A bacterial view of the periodic table: genes and proteins for toxic inorganic ions

Metabolic flexibility revealed in the genome of the cyst-forming alpha-1 proteobacterium Rhodospirillum centenum

Background

Rhodospirillum centenum is a photosynthetic non-sulfur purple bacterium that favors growth in an anoxygenic, photosynthetic N₂-fixing environment. It is emerging as a genetically amenable model organism for molecular genetic analysis of cyst formation, photosynthesis, phototaxis, and cellular development. Here, we present an analysis of the genome of this bacterium.

Results

R. centenum contains a singular circular chromosome of 4,355,548 base pairs in size harboring 4,105 genes. It has an intact Calvin cycle with two forms of Rubisco, as well as a gene encoding phosphoenolpyruvate carboxylase (PEPC) for mixotrophic CO₂ fixation. This dual carbon-fixation system may be required for regulating internal carbon flux to facilitate bacterial nitrogen assimilation. Enzymatic reactions associated with arsenate and mercuric detoxification are rare or unique compared to other purple bacteria. Among numerous newly identified signal transduction proteins, of particular interest is a putative bacteriophytochrome that is phylogenetically distinct from a previously characterized R. centenum phytochrome, Ppr. Genes encoding proteins involved in chemotaxis as well as a sophisticated dual flagellar system have also been mapped.

Conclusions

Remarkable metabolic versatility and a superior capability for photoautotrophic carbon assimilation is evident in R. centenum.

Heavy metal resistance in Arthrobacter ramosus strain G2 isolated from mercuric salt-contaminated soil

Present study describes isolation of a multiple metal-resistant Arthrobacter ramosus strain from mercuric salt-contaminated soil. The isolate was found to resist and bioaccumulate several metals, such as cadmium, cobalt, zinc, chromium and mercury. Maximum tolerated concentrations for above metals were found to be 37, 525, 348, 1530 and 369 microM, respectively. The isolate could also reduce and detoxify redox-active metals like chromium and mercury, indicating that it has great potential in bioremediation of heavy metal-contaminated sites. Chromate reductase and mercuric reductase (MerA) activities in protein extract of the culture were found to be 2.3 and 0.17 units mg(-1) protein, respectively. MerA enzyme was isolated from the culture by (NH(4))(2)SO(4) precipitation followed by dye affinity chromatography and its identity was confirmed by nano-LC-MS/MS. Its monomeric molecular weight, and optimum pH and temperature were 57kDa, 7.4 and 55 degrees C, respectively. Thus, the enzyme was mildly thermophilic as compared to other MerA enzymes. K(m) and V(max) of the enzyme were 16.9 microM HgCl(2) and 6.2 micromol min(-1)mg(-1) enzyme, respectively. The enzyme was found to be NADPH-specific. To our knowledge this is the first report on characterization of MerA enzyme from an Arthrobacter sp.

"In situ" phytostabilisation of heavy metal polluted soils using Lupinus luteus inoculated with metal resistant plant-growth promoting rhizobacteria

The aim of this work is the evaluation of metal phytostabilisation potential of Lupinus luteus inoculated with Bradyrhizobium sp. 750 and heavy metal resistant PGPRs (plant-growth promoting rhizobacteria), for in situ reclamation of multi-metal contaminated soil after a mine spill. Yellow lupines accumulated heavy metals mainly in roots (Cu, Cd and especially Pb were poorly translocated to shoots). This indicates a potential use of this plant in metal phytostabilisation. Furthermore, As accumulation was undetectable. On the other hand, zinc accumulation was 10-100 times higher than all other metals, both in roots and in shoots. Inoculation with Bradyrhizobium sp. 750 increased both biomass and nitrogen content, indicating that nitrogen fixation was effective in soils with moderate levels of contamination. Co-inoculation of lupines with a consortium of metal resistant PGPR (including Bradyrhizobium sp., Pseudomonas sp. and Ochrobactrum cytisi) produced an additional improvement of plant biomass. At the same time, a decrease in metal accumulation was observed, both in shoots and roots, which could be due to a protective effect exerted on plant rhizosphere. Our results indicate the usefulness of L. luteus inoculated with a bacterial consortium of metal resistant PGPRs as a method for in situ reclamation of metal polluted soils.

GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity

A new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with approximately 28 000 probes covering approximately 57 000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation. GeoChip 3.0 also has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating and the gyrB gene for phylogenetic analysis. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets. Experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036-0.025% false-positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which showed that the structure, composition and potential activity of soil microbial communities significantly changed with the plant species diversity. As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning.

Arsenic-resistant bacteria associated with roots of the wild Cirsium arvense (L.) plant from an arsenic polluted soil, and screening of potential plant growth-promoting characteristics

A rhizobacterial community, associated with the roots of wild thistle Cirsium arvense (L.) growing in an arsenic polluted soil, was studied by fluorescence in situ hybridization (FISH) analysis in conjunction with cultivation-based methods. In the bulk, rhizosphere, and rhizoplane fractions of the soil, the qualitative picture obtained by FISH analysis of the main phylogenetic bacterial groups was similar and was predominantly comprised of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. The arsenic-resistant isolates belonged to 13 genera, the most abundant being those of Bacillus, Achromobacter, Brevundimonas, Microbacterium, and Ochrobactrum. Most bacteria grew in the presence of high arsenic concentrations (over 100mM arsenate and 10mM arsenite). Most strains possessed the ArsC, ArsB and ACR3 genes homologous to arsenate reductase and to the two classes of arsenite efflux pumps, respectively, peculiar to the ars operon of the arsenic detoxification system. ArsB and ACR3 were present simultaneously in highly resistant strains. An inconsistency between 16S rRNA phylogenetic affiliations and the arsenate reductase sequences of the strains was observed, indicating possible horizontal transfer of arsenic resistance genes in the soil bacterial community. Several isolates were able to reduce arsenate and to oxidise arsenite. In particular, Ancylobacter dichloromethanicum strain As3-1b possessed both characteristics, and arsenite oxidation occurred in the strain also under chemoautotrophic conditions. Some rhizobacteria produced siderophores, indole acetic acid and 1-amino-cyclopropane-1-carboxylic acid deaminase, thus possessing potential plant growth-promoting traits.

Structure, function, and evolution of the Thiomonas spp. genome

Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome of one of these strains, Thiomonas sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive and grow in its highly toxic environment. In order to explore genomic diversity as well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH) approach was used on eight different strains of the Thiomonas genus, including five strains of the same species. Our results suggest that the Thiomonas genome has evolved through the gain or loss of genomic islands and that this evolution is influenced by the specific environmental conditions in which the strains live.

Surface display of metal fixation motifs of bacterial P1-type ATPases specifically promotes biosorption of Pb(2+) by Saccharomyces cerevisiae

Biosorption of metal ions may take place by different passive metal-sequestering processes such as ion exchange, complexation, physical entrapment, and inorganic microprecipitation or by a combination of these. To improve the biosorption capacity of the potential yeast biosorbent, short metal-binding NP peptides (harboring the CXXEE metal fixation motif of the bacterial Pb(2+)-transporting P1-type ATPases) were efficiently displayed and covalently anchored to the cell wall of Saccharomyces cerevisiae. These were fusions to the carboxyl-terminal part of the sexual adhesion glycoprotein alpha-agglutinin (AGalpha1Cp). Compared to yeast cells displaying the anchoring domain only, those having a surface display of NP peptides multiplied their Pb(2+) biosorption capacity from solutions containing a 75 to 300 microM concentration of the metal ion up to 5-fold. The S-type Pb(2+) biosorption isotherms, plus the presence of electron-dense deposits (with an average size of 80 by 240 nm, observed by transmission electron microscopy) strongly suggested that the improved biosorption potential of NP-displaying cells is due to the onset of microprecipitation of Pb species on the modified cell wall. The power of an improved capacity for Pb biosorption was also retained by the isolated cell walls containing NP peptides. Their Pb(2+) biosorption property was insensitive to the presence of a 3-fold molar excess of either Cd(2+) or Zn(2+). These results suggest that the biosorption mechanism can be specifically upgraded with microprecipitation by the engineering of the biosorbent with an eligible metal-binding peptide.

