Bacterial mercury resistance from atoms to ecosystems

Evidence for regulation of monomethyl mercury by nitrate in a seasonally stratified, eutrophic lake

The accumulation of monomethyl mercury (CH3Hg+) in aquatic ecosystems is a redox sensitive process that is accelerated under sulfate-reducing conditions. While nitrate (NO3-) reduction is energetically favored over sulfate reduction, the influence of NO3 on the accumulation of CH3Hg+ has not been reported in the literature. We examined temporal and vertical patterns in redox constituents and CH3Hg+ concentrations in the hypolimnion of a dimictic lake, Onondaga Lake, prior to and following increases in NO3- inputs. Detailed water-column profiles and a long-term record revealed marked decreases in the accumulation of CH3Hg+ in the anoxic hypolimnion coinciding with long-term decreases in the deposition of organic matter coupled with recent increases in NO3-concentrations. CH3Hg+ concentrations in the hypolimnion were substantially abated when No3 was present above the sediment-water interface. A decrease in the peak hypolimnetic mass of CH3Hg+ and shortening of the period of elevated CH3Hg+ concentrations resulted in more than a 50% decline in the accumulated CH3Hg+. N03- regulation of CH3Hg+ accumulation may be a widespread phenomenon in oxygen-limited freshwater and terrestrial environments, and could have an important notpreviously recognized, effect on the biogeochemistry of mercury.

Reduction of Hg(II) to Hg(0) by magnetite

Mercury (Hg) is a highly toxic element, and its contamination of groundwater presents a significant threat to terrestrial ecosystems. Understanding the geochemical processes that mediate mercury transformations in the subsurface is necessary to predict its fate and transport. In this study, we investigated the redox transformation of mercuric Hg (Hg[II]) in the presence of the Fe(II)/Fe(III) mixed valence iron oxide mineral magnetite. Kinetic and spectroscopic experiments were performed to elucidate reaction rates and mechanisms. The experimental data demonstrated that reaction of Hg(II) with magnetite resulted in the loss of Hg(II) and the formation of volatile elemental Hg (Hg[0]). Kinetic experiments showed that Hg(II) reduction occurred within minutes, with reaction rates increasing with increasing magnetite surface area (0.5 to 2 m2/L) and solution pH (4.8 to 6.7), and decreasing with increasing chloride concentration (10(-6) to 10(-2) mol/L). Mössbauer spectroscopic analysis of reacted magnetite samples revealed a decrease in Fe(II) content, corresponding to the oxidation of Fe(II) to Fe(III) in the magnetite structure. X-ray photoelectron spectroscopy detected the presence of Hg(II) on magnetite surfaces, implying that adsorption is involved in the electron transfer process. These results suggest that Hg(II) reaction with solid-phase Fe(II) is a kinetically favorable pathway for Hg(II) reduction in magnetite-hearing environmental systems.

Non mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus

Mycobacterium abscessus is an emerging rapidly growing mycobacterium (RGM) causing a pseudotuberculous lung disease to which patients with cystic fibrosis (CF) are particularly susceptible. We report here its complete genome sequence. The genome of M. abscessus (CIP 104536T) consists of a 5,067,172-bp circular chromosome including 4920 predicted coding sequences (CDS), an 81-kb full-length prophage and 5 IS elements, and a 23-kb mercury resistance plasmid almost identical to pMM23 from Mycobacterium marinum. The chromosome encodes many virulence proteins and virulence protein families absent or present in only small numbers in the model RGM species Mycobacterium smegmatis. Many of these proteins are encoded by genes belonging to a “mycobacterial” gene pool (e.g. PE and PPE proteins, MCE and YrbE proteins, lipoprotein LpqH precursors). However, many others (e.g. phospholipase C, MgtC, MsrA, ABC Fe(3+) transporter) appear to have been horizontally acquired from distantly related environmental bacteria with a high G+C content, mostly actinobacteria (e.g. Rhodococcus sp., Streptomyces sp.) and pseudomonads. We also identified several metabolic regions acquired from actinobacteria and pseudomonads (relating to phenazine biosynthesis, homogentisate catabolism, phenylacetic acid degradation, DNA degradation) not present in the M. smegmatis genome. Many of the “non mycobacterial” factors detected in M. abscessus are also present in two of the pathogens most frequently isolated from CF patients, Pseudomonas aeruginosa and Burkholderia cepacia. This study elucidates the genetic basis of the unique pathogenicity of M. abscessus among RGM, and raises the question of similar mechanisms of pathogenicity shared by unrelated organisms in CF patients.

Gaseous mercury emissions from unsterilized and sterilized soils: the effect of temperature and UV radiation

Mercury (Hg) emissions from the soils taken from two different sites (deciduous and coniferous forests) in the Adirondacks were measured in outdoor and laboratory experiments. Some of the soil samples were irradiated to eliminate biological activity. The result from the outdoor measurements with different soils suggests the Hg emission from the soils is partly limited by fallen leaves covering the soils which helps maintain relatively high soil moisture and limits the amount of heat and solar radiation reaching the soil surface. In laboratory experiments exposure to UV-A (365 nm) had no significant effect on the Hg emissions while the Hg emissions increased dramatically during exposure to UV-B (302 nm) light suggesting UV-B directly reduced soil-associated Hg. Overall these results indicate that for these soils biotic processes have a relatively constant and smaller influence on the Hg emission from the soil than the more variable abiotic processes.

