From industrial sites to environmental applications with Cupriavidus metallidurans

Proteomic and morphological insights into the exposure of Cupriavidus metallidurans CH34 planktonic cells and biofilms to aluminium

Aluminium (Al) is one of the most popular materials for industrial and domestic use. Nevertheless, research has proven that this metal can be toxic to most organisms. This light metal has no known biological function and to date very few aluminium-specific biological pathways have been identified. In addition, information about the impact of this metal on microbial life is scarce. Here, we aimed to study the effect of aluminium on the metal-resistant soil bacterium Cupriavidus metallidurans CH34 in different growth modes, i.e. planktonic cells, adhered cells and mature biofilms. Our results indicated that despite a significant tolerance to aluminium (minimal inhibitory concentration of 6.25 mM Al₂(SO₄)₃.18H₂O), the exposure of C. metallidurans to a sub-inhibitory dose (0.78 mM) caused early oxidative stress and an increase in hydrolytic activity. Changes in the outer membrane surface of planktonic cells were observed, in addition to a rapid disruption of mature biofilms. On protein level, aluminium exposure increased the expression of proteins involved in metabolic activity such as pyruvate kinase, formate dehydrogenase and poly(3-hydroxybutyrate) polymerase, whereas proteins involved in chemotaxis, and the production and transport of iron scavenging siderophores were significantly downregulated.

The Viable but Non-Culturable (VBNC) State, a Poorly Explored Aspect of Beneficial Bacteria

Many bacteria have the ability to survive in challenging environments; however, they cannot all grow on standard culture media, a phenomenon known as the viable but non-culturable (VBNC) state. Bacteria commonly enter the VBNC state under nutrient-poor environments or under stressful conditions. This review explores the concept of the VBNC state, providing insights into the beneficial bacteria known to employ this strategy. The investigation covers different chemical and physical factors that can induce the latency state, cell features, and gene expression observed in cells in the VBNC state. The review also covers the significance and applications of beneficial bacteria, methods of evaluating bacterial viability, the ability of bacteria to persist in environments associated with higher organisms, and the factors that facilitate the return to the culturable state. Knowledge about beneficial bacteria capable of entering the VBNC state remains limited; however, beneficial bacteria in this state could face adverse environmental conditions and return to a culturable state when the conditions become suitable and continue to exert their beneficial effects. Likewise, this unique feature positions them as potential candidates for healthcare applications, such as the use of probiotic bacteria to enhance human health, applications in industrial microbiology for the production of prebiotics and functional foods, and in the beer and wine industry. Moreover, their use in formulations to increase crop yields and for bacterial bioremediation offers an alternative pathway to harness their beneficial attributes.

Bioremediation potential of consortium Pseudomonas Stutzeri LBR and Cupriavidus Metallidurans LBJ in soil polluted by lead

Pollution by lead (Pb) is an environmental and health threat due to the severity of its toxicity. Microbial bioremediation is an eco-friendly technique used to remediate contaminated soils. This present study was used to evaluate the effect of two bacterial strains isolated and identified from Bizerte lagoon: Cupriavidus metallidurans LBJ (C. metallidurans LBJ) and Pseudomonas stutzeri LBR (P. stutzeri LBR) on the rate of depollution of soil contaminated with Pb from Tunisia. To determine this effect, sterile and non-sterile soil was bioaugmented by P. stutzeri LBR and C. metallidurans LBJ strains individually and in a mixture for 25 days at 30°C. Results showed that the bioaugmentation of the non-sterile soil by the mixture of P. stutzeri LBR and C. metallidurans LBJ strains gave the best rate of reduction of Pb of 71.02%, compared to a rate of 58.07% and 46.47% respectively for bioaugmentation by the bacterial strains individually. In the case of the sterile soil, results showed that the reduction rate of lead was in the order of 66.96% in the case of the mixture of the two bacterial strains compared with 55.66% and 41.86% respectively for the addition of the two strains individually. These results are confirmed by analysis of the leachate from the sterile and non-sterile soil which showed an increase in the mobility and bioavailability of Pb in soil. These promising results offer another perspective for a soil bioremediation bioprocess applying bacterial bioremediation.

PrsQ2, a small periplasmic protein involved in increased uranium resistance in the bacterium Cupriavidus metallidurans

Uranium contamination is a widespread problem caused by natural and anthropogenic activities. Although microorganisms thrive in uranium-contaminated environments, little is known about the actual molecular mechanisms mediating uranium resistance. Here, we investigated the resistance mechanisms driving the adaptation of Cupriavidus metallidurans NA4 to toxic uranium concentrations. We selected a spontaneous mutant able to grow in the presence of 1 mM uranyl nitrate compared to 250 µM for the parental strain. The increased uranium resistance was acquired via the formation of periplasmic uranium-phosphate precipitates facilitated by the increased expression of a genus-specific small periplasmic protein, PrsQ₂, regulated as non-cognate target of the CzcS₂-CzcR₂ two-component system. This study shows that bacteria can adapt to toxic uranium concentrations and explicates the complete genetic circuit behind the adaptation.

