'Proteomineering': has the mine been excavated?

Evaluation of: Di Girolamo F, Boschetti E, Chung MC, Guadagni F, Righetti PG. 'Proteomineering' or not? The debate on biomarker discovery in sera continues. J. Proteomics 74(5), 589-594 (2011). The combinatorial peptide ligand library in association with mass spectrometry can greatly enhance the dynamic range of the analysis of low- and very low-abundance proteins constituting the vast majority of species in any sample. When compared with untreated samples, the increment in detection of low-abundance species appears to be at least fourfold. Recently, the combinatorial peptide ligand library has been challenged; however, it has been clearly demonstrated in the evaluated paper that the protocols for elution of the captured polypeptides make the difference. Therefore, the solid-phase ligand library made of hexapeptides remains a promising and unique tool for biomarker discovery.     

A meta-taxonomic investigation of the prokaryotic diversity of water bodies impacted by acid mine drainage from the São Domingos mine in southern Portugal

Extremophiles - The prokaryotic communities of water bodies contaminated by acid mine drainage from the São Domingos mining area in southern Portugal were analyzed using a meta-taxonomics...     

Flora and dispersed cuticles from the coal seams in the Jan pit of the Šverma coal mine in Žacléř (Bashkirian,Intrasudetic Basin,Czech Republic)

The Lampertice Member in the ?aclé? coalfield represents the long-term coal-bearing deposition of nearly all Upper Bashkitian (Namurian to Ducmantian). Nearly the whole thickness, more than 600 m was revealed during the construction of the Jan pit of the Jan ?verma coal mine during 1958–1962. Z. Rieger collected stratigraphically determined plant remains for later evaluation and he also sampled individual coal seams. The plant material was evaluated again and four coal samples were macerated for cuticles to expand our knowledge of ?aclé? flora. The following local biozones are valid for the Lampertice Member. The Namutian (Yeadonian) Mariopteris glabra Zone lasts from the basal coal-barren rocks till lower coal seam 17 (there are 24 lower coal seams). The Langsettian is crowed by the LAD of Neuralethopteris schlehanii (Stur) Laveine at upper coal seam 20 (there are 32 upper coal seams). The Langsettian can be divided into the upper and lower parts by FAD of Lonchopteris Brongniart at about lower coal seam 8. The Upper Duckmantian is defined by the FAD of Linopteris neuropteroides Gutbier forma major Potonié from about upper coal seam 11 upwards. The results of cuticular analysis are as follows: Undeterminable cuticles with polygonal or tetragonal, randomly or parallel oriented cells dominate. Such cuticles predominantly belong to seeds. Cordaitalean cuticles are common in three of four samples. They are assigned to the genera Cordaites Unger, Cordaadaxicutis ?im?nek et Florjan, and Cordaabaxicutis ?im?nek et Florjan. Pteridosperm cuticles are very rare—Silesiacutis prosenchymatica Roselt et Schneider and undetermined cuticles with probably neuropterid cyclopterid affinity.     

Riparian plants on mine runoff in Zimapan,Hidalgo, Mexico: Useful for phytoremediation?

Dispersion and runoff of mine tailings have serious implications for human and ecosystem health in the surroundings of mines. Water, soils and plants were sampled in transects perpendicular to the Santiago stream in Zimapan, Hidalgo, which receives runoff sediments from two acidic and one alkaline mine tailing. Concentrations of potentially toxic elements (PTE) were measured in water, soils (rhizosphere and non-rhizosphere) and plants. Using diethylenetriaminepentaacetic acid (DTPA) extractable concentrations of Cu, Zn, Ni, Cd and Pb in rhizosphere soil, the bioconcentration and translocation factors were calculated. Ruderal annuals formed the principal element of the herbaceous vegetation. Accumulation was the most frequent strategy to deal with high concentrations of Zn, Cu, Ni, Cd and Pb. The order of concentration in plant tissue was Zn>Pb>Cu>Ni>Cd. Most plants contained concentrations of PTE considered as phytotoxic and behaved as metal tolerant species. Rorippa nasturtium-aquaticum accumulated particularly high concentrations of Cu. Parietaria pensylvanica and Commelina diffusa, common tropical weeds, behaved as Zn hyperaccumulators and should be studied further.     

Heavy metals and arsenic uptake by wild vegetation in the Guadiamar river area after the toxic spill of the Aznalcóllar mine

On 25 April 1998, approximately 4.5 hm(3) of pyritic sludge, containing 5000 mg of As kg(-1) among other pollutants, was spilled into the Agrio and Guadiamar rivers and the surrounding agricultural areas (Aznalcóllar, Seville, Southern Spain). Many trace metals such as Pb, Cu, Zn, Cd, Tl, Sb and As reached the Do?ana National Park, the largest wetland area in Europe, affecting soils, different plant and animal species. In order to recuperate the affected lands by employing plants capable of accumulating high levels of contaminants in shoots, periodical field surveys have been made to identify the metal-tolerant species that are spontaneously growing in the polluted soils, and are able to uptake one or various of the contaminants. Among the 99 different plant species studied, Anchusa azurea, Beta vulgaris, Chamaemelum fuscatum, Convolvulus arvensis, Cynodon dactylon, Diplotaxis virgata, Erodium aethiopicum, Lavatera cretica, Malva nicaeensis, Silybum marianum and, above all, Amaranthus blitoides highlight as the most promising to be used in the remediation of the affected area.     