Damage control: regulating defenses against toxic metals and metalloids

Some elements are essential for life and others closely related to them are very toxic. In exploiting unique ecological niches many prokaryotes have evolved the means to defend themselves against and even to derive energy from deleterious elements. Toxic metal defense systems are related to those providing homeostasis of essential metals and metalloid elements. Expression of these multiprotein systems is costly but they must respond rapidly and, so, all are well controlled. Seven diverse families of metalloregulators are presently recognized for essential metal homeostasis in prokaryotes. Two of these, the ArsR and MerR families, figure more often than the others in controlling responses to toxic transition metals and metalloids. This review emphasizes recent advances in these two metalloregulator families and highlights emerging regulatory motifs of other types.

A Tn5051-like mer-containing transposon identified in a heavy metal tolerant strain Achromobacter sp. AO22

BACKGROUND

Achromobacter sp. AO22 (formerly Alcaligenes sp. AO22), a bacterial strain isolated from a lead-contaminated industrial site in Australia, was previously found to be resistant to moderate to high levels of mercury, copper and other heavy metals. However, the nature and location of the genetic basis for mercuric ion resistance in this strain, had not been previously identified.

FINDINGS

Achromobacter sp. AO22 contains a functional mer operon with all four essential genes (merRTPA) and shows >99% DNA sequence identity to that of Tn501. The mer operon was present on a transposon, designated TnAO22, captured by introducing a broad-host-range IncP plasmid into Achromobacter sp. AO22 and subsequently transferring it to E. coli recipients. The transposition frequency of TnAO22 was 10-2 to 10-3 per target plasmid transferred. Analysis of TnAO22 sequence revealed it belonged to the Tn21 subgroup of the Tn3 superfamily of transposons, with the transposition module having >99% identity with Tn5051 of a Pseudomonas putida strain isolated from a water sample in New York.

CONCLUSION

TnAO22 is thus a new variant of Tn5051 of the Tn3 superfamily and the transposon and its associated mercury resistance system are among the few such systems reported in a soil bacterium. Achromobacter sp. AO22 can thus be exploited for applications such as in situ mercury bioremediation of contaminated sites, or the mobile unit and mer operon could be mobilized to other bacteria for similar purposes.

The MerE protein encoded by transposon Tn21 is a broad mercury transporter in Escherichia coli

In order to clarify the physiological role of the merE gene of transposon Tn21, a pE4 plasmid that contained the merR gene of plasmid pMR26 from Pseudomonas strain K-62, and the merE gene of Tn21 from the Shigella flexneri plasmid NR1 (R100) was constructed. Bacteria with plasmid pE4 (merR-o/p-merE) were more hypersensitive to CH(3)Hg(I) and Hg(II), and took up significantly more CH(3)Hg(I) and Hg(II), than the isogenic strain. The MerE protein encoded by pE4 was localized in the membrane cell fraction, but not in the soluble fraction. Based on these experimental results, we suggest for the first time that the merE gene is a broad mercury transporter mediating the transport of both CH(3)Hg(I) and Hg(II) across the bacterial membrane.

An initial characterization of the mercury resistance (mer) system of the thermophilic bacterium Thermus thermophilus HB27

The evolutionary origin of the broadly distributed mer system, which plays an important role in mercury detoxification and biogeochemistry, is presently unknown. The phylum Deinococcus/Thermus was found to be one of the deepest-branching bacterial lineage to have a homolog of merA, which specifies reduction of ionic to elemental mercury, and the mercuric reductase (MerA) of Thermus thermophilus HB27 was found to be basal to all bacterial MerA when this protein's phylogeny was constructed. A merA mutant of HB27 was fourfolds more sensitive to mercury toxicity than the wild type (wt), and lost detectable MerA-specific activities. The merA gene in HB27 was transcribed on a polycistronic message downstream from ORF encoding for homologs of O-acetyl-l-homoserine/O-acetyl-serine (OAH/OAS) sulfhydrylase and MerR, the mer operon transcription regulator, from a promoter located 69 nucleotides upstream of the sulfhydrylase translation start codon. The transcription of the putative mer operon in HB27 was induced 66.8+/-15.8-fold by exposure to 1 muM HgCl2. The optimal temperature for MerA-specific activity corresponded to this strain's optimal growth temperature, 70 degrees C. Thus, T. thermophilus is the earliest mercury-resistant bacterium identified to date, a finding consistent with the hypothesis that the mer system originated among thermophilic microorganisms from geothermal environments.

Gaseous mercury fluxes from the forest floor of the Adirondacks

The flux of gaseous elemental mercury (Hg(0)) from the forest floor of the Adirondack Mountains in New York (USA) was measured numerous times throughout 2005 and 2006 using a polycarbonate dynamic flux chamber (DFC). The Hg flux ranged between -2.5 and 27.2 ng m(-2) h(-1) and was positively correlated with temperature and solar radiation. The measured Hg emission flux was highest in spring, and summer, and lowest in winter. During leaf-off periods, the Hg emission flux was highly dependent on solar radiation and less dependent on temperature. During leaf-on periods, the Hg emission flux was fairly constant because the forest canopy was shading the forest floor. Two empirical models were developed to estimate yearly Hg(0) emissions, one for the leaf-off period and one for the leaf-on period. Using the U.S. EPA's CASTNET meteorological data, the cumulative estimated emission flux was approx. 7.0 microg Hg(0) m(-2) year(-1).

Expressing a bacterial mercuric ion binding protein in plant for phytoremediation of heavy metals

A specific mercuric ion binding protein (MerP) originating from transposon TnMERI1 of Bacillus megaterium strain MB1 isolated from Minamata Bay displayed good adsorption capability for a variety of heavy metals. In this study, the Gram-positive MerP protein was expressed in transgenic Arabidopsis to create a model system for phytoremediation of heavy metals. Under control of an actin promoter, the transgenic Arabidpsis showed higher tolerance and accumulation capacity for mercury, cadium and lead when compared with the control plant. Results from confocal microscopy analysis also indicate that MerP was localized at the cell membrane and vesicles of plant cells. The developed transgenic plants possessing excellent metal-accumulative ability could have potential applications in decontamination of heavy metals.

