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The use of information available in the organizations to understand what good performance looks like has been proposed for improving the decreased productivity in mine sector. Detailed monitoring has been performed at the heap bioleaching process in Minera Escondida since the start of the industrial operation in 2006. The huge industrial data recorded represents an opportunity to raise knowledge about complex bioleaching processes for improving the technology. A systematic approach using machine learning tools for the analysis of High Dimensional Feature Space is now being developed to deliver experience-based learning with the aim to serve as the foundation for optimal production planning and operational decision making, in the presence of inherent process variations. The construction of a Decision Support System (DSS) is reported, which considers a Real Time PCR array, a database for data logging and storage, the application of suitable statistical and computational tools for knowledge acquiring and finally the creation of a system of knowledge translation to transform it into action by applying recommendations that come to terms with operational limitations. The user can accurately retrieve data and design similar matches to the historic operation to get, for instance the expected metallurgical performance (such as copper recovery, acid consumption and bacterial activity) and recommendations. The process followed to construct the base of knowledge of the DSS is discussed.

Microorganisms, which play a key role during mineral dissolution in bioleaching processes, require O 2 to promote the oxidation processes of sulfide mineral dissolution and CO 2 or more complex molecules as carbon source for cell growth. Preliminary models have been proposed for relating the microbial succession in bioleaching heaps with the activity of different CO 2 fixation pathways. The increase of internal heap temperature during bioleaching improves the rate of chalcopyrite dissolution. However, it also negatively affects CO 2 and O 2 availability, consequently the microbial community changes and only the best adapted microorganisms are capable of growing under the limiting conditions. In this work we attempt to elucidate how microbiological succession proceeds in a semi-industrial bioleaching column test system, with emphasis in determining the identity of the microorganisms participating and the metabolic dynamics of carbon fixation pathways. In silico reconstruction of the carbon fixation metabolisms based on available genomes and the gene expression studies using microarray and RNA-seq were performed. The physicochemical conditions and the metallurgical parameters were also included in the analysis. Although the investigation is based on a non-homogeneous system - which leads to some seemingly contradictory data - the results showed a clear change in the structure of the microbial community as well as in the expression of pathways for CO 2 fixation, as the column test progressed. These changes were directly related to two factors, the temperature inside column and the CO 2 availability. The gene expression analyses confirmed the temporal distribution of microorganisms as a function of the temperature and the different pathways for CO 2 fixation. The evidences obtained here support the fact that low CO 2 availability becomes an important asset to the microbial population survival and growth promotion in the bioleaching environments. The determination of the expression level of the key genes is a good opportunity to improve a sound understanding of the high temperature bio-assisted heap leaching of chalcopyrite and to optimize the technology.

CLST is an extremely acidophilic gamma-proteobacteria that was isolated from the Gorbea salt flat, an acidic hypersaline environment in northern Chile. This kind of environment is considered a terrestrial analog of ancient Martian terrains and a source of new material for biotechnological applications. plays a key role in industrial bioleaching; it has the capacity of generating and maintaining acidic conditions by producing sulfuric acid and it can also remove sulfur layers from the surface of minerals, which are detrimental for their dissolution. CLST is a strain of able to tolerate moderate chloride concentrations (up to 15 g L−1 Cl−), a feature that is quite unusual in extreme acidophilic microorganisms. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 3,974,949 bp draft genome is arranged into 40 scaffolds of 389 contigs containing 3866 protein-coding genes and 75 RNAs encoding genes. This is the first draft genome of a halotolerant strain. The release of the genome sequence of this strain improves representation of these extreme acidophilic Gram negative bacteria in public databases and strengthens the framework for further investigation of the physiological diversity and ecological function of populations.

article i nfo Available online 5 October 2014 A comprehensive monitoring program has been performed at an industrial bioleaching heap at the Escondida mine in Chile since 2006, in order to study possible changes to the indigenous microbial population. In the initial stage of thebioleachingheapoperation,themicrobialpopulation wasdominatedby mesophilic microorganisms. When the height of the heap increased, the microbial population changed from predominantly mesophilic to thermotolerant and moderate thermophilic microorganisms. The results of molecular analyses indicated that under these conditions Leptospirillum ferriphilum and Sulfobacillus thermosulfidooxidans are the most abundant microorganisms. Those results obtained show that the highest ferrous iron oxidation activity at the third lift occurs at the same operational temperature window as that of the thermotolerant and moderate thermophiles. An increase in the expression of genes (including rfaF1) associated with cell envelope biogenesis was indicative of the active growth of L. ferriphilum. We conclude that the increasing heap height and the consequent increase in temperature within the heap triggered a change in the microbial community from mesophilic to moderate thermophilic microorganisms. Further, this shift had a relevant impact on the metallurgical performance of the industrial bioheap process at Escondida mine.

