PCR-mediated detection of acidophilic, bioleaching-associated bacteria.

The detection of acidophilic microorganisms from mining environments by culture methods is time consuming and unreliable. Several PCR approaches were developed to amplify small-subunit rRNA sequences from the DNA of six bacterial phylotypes associated with acidic mining environments, permitting the detection of the target DNA at concentrations as low as 10 fg.     

Sediment Contamination along Desert Wash Systems from Historic Mining Sites in a Hyperarid Region of Southern Nevada,USA

Abandoned mining sites in hyperarid environments are generally assumed to present an insignificant risk to water availability. This study investigated the impact abandoned mine sites in Southern Nevada can have on the wider environment. Southern Nevada is characterized with little precipitation and prolonged droughts. Precipitation in Southern Nevada is often in the form of short and intense events with the potential to mobilize and transport contaminated sediments down gradient. This work evaluated the movement of trace elements (Ag, As, Ba, Cd, Cr, Hg, Pb, and Se) and cyanide in surface sediments of three desert washes near the historic mining town of Nelson, a hyperarid region of Southern Nevada. Results indicate trace elements have been mobilized and transported down gradient from sources to areas not directly impacted by mining. Contaminants used in mining operations (Hg and CN^?) as well as those of geogenic nature migrated as far as 6000 m, providing evidence of their transport in hyperarid environments, contrary to the generally held belief. Although contaminants in this study are below levels that are environmentally significant, the findings show that transport is possible. This study demonstrates that large amounts of contaminant-laden sediments might be a significant threat in hyperarid environment and to areas down gradient from source materials.     

Restoration and management for cliff‐nesting birds in Mediterranean mining sites: the Sand Martin case study

Habitat enhancement for birds is frequently implemented during mine site restoration. Cliff‐nesting birds often colonize anthropogenic environments such as mining areas (aggregate sites and quarries for aggregate and cement production). Mining activity can compromise breeding success, causing cliff‐nesting birds to depend on the management and restoration of mining areas. The objective of our study is to assess the importance of mine site habitats for Sand Martin conservation and reconcile mining activity with breeding success in Mediterranean environments. We studied Sand Martin breeding habitat preferences in mining areas at three spatial scales. At the mining site scale, we compared 10 mining sites with Sand Martin burrows with 19 mining sites without burrows. At the colony scale (vertical structures with colonies), we evaluated the relationships between the number of breeding pairs, number of burrows, and colony characteristics within 30 distinct Sand Martin colonies. At the burrow scale, we compared the characteristics of the available vertical structure with the areas used by Sand Martins. At the mining site scale, Sand Martins preferred more surface of water bodies, shorter distances to flowing water, older sites, and mining sites which produce aggregates instead of cement. At the colony scale, Sand Martins preferred southwest orientations and stockpiles to vertical extraction faces. At the burrow scale, birds preferred the most vertical areas of the face. Our results support the need for effective habitat restoration and improved management for more effective Sand Martin conservation within mining areas. Simple interventions can enhance habitat quality and conservation of cliff‐nesting birds.     

Identification of Mn(II)-Oxidizing Bacteria from a Low-pH Contaminated Former Uranium Mine

Biological Mn oxidation is responsible for producing highly reactive and abundant Mn oxide phases in the environment that can mitigate metal contamination. However, little is known about Mn oxidation in low-pH environments, where metal contamination often is a problem as the result of mining activities. We isolated two Mn(II)-oxidizing bacteria (MOB) at pH 5.5 (Duganella isolate AB_14 and Albidiferax isolate TB-2) and nine strains at pH 7 from a former uranium mining site. Isolate TB-2 may contribute to Mn oxidation in the acidic Mn-rich subsoil, as a closely related clone represented 16% of the total community. All isolates oxidized Mn over a small pH range, and isolates from low-pH samples only oxidized Mn below pH 6. Two strains with different pH optima differed in their Fe requirements for Mn oxidation, suggesting that Mn oxidation by the strain found at neutral pH was linked to Fe oxidation. Isolates tolerated Ni, Cu, and Cd and produced Mn oxides with similarities to todorokite and birnessite, with the latter being present in subsurface layers where metal enrichment was associated with Mn oxides. This demonstrates that MOB can be involved in the formation of biogenic Mn oxides in both moderately acidic and neutral pH environments.     