Horizontal gene transfer in metal and radionuclide contaminated soils

The horizontal transfer of genes encoded on mobile genetic elements (MGEs) such as plasmids and phage and their associated hitchhiking elements (transposons, integrons, integrative and conjugative elements, and insertion sequences) rapidly accelerate genome diversification of microorganisms, thereby affecting their physiology, metabolism, pathogenicity,and ecological character. The analyses of completed prokaryotic genomes reveal that horizontal gene transfer (HGT) continues to be an important factor contributing to the innovation of microbial genomes. Indeed, microbial genomes are remarkably dynamic and a considerable amount of genetic information is inserted or deleted by HGT mechanisms. Thus, HGT and the vast pool of MGEs provide microbial communities with an unparalleled means by which to respond rapidly to changing environmental conditions and exploit new ecological niches. Metals and radionuclide contamination in soils, the subsurface, and aquifers poses a serious challenge to microbial growth and survival because these contaminants cannot be transformed or biodegraded into non-toxic forms as often occurs with organic xenobiotic contaminants. In this chapter we present cases in which HGT has been demonstrated to contribute to the dissemination of genes that provide adaptation to contaminant stress (i.e., toxic heavy metals and radionuclides). In addition, we present directions for future studies that could provide even greater insights into the contributions of HGT to adaptation for survival in mixed waste sites.

Dissolved gaseous mercury production in the dark: Evidence for the fundamental role of bacteria in different types of Mediterranean water bodies

It is well established that the dissolved gaseous mercury (DGM) production in waters is mainly driven by photochemical processes. The present paper provides evidence for a significant bacteria-mediated DGM production, occurring also under dark conditions in environmentally different types of coastal water bodies of the Mediterranean basin. The DGM production was laboratory determined in sea, lagoon-brackish and lake water samples, comparing the efficiency of the DGM production processes in darkness and in the light. This latter condition was established by exposing samples at solar radiation intensity in the Photosyntetical Active Radiation region (PAR) of 200 W m(-2). Mercury reduction rate in the dark was of the order of 2-4% of the DGM production in lightness, depending on the total mercury concentration in the water, rather than the bacterial abundance in it. Support for the active bacterial role in mercury reduction rate under dark conditions was provided by: 1) absence of significant DGM production in sterilized water samples (following filtration treatment or autoclaving), 2) restored DGM production efficiency, following re-inoculation into the same water samples of representatives of their bacterial community, previously isolated and separately cultured. Notwithstanding the low bacteria-mediated vs. the high photo-induced DGM production, whatever natural water body was considered, it is worth stressing the significant contribution of this organismal-mediated process to oceanic mercury evasion, since it occurs continuously along the entire water column throughout the 24 h of the day.

Mercury stable isotope fractionation during reduction of Hg(II) by different microbial pathways

Mercury (Hg) stable isotope fractionation has recently been developed as a tool in biogeochemistry. In this study, the extent of Hg stable isotope fractionation during reduction of ionic mercury [Hg(II)] by two Hg(II)-resistant strains, Bacillus cereus 5 and the thermophile Anoxybacillus sp. FB9 [which actively detoxify Hg(II) by the mer system] and a Hg(II)-sensitive metal-reducing anaerobe, Shewanella oneidensis MR-1 [which reduces Hg(II) at low concentrations], was investigated. In all cases, barring suppression of fractionation that is likely due to lower Hg(II) bioavailability, the Hg(II) remaining in the reactor became progressively enriched with heavy isotopes with time and underwent mass-dependent Rayleigh fractionation with alpha202/198 values of 1.0016 +/- 0.0004 (1 SD). Based on a multistep framework for the Hg(II) reduction pathways in the three strains, we constrain the processes that could contribute toward fractionation and suggest that for Hg(II)-resistant strains, reduction by mercuric reductase is the primary step causing fractionation. The proposed framework helps explain the variation in the extent of Hg stable isotope fractionation during microbial reduction of Hg(II), furthering the promise of Hg isotope ratios as a tool in determining the role of microbial Hg transformations in the environment.

Mercury biomethylation assessment in the estuary of Bilbao (North of Spain)

The relationship between the microbial methylation of mercury and the microbial activities in sediments and water collected from the estuary of Bilbao (North of Spain) was studied in three different sampling points and in two different seasons. Three different cultures were prepared with a sediment slurry to distinguish between biotic and abiotic methylation pathways and the variations of the methylmercury concentration and the variations of the population of total number of bacteria (TDC), anaerobic heterotrophic bacteria (AHB), sulphate-reducing bacteria (SRB) and Desulfovibrio were measured. From this work, it can be concluded that the variation of MeHg concentrations is a result of the methylation/demethylation processes in the sediments, and that the abiotic processes have a negligible contribution to those processes. According to the statistical analysis of the results (partial least squares analysis) a significant statistical correlation was established between methylmercury and the SRB counts.

Sequence and analysis of a plasmid-encoded mercury resistance operon from Mycobacterium marinum identifies MerH, a new mercuric ion transporter

In this study, we report the DNA sequence and biological analysis of a mycobacterial mercury resistance operon encoding a novel Hg(2+) transporter. MerH was found to transport mercuric ions in Escherichia coli via a pair of essential cysteine residues but only when coexpressed with the mercuric reductase.