Generation of electrical energy in a microbial fuel cell coupling acetate oxidation to Fe3+ reduction and isolation of the involved bacteria

An iron reducing enrichment was obtained from sulfate reducing sludge and was evaluated on the capability of reducing Fe³⁺ coupled to acetate oxidation in a microbial fuel cell (MFC). Three molar ratios for acetate/Fe³⁺ were evaluated (2/16, 3.4/27 and 6.9/55 mM). The percentages of Fe³⁺ reduction were in a range of 80-90, 60-70 and 40-50% for the MFCs at closed circuit for the molar ratios of 2/16, 3.4/27 and 6.9/55 mM, respectively. Acetate consumption was in a range of 80-90% in all cases. The results obtained at closed circuit for current density were: 11.37 mA/m², 4.5 mA/m² and 7.37 mA/m² for the molar ratios of 2/16, 3.4/27 and 6.9/55 mM, respectively. Some microorganisms that were isolated and identified in the MFCs were Azospira oryzae, Cupriavidus metallidurans CH34, Enterobacter bugandensis 247BMC, Citrobacter freundii ATCC8090 and Citrobacter murliniae CDC2970-59, these bacteria have been reported as exoelectrogens in MFC and in MFC involving metals removal but not all of them have been reported to utilize acetate as preferred substrate. The results demonstrate that the isolates can utilize acetate as the sole source of carbon and suggest that Fe³⁺ reduction was carried out by a combination of different mechanisms (direct contact and redox mediators) utilized by the bacteria identified in the MFC. Storage of the energy generated from the 2/16 mM MFC system arranged in a series of three demonstrated that it is possible to utilize the energy to charge a battery.

Cupriavidus metallidurans CH34, a historical perspective on its discovery, characterization and metal resistance

Cupriavidus metallidurans, and in particular type strain CH34, became a model bacterium to study bacterial resistance to metals. Although nowadays the routine use of a wide variety of omics and molecular techniques allow refining, deepening and expanding our knowledge on adaptation and resistance to metals, these were not available at the onset of C. metallidurans research starting from its isolation in 1976. This minireview describes the early research and legacy tools used to study its metal resistance determinants, characteristic megaplasmids, ecological niches and environmental applications.

Mycoremediation of heavy metals: processes, mechanisms, and affecting factors

Industrial processes and mining of coal and metal ores are generating a number of threats by polluting natural water bodies. Contamination of heavy metals (HMs) in water and soil is the most serious problem caused by industrial and mining processes and other anthropogenic activities. The available literature suggests that existing conventional technologies are costly and generated hazardous waste that necessitates disposal. So, there is a need for cheap and green approaches for the treatment of such contaminated wastewater. Bioremediation is considered a sustainable way where fungi seem to be good bioremediation agents to treat HM-polluted wastewater. Fungi have high adsorption and accumulation capacity of HMs and can be potentially utilized. The most important biomechanisms which are involved in HM tolerance and removal by fungi are bioaccumulation, bioadsorption, biosynthesis, biomineralisation, bioreduction, bio-oxidation, extracellular precipitation, intracellular precipitation, surface sorption, etc. which vary from species to species. However, the time, pH, temperature, concentration of HMs, the dose of fungal biomass, and shaking rate are the most influencing factors that affect the bioremediation of HMs and vary with characteristics of the fungi and nature of the HMs. In this review, we have discussed the application of fungi, involved tolerance and removal strategies in fungi, and factors affecting the removal of HMs.

Adaptation of Cupriavidus metallidurans CH34 to Toxic Zinc Concentrations Involves an Uncharacterized ABC-Type Transporter

Cupriavidus metallidurans CH34 is a well-studied metal-resistant β-proteobacterium and contains a battery of genes participating in metal metabolism and resistance. Here, we generated a mutant (CH34^ZnR) adapted to high zinc concentrations in order to study how CH34 could adaptively further increase its resistance against this metal. Characterization of CH34^ZnR revealed that it was also more resistant to cadmium, and that it incurred seven insertion sequence-mediated mutations. Among these, an IS1088 disruption of the glpR gene (encoding a DeoR-type transcriptional repressor) resulted in the constitutive expression of the neighboring ATP-binding cassette (ABC)-type transporter. GlpR and the adjacent ABC transporter are highly similar to the glycerol operon regulator and ATP-driven glycerol importer of Rhizobium leguminosarum bv. viciae VF39, respectively. Deletion of glpR or the ABC transporter and complementation of CH34^ZnR with the parental glpR gene further demonstrated that loss of GlpR function and concomitant derepression of the adjacent ABC transporter is pivotal for the observed resistance phenotype. Importantly, addition of glycerol, presumably by glycerol-mediated attenuation of GlpR activity, also promoted increased zinc and cadmium resistance in the parental CH34 strain. Upregulation of this ABC-type transporter is therefore proposed as a new adaptation route towards metal resistance.

