Copper resistance in Desulfovibrio strain R2

A sulfate-reducing bacterium, designated as strain R2, was isolated from wastewater of a ball-bearing manufacturing facility in Tomsk, Western Siberia. This isolate was resistant up to 800 mg Cu/l in the growth medium. By comparison, Cu-resistance of reference cultures of sulfate-reducing bacteria ranged from 50 to 75 mg Cu/l. Growth experiments with strain R2 showed that Cu was an essential trace element and, on one hand, enhanced growth at concentrations up to 10 mg/l but, on the other hand, the growth rate decreased and lag-period extended at copper concentrations of >50 mg/l. Phenotypic characteristics and a 1078 bp nucleotide sequence of the 16S rDNA placed strain R2 within the genus Desulfovibrio. Desulfovibrio R2 carried at least one plasmid of approximately of 23.1 kbp. A 636 bp fragment ot the pcoR gene of the pco operon that encodes Cu resistance was amplified by PCR from plasmid DNA of strain R2. The pco genes are involved in Cu-resistance in some enteric and aerobic soil bacteria. Desulfovibrio R2 is a prospective strain for bioremediation purposes and for developing a homologous system for transformation of Cu-resistance in sulfate-reducing bacteria. This revised version was published online in June 2006 with corrections to the Cover Date.     

Genomics, metagenomics and proteomics in biomining microorganisms

The use of acidophilic, chemolithotrophic microorganisms capable of oxidizing iron and sulfur in industrial processes to recover metals from minerals containing copper, gold and uranium is a well established biotechnology with distinctive advantages over traditional mining. A consortium of different microorganisms participates in the oxidative reactions resulting in the extraction of dissolved metal values from ores. Considerable effort has been spent in the last years to understand the biochemistry of iron and sulfur compounds oxidation, bacteria-mineral interactions (chemotaxis, quorum sensing, adhesion, biofilm formation) and several adaptive responses allowing the microorganisms to survive in a bioleaching environment. All of these are considered key phenomena for understanding the process of biomining. The use of genomics, metagenomics and high throughput proteomics to study the global regulatory responses that the biomining community uses to adapt to their changing environment is just beginning to emerge in the last years. These powerful approaches are reviewed here since they offer the possibility of exciting new findings that will allow analyzing the community as a microbial system, determining the extent to which each of the individual participants contributes to the process, how they evolve in time to keep the conglomerate healthy and therefore efficient during the entire process of bioleaching.     

Strength of Cu-efflux response in Escherichia coli coordinates metal resistance in Caenorhabditis elegans and contributes to the severity of environmental toxicity

Without effective homeostatic systems in place, excess copper (Cu) is universally toxic to organisms. While increased utilization of anthropogenic Cu in the environment has driven the diversification of Cu-resistance systems within enterobacteria, little research has focused on how this change in bacterial architecture impacts host organisms that need to maintain their own Cu homeostasis. Therefore, we utilized a simplified host–microbe system to determine whether the efficiency of one bacterial Cu-resistance system, increasing Cu-efflux capacity via the ubiquitous CusRS two-component system, contributes to the availability and subsequent toxicity of Cu in host Caenorhabditis elegans nematode. We found that a fully functional Cu-efflux system in bacteria increased the severity of Cu toxicity in host nematodes without increasing the C. elegans Cu-body burden. Instead, increased Cu toxicity in the host was associated with reduced expression of a protective metal stress-response gene, numr-1, in the posterior pharynx of nematodes where pharyngeal grinding breaks apart ingested bacteria before passing into the digestive tract. The spatial localization of numr-1 transgene activation and loss of bacterially dependent Cu-resistance in nematodes without an effective numr-1 response support the hypothesis that numr-1 is responsive to the bacterial Cu-efflux capacity. We propose that the bacterial Cu-efflux capacity acts as a robust spatial determinant for a host’s response to chronic Cu stress.     

Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments

Nitrate is an important nutrient and electron acceptor for microorganisms, having a key role in nitrogen (N) cycling and electron transfer in anoxic sediments. High-nitrate inputs into sediments could have a significant effect on N cycling and its associated microbial processes. However, few studies have been focused on the effect of nitrate addition on the functional diversity, composition, structure and dynamics of sediment microbial communities in contaminated aquatic ecosystems with persistent organic pollutants (POPs). Here we analyzed sediment microbial communities from a field-scale in situ bioremediation site, a creek in Pearl River Delta containing a variety of contaminants including polybrominated diphenyl ethers (PBDEs) and polycyclic aromatic hydrocarbons (PAHs), before and after nitrate injection using a comprehensive functional gene array (GeoChip 4.0). Our results showed that the sediment microbial community functional composition and structure were markedly altered, and that functional genes involved in N-, carbon (C)-, sulfur (S)-and phosphorus (P)- cycling processes were highly enriched after nitrate injection, especially those microorganisms with diverse metabolic capabilities, leading to potential in situ bioremediation of the contaminated sediment, such as PBDE and PAH reduction/degradation. This study provides new insights into our understanding of sediment microbial community responses to nitrate addition, suggesting that indigenous microorganisms could be successfully stimulated for in situ bioremediation of POPs in contaminated sediments with nitrate addition.     

Bioaccumulation of copper, lead and zinc by the bivalves Macomona liliana and Austrovenus stutchburyi

Aquatic organisms take up heavy metals from surrounding environments which accumulate in their body tissues. In the region of Auckland, New Zealand, the heavy metals, copper (Cu), lead (Pb) and zinc (Zn) are the primary sediment contaminants of concern. Previous investigations have revealed adverse effects of Cu and Zn, but not of Pb, on estuarine infauna and a higher sensitivity of the deposit-feeding bivalve Macomona liliana than the suspension-feeding bivalve Austrovenus stutchburyi to these metals. In order to further examine the bioavailability of Cu, Pb and/or Zn and their interactive effects, bioaccumulation of Cu, Pb and Zn was measured in M. liliana and A. stutchburyi after 10-day exposure to these metals in the laboratory. Both bivalves accumulated Pb and Zn, while bioaccumulation of Cu only occurred in A. stutchburyi in the presence of Zn. There was some evidence that the presence of Pb could increase bioaccumulation of Zn. Bioaccumulation was generally much higher in M. liliana than in A. stutchburyi, potentially suggesting their higher uptake rates of metals and thus explaining the higher sensitivity of M. liliana to these heavy metals. Bioaccumulation of Pb in the bivalves and its potential influences on the bioavailability of other metals indicated that, despite the lack of any evidence for acute toxicity of Pb in previous studies, it could still pose a potentially important environmental threat. Bioaccumulation of heavy metals found in the present study also highlights the needs for further investigations of potential chronic toxicity of these metals.     

A genomic island provides <Emphasis Type="Italic">Acidithiobacillus ferrooxidans</Emphasis> ATCC 53993 additional copper resistance: a possible competitive advantage

There is great interest in understanding how extremophilic biomining bacteria adapt to exceptionally high copper concentrations in their environment. Acidithiobacillus ferrooxidans ATCC 53993 genome possesses the same copper resistance determinants as strain ATCC 23270. However, the former strain contains in its genome a 160-kb genomic island (GI), which is absent in ATCC 23270. This GI contains, amongst other genes, several genes coding for an additional putative copper ATPase and a Cus system. A. ferrooxidans ATCC 53993 showed a much higher resistance to CuSO₄ (>100 mM) than that of strain ATCC 23270 (<25 mM). When a similar number of bacteria from each strain were mixed and allowed to grow in the absence of copper, their respective final numbers remained approximately equal. However, in the presence of copper, there was a clear overgrowth of strain ATCC 53993 compared to ATCC 23270. This behavior is most likely explained by the presence of the additional copper-resistance genes in the GI of strain ATCC 53993. As determined by qRT-PCR, it was demonstrated that these genes are upregulated when A. ferrooxidans ATCC 53993 is grown in the presence of copper and were shown to be functional when expressed in copper-sensitive Escherichia coli mutants. Thus, the reason for resistance to copper of two strains of the same acidophilic microorganism could be determined by slight differences in their genomes, which may not only lead to changes in their capacities to adapt to their environment, but may also help to select the more fit microorganisms for industrial biomining operations.     