Cyanobacteria Metal Interactions: Requirements, Toxicity, and Ecological Implications

The environmental health-related relevance of cyanobacteria is primarily related to their ability to produce a wide range of toxins, which are known to be hazardous to many organisms, including human beings. The occurrence of cyanobacterial blooms has been related to eutrophic surface water. In the bloom-forming process the levels of phosphorus and nitrogen have been well documented but information regarding concentrations of other chemicals (inorganic, organo-metallic, and organic) is still incipient. Several contaminants, like trace metals, elicit a variety of acute and chronic toxicity effects, but cyanobacteria also have the capability to accumulate, detoxify, or metabolize such substances, to some extent. The role of cyanobacterial exudates has been proved a means of both nutrient acquisition and detoxification. In addition, cyanobacteria are effective biological metal sorbents, representing an important sink for metals in aquatic environment. Understanding the fundamental physicochemical mechanisms of trace metal bio-uptake by cyanobacteria in natural systems is a step towards identifying under what conditions cyanobacterial growth is favored and to ascertain the mechanisms by which blooms (and toxin production) are triggered. In this review the cyanobacterial interactions with metals will be discussed, focusing on freshwater systems.

A Cu(I)-sensing ArsR family metal sensor protein with a relaxed metal selectivity profile

ArsR (or ArsR/SmtB) family metalloregulatory homodimeric repressors collectively respond to a wide range of metal ion inducers in regulating homeostasis and resistance of essential and nonessential metal ions in bacteria. BxmR from the cyanobacterium Osciliatoria brevis is the first characterized ArsR protein that senses both Cu (I)/Ag (I) and divalent metals Zn (II)/Cd (II) in cells by regulating the expression of a P-type ATPase efflux pump (Bxa1) and an intracellular metallothionein (BmtA). We show here that both pairs of predicted alpha3N and alpha5 sites bind metal ions, but with distinct physicochemical and functional metal specificities. Inactivation of the thiophilic alpha3N site via mutation (C77S) abolishes regulation by both Cd (II) and Cu (I), while Zn (II) remains a potent allosteric negative effector of operator/promoter binding (Delta G c >or= +3.2 kcal mol (-1)). In contrast, alpha5 site mutant retains regulation by all four metal ions, albeit with a smaller coupling free energy (Delta G c approximately +1.7 (+/-0.1) kcal mol (-1)). Unlike the other metals ions, the BxmR dimer binds 4 mol equiv of Cu (I) to form an alpha3N binuclear Cu (I) 2S 4 cluster by X-ray absorption spectroscopy. BxmR is thus distinguishable from other closely related ArsR family sensors, in having evolved a metalloregulatory alpha3N site that can adopt an expanded range of coordination chemistries while maintaining redundancy in the response to Zn (II). The evolutionary implications of these findings for the ArsR metal sensor family are discussed.

Candidate stress genes of Nitrosomonas europaea for monitoring inhibition of nitrification by heavy metals

Heavy metals have been shown to be strong inhibitors of nitrification in wastewater treatment plants. In this research, the effects of cadmium, copper, and mercury on Nitrosomonas europaea were studied in quasi-steady-state batch reactors. When cells were exposed to 1 microM CdCl2, 6 microM HgCl2, or 8 microM CuCl2, ammonia oxidation rates were decreased by about 90%. Whole-genome transcriptional and proteomic responses of N. europaea to cadmium were used to identify heavy metal stress response genes. When cells were exposed to 1 microM CdCl2 for 1 h, 66 genes (of the total of 2,460 genes) were upregulated, and 50 genes were downregulated more than twofold. Of these, the mercury resistance genes (merTPCADE) averaged 277-fold upregulation under 1 microM CdCl2, with merA (mercuric reductase) showing 297-fold upregulation. In N. europaea cells exposed to 6 microM HgCl2 or to 8 microM CuCl2, merA showed 250-fold and 1.7-fold upregulation, respectively. Cells showed the ability to recover quickly from Hg2+-related toxic effects, apparently associated with upregulation of the mercury resistance genes and amoA, but no such recovery was evident in Cd2+-exposed cells even though merTPCADE were highly upregulated. We suggest that the upregulation of merA in response to CdCl2 and HgCl2 exposure may provide a means to develop an early-warning indicator for inhibition of nitrification by these metals.

Detoxification of toxic heavy metals by marine bacteria highly resistant to mercury

Pollution in industrial areas is a serious environmental concern, and interest in bacterial resistance to heavy metals is of practical significance. Mercury (Hg), Cadmium (Cd), and lead (Pb) are known to cause damage to living organisms, including human beings. Several marine bacteria highly resistant to mercury (BHRM) capable of growing at 25 ppm (mg L(-1)) or higher concentrations of mercury were tested during this study to evaluate their potential to detoxify Cd and Pb. Results indicate their potential of detoxification not only of Hg, but also Cd and Pb. Through biochemical and 16S rRNA gene sequence analyses, these bacteria were identified to belong to Alcaligenes faecalis (seven isolates), Bacillus pumilus (three isolates), Bacillus sp. (one isolate), Pseudomonas aeruginosa (one isolate), and Brevibacterium iodinium (one isolate). The mechanisms of heavy metal detoxification were through volatilization (for Hg), putative entrapment in the extracellular polymeric substance (for Hg, Cd and Pb) as revealed by the scanning electron microscopy and energy dispersive x-ray spectroscopy, and/or precipitation as sulfide (for Pb). These bacteria removed more than 70% of Cd and 98% of Pb within 72 and 96 h, respectively, from growth medium that had initial metal concentrations of 100 ppm. Their detoxification efficiency for Hg, Cd and Pb indicates good potential for application in bioremediation of toxic heavy metals.