Impact of silver(I) on the metabolism of Shewanella oneidensis

Anaerobic cultures of Shewanella oneidensis MR-1 reduced toxic Ag(I), forming nanoparticles of elemental Ag(0), as confirmed by X-ray diffraction analyses. The addition of 1 to 50 microM Ag(I) had a limited impact on growth, while 100 microM Ag(I) reduced both the doubling time and cell yields. At this higher Ag(I) concentration transmission electron microscopy showed the accumulation of elemental silver particles within the cell, while at lower concentrations the metal was exclusively reduced and precipitated outside the cell wall. Whole organism metabolite fingerprinting, using the method of Fourier transform infrared spectroscopy analysis of cells grown in a range of silver concentrations, confirmed that there were significant physiological changes at 100 microM silver. Principal component-discriminant function analysis scores and loading plots highlighted changes in certain functional groups, notably, lipids, amides I and II, and nucleic acids, as being discriminatory. Molecular analyses confirmed a dramatic drop in cellular yields of both the phospholipid fatty acids and their precursor molecules at high concentrations of silver, suggesting that the structural integrity of the cellular membrane was compromised at high silver concentrations, which was a result of intracellular accumulation of the toxic metal.

Microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased colonies

A functional gene array (FGA), GeoChip 2.0, was used to assess the biogeochemical cycling potential of microbial communities associated with healthy and Caribbean yellow band diseased (YBD) Montastraea faveolata. Over 6700 genes were detected, providing evidence that the coral microbiome contains a diverse community of archaea, bacteria and fungi capable of fulfilling numerous functional niches. These included carbon, nitrogen and sulfur cycling, metal homeostasis and resistance, and xenobiotic contaminant degradation. A significant difference in functional structure was found between healthy and YBD M. faveolata colonies and those differences were specific to the physical niche examined. In the surface mucopolysaccharide layer (SML), only two of 31 functional categories investigated, cellulose degradation and nitrification, revealed significant differences, implying a very specific change in microbial functional potential. Coral tissue slurry, on the other hand, revealed significant changes in 10 of the 31 categories, suggesting a more generalized shift in functional potential involving various aspects of nutrient cycling, metal transformations and contaminant degradation. This study is the first broad screening of functional genes in coral-associated microbial communities and provides insights regarding their biogeochemical cycling capacity in healthy and diseased states.

Environmental pollution by antibiotics and by antibiotic resistance determinants

Antibiotics are among the most successful drugs used for human therapy. However, since they can challenge microbial populations, they must be considered as important pollutants as well. Besides being used for human therapy, antibiotics are extensively used for animal farming and for agricultural purposes. Residues from human environments and from farms may contain antibiotics and antibiotic resistance genes that can contaminate natural environments. The clearest consequence of antibiotic release in natural environments is the selection of resistant bacteria. The same resistance genes found at clinical settings are currently disseminated among pristine ecosystems without any record of antibiotic contamination. Nevertheless, the effect of antibiotics on the biosphere is wider than this and can impact the structure and activity of environmental microbiota. Along the article, we review the impact that pollution by antibiotics or by antibiotic resistance genes may have for both human health and for the evolution of environmental microbial populations.

An efflux transporter PbrA and a phosphatase PbrB cooperate in a lead-resistance mechanism in bacteria

The gene cluster pbrTRABCD from Cupriavidus metallidurans CH34 is thought to encode a unique, specific resistance mechanism for lead. However, the exact functions of these genes are unknown. In this study we examine the metal specificity and functions of pbrABCD by expressing these genes in different combinations and comparing their ability to restore Pb(2+), Zn(2+) and Cd(2+) resistance in a metal-sensitive C. metallidurans strain DN440. We show that lead resistance in C. metallidurans is achieved through the cooperation of the Zn/Cd/Pb-translocating ATPase PbrA and the undecaprenyl pyrophosphate phosphatase PbrB. While PbrA non-specifically exported Pb(2+), Zn(2+) and Cd(2+), a specific increase in lead resistance was observed when PbrA and PbrB were coexpressed. As a model of action for PbrA and PbrB we propose a mechanism where Pb(2+) is exported from the cytoplasm by PbrA and then sequestered as a phosphate salt with the inorganic phosphate produced by PbrB. Similar operons containing genes for heavy metal translocating ATPases and phosphatases were found in several different bacterial species, suggesting that lead detoxification through active efflux and sequestration is a common lead-resistance mechanism.