Acidithiobacillus ferrooxidans strain D2 was isolated from a copper bioleaching operation in Atacama Desert, Chile. Copper is widely used as cofactor in proteins but high concentrations of copper are toxic. Cells require certain mechanisms to maintain the copper homeostasis and avoid toxic effects of high intracellular concentration. The molecular response of A. ferrooxidans strain D2 grown in the presence/absence of copper was examined using a A. ferrooxidans whole-genome DNA microarrays. Roughly 23% of 3,147 genes represented on the microarray were differentially expressed; about 9% of them were upregulated in the presence of copper. Among the upregulated genes, those encoding for the copper efflux protein (CusA) and for the copper-translocating P-type ATPase (CopA) were upregulated. The expression of genes encoding proteins related to iron transport was repressed. Similarly, genes related with assimilative metabolism of sulfur (L-cysteine biosynthesis) cysB, cysJ, cysI, CysD-2 and cysN were upregulated. Our results show that when A. ferrooxidans strain D2 was challenged with high copper concentrations, genes related to copper stress response were upregulated as well as others that have not been reported to be related to that mechanism. In addition, some genes related to other metabolic pathways were repressed, probably because of the energy cost of the stress response.

The industrial run of mine (ROM) bioleaching heap of Escondida mine is monitored monthly from Pregnant Leach Solution (PLS) to assess concentration of microorganisms, microbial activity and physicochemical parameters generating a huge amount of information. To obtain a better description of the iron microbial activity and the dissolution rate of sulfide ores occurring in the leaching cycle, iterative process based on “Knowledge Discovery in Databases” (KDD) was used. A data mining technique, called “hierarchical clustering”, was employed with mineralogical characteristics of the ores loaded in the heap as input. Three different groups of strips were distinguished by this model. Chalcocite and chalcopyrite contents were the most relevant parameters selected by “decision tree” technique. The results showed that there was a good coincidence between the three groups defined and the metallurgical performance in terms of copper recovery. Moreover, another decision tree analysis was performed including the three mineralogical groups, the gathered data about physicochemical parameters and the microbial community composition and function from the PLS. The PLS temperature and the MPN were the most relevant factors selected to explain the differences between the operation of the defined groups of strips. The group with the lowest chalcocite and highest chalcopyrite content, reached the highest PLS temperature and the highest MPN of ferrous iron oxidizing microorganisms and also the fastest kinetics of copper recovery. The estimated temperature inside the heap following conservatively the available models for heaps loaded with agglomerated material, together with the sustainable occurrence of a moderate thermophile population and the confirmation of some chalcopyrite dissolution by analysis of tail allowed us to account the chalcopyrite as a microbial substrate in that industrial scale operation. Those results confirmed the relationship between the microbial community function and the copper release and the hypothesis that the substrate availability is an important parameter to describe the microbial activity. Nevertheless, the model is not yet able to explain the low bacterial growth in the group with the highest chalcocite content that is considered a good microbial substrate. Then it is needed to perform another cycle of the KDD process to complete the model. This kind of information should be considered in defining models to describe and to predict copper recovery in ROM industrial bioleaching processes.

