Isolation and characterization of a Geobacillus thermoleovorans strain from an ultra-deep South African gold mine

A thermophilic facultative bacterial isolate was recovered from 3.2km depth in a gold mine in South Africa. This isolate, designated GE-7, was cultivated from pH 8.0, 50 degrees C water from a dripping fracture near the top of an exploration tunnel. GE-7 grows optimally at 65 degrees C and pH 6.5 on a wide range of carbon substrates including cellobiose, hydrocarbons and lactate. In addition to O(2), GE-7 also utilizes nitrate as an electron acceptor. GE-7 is a long rod-shaped bacterium (4-6microm longx0.5microm wide) with terminal endospores and flagella. Phylogenetic analysis of GE-7 16S rDNA sequence revealed high sequence similarity with G. thermoleovorans DSM 5366(T) (99.6%), however, certain phenotypic characteristics of GE-7 were distinct from this and other previously described strains of G. thermoleovorans.     

Mineralogy and geochemistry of tailings from a gold mine in northeastern Thailand

Mineralogical and geochemical characteristics of tailings from a gold mine in northeastern Thailand were investigated in relation to acid mine drainage (AMD) and the release potentials of toxic elements. The tailings can be divided into upper tailings and lower tailings. The upper tailings usually contain pyrrhotite, pyrite ± chalcopyrite, calcite, quartz, andradite and diopside. The lower tailings mainly contain goethite, quartz, chlorite, muscovite, calcite and hematite ± pyrrhotite. These assemblages clearly relate to the original types of gold deposit prior to mining and mineral processing. The upper tailings are defined as potential acid forming (PAF), whereas the lower tailings are classified as non-acid forming (NAF). Regarding heavy metals, apart from high Mn level, the other heavy metals appear to have low concentrations in the upper tailings. On the other hand, the lower tailings contain high contents of As, Cu and Pb, which appear to be higher than the National Total Threshold Limit Concentrations. Goethite, the main mineral assemblage in the lower tailings, reveals characteristic of arsenic adsorbent. As a result, the tailing pond is recommended to be covered to prevent the oxidizing processes of the upper tailings; otherwise, AMD generation may take place soon after the mine closure. Land reclamation and monitoring plans must be planned very well and carried out with great care since arsenic contamination has been reported in steam water close to the tailing dam.     

Environmental exposure to uranium in a population living in close proximity to gold mine tailings in South Africa

BackgroundGold mining activities in South Africa resulted in contamination of residential environment with uranium-rich wastes from mine tailings. Health of the people living around the mine tailings could be affected by uranium exposure due to its hazardous chemotoxic and radiological properties.MethodsWe conducted a cross-sectional study to assess i) uranium (U) concentrations in individual hair samples of children and adults living in close proximity to mine tailings in Northeast- Soweto in Johannesburg, South Africa, and ii) the association between U concentrations in hair and various factors, including zone of residence, socio-demographic and housing characteristics. Sampling sites were divided into three zones based on the distance between a dwelling and a cluster of mine tailings (zone 1: <= 500 m, zone 2: 2–3 km away, zone 3: 4–5 km away). U concentrations in hair samples were measured using inductively coupled plasma mass spectrometry. To test the association between U concentrations and selected factors we used robust regression models with log-transformed U concentrations.ResultsAmong 128 subjects with available U measurements, 63 (49%) were children (ages 7–15 years) of which 38 were girls, the remaining 65 (51%) were adult females. Mean (median) U concentration in hair samples was 143 (92) µg/kg. In the mutually adjusted analyses, only an inverse association between age and U concentration in hair remained statistically significant, with geometric mean in children being 2.1 times higher compared to adults (P < 0.001). There was no evidence of an association between zones and U concentration (P = 0.42).ConclusionsThere was little evidence of association between U concentration in hair and distance from the mine tailings within the 5 km range, but overall concentrations were elevated compared to general population samples in other parts of the world. Children had statistically significantly higher geometric mean of uranium concentration in hair compared to adults. The results are important for improvement of mining waste policies and implementation of health monitoring and protective measures in populations at risk.Article categoryResearch Article     

Characterization of iron- and sulphide mineral-oxidizing moderately thermophilic acidophilic bacteria from an Indonesian auto-heating copper mine waste heap and a deep South African gold mine

Iron- and chalcopyrite-oxidizing enrichment cultures were obtained at 50°C from acidic, high-temperature, copper/gold mine environments in Indonesia and South Africa. Over 90% copper yield was obtained from chalcopyrite concentrate with the Indonesian enrichment in 3 months with 2% solids concentration, when pH was maintained at around 2. Neither addition of silver cations nor an enhanced nutrient concentration influenced chalcopyrite leaching. Excision and sequencing of bands from denaturing gradient gel electrophoresis of the amplified partial 16S rRNA gene showed that the enrichment cultures from different environments in South Africa and Indonesia were very simple, and similar. Chalcopyrite concentrate supported a simpler and different community than Fe²⁺. The members of the enrichment cultures were closely related to Sulfobacillus yellowstonensis and Sulfobacillus acidophilus.     