Review of rotifers and crustaceans in highly acidic environments of pH values ≤3

A review of the literature on rotifers and crustacean zooplankton in highly acidic environments revealed that data from eleven aquatic environments on three continents (America, Europe, Japan) with a pH 3 are available. Seven sites are influenced by volcanism or weathering processes in the catchment area, four others originated from human mining activities. Species richness was generally low. Only 16 species are found and 1–11 species are reported for each area. These studies clearly show that small littoral or benthic rotifers predominate over crustaceans under highly acidic conditions. In the Lusatian mining area (Germany), all lakes are colonized by zooplankton, even the most acidic one with a pH of 2.3. The core community consists of the rotifers Cephalodella hoodi, C. gibba, Elosa worallii and Rotaria rotatoria, with C. hoodi and E. worallii the most abundant. Larger species, such as the rotifer Brachionus sericus or the cladoceran Chydorus sphaericus, occur at a pH close to 3. A similar pattern is reported from acidic mining lakes in Illinois, U.S.A. Many of these species can also be found in less acidic softwater or even alkaline environments due to the tolerance of a broad range of pH values. Elosa worallii and Brachionus sericus are probably the most acidophilic rotifer species, though at least the latter can also grow at neutral pH in the laboratory. Clear understanding of the pH limits of B. sericus in nature may also have been complicated by the fact that it has probably in the past been wrongly named as B. urceolaris (phenotype `sericus'). The typical B. urceolaris cannot tolerate extremely low pH. Overall, generalist species with a worldwide distribution seem to play the major role in the colonization of anthropogenic highly acidic lakes.     

The influence of hydrogeological disturbance and mining on coal seam microbial communities

The microbial communities present in two underground coal mines in the Bowen Basin, Queensland, Australia, were investigated to deduce the effect of pumping and mining on subsurface methanogens and methanotrophs. The micro‐organisms in pumped water from the actively mined areas, as well as, pre‐ and post‐mining formation waters were analyzed using 16S rRNA gene amplicon sequencing. The methane stable isotope composition of Bowen Basin coal seam indicates that methanogenesis has occurred in the geological past. More recently at the mine site, changing groundwater flow dynamics and the introduction of oxygen in the subsurface has increased microbial biomass and diversity. Consistent with microbial communities found in other coal seam environments, pumped coal mine waters from the subsurface were dominated by bacteria belonging to the genera Pseudomonas and the family Rhodocyclaceae. These environments and bacterial communities supported a methanogen population, including Methanobacteriaceae, Methanococcaceae and Methanosaeta. However, one of the most ubiquitous micro‐organisms in anoxic coal mine waters belonged to the family ‘Candidatus Methanoperedenaceae’. As the Archaeal family ‘Candidatus Methanoperedenaceae’ has not been extensively defined, the one studied species in the family is capable of anaerobic methane oxidation coupled to nitrate reduction. This introduces the possibility that a methane cycle between archaeal methanogenesis and methanotrophy may exist in the anoxic waters of the coal seam after hydrogeological disturbance.     

Advantages and challenges of increased antimicrobial copper use and copper mining

