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Bioleaching genomics.

Siezen RJ, Wilson G - Microb Biotechnol (2009)

View Article: PubMed Central - PubMed

Affiliation: Kluyver Centre for Genomics of Industrial Fermentation, TI Food and Nutrition, 6700AN Wageningen, The Netherlands. r.siezen@cmbi.ru.nl

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Bioleaching is a natural process involving acidophilic bacteria and archaea, which have the ability to either oxidize metal sulfides or to oxidize reduced inorganic sulfur compounds (RISCs) to sulfuric acid, or both (Fig.  1, left panel)... Acid mine drainage liquors were found to contain bacteria responsible for producing iron‐rich acidic waters from coal and metal mines... These reactions take place in the extracellular polysaccharide laid down by cells growing in biofilms rather than cells in a planktonic lifestyle... Biofilm formation greatly accelerates the reactions... The role of the microbes is therefore to produce sulfuric acid for proton attack and to keep the iron in the oxidized ferric state for oxidative attack on the metal... Table 1 lists examples of acidophilic prokaryotes identified in stirred‐tank mineral bioleaching and bio‐oxidation operations... Table 2 summarizes genome sequencing projects of acidophilic microbes involved in oxidation/reduction of iron and/or RISCs, many of which were isolated from bioleaching operations... The long‐awaited, complete annotated genome sequence of the mesoacidophilic A. ferrooxidans ATCC 23270 (3.0 Mb, 58.8% GC) has only recently been published... As expected, the organism was found to have a complete repertoire of genes required for a free‐living, chemolithoautotrophic lifestyle, including CO2 fixation, nucleotide and cofactor biosynthesis... In the complete genome sequence of the extremely thermoacidophilic archaeon Metallosphaera sedula (2.2 Mb, 46% GC), genes were identified for iron and sulfur oxidation, autotrophic carbon fixation, metal tolerance and adhesion... Comparative genomics with A. ferriooxidans showed that M. sedula has different respiratory electron transport chain components, as it does not appear to contain cytochromes... A classical metagenome sequencing study of a low‐complexity, acid‐mine drainage microbial biofilm, growing within a pyrite ore body, allowed the reconstruction of near‐complete genomes of the iron oxidizers Leptospirillum group II and Ferroplasma type II... Surprisingly, Acidithiobacilli have a very large number of Fe(III)‐siderphore uptake systems, but they do not make siderophores – so in conditions of higher pH 4–5, which may occur in industrial bioleaching heaps, they may scavenge the siderophores of other organisms.

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Whole‐cell model for A. ferrooxidans ATCC 23270. Genome‐based model of the cellular metabolism, including predicted transport systems, chemolithoautotrophic components, carbon/nitrogen/sulfur metabolism, and biogeochemical cycling. Reproduced from Valdes and colleagues (2008a).
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f2: Whole‐cell model for A. ferrooxidans ATCC 23270. Genome‐based model of the cellular metabolism, including predicted transport systems, chemolithoautotrophic components, carbon/nitrogen/sulfur metabolism, and biogeochemical cycling. Reproduced from Valdes and colleagues (2008a).

Mentions: Table 2 summarizes genome sequencing projects of acidophilic microbes involved in oxidation/reduction of iron and/or RISCs, many of which were isolated from bioleaching operations. Acidithiobacillus ferrooxidans is a major member of microbial consortia used in the bioleaching industry (Table 1). It is abundant in environments associated with pyrite ore bodies, coal deposits and their acidified drainages. Acidithiobacillus ferrooxidans is a chemilitho‐autotrophic γ‐proteobacterium that acquires energy from the oxidation of iron‐ and sulfur‐containing minerals. It is capable of carbon and nitrogen fixation, and thrives at pH of 1–2. The long‐awaited, complete annotated genome sequence of the mesoacidophilic A. ferrooxidans ATCC 23270 (3.0 Mb, 58.8% GC) has only recently been published (Valdes et al., 2008a). As expected, the organism was found to have a complete repertoire of genes required for a free‐living, chemolithoautotrophic lifestyle, including CO2 fixation, nucleotide and cofactor biosynthesis. Three copies of the gene cluster for RUBISCO were identified, suggesting the ability to adapt to different levels of CO2. Electron transport from iron oxidation is through cytochromes and rusticyanin to cytochrome oxidase and NADH dehydrogenase. The organism can also grow anaerobically and the genome suggests that this is by using sulfur as the final electron acceptor. Figure 2 shows a schematic whole‐cell model of functions encoded in the A. ferrooxidans genome (Valdes et al., 2008a), and a first simple metabolic model using flux balance analysis has been reconstructed (Hold et al., 2009). Based on a high‐throughput proteomics study of periplasmic proteins, a detailed model was made of location and putative function of many of the periplasmic proteins, including those involved in iron and sulfur oxidation (Chi et al., 2007).


