metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	starch degradation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	alanine metabolism	65.52	19 of 29
66794	lipid metabolism	64.52	20 of 31
66794	vitamin B6 metabolism	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	gluconeogenesis	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	leucine metabolism	61.54	8 of 13
66794	sulfate reduction	61.54	8 of 13
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	cellulose degradation	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	pyrimidine metabolism	57.78	26 of 45
66794	oxidative phosphorylation	57.14	52 of 91
66794	propanol degradation	57.14	4 of 7
66794	citric acid cycle	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	metabolism of disaccharids	54.55	6 of 11
66794	tryptophan metabolism	52.63	20 of 38
66794	lysine metabolism	52.38	22 of 42
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	glycine metabolism	50	5 of 10
66794	selenocysteine biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	Entner Doudoroff pathway	50	5 of 10
66794	tyrosine metabolism	50	7 of 14
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	polyamine pathway	47.83	11 of 23
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	degradation of sugar alcohols	43.75	7 of 16
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	propionate fermentation	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	degradation of hexoses	38.89	7 of 18
66794	carnitine metabolism	37.5	3 of 8
66794	arachidonic acid metabolism	33.33	6 of 18
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	sphingosine metabolism	33.33	2 of 6
66794	pantothenate biosynthesis	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	carotenoid biosynthesis	31.82	7 of 22
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	lactate fermentation	25	1 of 4
66794	butanoate fermentation	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	cyclohexanol degradation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	phenol degradation	25	5 of 20
66794	androgen and estrogen metabolism	25	4 of 16
66794	toluene degradation	25	1 of 4
66794	vitamin B12 metabolism	20.59	7 of 34

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
1930	geothermally heated sea sediment	Vulcano, beach of Porto di Levante	Italy	ITA	Europe
67770	Shallow geothermally heated seafloor at the beach of Porto di Levante	Vulcano	Italy	ITA	Europe

Taxonmaps

69479

Global distribution of 16S sequence AY034139 (>99% sequence identity) for Acidihalobacter prosperus from Microbeatlas

Aquatic Samples	35
Soil Samples	12
Animal Samples	2
Plant Samples	2
Total Samples	51

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1930	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
67770	ASM75409v2 assembly for Acidihalobacter prosperus DSM 5130	contig	GCA_000754095	160660.30	2648501264	160660	70.62
66792	Thiobacillus prosperus strain DSM 5130	contig		160660.4		160660	46.9

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Thiobacillus prosperus 16S ribosomal RNA gene, partial sequence	AY034139	1433		160660
1930	Thiobacillus prosperus strain DSM 5130 16S ribosomal RNA gene, partial sequence	EU653291	1461		160660

GC content

@ref	GC-content (mol%)	Method
1930	64.0
67770	64.4	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Acidihalobacter prosperus DSM 5130
NCBI: GCA_000754095

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.20	no
125439	motility	BacteriaNetⓘ	yes	76.80	no
125439	gram_stain	BacteriaNetⓘ	negative	95.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	88.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thiobacillus prosperus strain DSM 5130
PATRIC: 160660.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.49	no
125438	anaerobic	anaerobicⓘ	no	84.87	no
125438	spore-forming	spore-formingⓘ	no	91.19	no
125438	aerobic	aerobicⓘ	yes	57.83	no
125438	thermophilic	thermophileⓘ	no	92.95	yes
125438	flagellated	motile2+ⓘ	yes	75.62	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Draft Genome Sequence of the Acidophilic, Halotolerant, and Iron/Sulfur-Oxidizing Acidihalobacter prosperus DSM 14174 (Strain V6).	Khaleque HN, Ramsay JP, Murphy RJ, Kaksonen AH, Boxall NJ, Watkin EL.	Genome Announc	10.1128/genomea.01469-16	2017
	Draft Genome Sequence of Acidihalobacter ferrooxidans DSM 14175 (Strain V8), a New Iron- and Sulfur-Oxidizing, Halotolerant, Acidophilic Species.	Khaleque HN, Ramsay JP, Murphy RJT, Kaksonen AH, Boxall NJ, Watkin ELJ.	Genome Announc	10.1128/genomea.00413-17	2017
	Examining the Osmotic Response of Acidihalobacter aeolianus after Exposure to Salt Stress.	Corbett MK, Anstiss L, Gifford A, Graham RM, Watkin ELJ.	Microorganisms	10.3390/microorganisms10010022	2021
Phylogeny	Genomic Comparison, Phylogeny and Taxonomic Reevaluation of the Ectothiorhodospiraceae and Description of Halorhodospiraceae fam. nov. and Halochlorospira gen. nov.	Imhoff JF, Kyndt JA, Meyer TE.	Microorganisms	10.3390/microorganisms10020295	2022
	In a quest for engineering acidophiles for biomining applications: challenges and opportunities.	Gumulya Y, Boxall NJ, Khaleque HN, Santala V, Carlson RP, Kaksonen AH.	Genes (Basel)	10.3390/genes9020116	2018
	Prediction and Inferred Evolution of Acid Tolerance Genes in the Biotechnologically Important Acidihalobacter Genus.	Boase K, Gonzalez C, Vergara E, Neira G, Holmes D, Watkin E	Front Microbiol	10.3389/fmicb.2022.848410	2022
Metabolism	Quantitative proteomics using SWATH-MS identifies mechanisms of chloride tolerance in the halophilic acidophile Acidihalobacter prosperus DSM 14174.	Khaleque HN, Shafique R, Kaksonen AH, Boxall NJ, Watkin ELJ	Res Microbiol	10.1016/j.resmic.2018.07.002	2018
Genetics	Draft Genome Sequence of the Iron-Oxidizing, Acidophilic, and Halotolerant "Thiobacillus prosperus" Type Strain DSM 5130.	Ossandon FJ, Cardenas JP, Corbett M, Quatrini R, Holmes DS, Watkin E	Genome Announc	10.1128/genomeA.01042-14	2014
Phylogeny	Reclassification of 'Thiobacillus prosperus' Huber and Stetter 1989 as Acidihalobacter prosperus gen. nov., sp. nov., a member of the family Ectothiorhodospiraceae.	Pablo Cardenas J, Ortiz R, Norris PR, Watkin E, Holmes DS	Int J Syst Evol Microbiol	10.1099/ijsem.0.000468	2015

References

#1930	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5130
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 .
#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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Acidihalobacter prosperus (DSM 5130, JCM 30709, LM3)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000754095

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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