An overview of mercury contamination research in the Amazon basin with an emphasis on Brazil

This article provides an overview of research on mercury contamination in the Amazon Basin and its evolution from 1990 to 2005. The assessment was based on an extensive and systematic review using bibliographic databases available online and a review of projects by research groups. Brazilian research groups were identified using the database of the Brazilian National Research Council (CNPq). A geographic information system was used to determine the location of the studies. Different aspects of mercury contamination were evaluated (environmental studies, impacts on human health, technological improvements). For 1990-2005, a total of 455 publications were identified. The main advances and remaining gaps in relation to environmental issues and human health were identified and discussed. Although the scientific output varied considerably over the period, there was a general increase in the total number of publications per year from the early 1990s (fewer than 20) until 2005 (more than 30), considering the articles published in indexed journals.

Long-term Hg pollution induced Hg tolerance in the terrestrial isopod Porcellio scaber (Isopoda, Crustacea)

The aim of our work was to assess the pollution-induced community tolerance (PICT) of isopod gut microbiota and pollution-induced isopod population tolerance (PIPT). Animals collected from a chronically Hg polluted and an unpolluted location were exposed for 14 days to 10microg Hg/g dry food under laboratory conditions. The lysosomal membrane stability, hepatopancreas epithelium thickness, feeding activity and animal bacterial gut microbiota composition were determined. The results confirm the hypothesis that the response to short-term Hg exposure differs for animals from the Hg polluted and the unpolluted field locations. The animals and their gut microbiota from the Hg polluted location were less affected by Hg in a short-term feeding experiment than those from the unpolluted environment. We discuss the pollution-induced population tolerance of isopods and their gut microbiota as a measure of effects of long-term environmental pollution. The ecological consequences of such phenomena are also discussed.

Relationships between hydrosedimentary processes and occurrence of mercury-resistant bacteria (merA) in estuary mudflats (Seine, France)

The Seine estuary (France) is one of the world's macrotidal systems that is most contaminated with heavy metals. To study the mercury-resistant bacterial community in such an environment, we have developed a molecular tool, based on competitive PCR, enabling the quantification of Gram-negative merA gene abundance. The occurrence of the Gram-negative merA gene in relation with the topology (erosion/deposit periods) and the mercury contamination of three contrasted mudflats was investigated through a multidisciplinary approach and compared with a non-anthropized site (Authie, France). The higher abundance of the Gram-negative merA gene in the Seine estuary mudflats indicates a relationship between the degree of anthropization and the abundance of the merA gene in the mudflat sediments. In the Seine mudflats, the maxima of abundance are always located in fresh sediment deposits. Therefore, the abundance is closely related with the hydrosedimentary processes, which thus seem to be determining factors in the occurrence of the Gram-negative merA gene in the surface sediments of the Seine's mudflat.

Dental Amalgam and Antibiotic- and/or Mercury-resistant Bacteria

Mercury emitted from dental amalgam may select for increased numbers of antibiotic- or mercury-resistant commensal bacteria in patients and increase their risk for bacterial diseases that are resistant to common therapies. We hypothesized that the presence of dental amalgams would increase the level of mercury-, tetracycline-, ampicillin-, erythromycin-, or chloramphenicol-resistant oral and urinary bacteria as compared with levels in children receiving composite fillings. Samples were collected at baseline, 3–6 months after the initial dental treatment, and annually for 7 years of follow-up. There were no statistically significant differences between treatment groups in the numbers of bacteria growing on antibiotic- or mercury-supplemented plates. This study provided no evidence that amalgam fillings on posterior teeth influenced the level of antibiotic- or mercury-resistant oral or urinary bacteria as detected by culture.

Cultivation of hard-to-culture subsurface mercury-resistant bacteria and discovery of new merA gene sequences

Mercury-resistant bacteria may be important players in mercury biogeochemistry. To assess the potential for mercury reduction by two subsurface microbial communities, resistant subpopulations and their merA genes were characterized by a combined molecular and cultivation-dependent approach. The cultivation method simulated natural conditions by using polycarbonate membranes as a growth support and a nonsterile soil slurry as a culture medium. Resistant bacteria were pregrown to microcolony-forming units (mCFU) before being plated on standard medium. Compared to direct plating, culturability was increased up to 2,800 times and numbers of mCFU were similar to the total number of mercury-resistant bacteria in the soils. Denaturing gradient gel electrophoresis analysis of DNA extracted from membranes suggested stimulation of growth of hard-to-culture bacteria during the preincubation. A total of 25 different 16S rRNA gene sequences were observed, including Alpha-, Beta-, and Gammaproteobacteria; Actinobacteria; Firmicutes; and Bacteroidetes. The diversity of isolates obtained by direct plating included eight different 16S rRNA gene sequences (Alpha- and Betaproteobacteria and Actinobacteria). Partial sequencing of merA of selected isolates led to the discovery of new merA sequences. With phylum-specific merA primers, PCR products were obtained for Alpha- and Betaproteobacteria and Actinobacteria but not for Bacteroidetes and Firmicutes. The similarity to known sequences ranged between 89 and 95%. One of the sequences did not result in a match in the BLAST search. The results illustrate the power of integrating advanced cultivation methodology with molecular techniques for the characterization of the diversity of mercury-resistant populations and assessing the potential for mercury reduction in contaminated environments.

A conservative region of the mercuric reductase gene (mera) as a molecular marker of bacterial mercury resistance

The most common bacterial mercury resistance mechanism is based on the reduction of Hg(II) to Hg(0), which is dependent of the mercuric reductase enzyme (MerA) activity. The use of a 431 bp fragment of a conservative region of the mercuric reductase (merA) gene was applied as a molecular marker of this mechanism, allowing the identification of mercury resistant bacterial strains.