Dielectrophoretic ultra-high-frequency characterization and in silico sorting on uptake of rare earth elements by Cupriavidus necator

Rare earth elements (REEs) are widely used across different industries due to their exceptional magnetic and electrical properties. In this work, Cupriavidus necator is characterized using dielectrophoretic ultra-high-frequency measurements, typically in MHz range to quantify the properties of cytoplasm in C. necator for its metal uptake/bioaccumulation capacity. Cupriavidus necator, a Gram-negative bacteria strain is exposed to REEs like europium, samarium, and neodymium in this study. Dielectrophoretic crossover frequency experiments were performed on the native C. necator species pre- and post-exposure to the REEs at MHz frequency range. The net conductivity of native C. necator, Cupriavidus europium, Cupriavidus samarium, and Cupriavidus neodymium are 15.95 ± 0.029 μS/cm, 16.15 ± 0.028 μS/cm, 16.05 ± 0.029 μS/cm, 15.61 ± 0.005 μS/cm respectively. The estimated properties of the membrane published by our group are used to develop a microfluidic sorter by modeling and simulation to separate REE absorbed C. necator from the unabsorbed native C. necator species using COMSOL Multiphysics commercial software package v5.5.

The Transcriptomic Landscape of Cupriavidus metallidurans CH34 Acutely Exposed to Copper

Bacteria are increasingly used for biotechnological applications such as bioremediation, biorecovery, bioproduction, and biosensing. The development of strains suited for such applications requires a thorough understanding of their behavior, with a key role for their transcriptomic landscape. We present a thorough analysis of the transcriptome of Cupriavidus metallidurans CH34 cells acutely exposed to copper by tagRNA-sequencing. C. metallidurans CH34 is a model organism for metal resistance, and its potential as a biosensor and candidate for metal bioremediation has been demonstrated in multiple studies. Several metabolic pathways were impacted by Cu exposure, and a broad spectrum of metal resistance mechanisms, not limited to copper-specific clusters, was overexpressed. In addition, several gene clusters involved in the oxidative stress response and the cysteine-sulfur metabolism were induced. In total, 7500 transcription start sites (TSSs) were annotated and classified with respect to their location relative to coding sequences (CDSs). Predicted TSSs were used to re-annotate 182 CDSs. The TSSs of 2422 CDSs were detected, and consensus promotor logos were derived. Interestingly, many leaderless messenger RNAs (mRNAs) were found. In addition, many mRNAs were transcribed from multiple alternative TSSs. We observed pervasive intragenic TSSs both in sense and antisense to CDSs. Antisense transcripts were enriched near the 5' end of mRNAs, indicating a functional role in post-transcriptional regulation. In total, 578 TSSs were detected in intergenic regions, of which 35 were identified as putative small regulatory RNAs. Finally, we provide a detailed analysis of the main copper resistance clusters in CH34, which include many intragenic and antisense transcripts. These results clearly highlight the ubiquity of noncoding transcripts in the CH34 transcriptome, many of which are putatively involved in the regulation of metal resistance.

Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site

The microbial oxidation of metal sulfides plays a major role in the formation of acid rock drainage (ARD). We aimed to broadly characterize the ARD at Ely Brook, which drains the Ely Copper Mine Superfund site in Vermont, USA, using metagenomics and metatranscriptomics to assess the metabolic potential and seasonal ecological roles of microorganisms in water and sediment. Using Centrifuge against the NCBI "nt" database, ~25% of reads in sediment and water samples were classified as acid-tolerant Proteobacteria (61 ± 4%) belonging to the genera Pseudomonas (2.6-3.3%), Bradyrhizobium (1.7-4.1%), and Streptomyces (2.9-5.0%). Numerous genes (12%) were differentially expressed between seasons and played significant roles in iron, sulfur, carbon, and nitrogen cycling. The most abundant RNA transcript encoded the multidrug resistance protein Stp, and most expressed KEGG-annotated transcripts were involved in amino acid metabolism. Biosynthetic gene clusters involved in secondary metabolism (BGCs, 449) as well as metal- (133) and antibiotic-resistance (8501) genes were identified across the entire dataset. Several antibiotic and metal resistance genes were colocalized and coexpressed with putative BGCs, providing insight into the protective roles of the molecules BGCs produce. Our study shows that ecological stimuli, such as metal concentrations and seasonal variations, can drive ARD taxa to produce novel bioactive metabolites.