Bioleaching genomics.

Siezen RJ, Wilson G - Microb Biotechnol (2009)

Whole‐cell model for A. ferrooxidans ATCC 23270. Genome‐based model of the cellular metabolism, including predicted transport systems, chemolithoautotrophic components, carbon/nitrogen/sulfur metabolism, and biogeochemical cycling. Reproduced from Valdes and colleagues (2008a).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815750&req=5

f2: Whole‐cell model for A. ferrooxidans ATCC 23270. Genome‐based model of the cellular metabolism, including predicted transport systems, chemolithoautotrophic components, carbon/nitrogen/sulfur metabolism, and biogeochemical cycling. Reproduced from Valdes and colleagues (2008a).
Mentions: Table 2 summarizes genome sequencing projects of acidophilic microbes involved in oxidation/reduction of iron and/or RISCs, many of which were isolated from bioleaching operations. Acidithiobacillus ferrooxidans is a major member of microbial consortia used in the bioleaching industry (Table 1). It is abundant in environments associated with pyrite ore bodies, coal deposits and their acidified drainages. Acidithiobacillus ferrooxidans is a chemilitho‐autotrophic γ‐proteobacterium that acquires energy from the oxidation of iron‐ and sulfur‐containing minerals. It is capable of carbon and nitrogen fixation, and thrives at pH of 1–2. The long‐awaited, complete annotated genome sequence of the mesoacidophilic A. ferrooxidans ATCC 23270 (3.0 Mb, 58.8% GC) has only recently been published (Valdes et al., 2008a). As expected, the organism was found to have a complete repertoire of genes required for a free‐living, chemolithoautotrophic lifestyle, including CO2 fixation, nucleotide and cofactor biosynthesis. Three copies of the gene cluster for RUBISCO were identified, suggesting the ability to adapt to different levels of CO2. Electron transport from iron oxidation is through cytochromes and rusticyanin to cytochrome oxidase and NADH dehydrogenase. The organism can also grow anaerobically and the genome suggests that this is by using sulfur as the final electron acceptor. Figure 2 shows a schematic whole‐cell model of functions encoded in the A. ferrooxidans genome (Valdes et al., 2008a), and a first simple metabolic model using flux balance analysis has been reconstructed (Hold et al., 2009). Based on a high‐throughput proteomics study of periplasmic proteins, a detailed model was made of location and putative function of many of the periplasmic proteins, including those involved in iron and sulfur oxidation (Chi et al., 2007).

View Article: PubMed Central - PubMed

Affiliation: Kluyver Centre for Genomics of Industrial Fermentation, TI Food and Nutrition, 6700AN Wageningen, The Netherlands. r.siezen@cmbi.ru.nl

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Bioleaching is a natural process involving acidophilic bacteria and archaea, which have the ability to either oxidize metal sulfides or to oxidize reduced inorganic sulfur compounds (RISCs) to sulfuric acid, or both (Fig.  1, left panel)... Acid mine drainage liquors were found to contain bacteria responsible for producing iron‐rich acidic waters from coal and metal mines... These reactions take place in the extracellular polysaccharide laid down by cells growing in biofilms rather than cells in a planktonic lifestyle... Biofilm formation greatly accelerates the reactions... The role of the microbes is therefore to produce sulfuric acid for proton attack and to keep the iron in the oxidized ferric state for oxidative attack on the metal... Table 1 lists examples of acidophilic prokaryotes identified in stirred‐tank mineral bioleaching and bio‐oxidation operations... Table 2 summarizes genome sequencing projects of acidophilic microbes involved in oxidation/reduction of iron and/or RISCs, many of which were isolated from bioleaching operations... The long‐awaited, complete annotated genome sequence of the mesoacidophilic A. ferrooxidans ATCC 23270 (3.0 Mb, 58.8% GC) has only recently been published... As expected, the organism was found to have a complete repertoire of genes required for a free‐living, chemolithoautotrophic lifestyle, including CO2 fixation, nucleotide and cofactor biosynthesis... In the complete genome sequence of the extremely thermoacidophilic archaeon Metallosphaera sedula (2.2 Mb, 46% GC), genes were identified for iron and sulfur oxidation, autotrophic carbon fixation, metal tolerance and adhesion... Comparative genomics with A. ferriooxidans showed that M. sedula has different respiratory electron transport chain components, as it does not appear to contain cytochromes... A classical metagenome sequencing study of a low‐complexity, acid‐mine drainage microbial biofilm, growing within a pyrite ore body, allowed the reconstruction of near‐complete genomes of the iron oxidizers Leptospirillum group II and Ferroplasma type II... Surprisingly, Acidithiobacilli have a very large number of Fe(III)‐siderphore uptake systems, but they do not make siderophores – so in conditions of higher pH 4–5, which may occur in industrial bioleaching heaps, they may scavenge the siderophores of other organisms.

Show MeSH