Two naphthalene degrading bacteria belonging to the genera Paenibacillus and Pseudomonas isolated from a highly polluted lagoon perform different sensitivities to the organic and heavy metal contaminants

Two bacterial strains were isolated in the presence of naphthalene as the sole carbon and energy source from sediments of the Orbetello Lagoon, Italy, which is highly contaminated with both organic compounds and metals. 16S rRNA gene sequence analysis of the two isolates assigned the strains to the genera Paenibacillus and Pseudomonas. The effect of different contaminants on the growth behaviors of the two strains was investigated. Pseudomonas sp. ORNaP2 showed a higher tolerance to benzene, toluene, and ethylbenzene than Paenibacillus sp. ORNaP1. In addition, the toxicity of heavy metals potentially present as co-pollutants in the investigated site was tested. Here, strain Paenibacillus sp. ORNaP1 showed a higher tolerance towards arsenic, cadmium, and lead, whereas it was far more sensitive towards mercury than strain Pseudomonas sp. ORNaP2. These differences between the Gram-negative Pseudomonas and the Gram-positive Paenibacillus strain can be explained by different general adaptive response systems present in the two bacteria.

Chromosomal antioxidant genes have metal ion-specific roles as determinants of bacterial metal tolerance

Microbiological metal toxicity involves redox reactions between metal species and cellular molecules, and therefore, we hypothesized that antioxidant systems might be chromosomal determinants affecting the susceptibility of bacteria to metal toxicity. Here, survival was quantified in metal ion-exposed planktonic cultures of several Escherichia coli strains, each bearing a mutation in a gene important for redox homeostasis. This characterized approximately 250 gene-metal combinations and identified that sodA, sodB, gor, trxA, gshA, grxA and marR have distinct roles in safeguarding or sensitizing cells to different toxic metal ions (Cr(2)O(7)(2-), Co(2+), Cu(2+), Ag(+), Zn(2+), AsO(2)(-), SeO(3)(2-) or TeO(3)(2-)). To shed light on these observations, fluorescent sensors for reactive oxygen species (ROS) and reduced thiol (RSH) quantification were used to ascertain that different metal ions exert oxidative toxicity through disparate modes-of-action. These oxidative mechanisms of metal toxicity were categorized as involving ROS and thiol-disulfide chemistry together (AsO(2)(-), SeO(3)(2-)), ROS predominantly (Cu(2+), Cr(2)O(7)(2-)) or thiol-disulfide chemistry predominantly (Ag(+), Co(2+), Zn(2+), TeO(3)(2-)). Corresponding to this, promoter-luxCDABE fusions showed that toxic doses of different metal ions up- or downregulate the transcription of gene sets marking distinct pathways of cellular oxidative stress. Altogether, our findings suggest that different metal ions are lethal to cells through discrete pathways of oxidative biochemistry, and moreover, indicate that chromosomally encoded antioxidant systems may have metal ion-specific physiological roles as determinants of bacterial metal tolerance.

Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains

The GntR superfamily of dimeric transcription factors, with more than 6200 members encoded in bacterial genomes, are characterized by N-terminal winged-helix DNA-binding domains and diverse C-terminal regulatory domains which provide a basis for the classification of the constituent families. The largest of these families, FadR, contains nearly 3000 proteins with all-alpha-helical regulatory domains classified into two related Pfam families: FadR_C and FCD. Only two crystal structures of FadR-family members, those of Escherichia coli FadR protein and LldR from Corynebacterium glutamicum, have been described to date in the literature. Here, the crystal structure of TM0439, a GntR regulator with an FCD domain found in the Thermotoga maritima genome, is described. The FCD domain is similar to that of the LldR regulator and contains a buried metal-binding site. Using atomic absorption spectroscopy and Trp fluorescence, it is shown that the recombinant protein contains bound Ni(2+) ions but that it is able to bind Zn(2+) with K(d) < 70 nM. It is concluded that Zn(2+) is the likely physiological metal and that it may perform either structural or regulatory roles or both. Finally, the TM0439 structure is compared with two other FadR-family structures recently deposited by structural genomics consortia. The results call for a revision in the classification of the FadR family of transcription factors.