Effect of simulated acid rain on the stability of calcium carbonate immobilized by microbial carbonate precipitation

The stability of carbonate products resulting from microbially induced carbonate precipitation (MICP) under acid rain is under question. The present study investigated the stability of CaCO₃ precipitated by MICP in soil under simulated acid rain (SAR). Soils were treated continuously for two months with four SAR pH levels: 3.5, 4.5, 5.5, and 7.0. During SAR, biostimulation using nutrient broth containing urea and calcium chloride was adopted to ensure CaCO₃ precipitation. At the end of treatments, soil samples from top and bottom layers were analyzed for bacterial diversity by Illumina MiSeq sequencing, Fourier transform infrared (FTIR) spectroscopy for identification of chemical functional groups related to calcite precipitation, and X-ray diffraction (XRD) for identification of the main crystalline phases. The analysis identified several ureolytic bacteria mainly from Arthrobacter and Sporosarcina genera in SAR-treated soils accelerated with biostimulation, and urease quantities of greater than 300 mg NH₄⁺ per kg soil at all pH levels. The precipitation of CaCO₃ was pronounced and its stability was maintained even when the pH was as low as 3.5. The results obtained in this study are helpful to the scientific community to ensure the immobilization of heavy metals with microbial carbonate precipitation in soil under acid rain.

A genomic perspective of metal-resistant bacteria from gold particles: Possible survival mechanisms during gold biogeochemical cycling

A bacterial consortium was enriched from gold particles that ‘experienced’ ca. 80 years of biotransformation within waste-rock piles (Australia). This bacterial consortium was exposed to 10 µM AuCl3 to obtain Au-tolerant bacteria. From these isolates, Serratia sp. and Stenotrophomonas sp. were the most Au-tolerant and reduced soluble Au as pure gold nanoparticles, indicating that passive mineralisation is a mechanism for mediating the toxic effect of soluble Au produced during particle dissolution. Genome-wide analysis demonstrated that these isolates also possessed various genes that could provide cellular defence enabling survival under heavy-metal stressed condition by mediating the toxicity of heavy metals through active efflux/reduction. Diverse metal-resistant genes or genes clusters (cop, cus, czc, zntand ars) were detected, which could confer resistance to soluble Au. Comparative genome analysis revealed that the majority of detected heavy-metal resistant genes were similar (i.e. orthologous) to those genes of Cupriavidus metallidurans CH34. The detection of heavy-metal resistance, nutrient cycling and biofilm formation genes (pgaABCD, bsmAandhmpS) may have indirect yet important roles when dealing with soluble Au during particle dissolution. In conclusion, the physiological and genomic results suggest that bacteria living on gold particles would likely use various genes to ensure survival during Au-biogeochemical cycling.

Biodegradation of polyvinyl chloride plastic films by enriched anaerobic marine consortia

Plastics remarkably contribute to marine litter, which is raising serious concerns. Currently, little is known about the fate of most plastics entering the marine environment and their potential biodegradation rate and extent under anoxic conditions. In this work, biodegradation of polyvinyl chloride (PVC) films by consortia enriched from marine samples (litter and water) was evaluated in anaerobic microcosms. After 7 months, three microcosms showed dense biofilms on plastic surfaces, gravimetric weight losses up to 11.7 ± 0.6%, marked decreases in thermal stability and average molecular weight of the polymer, suggesting microbial attack towards polymer chains. After 24 months, further three consortia showed the same abilities. Microbial communities analyzed at month 24 included taxa closely related to those previously reported as halogenated organic compounds degraders. The study is the first report on PVC biodegradation by marine anaerobic microbes and provides insights on potential biodegradation of the plastic film introduced into the sea by native microbes.

Comparative genome analysis of completely sequenced Cupriavidus genomes provides insights into the biosynthetic potential and versatile applications of Cupriavidus alkaliphilus ASC-732

The genome analysis of microorganisms provides valuable information to endorse more extensive research on their potential applications. In this paper, the genome of Cupriavidus alkaliphilus ASC-732, isolated from agave rhizosphere in northeastern Mexico, was analyzed and compared with the genomes of other Cupriavidus species to gain better insight into the parts in the genetic makeup responsible for essential metabolic pathways and others of biotechnological importance. Here, the key genes related to glycolysis, pentose phosphate, and the Entner-Doudoroff and tricarboxylic acid cycle pathways were predicted. Comparative genome analysis revealed that the key genes for hydrogenotrophic growth and carbon fixation pathway, i.e., those coding for hydrogenase and enzymes Calvin-Benson-Bassham cycle, are absent in C. alkaliphilus ASC-732. Furthermore, capabilities for producing polyhydroxyalkanoates and extracellular polysaccharide matrix and degrading xenobiotics were found, and the related pathways are explained. Moreover, biofilm formation and the production of exopolysaccharides and polyhydroxyalkanoates were corroborated with crystal violet staining, calcofluor, and Nile red fluorochromes, confirming the presence of the products of the active genes in these pathways and their related metabolic routes, respectively. Additionally, a large group of genes essential for the resistance and detoxification of several heavy metals were also found. Thus, the present study demonstrates that this strain can respond to various environmental signals, such as energy source, nutrient limitations, virulence, and extreme metals concentration, indicating the possibility to foster C. alkaliphilus ASC-732 in diverse biotechnological applications.