The multiple functions of the thiol-based electron flow pathways of Escherichia coli: Eternal concepts revisited

Electron flow via thiols is a theme with many variations in all kingdoms of life. The favourable physichochemical properties of the redox active couple of two cysteines placed in the optimised environment of the thioredoxin fold allow for two electron transfers in between top biological reductants and ultimate oxidants. The reduction of ribonucleotide reductases by thioredoxin and thioredoxin reductase of Escherichia coli (E. coli) was one of the first pathways to be elucidated. Diverse functions such as protein folding in the periplasm, maturation of respiratory enzymes, detoxification of hydrogen peroxide and prevention of oxidative damage may be based on two electron transfers via thiols. A growing field is the relation of thiol reducing pathways and the interaction of E. coli with different organisms. This concept combined with the sequencing of the genomes of different bacteria may allow for the identification of fine differences in the systems employing thiols for electron flow between pathogens and their corresponding mammalian hosts. The emerging possibility is the development of novel antibiotics.

Remediation aspect of microbial changes of plant rhizosphere in mercury contaminated soil

Phytoremediation, an approach that uses plants to remediate contaminated soil through degradation, stabilization or accumulation, may provide an efficient solution to some mercury contamination problems. This paper presents growth chamber experiments that tested the ability of plant species to stabilize mercury in soil. Several indigenous herbaceous species and Salix viminalis were grown in soil collected from a mercury-contaminated site in southern Poland. The uptake and distribution of mercury by these plants were investigated, and the growth and vitality of the plants through a part of one vegetative cycle were assessed. The highest concentrations of mercury were found at the roots, but translocation to the aerial part also occurred. Most of the plant species tested displayed good growth on mercury contaminated soil and sustained a rich microbial population in the rhizosphere. The microbial populations of root-free soil and rhizosphere soil from all species were also examined. An inverse correlation between the number of sulfur amino acid decomposing bacteria and root mercury content was observed. These results indicate the potential for using some species of plants to treat mercury contaminated soil through stabilization rather than extraction. The present investigation proposes a practical cost-effective temporary solution for phytostabilization of soil with moderate mercury contamination as well as the basis for plant selection.

The application of (199)Hg NMR and (199m)Hg perturbed angular correlation (PAC) spectroscopy to define the biological chemistry of Hg(II): a case study with designed two- and three-stranded coiled coils

The use of de novo designed peptides is a powerful strategy to elucidate Hg(II)-protein interactions and to gain insight into the chemistry of Hg(II) in biological systems. Cysteine derivatives of the designed alpha-helical peptides of the TRI family [Ac-G-(L(a)K(b)A(c)L(d)E(e)E(f)K(g))(4)-G-NH(2)] bind Hg(II) at high pH values and at peptide/Hg(II) ratios of 3:1 with an unusual trigonal thiolate coordination mode. The resulting Hg(II) complexes are good water-soluble models for Hg(II) binding to the protein MerR. We have carried out a parallel study using (199)Hg NMR and (199m)Hg perturbed angular correlation (PAC) spectroscopy to characterize the distinct species that are generated under different pH conditions and peptide TRI L9C/Hg(II) ratios. These studies prove for the first time the formation of [Hg{(TRI L9C)(2)-(TRI L9C-H)}], a dithiolate-Hg(II) complex in the hydrophobic interior of the three-stranded coiled coil (TRI L9C)(3). (199)Hg NMR and (199m)Hg PAC data demonstrate that this dithiolate-Hg(II) complex is different from the dithiolate [Hg(TRI L9C)(2)], and that the presence of third alpha-helix, containing a protonated cysteine, breaks the symmetry of the coordination environment present in the complex [Hg(TRI L9C)(2)]. As the pH is raised, the deprotonation of this third cysteine generates the trigonal thiolate-Hg(II) complex Hg(TRI L9C)(3)(-) on a timescale that is slower than the NMR timescale (0.01-10 ms). The formation of the species [Hg{(TRI L9C)(2)(TRI L9C-H)}] is the result of a compromise between the high affinity of Hg(II) to form dithiolate complexes and the preference of the peptide to form a three-stranded coiled coil.

Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation

Analysis of the structure and inventory of the genome of Nitrosomonas eutropha C91 revealed distinctive features that may explain the adaptation of N. eutropha-like bacteria to N-saturated ecosystems. Multiple gene-shuffling events are apparent, including mobilized and replicated transposition, as well as plasmid or phage integration events into the 2.66 Mbp chromosome and two plasmids (65 and 56 kbp) of N. eutropha C91. A 117 kbp genomic island encodes multiple genes for heavy metal resistance, including clusters for copper and mercury transport, which are absent from the genomes of other ammonia-oxidizing bacteria (AOB). Whereas the sequences of the two ammonia monooxygenase and three hydroxylamine oxidoreductase gene clusters in N. eutropha C91 are highly similar to those of Nitrosomonas europaea ATCC 19718, a break of synteny in the regions flanking these clusters in each genome is evident. Nitrosomonas eutropha C91 encodes four gene clusters for distinct classes of haem-copper oxidases, two of which are not found in other aerobic AOB. This diversity of terminal oxidases may explain the adaptation of N. eutropha to environments with variable O(2) concentrations and/or high concentrations of nitrogen oxides. As with N. europaea, the N. eutropha genome lacks genes for urease metabolism, likely disadvantaging nitrosomonads in low-nitrogen or acidic ecosystems. Taken together, this analysis revealed significant genomic variation between N. eutropha C91 and other AOB, even the closely related N. europaea, and several distinctive properties of the N. eutropha genome that are supportive of niche specialization.

