Structural and Functional Insights from the Metagenome of an Acidic Hot Spring Microbial Planktonic Community in the Colombian Andes

A taxonomic and annotated functional description of microbial life was deduced from 53 Mb of metagenomic sequence retrieved from a planktonic fraction of the Neotropical high Andean (3,973 meters above sea level) acidic hot spring El Coquito (EC). A classification of unassembled metagenomic reads using different databases showed a high proportion of Gammaproteobacteria and Alphaproteobacteria (in total read affiliation), and through taxonomic affiliation of 16S rRNA gene fragments we observed the presence of Proteobacteria, micro-algae chloroplast and Firmicutes. Reads mapped against the genomes Acidiphilium cryptum JF-5, Legionella pneumophila str. Corby and Acidithiobacillus caldus revealed the presence of transposase-like sequences, potentially involved in horizontal gene transfer. Functional annotation and hierarchical comparison with different datasets obtained by pyrosequencing in different ecosystems showed that the microbial community also contained extensive DNA repair systems, possibly to cope with ultraviolet radiation at such high altitudes. Analysis of genes involved in the nitrogen cycle indicated the presence of dissimilatory nitrate reduction to N2 (narGHI, nirS, norBCDQ and nosZ), associated with Proteobacteria-like sequences. Genes involved in the sulfur cycle (cysDN, cysNC and aprA) indicated adenylsulfate and sulfite production that were affiliated to several bacterial species. In summary, metagenomic sequence data provided insight regarding the structure and possible functions of this hot spring microbial community, describing some groups potentially involved in the nitrogen and sulfur cycling in this environment. Citation: Jimenez DJ, Andreote FD, Chaves D, Montana JS, Osorio-Forero C, et al. (2012) Structural and Functional Insights from the Metagenome of an Acidic Hot Spring Microbial Planktonic Community in the Colombian Andes. PLoS ONE 7(12): e52069. doi:10.1371/journal.pone.0052069

A primer for use of genetic tools in selecting and testing the suitability of set-aside sites protected from deep-sea seafloor massive sulfide mining activities

Seafloor massive sulfide (SMS) mining will likely occur at hydrothermal systems in the near future. Alongside their mineral wealth, SMS deposits also have considerable biological value. Active SMS deposits host endemic hydrothermal vent communities, whilst inactive deposits support communities of deep water corals and other suspension feeders. Mining activities are expected to remove all large organisms and suitable habitat in the immediate area, making vent endemic organisms particularly at risk from habitat loss and localised extinction. As part of environmental management strategies designed to mitigate the effects of mining, areas of seabed need to be protected to preserve biodiversity that is lost at the mine site and to preserve communities that support connectivity among populations of vent animals in the surrounding region. These "set-aside" areas need to be biologically similar to the mine site and be suitably connected, mostly by transport of larvae, to neighbouring sites to ensure exchange of genetic material among remaining populations. Establishing suitable set-asides can be a formidable task for environmental managers, however the application of genetic approaches can aid set-aside identification, suitability assessment and monitoring. There are many genetic tools available, including analysis of mitochondrial DNA (mtDNA) sequences (e.g. COI or other suitable mtDNA genes) and appropriate nuclear DNA markers (e.g. microsatellites, single nucleotide polymorphisms), environmental DNA (eDNA) techniques and microbial metagenomics. When used in concert with traditional biological survey techniques, these tools can help to identify species, assess the genetic connectivity among populations and assess the diversity of communities. How these techniques can be applied to set-aside decision making is discussed and recommendations are made for the genetic characteristics of set-aside sites. A checklist for environmental regulators forms a guide to aid decision making on the suitability of set-aside design and assessment using genetic tools. This non-technical primer document represents the views of participants in the VentBase 2014 workshop.