Biotransformation of arsenic by a Yellowstone thermoacidophilic eukaryotic alga

Arsenic is the most common toxic substance in the environment, ranking first on the Superfund list of hazardous substances. It is introduced primarily from geochemical sources and is acted on biologically, creating an arsenic biogeocycle. Geothermal environments are known for their elevated arsenic content and thus provide an excellent setting in which to study microbial redox transformations of arsenic. To date, most studies of microbial communities in geothermal environments have focused on Bacteria and Archaea, with little attention to eukaryotic microorganisms. Here, we show the potential of an extremophilic eukaryotic alga of the order Cyanidiales to influence arsenic cycling at elevated temperatures. Cyanidioschyzon sp. isolate 5508 oxidized arsenite [As(III)] to arsenate [As(V)], reduced As(V) to As(III), and methylated As(III) to form trimethylarsine oxide (TMAO) and dimethylarsenate [DMAs(V)]. Two arsenic methyltransferase genes, CmarsM7 and CmarsM8, were cloned from this organism and demonstrated to confer resistance to As(III) in an arsenite hypersensitive strain of Escherichia coli. The 2 recombinant CmArsMs were purified and shown to transform As(III) into monomethylarsenite, DMAs(V), TMAO, and trimethylarsine gas, with a T(opt) of 60-70 degrees C. These studies illustrate the importance of eukaryotic microorganisms to the biogeochemical cycling of arsenic in geothermal systems, offer a molecular explanation for how these algae tolerate arsenic in their environment, and provide the characterization of algal methyltransferases.

Arsenic-resistant bacteria isolated from agricultural soils of Bangladesh and characterization of arsenate-reducing strains

AIMS

To analyse the arsenic-resistant bacterial communities of two agricultural soils of Bangladesh, to isolate arsenic-resistant bacteria, to study their potential role in arsenic transformation and to investigate the genetic determinants for arsenic resistance among the isolates.

METHODS AND RESULTS

Enrichment cultures were performed in a minimal medium in the presence of As(III) and As(V) to isolate resistant bacteria. Twenty-one arsenic-resistant bacteria belonging to different genera of Gram-positive and Gram-negative bacteria were isolated. The isolates, with the exception of Oceanimonas doudoroffii Dhal Rw, reduced 2 mmol l(-1) As(V) completely to As(III) in aerobic conditions. Putative gene fragments for arsenite efflux pumps were amplified in isolates from Dhal soil and a putative arsenate reductase gene fragment was amplified from a Bacillus sp. from Rice soil.

CONCLUSIONS

Phylogenetically diverse arsenic-resistant bacteria present in agricultural soils of Bangladesh are capable of reducing arsenate to arsenite under aerobic conditions apparently for detoxification purpose.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides results on identification, levels of arsenic resistance and reduction of arsenate by the bacterial isolates which could play an important role in arsenic cycling in the two arsenic-contaminated soils in Bangladesh.

Functional role of bacterial multidrug efflux pumps in microbial natural ecosystems

Multidrug efflux pumps have emerged as relevant elements in the intrinsic and acquired antibiotic resistance of bacterial pathogens. In contrast with other antibiotic resistance genes that have been obtained by virulent bacteria through horizontal gene transfer, genes coding for multidrug efflux pumps are present in the chromosomes of all living organisms. In addition, these genes are highly conserved (all members of the same species contain the same efflux pumps) and their expression is tightly regulated. Together, these characteristics suggest that the main function of these systems is not resisting the antibiotics used in therapy and that they should have other roles relevant to the behavior of bacteria in their natural ecosystems. Among the potential roles, it has been demonstrated that efflux pumps are important for processes of detoxification of intracellular metabolites, bacterial virulence in both animal and plant hosts, cell homeostasis and intercellular signal trafficking.

Genes involved in arsenic transformation and resistance associated with different levels of arsenic-contaminated soils

Background

Arsenic is known as a toxic metalloid, which primarily exists in inorganic form [As(III) and As(V)] and can be transformed by microbial redox processes in the natural environment. As(III) is much more toxic and mobile than As(V), hence microbial arsenic redox transformation has a major impact on arsenic toxicity and mobility which can greatly influence the human health. Our main purpose was to investigate the distribution and diversity of microbial arsenite-resistant species in three different arsenic-contaminated soils, and further study the As(III) resistance levels and related functional genes of these species.

