Comparative genomics begins to unravel the ecophysiology of bioleaching

Valdés, Jorge Hernández; Cárdenas, Juan Pablo; Quatrini, Raquel; Esparza, Mario; Osório, Héctor S.; Duarte, F.; Lefimil, Claudia; Sepulveda, R.; Jedlicki, Eugenia; Holmes, David S.

doi:10.1016/j.hydromet.2010.03.028

Cited by 35 publications

(17 citation statements)

References 26 publications

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“…Genome sequencing can be an important first step in characterizing a new organism as it provides critical genetic information required to elucidate biochemical pathways underpinning its metabolic capabilities and survival mechanisms. Several acidophiles have been sequenced and comparative genomics has shed light on their metabolic processes (Tyson et al, 2004; Levicán et al, 2008; Valdés et al, 2008, 2010; Zhou et al, 2008; Cárdenas et al, 2010, 2012; Zhang et al, 2016a,b; Tran et al, 2017). The sequencing of the genomes of the members of the Acidihalobacter genus (Ossandon et al, 2014; Khaleque et al, 2017a,b,c) has provided an opportunity to better study the mechanisms of survival used by these acidophilic, halotolerant acidophiles.…”

Section: Introductionmentioning

confidence: 99%

Uncovering the Mechanisms of Halotolerance in the Extremely Acidophilic Members of the Acidihalobacter Genus Through Comparative Genome Analysis

Khaleque

González²,

Shafique³

et al. 2019

Front. Microbiol.

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There are few naturally occurring environments where both acid and salinity stress exist together, consequently, there has been little evolutionary pressure for microorganisms to develop systems that enable them to deal with both stresses simultaneously. Members of the genus Acidihalobacter are iron- and sulfur-oxidizing, halotolerant acidophiles that have developed the ability to tolerate acid and saline stress and, therefore, have the potential to bioleach ores with brackish or saline process waters under acidic conditions. The genus consists of four members, A. prosperus DSM 5130 T , A. prosperus DSM 14174, A. prosperus F5 and “ A. ferrooxidans ” DSM 14175. An in depth genome comparison was undertaken in order to provide a more comprehensive description of the mechanisms of halotolerance used by the different members of this genus. Pangenome analysis identified 29, 3 and 9 protein families related to halotolerance in the core, dispensable and unique genomes, respectively. The genes for halotolerance showed K a /K s ratios between 0 and 0.2, confirming that they are conserved and stabilized. All the Acidihalobacter genomes contained similar genes for the synthesis and transport of ectoine, which was recently found to be the dominant osmoprotectant in A. prosperus DSM 14174 and A. prosperus DSM 5130 T . Similarities also existed in genes encoding low affinity potassium pumps, however, A. prosperus DSM 14174 was also found to contain genes encoding high affinity potassium pumps. Furthermore, only A. prosperus DSM 5130 T and “ A. ferrooxidans ” DSM 14175 contained genes allowing the uptake of taurine as an osmoprotectant. Variations were also seen in genes encoding proteins involved in the synthesis and/or transport of periplasmic glucans, sucrose, proline, and glycine betaine. This suggests that versatility exists in the Acidihalobacter genus in terms of the mechanisms they can use for halotolerance. This information is useful for developing hypotheses for the search for life on exoplanets and moons.

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Section: Introductionmentioning

confidence: 99%

Uncovering the Mechanisms of Halotolerance in the Extremely Acidophilic Members of the Acidihalobacter Genus Through Comparative Genome Analysis

Khaleque

González²,

Shafique³

et al. 2019

Front. Microbiol.

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“…For example, bioinformatics-based analyses of important biochemical pathways have been made possible by the determination of the complete genome sequence of A. nferrooxidans ATCC 23270 Holmes and Bonnefoy, 2007). In addition, 11 metabolic and regulatory models, based on comparative genomic analyses and experimental studies, have been discussed, including carbon assimilation, tricarboxylic acid (TCA) cycle, sulfur oxidation, sulfur reduction, iron oxidation, iron assimilation, quorum sensing, hydrogen oxidation, flagella formation, Che signaling (chemotaxis), and nitrogen fixation (Vald es et al, 2008a;Vald es et al, 2010). In this review, we summarize currently available knowledge regarding the metabolic diversity and adaptive mechanisms of Acidithiobacillus and Leptospirillum spp.…”