Study on the Remediation of Cd Pollution by the Biomineralization of Urease-Producing Bacteria

Cadmium (Cd) is a highly toxic metal that can affect human health and environmental safety. The purpose of this study was to research the removal of Cd from an environmental perspective. In this article, four highly urease-active strains (CZW-2, CZW-5, CZW-9 and CZW-12) were isolated from an abandoned mine and their phylogenetic trees were analyzed. The maximum enzyme activities, the mineralized precipitate and the removal rates of these strains were compared. The results showed that CZW-2 had the highest urease activity at 51.6 U/mL, and the removal rates of CZW-2, CZW-5, CZW-9 and CZW-12 after 120 h were 80.10%, 72.64%, 76.70% and 73.40%, with an initial concentration of Cd of 2 mM in the Cd precipitation experiments. XRD (X-ray diffractometer), EDS (Energy dispersive spectrometer) and FTIR (Fourier transform infrared spectroscopy) analysis indicated that the mineralized precipitate was CdCO₃. SEM (Scanning electron microscopy) analysis revealed that the diameter of the oval-shaped mineralized product ranked from 0.5 to 2 μm. These strains were used to remedy Cd-contaminated soil, and five different fractions of Cd were measured. Compared with the control, the results of spraying pre-cultured strains containing 2% urea to remove Cd from contaminated soils showed that the exchangeable fraction of Cd decreased by 53.30%, 27.78%, 42.54% and 53.80%, respectively, whereas the carbonate-bound fraction increased by 55.42%, 20.27%, 39.67% and 34.36%, respectively, after one month. These data show that these strains can effectively reduce the bioavailability and mobility of Cd in contaminated soils. The results indicate that biomineralization based on the decomposition of substrate urea can be applied to remedy heavy contaminated soil and water.

Inorganic Polyphosphate, Exopolyphosphatase, and Pho84-Like Transporters May Be Involved in Copper Resistance in Metallosphaera sedula DSM 5348T

Polyphosphates (PolyP) are linear polymers of orthophosphate residues that have been proposed to participate in metal resistance in bacteria and archaea. In addition of having a CopA/CopB copper efflux system, the thermoacidophilic archaeon Metallosphaera sedula contains electron-dense PolyP-like granules and a putative exopolyphosphatase (PPX_Msed, Msed_0891) and four presumed pho84-like phosphate transporters (Msed_0846, Msed_0866, Msed_1094, and Msed_1512) encoded in its genome. In the present report, the existence of a possible PolyP-based copper-resistance mechanism in M. sedula DSM 5348^T was evaluated. M. sedula DSM 5348^T accumulated high levels of phosphorous in the form of granules, and its growth was affected in the presence of 16 mM copper. PolyP levels were highly reduced after the archaeon was subjected to an 8 mM CuSO₄ shift. PPX_Msed was purified, and the enzyme was found to hydrolyze PolyP in vitro. Essential residues for catalysis of PPX_Msed were E111 and E113 as shown by a site-directed mutagenesis of the implied residues. Furthermore, M. sedula ppx, pho84-like, and copTMA genes were upregulated upon copper exposure, as determined by qRT-PCR analysis. The results obtained support the existence of a PolyP-dependent copper-resistance system that may be of great importance in the adaptation of this thermoacidophilic archaeon to its harsh environment.

The role of non-spore-forming actinobacteria in cleaning up sites contaminated by persistent pollutants and the ability of these microorganisms to survive under unfavourable conditions

Years of research has shown that actinobacteria, including Rhodococcus, Gordonia, Arthrobacter, Microbacteria, play an important role in cleaning up sites contaminated by persistent organic pollutants. Under special conditions, actinobacteria of different genera are able to form specific forms, cyst-like resting cells (CLC), which maintain the viability during long-term storage (for at least 5–6 years, our unpublished results). These cells quickly germinate when conditions become favourable for growth. As a result, actinobacteria can be used as a basis for creating highly efficient biological preparations for cleaning up the soil with high levels of toxic contaminants such as (chloro)phenols, (chloro)biphenyls, polycyclic hydrocarbons, oil1.

Rapid bacteria identification from environmental mining samples using MALDI-TOF MS analysis

Copper mining has polluted soils and water, causing a reduction of the microbial diversity and a change in the structure of the resident bacterial communities. In this work, selective isolation combined with MALDI-TOF MS and the 16S rDNA method were used for characterizing cultivable bacterial communities from copper mining samples. The results revealed that MALDI-TOF MS analysis can be considered a reliable and fast tool for identifying copper-resistant bacteria from environmental samples at the genera level. Even though some results were ambiguous, accuracy can be improved by enhancing reference databases. Therefore, mass spectra analysis provides a reliable method to facilitate monitoring of the microbiota from copper-polluted sites. The understanding of the microbial community diversity in copper-contaminated sites can be helpful to understand the impact of the metal on the microbiome and to design bioremediation processes.