Bio-synthesis of nanosized semiconductors using mine wastes as material sources

This work describes the synthesis of nanosized metal sulfides and respective SiO2 and/or TiO2 composites in high yield via a straightforward process, under ambient conditions (temperature and pressure), by adding to aqueous metals a nutrient solution containing biologically generated sulfide from sulfate-reducing bacteria (SRB). The nanoparticles‘ (NPs) morphological properties were shown not to be markedly altered by the SRB growth media composition neither by the presence of bacterial cells. We further extended the work carried out, using the effluent of a bioremediation system previously established. The process results in the synthesis of added value products obtained from metal rich effluents, such as Acid Mine Drainage (AMD), when associated with the bioremediation process. Precipitation of metals using sulfide allows for the possibility of selective recovery, as different metal sulfides possess different solubilities. We have evaluated the selective precipitation of CuS, ZnS and FeS as nanosized metal sulfides. Again, we have also tested the precipitation of these metal sulfides in the presence of support structures, such as SiO2. Studies were carried out using both artificial and real solutions in a continuous bioremediation system. We found that this method allowed for a highly selective precipitation of copper and a lower selectivity in the precipitation of zinc and iron, though all metals were efficiently removed (>93% removal). This research has also demonstrated the potential of ZnS-TiO2 nanocomposites as catalysts in the photodegradation of organic pollutants using the cationic dye, Safranin-T, as a model contaminant. The influence of the catalyst amount, initial pH and dye concentration were also evaluated. Finally, the efficiency of the precipitates as catalysts in sunlight mediated photodegradation was investigated, using different volumes of dye-contaminated water (150 mL and 10 L). This work demonstrates that all tested composites have the potential to be used as photocatalysts for the degradation of Safranin-T.

The release of zinc and lead from mine tailings

Mining and processing of metal ores are important causes of soil and groundwater contamination in many regions worldwide. Metal contaminations are a serious risk for the environment and human health. The assessment of metal contaminations in the soil is therefore an important task. A common approach to assess the environmental risk emanating from inorganic contaminations to soil and groundwater is the use of batch or column leaching tests. In this regard, the suitability of leaching tests is a controversial issue. In the first part of this work the applicability and comparability of common leaching tests in the scope of groundwater risk assessment of inorganic contamination is reviewed and critically discussed. Soil water sampling methods (the suction cup method and centrifugation) are addressed as an alternative to leaching tests. Reasons for limitations of the comparability of leaching test results are exposed and recommendations are given for the expedient application of leaching tests for groundwater risk assessment. Leaching tests are usually carried out in open contact with the atmosphere disregarding possible changes of redox conditions. This can affect the original metal speciation and distribution, particularly when anoxic samples are investigated. The influence of sample storage on leaching test results of sulfide bearing anoxic material from a former flotation dump is investigated in a long-term study. Since the oxidation of the sulfide-bearing samples leads to a significant overestimation of metal release, a feasible modification for the conduction of common leaching tests for anoxic material is proposed, where oxidation is prevented efficiently. A comparison of leaching test results to soil water analyzes have shown that the modified saturation soil extraction (SSE) is found to be the only of the tested leaching procedures, which can be recommended for the assessment of current soil water concentrations at anoxic sites if direct investigation of the soil water is impossible due to technical reasons. The vertical distribution and speciation of Zn and Pb in the flotation residues as well as metal concentrations in soil water and plants were investigated to evaluate the environmental risk arising from this site due to the release of metals. The variations in pH and inorganic C content show an acidification of the topsoil with pH values down to 5.5 in the soil and a soil water pH of 6 in 1 m depth. This is due to the oxidation of sulfides and depletion in carbonates. In the anoxic subsoil pH conditions are still neutral and soil water collected with suction cups is in equilibrium with carbonate minerals. Results from extended x-ray absorption fine-structure (EXAFS) spectroscopy confirm that Zn is mainly bound in sphalerite in the subsoil and weathering reactions lead to a redistribution of Zn in the topsoil. A loss of 35% Zn and S from the topsoil compared to the parent material with 10 g/kg Zn has been observed. 13% of total Zn in the topsoil can be regarded as mobile or easily mobilizable according to sequential chemical extractions (SCE). Zn concentrations of 10 mg/L were found in the soil water, where pH is acidic. Electron supply and the buffer capacity of the soil were identified as main factors controlling Zn mobility and release to the groundwater. Variable Pb concentrations up to 30 µg/L were observed in the soil water. In contrast to Zn, Pb is enriched in the mobile fraction of the oxidized topsoil by a factor of 2 compared to the subsoil with 2 g/kg Pb. 80% of the cation exchange capacity in the topsoil is occupied by Pb. Therefore, plant uptake and bioavailability are of major concern. If the site is not prevented from proceeding acidification in the future, a significant release of Zn, S, and Pb to the groundwater has to be expected. Results from this study show that the assessment of metal release especially from sulfide bearing anoxic material requires an extensive comprehension of leaching mechanisms on the one hand and on weathering processes, which influence the speciation and the mobility of metals, on the other hand. Processes, which may change redox and pH conditions in the future, have to be addressed to enable sound decisions for soil and groundwater protection and remediation.