Section: Introductionmentioning

confidence: 99%

Metabolic diversity and adaptive mechanisms of iron‐ and/or sulfur‐oxidizing autotrophic acidophiles in extremely acidic environments

Zhang

Liu

Liang

et al. 2016

Environ Microbiol Rep

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Many studies have investigated the mechanisms underlying the survival and growth of certain organisms in extremely acidic environments known to be harmful to most prokaryotes and eukaryotes. Acidithiobacillus and Leptospirillum spp. are dominant bioleaching bacteria widely used in bioleaching systems, which are characterized by extremely acidic environments. To survive and grow in such settings, these acidophiles utilize shared molecular mechanisms that allow life in extreme conditions. In this review, we have summarized the results of published genomic analyses, which underscore the ability of iron- and/or sulfur-oxidizing autotrophic acidophiles belonging to the genera Acidithiobacillus and Leptospirillum to adapt to acidic environmental conditions. Several lines of evidence point at the metabolic diversity and multiplicity of pathways involved in the survival of these organisms. The ability to thrive in adverse environments requires versatile activation of structural and functional adaptive responses, including bacterial adhesion, motility, and resistance to heavy metals. We have highlighted recent developments centered on the key survival mechanisms employed by dominant extremophiles, and have laid the foundation for future studies focused on the ability of acidophiles to thrive in extremely acidic environments.

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“…A. ferrooxidans is an important microorganism in bioleaching operations due to its ability to interact directly with sulfidic ores through ferric iron (15,35). There have been some efforts to develop these cells as a platform for biofuel production (36)(37)(38)(39)(40).…”

Section: Discussionmentioning

confidence: 99%

Microbially Influenced Corrosion of Stainless Steel by Acidithiobacillus ferrooxidans Supplemented with Pyrite: Importance of Thiosulfate

Inaba

Vardner

et al. 2019

Appl Environ Microbiol

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Microbially influenced corrosion (MIC) results in significant damage to metallic materials in many industries. Anaerobic sulfate-reducing bacteria (SRB) have been well studied for their involvement in these processes. Highly corrosive environments are also found in pulp and paper processing, where chloride and thiosulfate lead to the corrosion of stainless steels. Acidithiobacillus ferrooxidans is a critically important chemolithotrophic acidophile exploited in metal biomining operations, and there is interest in using A. ferrooxidans cells for emerging processes such as electronic waste recycling. We explored conditions under which A. ferrooxidans could enable the corrosion of stainless steel. Acidic medium with iron, chloride, low sulfate, and pyrite supplementation created an environment where unstable thiosulfate was continuously generated. When combined with the chloride, acid, and iron, the thiosulfate enabled substantial corrosion of stainless steel (SS304) coupons (mass loss, 5.4 ± 1.1 mg/cm2 over 13 days), which is an order of magnitude higher than what has been reported for SRB. There results were verified in an abiotic flow reactor, and the importance of mixing was also demonstrated. Overall, these results indicate that A. ferrooxidans and related pyrite-oxidizing bacteria could produce aggressive MIC conditions in certain environmental milieus. IMPORTANCE MIC of industrial equipment, gas pipelines, and military material leads to billions of dollars in damage annually. Thus, there is a clear need to better understand MIC processes and chemistries as efforts are made to ameliorate these effects. Additionally, A. ferrooxidans is a valuable acidophile with high metal tolerance which can continuously generate ferric iron, making it critical to copper and other biomining operations as well as a potential biocatalyst for electronic waste recycling. New MIC mechanisms may expand the utility of these cells in future metal resource recovery operations.

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Comparative genomics begins to unravel the ecophysiology of bioleaching

Cited by 35 publications

References 26 publications

Uncovering the Mechanisms of Halotolerance in the Extremely Acidophilic Members of the Acidihalobacter Genus Through Comparative Genome Analysis

Uncovering the Mechanisms of Halotolerance in the Extremely Acidophilic Members of the Acidihalobacter Genus Through Comparative Genome Analysis

Metabolic diversity and adaptive mechanisms of iron‐ and/or sulfur‐oxidizing autotrophic acidophiles in extremely acidic environments

Microbially Influenced Corrosion of Stainless Steel by Acidithiobacillus ferrooxidans Supplemented with Pyrite: Importance of Thiosulfate

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