Siderophores as molecular tools in medical and environmental applications

Almost all life forms depend on iron as an essential micronutrient that is needed for electron transport and metabolic processes. Siderophores are low-molecular-weight iron chelators that safeguard the supply of this important metal to bacteria, fungi and graminaceous plants. Although animals and the majority of plants do not utilise siderophores and have alternative means of iron acquisition, siderophores have found important clinical and agricultural applications. In this review, we will highlight the different uses of these iron-chelating molecules.

Influence of Vinasse Application in the Structure and Composition of the Bacterial Community of the Soil under Sugarcane Cultivation

Although the use of vinasse as a waste helps replenish soil nutrients and improves the quality of the sugarcane crop, it is known that vinasse residues alter the diversity of bacteria naturally present in the soil. The actual impacts of vinasse application on the selection of bacterial taxa are not understood because no studies have addressed this phenomenon directly. Analysis of 16S rRNA gene clone sequences from four soil types showed that the soil planted with sugarcane and fertilized with vinasse has a high diversity of bacteria compared to other biomes, where Acidobacteria were the second most abundant phylum. Although the composition and structure of bacterial communities differ significantly in the four environments (Libshuff's test), forest soils and soil planted with sugarcane without vinasse fertilizer were similar to each other because they share at least 28 OTUs related to Rhizobiales, which are important agents involved in nitrogen fixation. OTUs belonging to Actinomycetales were detected more often in the soil that had vinasse applied, indicating that these groups are more favored by this type of land management.

Interactions of the metal tolerant heterotrophic microorganisms and iron oxidizing autotrophic bacteria from sulphidic mine environment during bioleaching experiments

Iron and sulfur oxidizing chemolithoautotrophic acidophilic bacteria, such as Acidithiobacillus species, hold the dominant role in mine environments characterized by low pH values and high concentrations of reduced sulfur and iron compounds, such as ores, rocks and acid drainage waters from mines. On the other hand, heterotrophic microorganisms, especially their biofilms, from these specific niches are receiving increased attention, but their potential eco-physiological roles have not been fully understood. Biofilms are considered a threat to human health, but biofilms also have beneficial properties as they are deployed in waste recycling and bioremediation systems. We have analyzed interactions of the metal tolerant heterotrophic microorganisms in biofilms with iron oxidizing autotrophic bacteria both from the sulphidic mine environment (copper mine Bor, Serbia). High tolerance to Cu(2+), Cd(2+) and Cr(6+) and the presence of genetic determinants for the respective metal tolerance and biofilm-forming ability was shown for indigenous heterotrophic bacteria that included strains of Staphylococcus and Rhodococcus. Two well characterized bacteria- Pseudomonas aeruginosa PAO1 (known biofilm former) and Cupriavidus metallidurans CH34 (known metal resistant representative) were also included in the study. The interaction and survivability of autotrophic iron oxidizing Acidithiobacillus bacteria and biofilms of heterotrophic bacteria during co-cultivation was revealed. Finally, the effect of heterotrophic biofilms on bioleaching process with indigenous iron oxidizing Acidithiobacillus species was shown not to be inhibitory under in vitro conditions.

Proteobacteria, extremophiles and unassigned species dominate in a tape-like showerhead biofilm

The development of showerhead biofilms exposes the user to repeated contact with potentially pathogenic microbes, yet we know relatively little about the content of these aggregates. The aim of the present study was to examine the microbial content of tape-like films found protruding from a domestic showerhead. Culturing showed that the films were dominated by aerobic α- and β-proteobacteria. Three isolates made up almost the entire plate count. These were a Brevundimonas species, a metalophilic Cupriavidus species and a thermophile, Geobacillus species. Furthermore, it was shown that the Cupriavidus isolate alone had a high capacity for biofilm formation and thus might be the initiator of biofilm production. A clone library revealed the same general composition. However, half of the 70 clones analyzed could not be assigned to a particular bacterial phylum and of these 29 differed from one another by only 1–2 base pairs, indicating a single species. Thus both the culture dependent and culture independent characterizations suggest a simple yet novel composition. The work is important as the biofilm is fundamentally different in form (tape-like) and content from that of all previously reported ones, where variously Mycobacterium, Methylobacterium and Xanthomonas species have dominated, and extremophiles were not reported.