Harnessing the mechanism of glutathione reductase for synthesis of active site bound metallic nanoparticles and electrical connection to electrodes

It is demonstrated herein that the FAD-dependent enzyme glutathione reductase (GR) catalyzes the NADPH-dependent reduction of AuCl4-, forming gold nanoparticles at the active site that are tightly bound through the catalytic cysteines. The nanoparticles can be removed from the GR active site with thiol reagents such as 2-mercaptoethanol. The deep enzyme active site cavity stabilizes very small metallic clusters and prevents them from aggregating in the absence of capping ligands. The behavior of the GR-nanoparticle complexes in solution, and their electrochemical properties when immobilized on graphite paper electrodes are presented. It is shown that the borohydride ion, a known reducing agent for GR, is catalytically oxidized by larger GR-nanoparticle (>or=150 gold atoms) complexes generating catalytic currents, whereas NADPH (the natural reducing agent for GR) is not. It is proposed that the surface of the Toray graphite paper electrode employed here interferes with NADPH binding to the GR-nanoparticle complex. The catalytic currents with borohydride begin at the potential of GR-bound FAD, showing that there is essentially zero resistance to electron transfer (i.e., zero overpotential) from GR-bound FAD through the gold nanoparticle to the electrode.

A study on the adsorption mechanism of mercury on Aspergillus versicolor biomass

The adsorption behavior of mercury on Aspergillus versicolor biomass (AVB) has been investigated in aqueous solution to understand the physicochemical process involved and to explore the potentiality of AVB in pollution control management. This biomass has been successfully used for reducing the mercury concentration level in the effluent of chloralkali and battery industries to a permissible limit. The results establish that 75.6 mg of mercury is adsorbed per gram of biomass. The adsorption process is found to be a function of pH of the solution, with the optimum range being pH 5.0-6.0. The process obeys the Langmuir-Freundlich isotherm model. Scanning electron microscopic analysis demonstrates a conspicuous surface morphology change of the mercury-adsorbed biomass. A nearly uniform distribution of metal ions on the mycelial surface excepting a few aggregation points is revealed by X-ray elemental mapping profiles. The results of zeta potential measurement, Fourier transform infrared (FTIR) spectroscopy, and blocking of the functional groups by chemical modification reflect the binding of mercury on the biomass occurs through electrostatic and complexation reactions. The accumulation of mercury on the cell wall associated with negligible diffusion and or transportation into cytoplasm finds support from the results of adsorption kinetics and transmission electron micrographs. Mercury adsorption on biomass also leads to elongation of cells and cytoplasmic aggregation of spheroplast/protoplasts, indicating that the cell wall acts as a permeation barrier against this toxic metal.

Effect of pH on intracellular accumulation of trace concentrations of Hg(II) in Escherichia coli under anaerobic conditions, as measured using a mer-lux bioreporter

The effects of pH on the uptake and accumulation of Hg(II) by Escherichia coli were determined at trace, environmentally relevant, concentrations of Hg and under anaerobic conditions. Hg(II) accumulation was measured using inducible light production from E. coli HMS174 harboring a mer-lux bioreporter plasmid (pRB28). The effect of pH on the toxicity of higher concentrations of Hg(II) was measured using a constitutive lux plasmid (pRB27) in the same bacterial host. In this study, intracellular accumulation and toxicity of Hg(II) under anaerobic conditions were both significantly enhanced with decreasing pH over the pH range of 8 to 5. The pH effect on Hg(II) accumulation was most pronounced at pHs of <6, which substantially enhanced the Hg(II)-dependent light response. This enhanced response did not appear to be due to pH stress, as similar results were obtained whether cells were grown at the same pH as the assay or at a different pH. The enhanced accumulation of Hg(II) was also not related to differences in the chemical speciation of Hg(II) in the external medium resulting from the changes in pH. Experiments with Cd(II), also detectable by the mer-lux bioreporter system, showed that Cd(II) accumulation responded differently to pH changes than the net accumulation of Hg(II). Potential implications of these findings for our understanding of bacterial accumulation of Hg(II) under anaerobic conditions and for bacteria-mediated cycling of Hg(II) in aquatic ecosystems are discussed. Arguments are provided suggesting that this differential accumulation is due to changes in uptake of mercury.

Functioning of the mercury resistance operon at extremely high Hg(II) loads in a chemostat: A proteome analysis

The transformation of extremely high concentrations of ionic mercury (up to 500 mg L(-1)) was investigated in a chemostat for two mercury-resistant Pseudomonas putida strains, the sediment isolate Spi3 carrying a regulated mercury resistance (mer) operon, and the genetically engineered strain KT2442Colon, two colonsmer73 expressing the mer operon constitutively. Both strains reduced Hg(II) with an efficiency of 99.9% even at the maximum load, but the concentration of particle bound mercury in the chemostat increased strongly. A proteome analysis using two-dimensional gel electrophoresis and mass spectrometry (2-DE/MS) showed constant expression of the MerA and MerB proteins in KT2442Colon, two colonsmer73 as expected, while in Spi3 expression of both proteins was strongly dependent on the Hg(II) concentration. The total cellular proteome of the two strains showed very little changes at high Hg(II) load. However, certain cellular responses of the two strains were identified, especially in membrane-related transport proteins. In Spi3, an up to 45-fold strong induction of a cation efflux transporter was observed, accompanied by a drastic downregulation (106-fold) of an outer membrane porin. In such a way, the cell complemented the highly specific mercury resistance mechanism with a general detoxification response. No indication of a higher demand on energy metabolism could be found for both strains.