Biogeography and species richness of endophagous insects associated with Proteaceae in South Africa

The endophagous insects associated with Proteaceae of the Cape fynbos were compared to endophage assemblages from more northern non-Capensis Proteaceae. Insects were collected from Proteaceae in the Cape on a regular basis and additional records obtained from insect collections. Northern samples were collected more opportunistically or records were obtained from collections or through personal communication. The Cape fynbos genus Protea is utilized by many more insect taxa than the non-fynbos Protea species. The fynbos Proteaceae has very few species in common with the northern Proteaceae, yet each has many of their own distinct species. This suggests that the fynbos endophage insect fauna is distinct from that of the other regions. It appears that the high diversity of host plants in the fynbos has contributed to generating high, local endophagous insect diversity.     

Biochemical changes in longear sunfish, Lepomis megalotis, associated with lead, cadmium and zinc from mine tailings

Longear sunfish were collected from a stream contaminated with mine tailings rich in lead (Pb), cadmium (Cd) and zinc (Zn). Blood samples were analysed for δ-aminolevulinic acid dehydratase (ALA-D) activity and Pb concentration. Vertebrae were tested for bone strength and composition, and Pb, Zn, and Cd concentrations were determined in muscle tissue. ALA-D activity was negatively correlated with blood Pb concentration ( r =–0.66), and enzyme activity was significantly higher and blood Pb significantly lower at the reference site than at the contaminated sites. Blood Pb was highly correlated with Pb in muscle tissue ( r = 0.72), and the concentrations of Pb and Cd in muscle tissues were themselves correlated ( r = 0.64). In fish from contaminated sites, two of the mechanical properties of the vertebrae measured (elastic limit and modulus of elasticity) were significantly different from values in fish from the reference site. These properties and one other (stress) were weakly correlated with muscle Cd concentration (0.42 < r < 0.46). Biochemical differences among fish from different sites were also evident; concentrations of calcium, phosphorus and collagen were lower in the vertebrae of fish from some of the contaminated sites than at the reference site, and bone phosphorus was negatively correlated with concentrations of Pb in both muscle ( r =– 0.62) and blood ( r =– 0.75). Collectively, these results indicate that, in addition to the well-documented effects of Pb on haem synthesis, other important biochemical pathways may be disrupted by continuous low-level exposure to elemental contaminants.     

Methanogenesis and sulfate reduction in timber and drainage water from a gold mine

Biogenesis of methane in the heartwood of diseased trees has been shown, but never in timber in service. Studies were undertaken to establish whether methan‐ogens and sulfate‐reducers were present in wooden pit props and drainage water from underground sites in a gold mine. The predominant methanogen in the mine ecosystem was tentatively identified as Methanobacterium bryantii. The sulfate‐reducers comprised Desulfovibrio desulfuricans and Desulfotomaculum antarcticum. Most probable numbers (MPN) of bacteria indicated that 3.5 × 10⁵ methanogenic and 7.9 × 10³ sulfate‐reducing bacteria were present per milliliter of stagnant drainage water. MPN values per gram of timber were lower for methanogens but comparable for sulfate‐reducers. Laboratory model systems predicted a maximum rate of methan‐ogenesis of 2.3 mL methane/g wood per day; however, rates would never attain this value because of nutrient limitations and environmental restrictions. Analysis of gas samples extracted from sealed areas of the gold mine verified the presence of methane.     