Molecular characterization influencing metal resistance in the Cupriavidus/Ralstonia genomes

Our environment is stressed with a load of heavy and toxic metals. Microbes, abundant in our environment, are found to adapt well to this metal-stressed condition. A comparative study among five Cupriavidus/Ralstonia genomes can offer a better perception of their evolutionary mechanisms to adapt to these conditions. We have studied codon usage among 1051 genes common to all these organisms and identified 15 optimal codons frequently used in highly expressed genes present within 1051 genes. We found the core genes of Cupriavidus metallidurans CH34 have a different optimal codon choice for arginine, glycine and alanine in comparison with the other four bacteria. We also found that the synonymous codon usage bias within these 1051 core genes is highly correlated with their gene expression. This supports that translational selection drives synonymous codon usage in the core genes of these genomes. Synonymous codon usage is highly conserved in the core genes of these five genomes. The only exception among them is C. metallidurans CH34. This genomewide shift in synonymous codon choice in C. metallidurans CH34 may have taken place due to the insertion of new genes in its genomes facilitating them to survive in heavy metal containing environment and the co-evolution of the other genes in its genome to achieve a balance in gene expression. Structural studies indicated the presence of a longer N-terminal region containing a copper-binding domain in the cupC proteins of C. metallidurans CH3 that helps it to attain higher binding efficacy with copper in comparison with its orthologs.

Metal resistance in acidophilic microorganisms and its significance for biotechnologies

Extremely acidophilic microorganisms have an optimal pH of <3 and are found in all three domains of life. As metals are more soluble at acid pH, acidophiles are often challenged by very high metal concentrations. Acidophiles are metal-tolerant by both intrinsic, passive mechanisms as well as active systems. Passive mechanisms include an internal positive membrane potential that creates a chemiosmotic gradient against which metal cations must move, as well as the formation of metal sulfate complexes reducing the concentration of the free metal ion. Active systems include efflux proteins that pump metals out of the cytoplasm and conversion of the metal to a less toxic form. Acidophiles are exploited in a number of biotechnologies including biomining for sulfide mineral dissolution, biosulfidogenesis to produce sulfide that can selectively precipitate metals from process streams, treatment of acid mine drainage, and bioremediation of acidic metal-contaminated milieux. This review describes how acidophilic microorganisms tolerate extremely high metal concentrations in biotechnological processes and identifies areas of future work that hold promise for improving the efficiency of these applications.

Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TB

Background

Adaptation of Pseudomonas aeruginosa to different living conditions is accompanied by microevolution resulting in genomic diversity between strains of the same clonal lineage. In order to detect the impact of colonized habitats on P. aeruginosa microevolution we determined the genomic diversity between the highly virulent cystic fibrosis (CF) isolate CHA and two temporally and geographically unrelated clonal variants. The outcome was compared with the intraclonal genome diversity between three more closely related isolates of another clonal complex.

Results

The three clone CHA isolates differed in their core genome in several dozen strain specific nucleotide exchanges and small deletions from each other. Loss of function mutations and non-conservative amino acid replacements affected several habitat- and lifestyle-associated traits, for example, the key regulator GacS of the switch between acute and chronic disease phenotypes was disrupted in strain CHA. Intraclonal genome diversity manifested in an individual composition of the respective accessory genome whereby the highest number of accessory DNA elements was observed for isolate PT22 from a polluted aquatic habitat. Little intraclonal diversity was observed between three spatiotemporally related outbreak isolates of clone TB. Although phenotypically different, only a few individual SNPs and deletions were detected in the clone TB isolates. Their accessory genome mainly differed in prophage-like DNA elements taken up by one of the strains.

Conclusions

The higher geographical and temporal distance of the clone CHA isolates was associated with an increased intraclonal genome diversity compared to the more closely related clone TB isolates derived from a common source demonstrating the impact of habitat adaptation on the microevolution of P. aeruginosa. However, even short-term habitat differentiation can cause major phenotypic diversification driven by single genomic variation events and uptake of phage DNA.

Polyamidoamine dendronized hollow fiber membranes in the recovery of heavy metal ions

Polyamidoamine (PAMAM) dendronized hollow fiber membranes (HFMs) were synthesized and used in the recovery of heavy metal ions. The dendronized HFMs showed strong binding ability with Cu(2+), Pb(2+), and Cd(2+) ions. Generation 3 (G3) PAMAM dendronized HFM (G3-HFM) retained 72% of its Cu(2+) binding capacity after five cycles of use and recovery. Interestingly, Cu2(OH)3Cl, Pb3(CO3)2(OH)2, and CdCO3 crystals were grown on G3-HFM surface when G3-HFMs were immersed in CuCl2, Pb(NO3)2, and CdCl2 solutions, respectively, while no crystal was observed with nonmodified HFMs. The results provide new insights into the applications of membrane-supported dendrimers in the recovery of heavy metal ions.

