Superoxide dismutases of heavy metal resistant streptomycetes

Biodiversity of Actinomycetes from Heavy Metal Contaminated Technosols

Technosols are artificial soils generated by diverse human activities and frequently contain toxic substances resulting from industrial processes. Due to lack of nutrients and extreme physico-chemical properties, they represent environments with limited bacterial colonization. Bacterial populations of technosols are dominated usually by Actinobacteria, including streptomycetes, known as a tremendous source of biotechnologically important molecules. In this study, the biodiversity of streptomycete-like isolates from several technosols, mainly mine soils and wastes (landfills and sludge) in Slovakia, was investigated. The combination of basic morphological and biochemical characterisations, including heavy metal resistance determination, and molecular approaches based on 16S rRNA gene analysis were used for the identification of the bacterial strains. From nine isolates of Actinobacteria collected from different habitats, one was found to represent a new species within the Crossiella genus. Eight other isolates were assigned to the genus Streptomyces, of which at least one could represent a new bacterial species. Some isolates showed high resistance to Pb, Zn, Cu or Ni. The most tolerated metal was Pb. The results obtained in this study indicate that technosols are a prospective source of new actinomycete species resistant to heavy metals what underlines their bioremediation potential.

Microfluidically supported characterization of responses of Rhodococcus erythropolis strains isolated from different soils on Cu-, Ni-, and Co-stress

We present a new methodological approach for the assessment of the susceptibility of Rhodococcus erythropolis strains from specific sampling sites in response to increasing heavy metal concentration (Cu²⁺, Ni²⁺, and Co²⁺) using the droplet-based microfluid technique. All isolates belong to the species R. erythropolis identified by Sanger sequencing of the 16S rRNA. The tiny step-wise variation of metal concentrations from zero to the lower mM range in 500 nL droplets not only provided accurate data for critical metal ion concentrations but also resulted in a detailed visualization of the concentration-dependent response of bacterial growth and autofluorescence activity. As a result, some of the isolates showed similar characteristics in heavy metal tolerance against Cu²⁺, Ni²⁺, and Co²⁺. However, significantly different heavy metal tolerances were found for other strains. Surprisingly, samples from the surface soil of ancient copper mining areas supplied mostly strains with a moderate sensitivity to Cu²⁺, Ni²⁺, and Co²⁺, but in contrast, a soil sample from an excavation site of a medieval city that had been covered for about eight centuries showed an extremely high tolerance against cobalt ion (up to 36 mM). The differences among the strains not only may be regarded as results of adaptation to the different environmental conditions faced by the strains in nature but also seem to be related to ancient human activities and temporal partial decoupling of soil elements from the surface. This investigation confirmed that microfluidic screening offers empirical characterization of properties from same species which has been isolated from sites known to have different human activities in the past.

Natural attenuation of lead by microbial manganese oxides in a karst aquifer

Lead is a toxic environmental contaminant associated with current and historic mine sites. Here we studied the natural attenuation of Pb in a limestone cave system that receives drainage from the ancient Priddy Mineries, UK. Extensive deposits of manganese oxides were observed to be forming on the cave walls and as coatings in the stream beds. Analysis of these deposits identified them as birnessite (δ-MnO₂), with some extremely high concentrations of sorbed Pb (up to 56 wt%) also present. We hypothesised that these cave crusts were actively being formed by microbial Mn(II)-oxidation, and to investigate this the microbial communities were characterised by DNA sequencing, enrichment and isolation experiments. The birnessite deposits contained abundant and diverse prokaryotes and fungi, with ~5% of prokaryotes and ~ 10% of fungi closely related to known heterotrophic Mn(II)-oxidisers. A substantial proportion (up to 17%) of prokaryote sequences were assigned to groups known as autotrophic ammonia and nitrite oxidisers, suggesting that nitrogen cycling may play an important role in contributing energy and carbon to the cave crust microbial communities and consequently the formation of Mn(IV) oxides and Pb attenuation. Enrichment and isolation experiments showed that the birnessite deposits contained Mn(II)-oxidising microorganisms, and two isolates (Streptomyces sp. and Phyllobacterium sp.) could oxidise Mn(II) in the presence of 0.1 mM Pb. Supplying the enrichment cultures with acetate as a source of energy and carbon stimulated Mn(II)-oxidation, but excess organics in the form of glucose generated aqueous Mn(II), likely via microbial Mn(IV)-reduction. In this karst cave, microbial Mn(II)-oxidation contributes to the active sequestration and natural attenuation of Pb from contaminated waters, and therefore may be considered a natural analogue for the design of wastewater remediation systems and for understanding the geochemical controls on karst groundwater quality, a resource relied upon by billions of people across the globe.