Thermophilic microorganisms in biomining

Biomining is an applied biotechnology for mineral processing and metal extraction from ores and concentrates. This alternative technology for recovering metals involves the hydrometallurgical processes known as bioleaching and biooxidation where the metal is directly solubilized or released from the matrix for further solubilization, respectively. Several commercial applications of biomining can be found around the world to recover mainly copper and gold but also other metals; most of them are operating at temperatures below 40–50 °C using mesophilic and moderate thermophilic microorganisms. Although biomining offers an economically viable and cleaner option, its share of the world´s production of metals has not grown as much as it was expected, mainly considering that due to environmental restrictions in many countries smelting and roasting technologies are being eliminated. The slow rate of biomining processes is for sure the main reason of their poor implementation. In this scenario the use of thermophiles could be advantageous because higher operational temperature would increase the rate of the process and in addition it would eliminate the energy input for cooling the system (bioleaching reactions are exothermic causing a serious temperature increase in bioreactors and inside heaps that adversely affects most of the mesophilic microorganisms) and it would decrease the passivation of mineral surfaces. In the last few years many thermophilic bacteria and archaea have been isolated, characterized, and even used for extracting metals. This paper reviews the current status of biomining using thermophiles, describes the main characteristics of thermophilic biominers and discusses the future for this biotechnology.     

Cytoplasmic membrane response to copper and nickel in Acidithiobacillus ferrooxidans

Metal tolerance has been found to vary among Acidithiobacillus ferrooxidans strains and this can impact the efficiency of biomining practices. To explain observed strain variability for differences in metal tolerance we examined the effects of Cu²⁺ and Ni²⁺ concentrations (1-200 mM) on cytoplasmic membrane properties of two A. ferrooxidans type strains (ATCC 23270 and 19859) and four strains isolated from AMD water around Sudbury, Ontario, Canada. Growth rate, membrane fluidity and phase, determined from the fluorescence polarization of 1,6-diphenyl-1,3,5-hexatriene (DPH), and fatty acid profiles indicated that three different modes of adaptation were present and could separate between strains showing moderate, or high metal tolerance from more sensitive strains. To compensate for the membrane ordering effects of the metals, significant remodelling of the membrane was used to either maintain homeoviscous adaptation in the moderately tolerant strains or to increase membrane fluidity in the sensitive strains. Shifts in the gel-to-liquid crystalline transition temperature in the moderately tolerant strains led to multiple phase transitions, increasing the potential for phase separation and compromised membrane integrity. The metal-tolerant strain however, was able to tolerate increases in membrane order without significant compensation via fatty acid composition. Our multivariate analyses show a common adaptive response which involves changes in the abundant 16:0 and 18:1 fatty acids. However, fatty acid composition and membrane properties showed no difference in response to either copper or nickel suggesting that adaptive response was non-specific and tolerance dependent. We demonstrate that strain variation can be evaluated using differences in membrane properties as intrinsic determinants of metal susceptibility.     

Manganese biomining: A review

Biomining comprises of processing and extraction of metal from their ores and concentrates using microbial techniques. Currently this is used by the mining industry to extract copper, uranium and gold from low grade ores but not for low grade manganese ore in industrial scale. The study of microbial genomes, metabolites and regulatory pathways provide novel insights to the metabolism of bioleaching microorganisms and their synergistic action during bioleaching operations. This will promote understanding of the universal regulatory responses that the biomining microbial community uses to adapt to their changing environment leading to high metal recovery. Possibility exists of findings ways to imitate the entire process during industrial manganese biomining endeavor. This paper reviews the current status of manganese biomining research operations around the world, identifies factors that drive the selection of biomining as a processing technology, describes challenges in exploiting these innovations, and concludes with a discussion of Mn biomining’s future.     