Microbial diversity in acid mineral bioleaching systems of dongxiang copper mine and Yinshan lead–zinc mine

To understand the composition and structure of microbial communities in acid mineral bioleaching systems, the molecular diversity of 16S rDNA genes was examined using a PCR-based cloning approach. A total of 31 Operational Taxonomic Units (OTUs) were obtained from the four samples taken from four different bioleaching sites in Yinshan lead–zinc mine and Dongxiang copper mine in Jiangxi Province, China. The percentages of overlapping OTUs between sites ranged from 22.2 to 50.0%. Phylogenetic analysis revealed that the bacteria present at the four bioleaching sites fell into six divisions, α-Proteobacteria (1.1%), β-Proteobacteria (2.3%), γ-Proteobacteria (30.8%), Firmicutes (15.4%), Actinobacteria (0.3%) and Nitrospira (50.1%). Organisms of genera Leptospirillum, Acidithiobacillus, and Sulfobacillus, which were in Nitrospira, γ-Proteobacteria, and Firmicutes divisions, respectively, were the most dominant. The results of principal component analysis based on the six phylogenetic divisions and biogeochemical data indicated that the microbial community structure of a site was directly related to the biogeochemical characteristic of that site. It follows therefore that sites with similar biogeochemical characteristics were comprised of similar microbial community structures. The results in our study also suggest that the elements copper and arsenic appear to be the key factors affecting the compositions and structures of microbial community in the four bioleaching sites. Zhiguo He, Shengmu Xiao, Xuehui Xie are equally contributed to this work.     

Distribution and mobility of toxic metals in Thymus alsarensis Ronniger in the Allchar As–Sb–Tl mine,Republic of Macedonia

Abstract

The Allchar district is an abandoned antimony–arsenic–thallium deposit located in the north-western region of Ko?uf mountain in the Republic of Macedonia. The locality of Allchar has a complex and unique mineral composition. The current study sought to investigate the levels of uptake and distribution of different heavy metals, such as As, Sb and Tl, in the different organs of Thymus alsarensis Ronniger, an endemic plant species of the area. Root, stem, leaf and flower samples, as well as corresponding soils, were processed, digested and then analysed by inductively coupled plasma atomic emission spectrometry. Significant accumulation of As, Sb and Tl in this endemic species was observed. Total As content in the soil ranged from 34.7 to 5288 mg kg^–1, and the content of As in plants ranged from 0.25 to 140 mg kg^–1. The content of Sb in soil and plants ranged from 6.3 to 130 mg kg^–1 and 0.25 to 1.51 mg kg^–1, respectively. Lastly, the content of Tl in soil and plants ranged from 2.0 to 330 mg kg^–1 and 0.10 to 496 mg kg^–1, respectively. Similar results were obtained from extraction tests of soil samples using various solvents.     

Isolation and characterization of aerobic,culturable, arsenic-tolerant bacteria from lead–zinc mine tailing in southern China

Bioremediation of arsenic (As) pollution is an important environmental issue. The present investigation was carried out to isolate As-resistant novel bacteria and characterize their As transformation and tolerance ability. A total of 170 As-resistant bacteria were isolated from As-contaminated soils at the Kangjiawan lead–zinc tailing mine, located in Hunan Province, southern China. Thirteen As-resistant isolates were screened by exposure to 260 mM Na₂HAsO₄·7H₂O, most of which showed a very high level of resistance to As⁵⁺ (MIC?≥?600 mM) and As³⁺ (MIC?≥?10 mM). Sequence analysis of 16S rRNA genes indicated that the 13 isolates tested belong to the phyla Firmicutes, Proteobacteria and Actinobacteria, and these isolates were assigned to eight genera, Bacillus, Williamsia, Citricoccus, Rhodococcus, Arthrobacter, Ochrobactrum, Pseudomonas and Sphingomonas. Genes involved in As resistance were present in 11 of the isolates. All 13 strains transformed As (1 mM); the oxidation and reduction rates were 5–30% and 10–51.2% within 72 h, respectively. The rates of oxidation by Bacillus sp. Tw1 and Pseudomonas spp. Tw224 peaked at 42.48 and 34.94% at 120 h, respectively. For Pseudomonas spp. Tw224 and Bacillus sp. Tw133, the highest reduction rates were 52.01% at 48 h and 48.66% at 144 h, respectively. Our findings will facilitate further research into As metabolism and bioremediation of As pollution by genome sequencing and genes modification.     

Intracellular Leishmania: your iron or mine?