Fence management and time since pack formation influence African wild dog escapes from protected areas in South Africa

In human-dominated and highly fragmented landscapes, keeping wildlife within reserve boundaries is vital for conservation success. In South Africa, fences are a widely employed conservation management tool for protected areas and are successful in mitigating human-wildlife conflict. However, fences are permeable, and predators are able to cross through reserve fences. African wild dogs (Lycaon pictus) often leave fenced boundaries, resulting in high capture and translocation costs. Moreover, when wild dog packs (up to 30 individuals) leave fenced reserves they enter human-dominated landscapes where they face strong persecution and livestock predation incurs high costs. The factors driving packs to leave managed reserves are poorly understood, thus, to effectively manage wild dogs in fenced systems, it is important to understand why they leave reserve boundaries. There are several hypotheses as to why wild dogs cross through reserve fences, including inter- and intra-specific competition, social behaviour, management, prey density and environmental variability. Using a long-term dataset comprising 32 resident packs across five reserves, we investigated the relative strength of these hypotheses on the probability of wild dogs exiting a fenced reserve. During the 14-year study period, we recorded 154 exit events. We found that the interaction of fence integrity and time since pack formation were the primary factors affecting the probability of a pack leaving a reserve. When fence integrity was poor, escape probability decreased with pack age likely due to the exploratory behaviour of new packs. When fence integrity was average, escape probability increased with pack age likely due to the fitness benefits of holding larger and more exclusive territories as packs age. When fence integrity was good, the probability of a pack escaping was very low (only 1% occurrence). The implications of this research suggest that the primary management consideration for reducing wild dog escapes from fenced reserves should be maintaining adequate reserve-wide fence integrity, rather than focusing on social structure or drivers of inter- and intra-specific competition.     

Cryptosporidiosis associated with emaciation and proliferative gastritis in a laboratory-reared South African clawed frog (Xenopus laevis)

A 2-year-old emaciated female South African clawed frog (Xenopus laevis) was euthanized because of chronic weight loss. At necropsy, there was no evidence of bacterial, fungal or viral disease; however, the histopathologic findings indicated a proliferative gastritis and the presence of numerous cryptosporidial stages throughout the intestinal tract. Crytosporidial oocysts were present in the water taken from the aquarium housing the infected frog and were likely shed by the sick frog; however, the exact source of the oocysts could not be identified. Water samples from other frog aquaria in the facility did not contain cryptosporidial oocysts. Some Cryptosporidium species are important zoonotic pathogens and, to our knowledge, this is the first report of disease associated with Cryptosporidium infection in a laboratory Xenopus laevis.     

Convergent evolution of alternative developmental trajectories associated with diapause in African and South American killifish

Annual killifish adapted to life in seasonally ephemeral water-bodies exhibit desiccation resistant eggs that can undergo diapause, a period of developmental arrest, enabling them to traverse the otherwise inhospitable dry season. Environmental cues that potentially indicate the season can govern whether eggs enter a stage of diapause mid-way through development or skip this diapause and instead undergo direct development. We report, based on construction of a supermatrix phylogenetic tree of the order Cyprinodontiformes and a battery of comparative analyses, that the ability to produce diapause eggs evolved independently at least six times within African and South American killifish. We then show in species representative of these lineages that embryos entering diapause display significant reduction in development of the cranial region and circulatory system relative to direct-developing embryos. This divergence along alternative developmental pathways begins mid-way through development, well before diapause is entered, during a period of purported maximum developmental constraint (the phylotypic period). Finally, we show that entering diapause is accompanied by a dramatic reduction in metabolic rate and concomitant increase in long-term embryo survival. Morphological divergence during the phylotypic period thus allows embryos undergoing diapause to conserve energy by shunting resources away from energetically costly organs thereby increasing survival chances in an environment that necessitates remaining dormant, buried in the soil and surrounded by an eggshell for much of the year. Our results indicate that adaptation to seasonal aquatic environments in annual killifish imposes strong selection during the embryo stage leading to marked diversification during this otherwise conserved period of vertebrate development.     

Cultivation-dependent and cultivation-independent characterization of the microbial community in acid mine drainage associated with acidic Pb/Zn mine tailings at Lechang, Guangdong, China

Cultivation-based and molecular approaches were used to characterize the phylogenetic composition and structure of the microbial community in an extremely acidic (pH 2.0) acid mine drainage (AMD) associated with Pb/Zn mine tailings that were undergoing vigorous acid generation. Acidophilic bacteria were isolated and enumerated on solid media, and were found to be restricted to isolates related to Acidithiobacillus ferrooxidans and Acidiphilium cryptum. By contrast, cloning and phylogenetic analysis of 16S rRNA genes revealed that, although low in total taxonomically distinct groups, the tailings AMD ecosystem harbored a wide range of phylogenetically diverse microbes. Of the 141 clones examined, 104 were phylogenetically affiliated with the recently discovered, iron-oxidizing Leptospirillum group III within the Nitrospira. It thus appears that iron serves as the major electron donor in this habitat. Thirty clones were affiliated with the Proteobacteria, half of which belonged to organisms related to Alphaproteobacteria species capable of ferric iron reduction. Other clones were grouped with Betaproteobacteria and Gammaproteobacteria (six clones each), and even with Deltaproteobacteria (three clones), a subdivision with anaerobic sulfate or metal (iron) reduction as the predominant physiological trait of its members. Finally, four clones were clustered within the Firmicutes and the Acidobacteria. Approximately half of the sequence types representing the majority of the total clones fell into lineages that are poorly represented by cultured organisms or have thus far been represented by only a few environmental sequences. Thus, the present study extends our knowledge of the biodiversity of microorganisms populating highly acidic AMD environments.     

