Genetic variability in Acidithiobacillus spp. – a working horse of environmental biotechnologies

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The genus Acidithiobacillus comprises 7 species of Gram-negative obligatory acidophilic chemolithotrophic bacteria that derive energy mainly from the oxidation of reduced sulphur compounds. Four of the species also catalyse the dissimilatory oxidation of ferrous iron while three (A. thiooxidans, A. albertensis, and A. caldus) do not. Bacteria from the genus Acidithiobacillus are often associated with mineral biotechnologies (biomining) and acid mine drainage. While acceleration of mineral solubilisation is a positive aspect in environmental biotechnologies, it is undesirable in acid mine drainage with strong negative ecological impact and there is profound interest in genetics and genomics of these bacteria. Representatives of Acidithiobacillus genus occur world-wide, however there are limited data on Acidithiobacillus spp. variability from Slovakia. In our work the variability of Acidithiobacillus spp., from Slovakia was analysed and the presence of A ferrooxidans was detected. In addition, for the first time we report here on the occurrence of A. albertensis as well. Comparative analyses confirmed pronounced genetic and genomic diversity within the genus, especially within A. ferrooxidans and A. thioxidans complexes. Based on data presented, several Acidithiobacillus species could be considered as a complex species and the description of several new species is very probable in the near future.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J. Mol. Biol. 215: 403-410.

Bryant RD, McGroarty KM, Costerton JW, Laishley EJ (1983) Isolation and characterization of a new acidophilic Thiobacillus species (T. albertis). Can. J. Microbiol. 29: 1159-1170.

Cárdenas JP, Quatrini R, Holmes DS (2016) Progress in acidophile genomics. In Quatrini R, Johnson DB (Eds.), Acidophiles: life in extremely acidic environments, Caister Academic Press, UK, pp. 179-198.

Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje TM (2014). Ribosomal Database Project: data and tools for high throughput rRNA analysis Nucl. Acids Res. 42 (Database issue): D633-D642.

Dold B, Blowes DW, Dickhout R, Spangenberg JE, Pfeifer HR (2005). Low molecular weight carboxylic acids in oxidizing porphyry copper tailings. Environ. Sci. Technol. 39: 2515-2521.

Hallberg KB, González-Toril E, Johnson DB (2010) Acidithiobacillus ferrivorans sp. nov.; facultatively anaerobic, psychrotolerant iron-, and sulfur-oxidizing acidophiles isolated from metal mine-impacted environments. Extremophiles 14: 9-19.

Hedrich S, Johnson DB (2013) Acidithiobacillus ferridurans sp. nov., an acidophilic iron-, sulfur- and hydrogenmetabolizing chemolithotrophic gammaproteobacterium. Int. J. Syst. Evol. Microbiol. 63: 4018-4025.

Falagan C, Johnson DB (2016) Acidithiobacillus ferriphilus sp. nov., a facultatively anaerobic iron- and sulfurmetabolizing extreme acidophile. Int. J. Syst. Evol. Microbiol. 66: 206-211.

Figueras MJ, Beaz-Hidalgo R, Hossain MJ, Liles MR (2014) Taxonomic affiliation of new genomes should be verified using average nucleotide identity and multilocus phylogenetic analysis. Genome Announc. 2: e00927-14.

Gonzalez-Toril E, Llobet-Brossa E, Casamayor EO, Amann R, Amils R (2003) Microbial ecology of an extreme acidic environment, the Tinto River. Appl. Environ. Microbiol. 69: 4853-4865.

Jain C, Rodriguez RLM, Phillippy AM, Konstantinidis KT, Aluru S (2018) High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nature Comm. 9: Article number: 5114.

Johnson DB (2014) Biomining-biotechnologies for extracting and recovering metals from ores and waste materials. Curr. Opin. Biotechnol. 30: 24-31.

Jones DS, Schaperdoth I, Macalady JL (2016) Biogeography of sulfur-oxidizing Acidithiobacillus populations in extremely acidic cave biofilms. The ISME Journal 10: 2879-2891.

Kamimura K, Higashino E, Moriya S, Sugio T (2003). Marine acidophilic sulfur oxidizing bacterium requiring salts for the oxidation of reduced inorganic sulfur compounds. Extremophiles 7: 95-99.

Karavaiko GI, Turova TP, Kondraeva TF, Lysenko AM, Kolganova TV, Ageeva SN, Muntyan LN, Pivovarova TA (2003) Phylogenetic heterogeneity of the species Acidithiobacillus ferrooxidans. Int. J. Syst. Evol. Microbiol. 53: 113-119.

Kelly DP, Wood AP (2000) Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov. Int. J. Syst. Evol. Microbiol. 50: 511-516.

Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol. Biol. Evol. 33: 1870-1874.

Luptakova A, Prascakova M, Kotulicova I (2012) Occurrence of Acidithiobacillus Ferrooxidans bacteria in sulfide mineral deposits of Slovak Republic. Chem. Eng. Trans. 28: 31-36.

Ni YQ, He KY, Bao, JT, Yang Y, Wan DS, Li HY (2008) Genomic and phenotypic heterogeneity of Acidithiobacillus spp. strains isolated from diverse habitats in China FEMS Microbiol. Let. 64: 248-259.

Nunez H, Moya-Beltran A, Covarrubias PC, Issotta F, Cardenas JP, Gonzalez M, Atavales J, Acuna LG, Johnson DB, Quatrini R (2017) Molecular systematics of the genus Acidithiobacillus: insights into the phylogenetic structure and diversification of the taxon. Front. Microbiol. 8: 30.

Ohmura N, Sasaki K, Matsumoto N, Saiki H (2002). Anaerobic respiration using Fe3+, S0 and H2 in the chemolithotrophic bacterium Acidithiobacillus ferrooxidans. J. Bacteriol. 184: 2081-2087.

Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R (2014) The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 42 (Database issue): D206-D214.

Waksman SA, Joffe JS (1922) Thiobacillus thiooxidans, a new sulfur-oxidizing organism isolated from the soil. J. Bacteriol. 7: 239-256.

Yarza P, Yilmaz P, Pruesse, E, Glöckner FO, Ludwig W, Schleifer KH, Whitman WB, Euzeby J, Amann R, Rossello-Mora R (2014) Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat. Rev. Microbiol. 12: 635-645.

Yoon SH, Ha SM, Lim JM, Kwon SJ, Chun J (2017). A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Leeuwenhoek 110: 1281-1286.

Nova Biotechnologica et Chimica

The Journal of University of SS. Cyril and Methodius

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CiteScore 2018: 0.68

SCImago Journal Rank (SJR) 2018: 0.173
Source Normalized Impact per Paper (SNIP) 2018: 0.288


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