Results

A total of 58 arsenite-resistant bacteria were identified from soils with three different arsenic-contaminated levels. Highly arsenite-resistant bacteria (MIC > 20 mM) were only isolated from the highly arsenic-contaminated site and belonged to Acinetobacter, Agrobacterium, Arthrobacter, Comamonas, Rhodococcus, Stenotrophomonas and Pseudomonas. Five arsenite-oxidizing bacteria that belonged to Achromobacter, Agrobacterium and Pseudomonas were identified and displayed a higher average arsenite resistance level than the non-arsenite oxidizers. 5 aoxB genes encoding arsenite oxidase and 51 arsenite transporter genes [18 arsB, 12 ACR3(1) and 21 ACR3(2)] were successfully amplified from these strains using PCR with degenerate primers. The aoxB genes were specific for the arsenite-oxidizing bacteria. Strains containing both an arsenite oxidase gene (aoxB) and an arsenite transporter gene (ACR3 or arsB) displayed a higher average arsenite resistance level than those possessing an arsenite transporter gene only. Horizontal transfer of ACR3(2) and arsB appeared to have occurred in strains that were primarily isolated from the highly arsenic-contaminated soil.

Conclusion

Soils with long-term arsenic contamination may result in the evolution of highly diverse arsenite-resistant bacteria and such diversity was probably caused in part by horizontal gene transfer events. Bacteria capable of both arsenite oxidation and arsenite efflux mechanisms had an elevated arsenite resistance level.

Quantum dot weathering results in microbial toxicity

Quantum dots (QDs) are increasingly being used for electronics, solar energy generation, and medical imaging applications. Most QDs consist of a heavy metal core/shell coated with amphiphilic organics that stabilize the nanoparticles and allow conjugation with biological molecules. In this study, QDs were evaluated for their effects on bacterial pure cultures, which serve as models of cell toxicity and indicators of potential impact to ecosystem health. QDs with intact surface coatings decreased growth rates of Gram positive Bacillus subtilis and Gram negative Escherichia coli but were not bactericidal. In contrast, weathering of various types of QDs under acidic (pH < or = 4) or alkaline (pH > or = 10) conditions significantly increased bactericidal activity due to the rapid (< 1 min) release of cadmium and selenite ions following QD destabilization upon loss of the organic coating. Toxicity was mitigated by humic acids, proteins, and other organic ligands that reduced metal bioavailability. The best available science, which is limited, suggests that QDs are potentially safe materials when used in their intended applications at near-neutral pH. These results forewarn us that even moderately acidic or alkaline conditions could lead to significant and localized organism effects due to toxic exposure to dissolved heavy metals. Thus, biocompatibility and ecotoxicity tests for QDs should consider in vivo and/or in situ transformations to fully characterize the potential risks to environmental health.

Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications

BACKGROUND

Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1-2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism.

RESULTS

The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes.

CONCLUSION

Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.

Calcium efflux is essential for bacterial survival in the eukaryotic host

In dynamic environments, intracellular homeostasis is maintained by transport systems found in all cells. While bacterial influx systems for essential trace cations are known to contribute to pathogenesis, efflux systems have been characterized mainly in contaminated environmental sites. We describe that the high calcium concentrations in the normal human host were toxic to pneumococci and that bacterial survival in vivo depended on CaxP, the first Ca2+ exporter reported in bacteria. CaxP homologues were found in the eukaryotic sacroplasmic reticulum and in many bacterial genomes. A caxP- mutant accumulated intracellular calcium, a state that was used to reveal signalling networks responsive to changes in intracellular calcium concentration. Chemical inhibition of CaxP was bacteriostatic in physiological calcium concentrations, suggesting a new antibiotic target uncovered under conditions in the eukaryotic host.

Escherichia coli heat-shock proteins IbpA/B are involved in resistance to oxidative stress induced by copper

The small heat-shock proteins IbpA/B are molecular chaperones that bind denatured proteins and facilitate their subsequent refolding by the ATP-dependent chaperones DnaK, DnaJ, GrpE and ClpB. In this report, we demonstrate that IbpA/B participate in the defence against copper-induced stress under aerobic conditions. In the presence of oxygen, DeltaibpA/B cells exhibit increased sensitivity to copper ions and accumulate elevated amounts of oxidized proteins, while under oxygen depletion, the DeltaibpA/B mutation has no effect on copper tolerance. This indicates that IbpA/B protect Escherichia coli cells from oxidative damage caused by copper. We show that AdhE, one of the proteins exposed to oxidation, is protected by IbpA/B against copper-mediated inactivation both in vivo and in vitro.