Nutrient availability and maize growth in a soil amended with earthworm casts from a South African indigenous species

The study was undertaken to assess the availability to maize of nutrients from earthworm casts (wormcasts) collected from a grazing paddock in the Eastern Cape province of South Africa. Maize (cv PAN 473) was grown in pots filled with ground wormcasts, non-casted surrounding soil and a mixture of the two media. Fertiliser application increased growth and uptake of nutrients by maize grown on both wormcast and non-casted soil. Maize grown on wormcasts had significantly (p < 0.05) higher plant height, stem diameter, dry weight and showed higher nutrient uptake and lower fertiliser response than that grown on corresponding non-casted surface soil. The uptakes of plant nutrients, growth and dry matter yields were in the order fertiliser>wormcasts>non-casted soil. Mixing worm casts with non-casted soil improved maize growth and nutrient uptake over non-casted soil. It is concluded that wormcasts could be used as a soil amendment for crop production, especially in small-scale production systems.     

Reduction of vanadium(V) by <Emphasis Type="Italic">Enterobacter cloacae</Emphasis> EV-SA01 isolated from a South African deep gold mine

Dissimilatory reduction of vanadium(V) by Enterobacter cloacae EV-SA01, isolated from a gold mine at 1.6 km below surface, is shown to occur anaerobically as well as aerobically. Growth rates were unaffected by up to 2 mM V₂O₅. Reduction of vanadium(V) was growth phase-dependent and resulted in cell deformities and precipitation of the vanadium in its lower oxidation states. The vanadate reductase activity was membrane-associated and coupled the oxidation of NADH to the reduction of vanadate.     

Isolation and characterization of cellulose-degrading bacteria from the deep subsurface of the Homestake gold mine,Lead, South Dakota,USA

The present study investigated the cultivable mesophilic (37°C) and thermophilic (60°C) cellulose-degrading bacterial diversity in a weathered soil-like sample collected from the deep subsurface (1.5 km depth) of the Homestake gold mine in Lead, South Dakota, USA. Chemical characterization of the sample by X-ray fluorescence spectroscopy revealed a high amount of toxic heavy metals such as Cu, Cr, Pb, Ni, and Zn. Molecular community structures were determined by phylogenetic analysis of 16S rRNA gene sequences retrieved from enrichment cultures growing in presence of microcrystalline cellulose as the sole source of carbon. All phylotypes retrieved from enrichment cultures were affiliated to Firmicutes. Cellulose-degrading mesophilic and thermophilic pure cultures belonging to the genera Brevibacillus, Paenibacillus, Bacillus, and Geobacillus were isolated from enrichment cultures, and selected cultures were studied for enzyme activities. For a mesophilic isolate (DUSELG12), the optimum pH and temperature for carboxymethyl cellulase (CMCase) were 5.5 and 55°C, while for a thermophilic isolate (DUSELR7) they were 5.0 and 75°C, respectively. Furthermore, DUSELG12 retained about 40% CMCase activity after incubation at 60°C for 8 h. Most remarkably, thermophilic isolate, DUSELR7 retained 26% CMCase activity at 60°C up to a period of 300 h. Overall, the present work revealed the presence of different cellulose-degrading bacterial lineages in the unique deep subsurface environment of the mine. The results also have strong implications for biological conversion of cellulosic agricultural and forestry wastes to commodity chemicals including sugars.     