Copper is a highly utilized metal for electrical, automotive, household objects, and more recently as an effective antimicrobial surface. Copper-containing solutions applied to fruits and vegetables can prevent bacterial and fungal infections. Bacteria, such as Salmonellae and Cronobacter sakazakii, often found in food contamination, are rapidly killed on contact with copper alloys. The antimicrobial effectiveness of copper alloys in the healthcare environment against bacteria causing hospital-acquired infections such as methicillin-resistant Staphylococcus aureus (MRSA), Escherichia coli O157:H7, and Clostridium difficile has been described recently. The use of copper and copper-containing materials will continue to expand and may lead to an increase in copper mining and production. However, the copper mining and manufacturing industry and the consumer do not necessarily enjoy a favorable relationship. Open pit mining, copper mine tailings, leaching products, and deposits of toxic metals in the environment often raises concerns and sometimes public outrage. In addition, consumers may fear that copper alloys utilized as antimicrobial surfaces in food production will lead to copper toxicity in humans. Therefore, there is a need to mitigate some of the negative effects of increased copper use and copper mining. More thermo-tolerant, copper ion-resistant microorganisms could improve copper leaching and lessen copper groundwater contamination. Copper ion-resistant bacteria associated with plants might be useful in biostabilization and phytoremediation of copper-contaminated environments. In this review, recent progress in microbiological and biotechnological aspects of microorganisms in contact with copper will be presented and discussed, exploring their role in the improvement for the industries involved as well as providing better environmental outcomes.     

A review on the occurrence and taxonomy of heterotrophic protists in extreme acidic environments of pH values ≤ 3

The occurrence and some important taxonomic problems of heterotrophic protists from extremely acidic (pH 3) environments are briefly discussed. Almost all information on the occurrence of heterotrophic protists from extremely acidic environments is restricted to acid mine drainage (AMD) or streams influenced by AMD. Most of the information is provided for ciliates. Very little information is available on the occurrence of flagellates, rhizopods and heliozoa in this environment. Within the ciliates Urotricha, Vorticella and Oxytricha dominate in acidic mining lakes. Actinophrys sp. is the most important heliozoan in these environments. There are many taxonomic problems which are not solved so far. Live observations and taxonomic methods adapted to the extreme chemical matrix are necessary for correct identification.     

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.     

Differential heavy metal sensitivity in seven algal species from the NIES culture collection based on delayed fluorescence assays

Seafloor massive sulfide (SMS) deposits are the target of available metallic resources. The toxic impacts of leachable metals from hydrothermal ore by mining operations in marine environments are a concern. However, ecotoxicological knowledge about marine algae, and particularly open ocean species, is still limited. Here, we evaluated the toxic effects of three leachable metals (i.e. Zn, Cu, and Pb) on seven marine algae, including cyanobacteria and eukaryotes, by a delayed fluorescence method. Cyanobacterial Synechococcus and Cyanobium species were sensitive to Zn and Cu, while eukaryotic algae showed various responses to heavy metal species. The prasinophycean Bathycoccus prasinos NIES‐2670 was sensitive to all metal species; this strain is a potential test strain to detect the leachable metals. A co‐culture experiment showed that the impact on community structure varies depending on leachable metal species. This study demonstrates that surveys across multiple taxonomic groups are necessary to assess the impact of SMS‐mining operations on marine ecosystems as a whole.     

Nonribosomal peptides in fungal cell factories: from genome mining to optimized heterologous production

Fungi are notoriously prolific producers of secondary metabolites including nonribosomal peptides (NRPs). The structural complexity of NRPs grants them interesting activities such as antibiotic, anti-cancer, and anti-inflammatory properties. The discovery of these compounds with attractive activities can be achieved by using two approaches: either by screening samples originating from various environments for their biological activities, or by identifying the related clusters in genomic sequences thanks to bioinformatics tools. This genome mining approach has grown tremendously due to recent advances in genome sequencing, which have provided an incredible amount of genomic data from hundreds of microbial species. Regarding fungal organisms, the genomic data have revealed the presence of an unexpected number of putative NRP-related gene clusters. This highlights fungi as a goldmine for the discovery of putative novel bioactive compounds. Recent development of NRP dedicated bioinformatics tools have increased the capacity to identify these gene clusters and to deduce NRPs structures, speeding-up the screening process for novel metabolites discovery. Unfortunately, the newly identified compound is frequently not or poorly produced by native producers due to a lack of expression of the related genes cluster. A frequently employed strategy to increase production rates consists in transferring the related biosynthetic pathway in heterologous hosts. This review aims to provide a comprehensive overview about the topic of NRPs discovery, from gene cluster identification by genome mining to the heterologous production in fungal hosts. The main computational tools and methods for genome mining are herein presented with an emphasis on the particularities of the fungal systems. The different steps of the reconstitution of NRP biosynthetic pathway in heterologous fungal cell factories will be discussed, as well as the key factors to consider for maximizing productivity. Several examples will be developed to illustrate the potential of heterologous production to both discover uncharacterized novel compounds predicted in silico by genome mining, and to enhance the productivity of interesting bio-active natural products.     