Changes in element availability induced by sterilization in heavy metal contaminated substrates: A comprehensive study

Microbiome analyses of soils and microcosm experiments depend on conditions that include sterilization in order to perform experimental manipulation of microbial communities. Still, they should represent conditions close to nature. When using metal contaminated soils, sterilization methods might alter metal availability. Here, four typical metal contaminated substrates were analyzed, representing different contamination histories and soil types. They included two very poor substrates, as they are often found at metal contaminated sites. The low contents in organic carbon and nitrogen as well as two substrates with slightly higher nutrient availability were used to perform a comprehesive study for element availability changes induced by sterilization. Autoclaving, dry heat or gamma raγ sterilization were applied and compared to a non-treated control. The sterile substrates were analyzed using sequential extraction to account for different associations of the elements. Metals forming specific (hydro)oxide layers were specifically analyzed since they in turn may also impact other metals or ions. In addition, (heavy) metals and (micro)nutrients were analyzed for changes in speciation. The effects of autoclaving (wet heat) was found acceptable, while γ-ray irradiation did show unexpected changes in metal associations, especially for one substrate. Dry heat changed metal availability to the highest degree.

Effects of arsenite stress on growth and proteome of Klebsiella pneumoniae

In the present study an arsenite, As(III), tolerating bacterium, MR4, was isolated from Mulla River Pune, India, capable of reducing arsenate to arsenite and identified as Klebsiella pneumoniae (HQ857583). Comparative proteomic analysis using two-dimensional gel electrophoresis (2-DGE) and matrix assisted laser desorption ionization-time of flight-time of flight (MALDI-TOF/TOF) was used to monitor the proteins undergoing changes in expression levels under 2.5 mM As(III) stress. The 2-DGE proteome map has shown that 60 proteins were differentially expressed under As(III) stress, of which 39 proteins were successfully identified with a MASCOT score greater than 70 (p<0.05). Among the identified proteins, membrane transport/binding proteins, porins, and amino acid metabolism enzymes were down-regulated while stress responsive proteins and antioxidant enzymes were up-regulated. Proteins involved in carbohydrate metabolism, particularly those in pentose phosphate pathway were also up-regulated while those involved in pyruvate metabolism were down-regulated. However, proteins involved in glycolysis and tricarboxylic acid cycle showed a mixed regulation response. These findings provide new insights into the probable mechanisms by which K. pneumoniae (HQ857583) could be adapting to As(III) stress.