Life-history traits of a tube-dwelling corophioid amphipod, Paracorophium excavatum, exposed to sediment copper

This is the first demonstration that sediment contaminants can influence the reproduction of amphipods. Groups of Paracorophium excavatum from a slightly contaminated estuarine site were held within laboratory mesocosms containing four copper-spiked estuarine sediments (Cu 14-46 μg g⁻¹ dry weight) and a control sediment (Cu 5 μg g⁻¹ dry weight) at 15 °C for 28 days. Copper sediment concentration did not affect the amphipod sex ratio. Female maturation was inhibited within copper-spiked sediments but female length was similar. Juvenile recruitment occurred only in sediments containing less than 20 μg g⁻¹. Males were significantly larger than females in the control sediment (Cu 5 μg g⁻¹ dry weight) and male length decreased linearly with increasing copper concentration. The copper concentration within whole body tissues increased with dry body dry weight in all sediments except the highest copper concentration. Following 28 days of exposure, none of the female amphipods from the copper-dosed sediments was brooding embryos. In contrast, brood size of females in the control sediment (Cu 5 μg g⁻¹) was similar to field samples. Because low concentrations of sediment copper affect the maturation and growth rates of male and female amphipods differently, these life-history traits could affect the population structure of amphipods exposed to copper contaminated sediments.     

Characteristics and adaptability of iron- and sulfur-oxidizing microorganisms used for the recovery of metals from minerals and their concentrates

Microorganisms are used in large-scale heap or tank aeration processes for the commercial extraction of a variety of metals from their ores or concentrates. These include copper, cobalt, gold and, in the past, uranium. The metal solubilization processes are considered to be largely chemical with the microorganisms providing the chemicals and the space (exopolysaccharide layer) where the mineral dissolution reactions occur. Temperatures at which these processes are carried out can vary from ambient to 80°C and the types of organisms present depends to a large extent on the process temperature used. Irrespective of the operation temperature, biomining microbes have several characteristics in common. One shared characteristic is their ability to produce the ferric iron and sulfuric acid required to degrade the mineral and facilitate metal recovery. Other characteristics are their ability to grow autotrophically, their acid-tolerance and their inherent metal resistance or ability to acquire metal resistance. Although the microorganisms that drive the process have the above properties in common, biomining microbes usually occur in consortia in which cross-feeding may occur such that a combination of microbes including some with heterotrophic tendencies may contribute to the efficiency of the process. The remarkable adaptability of these organisms is assisted by several of the processes being continuous-flow systems that enable the continual selection of microorganisms that are more efficient at mineral degradation. Adaptability is also assisted by the processes being open and non-sterile thereby permitting new organisms to enter. This openness allows for the possibility of new genes that improve cell fitness to be selected from the horizontal gene pool. Characteristics that biomining microorganisms have in common and examples of their remarkable adaptability are described.     

Growth, reproductive and photosynthetic responses to copper in the yellow-horned poppy, Glaucium flavum Crantz.

Glaucium flavum Crantz. is found in an anthropized coastal grassland at the joint estuary of the Tinto and Odiel rivers (SW Spain), growing under the influence of high levels of copper contamination derived from nearby petrochemical industries, with no obvious adverse affects on the performance of the plant. In addition, this species exhibits a series of ecological characteristics which may render it appropriate for use in the phytoremediation of contaminated areas. Nonetheless, the response of G. flavum to elevated copper concentrations has not been studied. A greenhouse experiment was conducted to investigate the effects of a range of Cu concentrations (0 to 47 mmol l⁻¹) on the growth, reproduction and photosynthetic performance of G. flavum, by measuring relative growth rate, fruit and seed production, chlorophyll fluorescence parameters, gas exchange and photosynthetic pigment concentrations. We also determined total copper, nitrogen, phosphorous, sulphur, calcium and magnesium concentrations. G. flavum survived with concentrations of up to 730 mg Cu kg⁻¹ DW in the leaves, when treated with 30 mmol Cu l⁻¹ (2000 mg l⁻¹). Quantum efficiency of PSII, net photosynthesis rate, as well as leaf Ca and Mg concentrations were all negatively affected by Cu concentrations greater than 9 mmol l⁻¹ in the nutrient solution. Our results indicate that the reduction in photosynthetic performance may be attributed to the adverse effect of excess Cu on the photosynthetic apparatus of the plant, both directly, via a decrease in pigment concentrations, and indirectly, via interference of Cu with Ca ions of PSII. Growth and seed production were only slightly affected by leaf tissue concentrations as high as 230 mg Cu kg⁻¹ dry mass, which suggests that this species could play an important role in phytoremediation of Cu-contaminated soils.     