Regional distribution characteristics and ecological risk assessment of heavy metal pollution of different land use in an antimony mining area – Xikuangshan,China

Abstract

Mining activities have introduced various heavy metals and metalloids to surrounding soil environments, causing adverse impacts to the ecological environment system. The extremely high concentration of various heavy metals and metalloids make the Xikuangshan (Hunan, China) an excellent model to assess their ecological risk. In this study, the soil samples from 26 locations of different land use methods in four areas (smelting area, road nearby ore, mining area, and ore tailing area) in Xikuangshan with different levels of various heavy metals and metalloids (Sb, As, Pb, and Cd) were analyzed; in addition, the index of geo-accumulation and the potential ecological risk index were used to evaluate ecological risk. The results showed that the average contents of Sb, As, Pb, and Cd in all soil samples were 4368.222?mg·kg^?1, 40.722?mg·kg^?1, 248.013?mg·kg^?1, and 40.941?mg·kg^?1, respectively, implying serious contamination of compound pollution of heavy metals in soil. The concentration of heavy metals in soil among smelting area, road nearby ore, mining area, and ore tailing area showed significant distribution characteristics of region because different mining activities such as smelting, mining, transportation, and stacking caused different pollution intensity. Moreover, the contents of Sb in soil samples decreased successively in residue field, wasteland, forestland, sediment, grassland, and vegetable field, and the contents of Sb in vegetable-field and ecological restoration grassland were relatively low, which indicate that the method of grassland ecological restoration is an effective method to control antimony pollution in soil. The results of ecological risk assessment showed that the antimony mining area was seriously polluted by Sb, As, Pb, and Cd, and had strong ecological risk, and Sb and Cd were the most important pollution factors, which indicated that the pollution of Sb and Cd should be a major concern of relevant departments of environment and health.     

Risk Factors for Mercury Exposure of Children in a Rural Mining Town in Northern Chile

Objective

Traditional gold mining is associated with mercury exposure. Especially vulnerable to its neurotoxic effects is the developing nervous system of a child. We aimed to investigate risk factors of mercury exposure among children in a rural mining town in Chile.

Methods

Using a validated questionnaire distributed to the parents of the children, a priori mercury risk factors, potential exposure pathways and demographics of the children were obtained. Mercury levels were measured through analyzing fingernail samples. Logistic regression modeling the effect of risk factors on mercury levels above the 75^th percentile were made, adjusted for potential confounders.

Results

The 288 children had a mean age of 9.6 years (SD = 1.9). The mean mercury level in the study population was 0.13 µg/g (SD 0.11, median 0.10, range 0.001–0.86 µg/g). The strongest risk factor for children’s odds of high mercury levels (>75^th percentile, 0.165 µg/g) was to play inside a house where a family member worked with mercury (OR adjusted 3.49 95% CI 1.23–9.89). Additionally, children whose parents worked in industrial gold mining had higher odds of high mercury levels than children whose parents worked in industrial copper mining or outside mining activities.

Conclusion

Mercury exposure through small-scale gold mining might affect children in their home environments. These results may further help to convince the local population of banning mercury burning inside the households.     