Responses of environmental Amycolatopsis strains to copper stress

Copper is a redox-active metal, which acts as a catalyst in the formation of Reactive Oxygen Species (ROS) encouraging oxidative stress. Protection against oxidants is intrinsic to every living cell; however, in stress conditions, cells are forced to increase and expand their antioxidative network. In this work, the novel copper-resistant strain Amycolatopsis tucumanensis and the copper-sensitive Amycolatopsis eurytherma were grown under copper increasing concentrations in order to elucidate the dissimilar effects of the metal on the strains viability, mainly on morphology and antioxidant capacity. Although biosorbed copper encouraged ROS production in a dose-dependent manner in both strains, the increase in ROS production from the basal level to the stress conditions in A. tucumanensis is lesser than in the copper-sensitive strain; likewise, in presence of copper A. eurytherma suffered inexorable morphological alteration while A. tucumanensis was not affected. The levels of antioxidant enzymes and metallothioneins (MT) were all greater in A. tucumanensis than in A. eurytherma; in addition MT levels as well as superoxide dismutase and thioredoxin reductase activities in A. tucumanensis, were higher as higher the concentration of copper in the culture medium. This work has given evidence that an efficient antioxidant defense system might aid microorganisms to survive in copper-stress conditions; besides it constitutes the first report of oxidative stress study in the genus Amycolatopsis and contributes to enlarge the knowledge on the copper-resistance mechanisms of A. tucumanensis.

Essential roles and hazardous effects of nickel in plants

With the world's ever increasing human population, the issues related to environmental degradation of toxicant chemicals are becoming more serious. Humans have accelerated the emission to the environment of many organic and inorganic pollutants such as pesticides, salts, petroleum products, acids, heavy metals, etc. Among different environmental heavy-metal pollutants, Ni has gained considerable attention in recent years, because of its rapidly increasing concentrations in soil, air, and water in different parts of the world. The main mechanisms by which Ni is taken up by plants are passive diffusion and active transport. Soluble Ni compounds are preferably absorbed by plants passively, through a cation transport system; chelated Ni compounds are taken up through secondary, active-transport-mediated means, using transport proteins such as permeases. Insoluble Ni compounds primarily enter plant root cells through endocytosis. Once absorbed by roots, Ni is easily transported to shoots via the xylem through the transpiration stream and can accumulate in neonatal parts such as buds, fruits, and seeds. The Ni transport and retranslocation processes are strongly regulated by metal-ligand complexes (such as nicotianamine, histidine, and organic acids) and by some proteins that specifically bind and transport Ni. Nickel, in low concentrations, fulfills a variety of essential roles in plants, bacteria, and fungi. Therefore, Ni deficiency produces an array of effects on growth and metabolism of plants, including reduced growth, and induction of senescence, leaf and meristem chlorosis, alterations in N metabolism, and reduced Fe uptake. In addition, Ni is a constituent of several metallo-enzymes such as urease, superoxide dismutase, NiFe hydrogenases, methyl coenzyme M reductase, carbon monoxide dehydrogenase, acetyl coenzyme-A synthase, hydrogenases, and RNase-A. Therefore, Ni deficiencies in plants reduce urease activity, disturb N assimilation, and reduce scavenging of superoxide free radical. In bacteria, Ni participates in several important metabolic reactions such as hydrogen metabolism, methane biogenesis, and acetogenesis. Although Ni is metabolically important in plants, it is toxic to most plant species when present at excessive amounts in soil and in nutrient solution. High Ni concentrations in growth media severely retards seed germinability of many crops. This effect of Ni is a direct one on the activities of amylases, proteases, and ribonucleases, thereby affecting the digestion and mobilization of food reserves in germinating seeds. At vegetative stages, high Ni concentrations retard shoot and root growth, affect branching development, deform various plant parts, produce abnormal flower shape, decrease biomass production, induce leaf spotting, disturb mitotic root tips, and produce Fe deficiency that leads to chlorosis and foliar necrosis. Additionally, excess Ni also affects nutrient absorption by roots, impairs plant metabolism, inhibits photosynthesis and transpiration, and causes ultrastructural modifications. Ultimately, all of these altered processes produce reduced yields of agricultural crops when such crops encounter excessive Ni exposures.