Indexación: Web of Science; PubMed Leptospirillum ferriphilum Sp-Cl is a Gram negative, thermotolerant, curved, rod- shaped bacterium, isolated from an industrial bioleaching operation in northern Chile, where chalcocite is the major copper mineral and copper hydroxychloride atacamite is present in variable proportions in the ore. This strain has unique features as compared to the other members of the species, namely resistance to elevated concentrations of chloride, sulfate and metals. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 2,475,669 bp draft genome is arranged into 74 scaffolds of 74 contigs. A total of 48 RNA genes and 2,834 protein coding genes were predicted from its annotation; 55 % of these were assigned a putative function. Release of the genome sequence of this strain will provide further understanding of the mechanisms used by acidophilic bacteria to endure high osmotic stress and high chloride levels and of the role of chloride-tolerant iron-oxidizers in industrial bioleaching operations. https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0142-1

During the past few decades the microbial bioleaching of metallic sulphide ores has become a very important process utilized by the mining industry. The biodiversity studies of industrial systems have revealed the occurrence of acidophilic microorganisms, forming dynamic communities that include bacteria and archaea. A combination of molecular and cultivation-based approaches has been used during the leaching cycle to understand the key microorganisms present and their function in the Escondida. Sulphide Leach Plant. The global genomic expression in solution samples has been analyzed by random arbitrary primed polymerase chain reaction (RAP-PCR), to pinpoint those microorganisms with active metabolism in the communities present in regions of the heap leach operation of different ages. Four random primers were used and one hundred and twenty RAP-PCR products were cloned, sequenced and compared to databases using the BLAST search algorithm. Approximately 48% of the RAP-PCR products were 16S and 23S rRNA genes, and many of these results are consistent with community analysis carried out on the same heap using 16S rRNA gene libraries and real-time PCR. Interestingly, different microorganisms to those previously detected by 16S rRNA PCR-DGGE, represented by sequences distantly related to the archaea Picrophilus torridus, and Thermoplasma acidophilum sequences, were detected using RNA analysis. Eight different RAP-PCR products shared similarity with functional genes, and sequence analysis revealed the expression of genes associated with transcription (RNA polymerase) and translation (elongation factor and ribosomal protein) components, metabolic function (2-methylisocitrate synthase and pyruvate dehydrogenase), and electron transport (cytochrome). Other genes such as mercuric reductase and ABC transporter ATP-binding proteins were also detected. However, 30% of RAP-PCR products showed no similarity with any sequences currently in the database. This report represents the first transcriptomic study of the microbial community inhabiting an industrial bioleaching system. The data suggest that the functional spectrum of expressed genes was consistent with genomic and proteomic reports from pure cultures and environmental AMD samples containing microorganisms involved in bioleaching processes. Both studies revealed the expression of genes mainly related to energetic metabolisms and stress responses. (C) 2008 Published by Elsevier B.V.

Microbial heap bioleaching is being used as an industrial process to recover copper from low grade ores. It is known that a consortium of different microorganisms participates in this process. Therefore identification and quantification of communities inhabiting heap bioleaching operations is a key step for understanding the dynamics and role of these microorganisms in the process. A quantitative real-time PCR approach was used to investigate the microbial dynamics in this process. To study the microbial population inhabiting a low-grade copper sulphide ore bioleaching industrial heap process at Escondida Mine in Chile, 16S rRNA genetic libraries were constructed using bacterial and archaeal universal primers. Phylogenetic analyses of sequences retrieved from genetic libraries showed that the community is mainly composed by microoganisms related to Acidithiobacillus ferrooxidans (2 strains), Acidithiobacillus thiooxidans, Leptospirillum ferrooxidans, Leptospirillum ferriphilum and the archaea Ferroplasma. Specific primers for real-time PCR determination were designed and tested to amplify each of the sequences obtained by cloning. Standard curves for real time PCR were performed using plasmid DNA from selected clones. This methodology is actually being used to monitor relevant microorganisms inhabiting this low-grade copper sulphide ore bioleaching industrial heap.

A comprehensive monitoring program by culturing and molecular techniques, physicochemical analysis plus the record of the operational conditions have been performed at an industrial bioleaching process for run-of-mine (ROM) material at Escondida mine since 2006. The data collected have been systematized in a data base to allow further analysis for advancing the understanding of commercial bioheap applications. The microbial succession during a heap bioleaching cycle has been formerly described by means of the analysis of the data obtained from the first lift of the industrial process. Data visualization techniques were used to analyze the information and to find patterns in the data. When only the first and second floor of the heap was operative, the mesophile population, Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans, was predominant in the microbial community. After the start of the third lift operation, a relevant change in the abundance of the moderate thermophile population was evident. Leptospirillum ferriphilum (optimum temperature 35-39°C) and Sulfobacillus thermosulfidooxidans (optimum temperature 45-50°C) became the most abundant microorganism. In addition, the specific iron oxidation activity showed by the moderate thermophilic dominated community is higher than the mesophilic dominated one. A patched distribution of Sulfolobus allowed us to infer the temporal occurrence of small niches with temperature over 50°C inside the heap. The temperature turned out to be a key factor driving the dynamic of the microbial community mainly after the start of the third lift. That shift had a relevant impact on the metallurgical performance of the industrial process.