BIOACTIVE PROTEINS,PEPTIDES, AND AMINO ACIDS FROM MACROALGAE1

Macroalgae are a diverse group of marine organisms that have developed complex and unique metabolic pathways to ensure survival in highly competitive marine environments. As a result, these organisms have been targeted for mining of natural biologically active components. The exploration of marine organisms has revealed numerous bioactive compounds that are proteinaceous in nature. These include proteins, linear peptides, cyclic peptides and depsipeptides, peptide derivatives, amino acids, and amino acid–like components. Furthermore, some species of macroalgae have been shown to contain significant levels of protein. While some protein‐derived bioactive peptides have been characterized from macroalgae, macroalgal proteins currently still represent good candidate raw materials for biofunctional peptide mining. This review will provide an overview of the important bioactive amino‐acid‐containing compounds that have been identified in macroalgae. Moreover, the potential of macroalgal proteins as substrates for the generation of biofunctional peptides for utilization as functional foods to provide specific health benefits will be discussed.     

GeneChip Expression Profiling Reveals the Alterations of Energy Metabolism Related Genes in Osteocytes under Large Gradient High Magnetic Fields

The diamagnetic levitation as a novel ground-based model for simulating a reduced gravity environment has recently been applied in life science research. In this study a specially designed superconducting magnet with a large gradient high magnetic field (LG-HMF), which can provide three apparent gravity levels (μ-g, 1-g, and 2-g), was used to simulate a space-like gravity environment. Osteocyte, as the most important mechanosensor in bone, takes a pivotal position in mediating the mechano-induced bone remodeling. In this study, the effects of LG-HMF on gene expression profiling of osteocyte-like cell line MLO-Y4 were investigated by Affymetrix DNA microarray. LG-HMF affected osteocyte gene expression profiling. Differentially expressed genes (DEGs) and data mining were further analyzed by using bioinfomatic tools, such as DAVID, iReport. 12 energy metabolism related genes (PFKL, AK4, ALDOC, COX7A1, STC1, ADM, CA9, CA12, P4HA1, APLN, GPR35 and GPR84) were further confirmed by real-time PCR. An integrated gene interaction network of 12 DEGs was constructed. Bio-data mining showed that genes involved in glucose metabolic process and apoptosis changed notablly. Our results demostrated that LG-HMF affected the expression of energy metabolism related genes in osteocyte. The identification of sensitive genes to special environments may provide some potential targets for preventing and treating bone loss or osteoporosis.     

Degradation of cultivated bench terraces in the Three Gorges Area: Field mapping and data mining

Due to resettlements, construction of new infrastructure, and new land reclamation the rapid agricultural changes in the Three Georges Area (TGA) in Central China are expected to force the degradation of the cultivated terraced landscape. Consequently, increased soil erosion can hamper a sustainable land management in the mountainous TGA. This paper presents the model framework TerraCE (Terrace Condition Erosion) for determining the causes for different terrace conditions and terrace degradation based on field surveys and spatial data mining. For a total of 987 bench terrace plots in the Xiangxi catchment we collected data on their state of maintenance and terrace design to account for terrace stability and thus capability of soil conservation. Assessing the driving factors of terrace degradation was done by embedding terrain-based predictors and distance-transforms of remote-sensing data as indicators of environmental and anthropogenic influences. Random forests classification and regression models were applied for data mining. Terrace degradation in the Xiangxi catchment is obvious. The sequence of degradation ranges from ‘well maintained’ (21%), ‘fairly maintained’ (44%), and ‘partially collapsed’ (23%) to ‘completely collapsed’ (11%) terraces. The cross-validation error of the supervised TerraCE model is below 8%, allowing for reasonable and valid interpretations of the causes of terrace degradation. Data mining reveals indicators for anthropogenic effects such as the distance to settlements or to roads as major drivers for the spatial distribution of terrace conditions. The effect of relief, which can be regarded as the major natural driver for terrace degradation by erosive action is tributary but altered and overlaid by land use dynamics associated with the Three Gorges Dam. An important indicator representing a combined effect of terrain and human activity is the distance to stream channels of different orders. Applying TerraCE we reveal mechanisms of terrace degradation in disturbed environments and present a framework for standardized mapping and analysis of terrace degradation under cultivation. The approach might also be used to develop guidelines for terrace planning in mountainous terraced landscapes of limited carrying capacity, with respect to socio-economic as well as environmental conditions.