Roberto A. Bobadilla-Fazzini

A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment.

Acidithiobacillus thiooxidans is a sulfur oxidizing acidophilic bacterium found in many sulfur-rich environments. It is particularly interesting due to its role in bioleaching of sulphide minerals. In this work, we report the genome sequence of At. thiooxidans Licanantay, the first strain from a copper mine to be sequenced and currently used in bioleaching industrial processes. Through comparative genomic analysis with two other At. thiooxidans non-metal mining strains (ATCC 19377 and A01) we determined that these strains share a large core genome of 2109 coding sequences and a high average nucleotide identity over 98%. Nevertheless, the presence of 841 strain-specific genes (absent in other At. thiooxidans strains) suggests a particular adaptation of Licanantay to its specific biomining environment. Among this group, we highlight genes encoding for proteins involved in heavy metal tolerance, mineral cell attachment and cysteine biosynthesis. Several of these genes were located near genetic motility genes (e.g. transposases and integrases) in genomic regions of over 10 kbp absent in the other strains, suggesting the presence of genomic islands in the Licanantay genome probably produced by horizontal gene transfer in mining environments.

Draft Genome Sequence of the Sulfobacillus thermosulfidooxidans Cutipay Strain, an Indigenous Bacterium Isolated from a Naturally Extreme Mining Environment in Northern Chile

Sulfobacillus thermosulfidooxidans strain Cutipay is a mixotrophic, acidophilic, moderately thermophilic bacterium isolated from mining environments of the north of Chile, making it an interesting subject for studying the bioleaching of copper. We introduce the draft genome sequence and annotation of this strain, which provide insights into its mechanisms for heavy metal resistance.

The bioleaching potential of a bacterial consortium

This work presents the molecular foundation of a consortium of five efficient bacteria strains isolated from copper mines currently used in state of the art industrial-scale biotechnology. The strains Acidithiobacillus thiooxidans Licanantay, Acidiphilium multivorum Yenapatur, Leptospirillum ferriphilum Pañiwe, Acidithiobacillus ferrooxidans Wenelen and Sulfobacillus thermosulfidooxidans Cutipay were selected for genome sequencing based on metal tolerance, oxidation activity and bioleaching of copper efficiency. An integrated model of metabolic pathways representing the bioleaching capability of this consortium was generated. Results revealed that greater efficiency in copper recovery may be explained by the higher functional potential of L. ferriphilum Pañiwe and At. thiooxidans Licanantay to oxidize iron and reduced inorganic sulfur compounds. The consortium had a greater capacity to resist copper, arsenic and chloride ion compared to previously described biomining strains. Specialization and particular components in these bacteria provided the consortium a greater ability to bioleach copper sulfide ores.

Global transcriptional responses of Acidithiobacillus ferrooxidans Wenelen under different sulfide minerals

In order to provide new information about the adaptation of Acidithiobacillus ferrooxidans during the bioleaching process, the current analysis presents the first report of the global transcriptional response of the native copper mine strain Wenelen (DSM 16786) oxidized under different sulfide minerals. Microarrays were used to measure the response of At. ferrooxidans Wenelen to shifts from iron supplemented liquid cultures (reference state) to the addition of solid substrates enriched in pyrite or chalcopyrite. Genes encoding for energy metabolism showed a similar transcriptional profile for the two sulfide minerals. Interestingly, four operons related to sulfur metabolism were over-expressed during growth on a reduced sulfur source. Genes associated with metal tolerance (RND and ATPases type P) were up-regulated in the presence of pyrite or chalcopyrite. These results suggest that At. ferrooxidans Wenelen presents an efficient transcriptional system developed to respond to environmental conditions, namely the ability to withstand high copper concentrations.

Sulfobacillus thermosulfidooxidans strain Cutipay enhances chalcopyrite bioleaching under moderate thermophilic conditions in the presence of chloride ion

Currently more than 90% of the world’s copper is obtained through sulfide mineral processing. Among the copper sulfides, chalcopyrite is the most abundant and therefore economically relevant. However, primary copper sulfide bioleaching is restricted due to high ionic strength raffinate solutions and particularly chloride coming from the dissolution of ores. In this work we describe the chalcopyrite bioleaching capacity of Sulfobacillus thermosulfidooxidans strain Cutipay (DSM 27601) previously described at the genomic level (Travisany et al. (2012) Draft genome sequence of the Sulfobacillus thermosulfidooxidans Cutipay strain, an indigenous bacterium isolated from a naturally extreme mining environment in Northern Chile. J Bacteriol 194:6327–6328). Bioleaching assays with the mixotrophic strain Cutipay showed a strong increase in copper recovery from chalcopyrite concentrate at 50°C in the presence of chloride ion, a relevant inhibitory element present in copper bioleaching processes. Compared to the abiotic control and a test with Sulfobacillus acidophilus DSM 10332, strain Cutipay showed an increase of 42 and 69% in copper recovery, respectively, demonstrating its high potential for chalcopyrite bioleaching. Moreover, a genomic comparison highlights the presence of the 2-Haloacid dehalogenase predicted-protein related to a potential new mechanism of chloride resistance in acidophiles. This novel and industrially applicable strain is under patent application CL 2013–03335.

Biomass Production and Inoculation of Industrial Bioleaching Processes

Microbial activity inleaching processes accounts for 4% of today’s copper produced in the world. Factorsrelated with lesser overall metal recoveries, no recovery of precious metalsand molybdenum in comparison with conventional concentration/smelting &refining technologies and the high prices of metals inhibit the use of bioleachingat a larger scale. In order to increase bioleaching rates and overall metal recoveries,continuous inoculation of the ore with a leaching solution containing specific adaptedconsortium of microorganisms, allows an early expression of microbial activity,reducing 2-3 fold the time required by ore native bearing microflora to grow.This leaching solution concentrated in microorganisms can be produced by meansof bioreactors operated in continuous regime. Unfortunately biomining microorganisms have a very low duplication timewhen comparing to common microbes like E.colior B. subtilis, that forces the useof huge volume bioreactors in the case of conventional bioreactors, to ensurethe growth of microorganisms have sufficient residence time. To overcome thisproblem, we have designed a very efficient air-lift bioreactor (Patent Registration No. CL 48319), that can be used at industrial operations for the production ofsolutions with a high concentration of biomining microorganisms, for theinoculation of bioleaching heaps, with lesser residence time in comparison toconventional bioreactors. Ourbioreactor has an internal recirculation for producing sulfide-ore bioleachingsolutions, with a phase-separating and solids-recirculation system, without theneed to impel the suspension containing the solids towards the bioreactor withpumps, using diatomaceous earth, ferric precipitates and/or elemental sulfur asa solid support to immobilize iron and/or sulfur-oxidizing microorganisms. Dependingon the source of energy supplied for the growth of the microorganisms, thebioreactor can produce either a solution concentrated in ferric ions andiron-oxidizing bacteria or sulfur oxidizing bacteria. In order to validate ourbioreactor design at industrial scale, a trial was carried out in an air-liftbioreactor of 35 m3 nominal capacity, which is part of a biomassplant located in Radomiro Tomic Division of CODELCO. In this article, theresults of the test proving the advantages and satisfactory design of ourbioreactor for producing continuously iron-oxidizing bacteria and sulfuroxidizing bacteria for inoculation and irrigation of heaps and dumps are shown.