13 pages, 5 figures, 3 tables, Athalassohaline lakes are inland saline aquatic environments with ionic proportions quite different from the dissolved salts in seawater. Prokaryotes inhabiting athalassohaline environments are poorly known and very few of such places have been surveyed for microbial diversity studies around the world. We analyzed the planktonic bacterial and archaeal assemblages inhabiting several of these evaporitic basins in a remote and vast area in northern Chile by PCR-denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rRNA gene fragments. Most systems were springs and athalassohaline ponds in different saltflats of the Atacama Desert region, including Salar de Llamará (in the Central Depression), Salar de Atacama (in the Pre-Andean Depression) and Salar de Ascotán (in the Altiplano). Overall, we analyzed more than 25 samples from 19 different environments with strong gradients of altitude, qualitative ionic compositions and UV influence. Between 4 and 25 well-defined DGGE bands were detected for Bacteria in each sample, whereas Archaea ranged between 1 and 5. Predominant DGGE bands (defined by intensity and frequency of appearance) were excised from the gel and sequenced. Bacterial assemblages were dominated by the Cytophaga-Flavobacterium- Bacteroides (CFB) phylum and a few Proteobacteria. There was a tendency for increasing contribution of CFB with higher salinities and altitude. Thus, CFB accounted for the major fraction of band intensity in the Ascotán samples and for lower percentages in Atacama and Llamará. When the distribution of particular CFB sequences was examined, there were several relatives of Psychroflexus torquis substituting each other as salinity changed in Ascotán. Another set of CFB sequences, very distantly related to Cytophaga marinovorus, was abundant in both Llamará and Atacama at salinities lower than 7%. Archaeal assemblages were dominated by uncultured haloarchaea distantly related to cultured strains mostly obtained from thalassohaline environments. Most of the archaeal sequences did not have a close match with environmental 16S rRNA genes deposited in the database either. Therefore, athalassohaline environments are excellent sources of new microorganisms different from their counterparts in thalassohaline sites and useful tools to relate microbial genetic diversity and environmental characteristics such as changes in salinity (both qualitative and quantitative) and altitude. © 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved, Sampling and measurements carried out in Chile were funded by projects FONDEF D97F1078 and D99I1026. Measurements carried out in Barcelona were funded by project MicroDIFF (REN2001-2120/MAR) from the Spanish Ministerio de Ciencia y Tecnología. Exchange agreements between Chilean CONICYT (#1999 2 02 136) and the Generalitat de Catalunya (ACI99-27) and CSIC (2001CL0020) provided funds for travels between Spain and Chile. [...] EOC was supported by the Programa Ramón y Cajal from the Spanish Ministerio de Ciencia y Tecnología

In order to explore new options to optimize the low-grade copper ore bioleaching process, it is important to understand the kinetics of microbial oxidation at industrial level. This work studies the changes of iron and sulfur oxidation rates of microbial communities in solution from an industrial low grade copper bioleaching heap process at Escondida Mine in Chile. Pregnant leach solution (PLS) samples were analyzed periodically to determine physico-chemical parameters. The total numbers of the different microorganism species in industrial samples were determined by Real Time PCR. In addition, Most Probable Number assays (MPN) were performed for iron and sulfur oxidizing microorganisms. Kinetics incubation tests of PLS in the presence of iron or sulfur were performed to study the iron and sulfur oxidation, in total, 102 oxidation profile tests were obtained. Based on the oxidation profiles obtained, the tests were divided into four groups, labeled as fast, normal, stepped shape, and incomplete. The grouping system was established by considering oxidation time and rates, during the initial oxidation stages and accounted for any lag phase. A data mining technique, called decision trees was used to analyze the data and to generate rules that represented patterns in the data. Strong correlations were found between the predominant microorganisms and the behavior of the oxidation tests. Preliminary results indicate that the magnitude order of MPN of the iron oxidizing microorganisms is an important factor in the microbial oxidizing activity, followed by the predominant specie within the microbial population, PLS temperature and Eh.