Structural determination of the O-chain polysaccharide from the haloalkaliphilic Halomonas alkaliantarctica bacterium strain CRSS

In hypersaline environments there are plenty of microorganisms belonging to both Bacteria and Archaea domains. These extremophiles have developed biochemical adaptations which comprise the accumulation of molar concentrations of potassium and chloride and the biosynthesis and/or the accumulation of organic osmotic solutes (osmolytes) within the cytoplasm. Moreover, to maintain the turgor of the cells halophiles enhance the production of anionic phospholipids and alter the fatty acid composition of the membrane lipids, but very little is known about adaptational structural changes of the lipopolysaccharides (LPS), the main constituent of the outer leaflet of the outer membrane of Gram-negative bacteria. The aim of this work is to investigate the chemical structure of these LPS in order to provide insight into the adaptation mechanism of halophiles to live at high salt concentration. For this, Halomonas alkaliantarctica, a haloalkaliphilic Gram-negative bacterium isolated from salt sediments of a saline lake in Cape Russell in the Antarctic continent, was cultivated and the LPS were extracted and analysed. The structure of the O-chain of the LPS from H. alkaliantarctica was determined by chemical analysis, 1-D and 2-D NMR spectroscopy. The polysaccharide was constituted of a linear trisaccharidic repeating unit as follows:→3)-β-l-Rhap-(1→4)-α-l-Rhap-(1→3)-α-l-Rhap-(1→A comparison among the O-chain structures of H. alkaliantarctica and other Halomonas species is also reported.     

NMR and homology modeling studies of copper(II)-halocyanin from Natronobacterium pharaonis bacteria

Halocyanin from the haloalkaliphilic archaean Natronobacterium pharaonis is a peripheral membrane type 1 blue copper protein with a single polypeptide chain of 163 amino acid residues. Halocyanin participates as putative electron carrier protein associated to an electron acceptor role for a terminal oxidase and has the lowest redox potential value reported to date for a BCP. NMR studies and homology modeling calculations were performed to evaluate the electronic properties of Cu(II)-halocyanin from Natronobacterium pharaonis. The copper coordination site properties of Cu(II)-halocyanin are discussed. The ¹H NMR spectra, isotropic chemical shifts and relaxation times for halocyanin are compared with those of other BCPs such as azurin, amicyanin, plastocyanin and stellacyanin. The wild-type Cu(II)-halocyanin presents almost the same ¹H NMR spectra in comparison with Cu(II)-plastocyanin as expected from a similar coordination symmetry. However, minor differences were found. In order to get some insight on these differences, a computational model for Cu(II)-halocyanin from N. pharaonis was built. Model is based on sequential homology of halocyanin with two different families of proteins: plastocyanins and pseudoazurins. Homology modeling was performed using two different structural templates and copper ion was added for further refinement of the coordination site. Proposed structure was in good agreement with NMR experimental information and is the first three-dimensional model reported to date of an halocyanin. Small differences were found in the copper coordination site with respect to other BCP with known structure. This work is also an interesting example of expertise-driven homology modeling across different protein families.     