Transporters of arsenite in rice and their role in arsenic accumulation in rice grain

Arsenic poisoning affects millions of people worldwide. Human arsenic intake from rice consumption can be substantial because rice is particularly efficient in assimilating arsenic from paddy soils, although the mechanism has not been elucidated. Here we report that two different types of transporters mediate transport of arsenite, the predominant form of arsenic in paddy soil, from the external medium to the xylem. Transporters belonging to the NIP subfamily of aquaporins in rice are permeable to arsenite but not to arsenate. Mutation in OsNIP2;1 (Lsi1, a silicon influx transporter) significantly decreases arsenite uptake. Furthermore, in the rice mutants defective in the silicon efflux transporter Lsi2, arsenite transport to the xylem and accumulation in shoots and grain decreased greatly. Mutation in Lsi2 had a much greater impact on arsenic accumulation in shoots and grain in field-grown rice than Lsi1. Arsenite transport in rice roots therefore shares the same highly efficient pathway as silicon, which explains why rice is efficient in arsenic accumulation. Our results provide insight into the uptake mechanism of arsenite in rice and strategies for reducing arsenic accumulation in grain for enhanced food safety.

Enzyme phylogenies as markers for the oxidation state of the environment: the case of respiratory arsenate reductase and related enzymes

Background

Phylogenies of certain bioenergetic enzymes have proved to be useful tools for deducing evolutionary ancestry of bioenergetic pathways and their relationship to geochemical parameters of the environment. Our previous phylogenetic analysis of arsenite oxidase, the molybdopterin enzyme responsible for the biological oxidation of arsenite to arsenate, indicated its probable emergence prior to the Archaea/Bacteria split more than 3 billion years ago, in line with the geochemical fact that arsenite was present in biological habitats on the early Earth. Respiratory arsenate reductase (Arr), another molybdopterin enzyme involved in microbial arsenic metabolism, serves as terminal oxidase, and is thus situated at the opposite end of bioenergetic electron transfer chains as compared to arsenite oxidase. The evolutionary history of the Arr-enzyme has not been studied in detail so far.

Results

We performed a genomic search of genes related to arrA coding for the molybdopterin subunit. The multiple alignment of the retrieved sequences served to reconstruct a neighbor-joining phylogeny of Arr and closely related enzymes. Our analysis confirmed the previously proposed proximity of Arr to the cluster of polysulfide/thiosulfate reductases but also unravels a hitherto unrecognized clade even more closely related to Arr. The obtained phylogeny strongly suggests that Arr originated after the Bacteria/Archaea divergence in the domain Bacteria, and was subsequently laterally distributed within this domain. It further more indicates that, as a result of accumulation of arsenate in the environment, an enzyme related to polysulfide reductase and not to arsenite oxidase has evolved into Arr.

Conclusion

These findings are paleogeochemically rationalized by the fact that the accumulation of arsenate over arsenite required the increase in oxidation state of the environment brought about by oxygenic photosynthesis.

Toxic effects of arsenic on Sinorhizobium-Medicago sativa symbiotic interaction

Recently, the Rhizobium-legume symbiotic interaction has been proposed as an interesting tool in bioremediation. However, little is known about the effect of most common contaminants on this process. The phytotoxic effects of arsenic on nodulation of Medicago sativa have been examined in vitro using the highly arsenic resistant and symbiotically effective Sinorhizobium sp. strain MA11. The bacteria were able to grow on plates containing As concentrations as high as 10 mM. Nevertheless, as little as 25-35 microM arsenite produced a 75% decrease in the total number of nodules, due to a 90% reduction in the number of rhizobial infections, as could be determined using the strain MA11 carrying a lacZ reporter gene. This effect was associated to root hair damage and a shorter infective root zone. However, once nodulation was established nodule development seemed to continue normally, although earlier senescence could be observed in nodules of arsenic-grown plants.