Synergism of Pseudomonas aeruginosa and Fe0 for treatment of heavy metal contaminated effluents using small scale laboratory reactor

In this study Pseudomonas aeruginosa a metal tolerant strain was not only applied for heavy metal removal but also to the solublization performance of the precipitated metal ions during effluent treatment. The synergistic effect of the isolate and Fe(0) enhanced the metal removal potential to 72.97% and 87.63% for Cr(VI) and cadmium, respectively. The decrease in cadmium ion removal to 43.65% (aeration+stirring reactors), 21.33% (aerated reactors), and 18.95% (without aerated+without stirring) with an increase in incubation period not only indicate the presence of soluble less toxic complexes, but also help in exploration of the balancing potential for valuable metal recovery. A relatively best fit and significant values of the correlation coefficient 0.912, 0.959, and 0.9314 for mixed effluent (Paint Industry effluent+CETP Wazirpur, effluent), CETP, Wazirpur, and control effluents, respectively, indicating first-order formulation and provide a reasonable description of COD kinetic data.

Synthetic phytochelatin surface display in Cupriavidus metallidurans CH34 for enhanced metals bioremediation

This work describes the effects of the cell surface display of a synthetic phytochelatin in the highly metal tolerant bacterium Cupriavidus metallidurans CH34. The EC20sp synthetic phytochelatin gene was fused between the coding sequences of the signal peptide (SS) and of the autotransporter β-domain of the Neisseria gonorrhoeae IgA protease precursor (IgAβ), which successfully targeted the hybrid protein toward the C. metallidurans outer membrane. The expression of the SS-EC20sp-IgAβ gene fusion was driven by a modified version of the Bacillus subtilis mrgA promoter showing high level basal gene expression that is further enhanced by metal presence in C. metallidurans. The recombinant strain showed increased ability to immobilize Pb(2+), Zn(2+), Cu(2+), Cd(2+), Mn(2+), and Ni(2+) ions from the external medium when compared to the control strain. To ensure plasmid stability and biological containment, the MOB region of the plasmid was replaced by the E. coli hok/sok coding sequence.

Mechanisms of nickel toxicity in microorganisms

Nickel has long been known to be an important human toxicant, including having the ability to form carcinomas, but until recently nickel was believed to be an issue only to microorganisms living in nickel-rich serpentine soils or areas contaminated by industrial pollution. This assumption was overturned by the discovery of a nickel defense system (RcnR/RcnA) found in microorganisms that live in a wide range of environmental niches, suggesting that nickel homeostasis is a general biological concern. To date, the mechanisms of nickel toxicity in microorganisms and higher eukaryotes are poorly understood. In this review, we summarize nickel homeostasis processes used by microorganisms and highlight in vivo and in vitro effects of exposure to elevated concentrations of nickel. On the basis of this evidence we propose four mechanisms of nickel toxicity: (1) nickel replaces the essential metal of metalloproteins, (2) nickel binds to catalytic residues of non-metalloenzymes; (3) nickel binds outside the catalytic site of an enzyme to inhibit allosterically and (4) nickel indirectly causes oxidative stress.

Specific PCR to identify the heavy-metal-resistant bacterium Cupriavidus metallidurans

The aim of this study is to develop a polymerase chain reaction (PCR) assay for rapid detection of Cupriavidus metallidurans. PCR primers targeting the Signal transduction histidine kinase gene were designed and designated Cm-F1/Cm-R1. Strains of C. metallidurans were positively identified. The size of the PCR products was 437 bp, as expected. This PCR method enables monitoring of industrial, environmental and clinical sources for presence of C. metallidurans.

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.

The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments

Many bacteria in the environment have adapted to the presence of toxic heavy metals. Over the last 30 years, this heavy metal tolerance was the subject of extensive research. The bacterium Cupriavidus metallidurans strain CH34, originally isolated by us in 1976 from a metal processing factory, is considered a major model organism in this field because it withstands milli-molar range concentrations of over 20 different heavy metal ions. This tolerance is mostly achieved by rapid ion efflux but also by metal-complexation and -reduction. We present here the full genome sequence of strain CH34 and the manual annotation of all its genes. The genome of C. metallidurans CH34 is composed of two large circular chromosomes CHR1 and CHR2 of, respectively, 3,928,089 bp and 2,580,084 bp, and two megaplasmids pMOL28 and pMOL30 of, respectively, 171,459 bp and 233,720 bp in size. At least 25 loci for heavy-metal resistance (HMR) are distributed over the four replicons. Approximately 67% of the 6,717 coding sequences (CDSs) present in the CH34 genome could be assigned a putative function, and 9.1% (611 genes) appear to be unique to this strain. One out of five proteins is associated with either transport or transcription while the relay of environmental stimuli is governed by more than 600 signal transduction systems. The CH34 genome is most similar to the genomes of other Cupriavidus strains by correspondence between the respective CHR1 replicons but also displays similarity to the genomes of more distantly related species as a result of gene transfer and through the presence of large genomic islands. The presence of at least 57 IS elements and 19 transposons and the ability to take in and express foreign genes indicates a very dynamic and complex genome shaped by evolutionary forces. The genome data show that C. metallidurans CH34 is particularly well equipped to live in extreme conditions and anthropogenic environments that are rich in metals.