Iron is a co-factor for several essential enzymes and biochemical pathways, including those required for replication of pathogens such as Leishmania in macrophages. Iron acquisition is emerging as a key battleground in which the iron import systems of microbes are pitted against the iron withdrawal and sequestration systems of macrophages, with both competing for iron at the interface of host-pathogen interaction. The recent characterization of a ferrous iron transport system (LIT1) in Leishmania amazonensis that is induced intracellularly and is required for survival in macrophages and for virulence in vivo provides an elegant example of the adaptation of protozoa to the iron-poor phagosomal environment.     

Dark septate endophytes colonizing the roots of ‘non-mycorrhizal’ plants in a mine tailing pond and in a relatively undisturbed environment,Southwest China

Dark septate endophytes (DSEs), one of the most common fungal colonizers of roots, are considered to overlap in function with mycorrhizal fungi. However, there is little knowledge on the distribution and identity of DSEs in ‘non-mycorrhizal’ plants. In the current study, colonization and diversity of DSEs colonizing the roots of eight typically ‘non-mycorrhizal’ families were assessed. In total, 120 root samples of 31 plant species were all colonized by DSEs. Intensity of DSE colonization varied greatly among different plant species, with a range of 0.56–47.56%, 8.13% on average. Cladosporium, Cyphellophora and Phialophora were the dominant genera, with a relative abundance of more than 60% over a total of 90 isolates. Our results showed that diverse DSE species colonized the roots of ‘non-mycorrhizal’ plants, especially they were more common in degraded mine tailings than in the undisturbed site, but their integral roles to the functional roots are in need of further experimental demonstration.     

How does storage affect the quality and quantity of organic carbon in sewage for use in the bioremediation of acidic mine waters?

Pit lakes (abandoned flooded mine pits) represent a potentially valuable water resource. However, acid mine drainage (AMD) generation due to mining activities often results in pit lake waters with low pH, high sulphate and dissolved metal concentrations. Sulphate reduction-based bioremediation offers tremendous scope for removal of acidity and metals from pit lake water. In this study, the effect of storing sewage on its carbon quality for bioremediation of acidic pit lake water was studied. In addition, the effectiveness of labile organic carbon (lactic acid and ethanol) on SRB activity was tested. Bioremediation experiments were performed in controlled and replicated microcosms with acidic (pH 2.2) water from a pit lake by addition of stored (3 years at 4 °C) sewage for stimulation of sulphate reducing bacteria (SRB) activity. This sewage had been previously used successfully in remediating to pH 7 water from this pit lake. The initial aim was to test the sewage at lower doses (18 and 28 g/L) and in a pulsed addition (over 5 weeks). Bioremediation efficacy was evaluated by measuring pit lake water pH increase, redox potential decrease, and acidity and sulphate removal. Though the stored sewage had retained a very similar high total organic carbon (TOC) equivalent to prior to storage, it failed to increase dissolved organic carbon (DOC) levels in pit lake water. Microcosms amended with doubled doses of sewage and an extended remediation time still failed to demonstrate any substantial improvement in water quality, other than a small amount of sulphate reduction and direct neutralisation by the sewage. In order to determine if low DOC concentrations in sewage were the cause of the bioremediation failure, labile organic carbon (LOC), consisting of 50:50 (w/w) lactic acid and ethanol, was added to all microcosm treatments at concentrations of 3000, 6000 and 9000 mg/L. After LOC addition, water quality improved with effective removal of acidity, sulphate and metals in the lowest carbon concentration (3000 mg/L). However, 6000 and 9000 mg/L LOC concentrations showed a delay in response due to the increased acidity associated with the lactic acid addition. The experiments showed that pulsed dosing of carbon simply slowed the commencement of remediation but it was ultimately able to reach the same effectiveness as the equivalent quantity added all at once. Prolonged storage of sewage leads to loss of LOC. In situ pit lake remediations which aim to make use of sewage as the main carbon source will need to factor in the storage time required to obtain sufficient sewage for the treatment into the design. Pulsing may help reduce issues with storage or supplementation with LOC may need to be considered. Results highlight that LOC is a more useful indicator of material effectiveness compared to a simple measures of TOC.     

Phytochemicals: the good, the bad and the ugly?

Phytochemicals are constitutive metabolites that enable plants to overcome temporary or continuous threats integral to their environment, while also controlling essential functions of growth and reproduction. All of these roles are generally advantageous to the producing organisms but the inherent biological activity of such constituents often causes dramatic adverse consequences in other organisms that may be exposed to them. Nevertheless, such effects may be the essential indicator of desirable properties, such as therapeutic potential, especially when the mechanism of bioactivity can be delineated. Careful observation of cause and effect, followed by a coordinated approach to identify the responsible entities, has proved extremely fruitful in discovering roles for phytochemical constituents. The process is illustrated by selected examples of plants poisonous to animals and include the steroidal alkaloid toxin of Veratrum californicum (Western false hellebore), piperidine alkaloids of Lupinus species (lupines), and polyhydroxy indolizidine, pyrrolizidine and nortropane alkaloids of Astragalus and Oxytropis species (locoweeds), Castanospermum australe (Moreton Bay chestnut) and Ipomoea species (morning glories).