14.1 IntroductionA series of astrobiological high-altitude expeditions to the South AmericanAndean Mountains were initiated in 2002 to explore the highest perenniallakes on Earth, including several volcanic crater lakes at or above 6000 min elevation. During the next five years, they will provide the first integratedlong-term astrobiological characterization and monitoring of lacustrineenvironments and their biology at such an altitude. These extreme lakesare natural laboratories that provide the field data, currently missingabove 4000 m, to complete our understanding of terrestrial lakes and biota.Research is being performed on the effects of UV in low-altitude lakesand models of UV flux over time have been developed (Cockell, 2000). Thelakes showing a high content of dissolved organic material (DOM) shieldorganisms from UV effects (McKenzie et al., 1999; Rae et al., 2000). DOMacts as a natural sunscreen by influencing water transparency, and thereforeis a determinant of photic zone depth (Reche et al., 2000). In sparselyvegetated alpine areas, lakes tend to be clearer and offer less protectionfrom UV to organisms living in the water. Transparent water, combinedwith high UV irradiance may maximize the penetration and effect of UVradiation as shown for organisms in alpine lakes (e.g., Vincent et al., 1984;Vinebrook and Leavitt, 1996). Shallow-water benthic communities in theselakes are particularly sensitive to UV radiation. Periphyton, which definescommunities of microorganisms in bodies of water, can live on varioussusbtrates. While on rocks, they include immobile species that cannot seeklow UV refuges unlike sediment-dwelling periphyton (Happey-Wood, 1988;Vincent et al., 1993) or alpine phytoflagellates (Rott, 1988) which bothundergo vertical migration. Inhibition of algal photosynthesis by UV radia-tion has been documented in the laboratory (Ha ¬der, 1993) and it has beenshown that phytoplankton production is reduced by formation of nucleic acidlesions (Karentz et al., 1991) or production of peroxides and free oxygenradicals (Cooper et al., 1989). Most of the experiments that have demon-strated in situ suppression of algal growth by UV radiation have eitherused artificially enhanced UV irradiance (Worrest et al., 1978) or shallowsystems (

Se estudiaron las comunidades estratificadas de microorganismos fotosintéticos que se encuentran en el Salar de Llamará ubicado en el desierto de Atacama, norte de Chile, mediante métodos microscópicos y espectrofotométricos. El espesor de la zona fótica de los tapetes descritos varió entre 8 y 30 mm lo cual podría atribuirse a la granulometría y la composición mineralógica de los sedimentos. Se diferencian tres tipos de tapetes. El primero con una única capa pigmentada de color verde; el segundo con capas de colores verde y naranja y un tercero en el que se observa, además de las capas verde y naranja, una de color púrpura. En uno de los sitios muestreados no se encontraron capas pigmentadas. Debajo de la zona pigmentada el sedimento es de color blanco, excepto en uno de los sectores donde se observó una coloración negra atribuible a sulfuro de hierro. Los microorganismos predominantes de la capa naranja fueron diatomeas y cianobacterias unicelulares principalmente de los grupos Cyanothece y Synechococcus. Las cianobacterias filamentosas Microccoleus sp. y Oscillatoria sp. fueron las más abundantes en la capa verde. No se observaron diatomeas en los sitios estudiados donde la salinidad del agua intersticial osciló entre 12 y 33 %. En la capa verde de estos sitios predominaron las cianobacterias cocoides, de los grupos Synechococcus, Cyanothece y Gloeocapsa y del género Gloeobacter, sobre las cianobacterias filamentosas. La capa púrpura estuvo compuesta principalmente por bacterias fototróficas anoxigénicas similares a células de los géneros Chromatium y Thiocapsa. Los espectros de absorción revelaron que la clorofila a es el pigmento más abundante en la mayoría de las muestras analizadas. Los valores integrados de clorofila a y bacterioclorofila a alcanzaron 230 y 144 mg m-2 en el espesor de la zona pigmentada, respectivamente. También se detectaron abundantes microorganismos no fotosintéticos en los tapetes incluyendo cocos y bacilos no identificados. En todos los tapetes muestreados en el Salar se encontraron bacterias reductoras de sulfato.