Development of a functional cis-prolyl bond biomimetic and mechanistic implications for nickel superoxide dismutase

During recent years several peptide-based Ni superoxide dismutase (NiSOD) models have been developed. These NiSOD models show an important structural difference compared to the native NiSOD enzyme, which could cause a completely different mechanism of superoxide dismutation. In the native enzyme the peptide bond between Leu4 and Pro5 is cis-configured, while the NiSOD models exhibit a trans-configured peptide bond between these two residues. To shed light on how the configuration of this single peptide bond influences the activity of the NiSOD model peptides, a new cis-prolyl bond surrogate was developed. As surrogate we chose a leucine/alanine-based disubstituted 1,2,3-triazole, which was incorporated into the NiSOD model peptide replacing residues Leu4 and Pro5. The yielded 1,5-disubstituted triazole nickel peptide exhibited high SOD activity, which was approximately the same activity as its parent trans-configured analogue. Hence, the conformation of the prolyl peptide bond apparently has of minor importance for the catalytic activity of the metallopeptides as postulated in literature. Furthermore, it is shown that the triazole metallopeptide is forming a stable cyanide adduct as a substrate analogue model complex.

Metallomics: lessons for metalliferous soil remediation

The term metallomics has been established for the investigation of transcriptome, proteome, and metabolome changes induced by metals. The mechanisms allowing the organisms to cope with metals in the environment, metal resistance factors, will in turn change biogeochemical cycles of metals in soil, coupling the metal pool with the root system of plants. This makes microorganisms key players in introducing metals into food webs, as well as for bioremediation strategies. Research on physiological and metabolic responses of microorganisms on metal stress in soil is thus essential for the selection of optimized consortia applicable in bioremediation strategies such as bioaugmentation or microbially enhanced phytoextraction. The results of metallomics studies will help to develop applications including identification of biomarkers for ecotoxicological studies, bioleaching, in situ soil regeneration, and microbially assisted phytoremediation of contaminated land. This review will therefore focus on the molecular understanding of metal resistance in bacteria and fungi, as can be derived from metallomics studies.

New insight into the mode of action of nickel superoxide dismutase by investigating metallopeptide substrate models

For the first time, the existence of a substrate adduct of a nickel superoxide dismutase (NiSOD) model, based on the first nine residues from the N terminus of the active form of Streptomyces coelicolor NiSOD, has been proven and the adduct has been isolated. This adduct is based on the cyanide anion (CN(-)), as a substrate analogue of the superoxide anion (O(2)(*-)), and the nickel metallopeptide H-HCDLPCGVY-NH(2)-Ni. Spectroscopic studies, including IR, UV/Vis, and liquid- and solid-state NMR spectroscopy, show a single nickel-bound cyanide anion, which is embedded in the metallopeptide structure. This complex sheds new light on the question of whether the mode of action of the NiSOD enzyme is an inner- or outer-sphere mechanism. Whereas discussion was previously biased in favor of an outer-sphere electron-transfer mechanism due to the fact that binding of cyanide or azide moieties to the nickel active site had never been observed, our results are a clear indication in favor of the inner-sphere electron-transfer mechanism for the disproportionation of the O(2)(*-) ion, whereby the substrate is attached to the Ni atom in the active site of the NiSOD.

Solution structure of a functional biomimetic and mechanistic implications for nickel superoxide dismutases

The nickel complex of a synthetic nonapeptide (HCDLPCFVY-NH2) is capable of catalytically disproportionating O2(.-) and is thus a functional biomimetic for nickel superoxide dismutases. This represents a simplification as compared to a NiSOD "maquette" that is based on a dodecapeptide that was recently reported [Inorg. Chem. 2006, 45, 2358]. The 3D solution structure reveals that the first six residues form a stable macrocyclic structure with a preformed binding site for Ni(II). Proline 5 exhibits a trans peptide linkage in the biomimetic and a cis conformation in NiSOD enzymes. DFT calculations reveal the source of this preference. Mechanistic consequences for the mode of action (identity of the fifth ligand) are discussed. The SOD activity is compared to enzymatic systems, and selected modifications allowed the biomimetic to be reduced to a functional minimal motif of only six amino acids (ACAAPC-NH2).