Metabolic Response to a Mixed Meal in Obese and Lean Women from Two South African Populations

Objective: Lower lipid and insulin levels are found during a glucose-tolerance test in obese black than obese white South African women. Therefore, β-cell function and lipid metabolism were compared in these populations during a mixed meal. Research Methods and Procedures: Blood concentrations of glucose, free fatty acids (FFAs), insulin, lipograms, and in vivo FFA oxidation were determined at fasting and for 7 hours after oral administration of a mixed emulsion containing glucose-casein-sucrose-lipid and [1-¹³C] palmitic acid in 8 lean black women (LBW), 10 obese black women (OBW), 9 lean white women (LWW), and 10 obese white women (OWW). Subcutaneous and visceral fat mass was assessed by computerized tomography. Results: Visceral fat area was higher in OWW (152.7 ± 17.0 cm²) than OBW (80.0 ± 6.7 cm²; p < 0.01). In OBW, 30-minute insulin levels were higher (604.3 ± 117.6 pM) than OWW (311.0 ± 42.9 pM; p < 0.05). Total triglyceride was higher in OWW (706.7 ± 96.0 mM × 7 hours) than OBW (465.7 ± 48.2 mM × 7 hours; p < 0.05) and correlated with visceral fat area (β = 0.38, p = 0.05). Palmitate oxidation was higher in lean than obese women in both ethnic groups and correlated negatively with fat mass (β = −0.58, p < 0.005). Discussion: The higher 30-minute insulin response in OBW may reflect a higher insulinotropic effect of FFAs or glucose. The elevated triglyceride level of OWW may be due to their higher visceral fat mass and possibly reduced clearance by adipose tissue.     

Additional fossil Theropithecus from Hopefield, South Africa: a comparison with other African sites and a reevaluation of its taxonomic status

Additional fossil Theropithecus remains, recovered from mid to late Pleistocene deposits near Hopefield , South Africa, include portions of the jaws of at least five individuals. Extensive comparisons with fossil Theropithecus from other African sites, including Makapan , Swartkrans , Kanjera , Olorgesailie , and Olduvai , reveal few morphological differences, especially when variation in modern gelada baboons ( Theropithecus gelada ) and savannah baboons (Papio) is considered. The most pronounced differences between fossil forms are overall size and relative P3 length. However, these traits do not separate the fossil forms either chronologically or geographically. Other traits, such as depth of the fossa of the mandibular corpus, slope of the upper symphyseal shelf, and variation in the depth of the mandibular corpus, do not distinguish alleged primitive forms ( Makapan and lower beds at Olduvai ) from remains found at Hopefield , Swartkrans , Kanjera , Olorgesailie , Olduvai Bed IV, or the lower Ndutu Beds. Other traits, such as canine crown height and incisor size, are poorly documented for fossil Theropithecus . Thus, the available evidence suggests that Theropithecus darti and its successional species, T. oswaldi , can best be considered as a single fossil species, T. oswaldi , of which the remains from Hopefield are a late representative. Furthermore, lack of morphological differences dictates that Hopefield Theropithecus not be considered a distinct subspecies. Variation within the Hopefield sample shows that only one taxa is found at this site. Hypothesized physical and climatic conditions at Hopefield during the Pleistocene suggest that T. oswaldi lived near vleis or fresh water lagoons. Comparisons with modern T. gelada suggest a graminivorous diet for the fossil form.     

Characterization and sequence elucidation of a novel peptide with molt-inhibiting activity from the South African spiny lobster, Jasus lalandii

We have isolated a peptide from extracts of sinus glands from a South African spiny lobster species, Jasus lalandii, by high-performance liquid chromatography (HPLC) and identified it as a putative molt-inhibiting hormone (MIH) by (i) an in vitro assay with J. lalandii Y-organs to measure the inhibition of ecdysteroid synthesis and (ii) an immunoassay using antiserum raised against MIH of the edible crab. The MIH of J. lalandii has 74 amino acid residues, a molecular mass of 9006 Da, a free N-terminus and an amidated C-terminus. The full primary sequence has been obtained from sequencing various digest fragments (tryptic, endoproteinase Asp-N, cyanogen bromide) of the unreduced (native) peptide: RFTFDCPGMMGQRYLYEQVEQVCDDCYNLYREEKIAVNCRENCFLNSWFTVCLQATMREHETPRFDIWR SIILKA-NH(2). Structural comparisons with other peptides show that the J. lalandii MIH belongs to the peptide family which includes the crustacean hyperglycemic hormone, molt-inhibiting hormone and vitellogenesis-inhibiting hormone (cHH/MIH/VIH). This novel peptide has 36-43% sequence identity to putative MIHs from other decapod crustaceans and 32-34% identity to the two cHH peptides previously identified in this spiny lobster species. This is the first report of a peptide with MIH activity in the Palinuridae infraorder.