Engineered holliday junctions as single-molecule reporters for protein-DNA interactions with application to a MerR-family regulator

Protein-DNA interactions are essential for gene maintenance, replication, and expression. Characterizing how proteins interact with and change the structure of DNA is crucial in elucidating the mechanisms of protein function. Here, we present a novel and generalizable method of using engineered DNA Holliday junctions (HJs) that contain specific protein-recognition sequences to report protein-DNA interactions in single-molecule FRET measurements, utilizing the intrinsic structural dynamics of HJs. Because the effects of protein binding are converted to the changes in the structure and dynamics of HJs, protein-DNA interactions that involve small structural changes of DNA can be studied. We apply this method to investigate how the MerR-family regulator PbrR691 interacts with DNA for transcriptional regulation. Both apo- and holo-PbrR691 bind the stacked conformers of the engineered HJ, change their structures, constrain their conformational distributions, alter the kinetics, and shift the equilibrium of their structural dynamics. The information obtained maps the potential energy surfaces of HJ before and after PbrR691 binding and reveals the protein actions that force DNA structural changes for transcriptional regulation. The ability of PbrR691 to bind both HJ conformers and still allow HJ structural dynamics also informs about its conformational flexibility that may have significance for its regulatory function. This method of using engineered HJs offers quantification of the changes both in structure and in dynamics of DNA upon protein binding and thus provides a new tool to elucidate the correlation of structure, dynamics, and function of DNA-binding proteins.

Sequence-based analysis of pQBR103; a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet

The plasmid pQBR103 was found within Pseudomonas populations colonizing the leaf and root surfaces of sugar beet plants growing at Wytham, Oxfordshire, UK. At 425 kb it is the largest self-transmissible plasmid yet sequenced from the phytosphere. It is known to enhance the competitive fitness of its host, and parts of the plasmid are known to be actively transcribed in the plant environment. Analysis of the complete sequence of this plasmid predicts a coding sequence (CDS)-rich genome containing 478 CDSs and an exceptional degree of genetic novelty; 80% of predicted coding sequences cannot be ascribed a function and 60% are orphans. Of those to which function could be assigned, 40% bore greatest similarity to sequences from Pseudomonas spp, and the majority of the remainder showed similarity to other gamma-proteobacterial genera and plasmids. pQBR103 has identifiable regions presumed responsible for replication and partitioning, but despite being tra+ lacks the full complement of any previously described conjugal transfer functions. The DNA sequence provided few insights into the functional significance of plant-induced transcriptional regions, but suggests that 14% of CDSs may be expressed (11 CDSs with functional annotation and 54 without), further highlighting the ecological importance of these novel CDSs. Comparative analysis indicates that pQBR103 shares significant regions of sequence with other plasmids isolated from sugar beet plants grown at the same geographic location. These plasmid sequences indicate there is more novelty in the mobile DNA pool accessible to phytosphere pseudomonas than is currently appreciated or understood.

19F-NMR Reveals Metal and Operator-induced Allostery in MerR

Metalloregulators of the MerR family activate transcription upon metal binding by underwinding the operator-promoter DNA to permit open complex formation by pre-bound RNA polymerase. Historically, MerR's allostery has been monitored only indirectly via nuclease sensitivity or by fluorescent nucleotide probes and was very specific for Hg(II), although purified MerR binds several thiophilic metals. To observe directly MerR's ligand-induced behavior we made 2-fluorotyrosine-substituted MerR and found similar, minor changes in (19)F chemical shifts of tyrosine residues in the free protein exposed to Hg(II), Cd(II) or Zn(II). However, DNA binding elicits large chemical shift changes in MerR's tyrosine residues and in DNA-bound MerR Hg(II) provokes changes very distinct from those of Cd(II) or Zn(II). These chemical shift changes and other biophysical and phenotypic properties of wild-type MerR and relevant mutants reveal elements of an allosteric network that enables the coordination state of the metal binding site to direct metal-specific movements in the distant DNA binding site and the DNA-bound state also to affect the metal binding domain.

High diversity of bacterial mercuric reductase genes from surface and sub-surface floodplain soil (Oak Ridge, USA)

DNA was extracted from different depth soils (0-5, 45-55 and 90-100 cm below surface) sampled at Lower East Fork Poplar Creek floodplain (LEFPCF), Oak Ridge (TN, USA). The presence of merA genes, encoding the mercuric reductase, the key enzyme in detoxification of mercury in bacteria, was examined by PCR targeting Actinobacteria, Firmicutes or beta/gamma-Proteobacteria. beta/gamma-Proteobacteria merA genes were successfully amplified from all soils, whereas Actinobacteria were amplified only from surface soil. merA clone libraries were constructed and sequenced. beta/gamma-Proteobacteria sequences revealed high diversity in all soils, but limited vertical similarity. Less than 20% of the operational taxonomic units (OTU) (DNA sequences > or = 95% identical) were shared between the different soils. Only one of the 62 OTU was > or = 95% identical to a GenBank sequence, highlighting that cultivated bacteria are not representative of what is found in nature. Fewer merA sequences were obtained from the Actinobacteria, but these were also diverse, and all were different from GenBank sequences. A single clone was most closely related to merA of alpha-Proteobacteria. An alignment of putative merA genes of genome sequenced mainly marine alpha-Proteobacteria was used for design of merA primers. PCR amplification of soil alpha-Proteobacteria isolates and sequencing revealed that they were very different from the genome-sequenced bacteria (only 62%-66% identical at the amino-acid level), although internally similar. In light of the high functional diversity of mercury resistance genes and the limited vertical distribution of shared OTU, we discuss the role of horizontal gene transfer as a mechanism of bacterial adaptation to mercury.