Mineralization of the Bonanza Mine

The Bonanza mine of the Emery mining district in Powell County is on the largest veins in the area, and is developed to a depth of 680 feet by an incline shaft following the dip of the structure. Sulfide ores carrying gold and silver values are mined throughout the area which is easily accessible by road from Deerlodge, Montana, ten miles west of the district.

Geochemistry and mineralogy of coal samples from Dingji Mine, Huainan Coalfield, China

To investigate the geochemistry of trace elements in coals from the Dingji Mine of the Huainan Coalfield, Anhui province, China, 416 borehole samples of coal, one parting, two floor and two roof mudstones were collected from 9 minable coal seams in 24 boreholes drilled during exploration. The abundances of 47 elements in each sample were determined by various instruments. The boron concentration in the coals suggests that marine influence decreased from coal seam 1 to 13-1. The geometric means of the elements Sn, Bi, Sb, and B are higher than the average for the corresponding elements in the coals from China, the U.S., and world. The enrichment of certain elements in the Shanxi or Upper Shihezi Formations is related to their depositional environment. The roof, floor and parting samples have higher contents of some elements than coal seams. The mineral matters in the coals from the Dingji Mine were found to consist mainly of granular quartz, clay minerals, and carbonate minerals. The elements are classified into two groups based on their stratigraphic distribution from coal seam 1 to 13-1, and the characteristics of each group are discussed. Based on the correlation coefficients of elemental concentrations with ash yield, four groups of elements with different affinities were identified.

In situ assessment of initial seafloor massive sulfide mining operation in Papua New Guinea using a cabled autonomous underwater vehicle system: a proposition

Senior thesis written for Oceanography 445

The Application of wireless LANS in mine automation

The objective of this paper is to provide an overview of mine automation applications, developed at the Queensland Centre for Advanced Technology (QCAT), which make use of IEEE 802.11b wireless local area networks (WLANs). The paper has been prepared for a 2002 conference entitled "Creating the Virtual Enterprise - Leveraging wireless technology within existing business models for corporate advantage". Descriptions of the WLAN components have been omitted here as such details are presented in the accompanying papers. The structure of the paper is as follows. Application overviews are provided in Sections 2 to 7. Some pertinent strengths and weaknesses are summarised in Section 8. Please refer to http://www.mining-automation.com/ or contact the authors for further information.

The emotional geography of a mine closure: a study of the Ravensthorpe nickel mine in Western Australia

This paper engages with the literature on emotional geographies to report on a case study of the emotions surrounding the closure of a nickel mine in the shire of Ravensthorpe in the south-west of Western Australia in January 2009. Two themes from the affect-infused narratives of pre- and post-mine community members are outlined. The first, which challenges constructions of the closure as a purely industrial and economic concern, focuses on the intense feelings the shut-down invoked amongst participants. The second theme explores the way in which the owner of the mine, BHP Billiton, worked to suppress and regulate affective reactions to the closure and thus reveals the highly political nature of emotions.