Effects of copper sulphate concentrations during in vitro maturation of bovine oocytes

The objectives were to evaluate

1) copper (Cu) concentrations in plasma and follicular fluid (FF) from cattle ovaries; 2) the effects of supplemental Cu during in vitro maturation (IVM) on DNA damage of cumulus cells and glutathione (GSH) content in oocytes and cumulus cells; and 3) supplementary Cu during IVM on subsequent embryo development. Copper concentrations in heifer plasma (116 ± 27.1 μg/dL Cu) were similar (P > 0.05) to concentrations in FF from large (90 ± 20.4 μg/dL Cu) and small (82 ± 22.1 μg/dL Cu) ovarian follicles in these heifers. The DNA damage in cumulus cells decreased with supplemental Cu concentrations of 4 and 6 μg/mL (P < 0.01) in the IVM medium (mean ± SEM index of DNA damage was: 200.0 ± 27.6, 127.6 ± 6.0, 46.4 ± 4.8, and 51.1 ± 6.0 for supplementation with 0, 2, 4, and 6 μg/mL Cu respectively). Total GSH concentrations increased following supplementation with 4 μg/mL Cu (4.7 ± 0.4 pmol in oocytes and 0.4 ± 0.04 nmol/10⁶ cumulus cells) and 6 μg/mL Cu (5.0 ± 0.5 pmol in oocytes and 0.5 ± 0.05 nmol/10⁶ cumulus cells, P < 0.01) compared with the other classes. Cleavage rates were similar (P ≥ 0.05) when Cu was added to the IVM medium at any concentration (65.1 ± 2.0, 66.6 ± 1.6, 72.0 ± 2.1, and 70.7 ± 2.1 for Cu concentrations of 0, 2, 4, and 6 μg/mL). Percentages of matured oocytes that developed to the blastocyst stage were 18.7 ± 0.6, 26.4 ± 0.03, and 29.0 ± 1.7% for 0, 2, and 4 μg/mL Cu, and was highest (33.2 ± 1.6 %) in oocytes matured with 6 μg/mL Cu (P > 0.01). There was an increase (P > 0.05) in mean cell number per blastocyst obtained from oocytes matured with 4 and 6 μg/mL Cu relative to 0 Cu (IVM alone) and 2 μg/mL Cu. In conclusion, Cu concentrations in the FF and plasma of heifers were similar. Adding copper during oocyte maturation significantly increased both intracellular GSH content and DNA integrity of cumulus cells. Since embryo development was responsive to copper supplementation, we inferred that optimal embryo development to the blastocyst stage was partially dependent on the presence of adequate Cu concentrations during IVM.     

Effect of copper exposure on GST activity and on the expression of four GSTs under oxidative stress condition in the monogonont rotifer, Brachionus koreanus

Glutathione S-transferases (GSTs; EC 2.5.1.18) are major enzymes that function in Phase II detoxification reactions by catalyzing the conjugation of reduced glutathione through cysteine thiol. In this study, we cloned and sequenced four GST genes from the monogonont rotifer Brachionus koreanus. The domain regions of four Bk-GSTs showed a high similarity to those of other species. In addition, to evaluate the potential of GST genes as an early warning signal for oxidative stress, we exposed sublethal concentrations of copper (Cu) to B. koreanus and measured glutathione (GSH) contents and several antioxidant enzymes such as glutathione S-transferase (GST), glutathione peroxidase (GPx; EC 1.11.1.9), and glutathione reductase (GR; EC 1.8.1.7). The reactive oxygen species (ROS) at 12 h and 24 h after copper exposure increased significantly. GSH contents however did not increase significantly and even it decreased at 0.24 mg/L at 12 h. The activities of several antioxidant enzymes, particularly GPx and GR, showed a dramatic increase in 0.24 mg/L of CuCl₂. Messenger RNAs of each Bk-GST showed different patterns of modulations according to GST types, and particularly, Bk-GST-omega, Bk-GST-sigma, and Bk-GST zeta genes were highly sensitive to Cu. These results indicate that Bk-GSTs, functioning as one of the enzymatic defense mechanisms particularly in the early stage of oxidative stress response, were induced by Cu exposure. This also suggests that these genes and related enzymes have a potential as biomarkers for a more sensitive initial stress response.