What can be inferred from bacterium-nanoparticle interactions about the potential consequences of environmental exposure to nanoparticles?

This article collates published information regarding the in vitro antibacterial activity of both metal and carbon nanoparticles. The aims are to establish a consensus regarding modes of antibacterial activity, and to evaluate the applicability of current knowledge to prediction of likely effects of nanoparticles upon important microbial processes in environmental exposures. The majority of studies suggest that nanoparticles cause disruption to bacterial membranes, probably by production of reactive oxygen species. Contact between the nanoparticle and bacterial membrane appears necessary for this activity to be manifested. Interfacial forces such as electrostatic interactions are probably important in this respect. However, the toxicity of free metal ions originating from the nanoparticles cannot be discounted. Passage of nanoparticles across intact membranes appears to be unlikely, although accumulation within the cytoplasm, probably after membrane disruption, is often observed. To date, published studies have not been designed to mimic natural systems and therefore provide poor understanding of the likely consequences of intentional or unintentional environmental release. The limited studies currently available fail to identify any significant effects at the microbial level of nanoparticles in more complex systems.

Expression of the novel wheat gene TM20 confers enhanced cadmium tolerance to bakers' yeast

Cadmium causes the generation of reactive oxygen species, which in turn causes cell damage. We isolated a novel gene from a wheat root cDNA library, which conferred Cd(II)-specific tolerance when expressed in yeast (Saccharomyces cerevisiae). The gene, which we called TaTM20, for Triticum aestivum transmembrane 20, encodes a putative hydrophobic polypeptide of 889 amino acids, containing 20 transmembrane domains arranged as a 5-fold internal repeating unit of 4 transmembrane domains each. Expression of TaTM20 in yeast cells stimulated Cd(II) efflux resulting in a decrease in the content of yeast intracellular cadmium. TaTM20-induced Cd(II) tolerance was maintained in yeast even under conditions of reduced GSH. These results demonstrate that TaTM20 enhances Cd(II) tolerance in yeast through the stimulation of Cd(II) efflux from the cell, partially independent of GSH. Treatment of wheat seedlings with Cd(II) induced their expression of TaTM20, decreasing subsequent root Cd(II) accumulation and suggesting a possible role for TaTM20 in Cd(II) tolerance in wheat.

Comparative genomic analyses of copper transporters and cuproproteomes reveal evolutionary dynamics of copper utilization and its link to oxygen

Copper is an essential trace element in many organisms and is utilized in all domains of life. It is often used as a cofactor of redox proteins, but is also a toxic metal ion. Intracellular copper must be carefully handled to prevent the formation of reactive oxygen species which pose a threat to DNA, lipids, and proteins. In this work, we examined patterns of copper utilization in prokaryotes by analyzing the occurrence of copper transporters and copper-containing proteins. Many organisms, including those that lack copper-dependent proteins, had copper exporters, likely to protect against copper ions that inadvertently enter the cell. We found that copper use is widespread among prokaryotes, but also identified several phyla that lack cuproproteins. This is in contrast to the use of other trace elements, such as selenium, which shows more scattered and reduced usage, yet larger selenoproteomes. Copper transporters had different patterns of occurrence than cuproproteins, suggesting that the pathways of copper utilization and copper detoxification are independent of each other. We present evidence that organisms living in oxygen-rich environments utilize copper, whereas the majority of anaerobic organisms do not. In addition, among copper users, cuproproteomes of aerobic organisms were larger than those of anaerobic organisms. Prokaryotic cuproproteomes were small and dominated by a single protein, cytochrome c oxidase. The data are consistent with the idea that proteins evolved to utilize copper following the oxygenation of the Earth.

The safety and efficacy of dressings with silver - addressing clinical concerns

With the increasing use of silver as a topical application in wound care, concerns focussing on its role are bound to arise. These concerns, which centre on issues such as resistance and toxicity, clinical efficacy and cost-effectiveness, need to be addressed and openly discussed so that they are viewed from a rational perspective. While clinical efficacy and safety, along with cost-benefit, are of obvious interest, the origin of some of these concerns is a matter of debate. The silver-containing dressing segment of the medical device market is of huge commercial importance, and, consequently, marketing and promotional issues occasionally obscure the evidence that clinicians need to have in order that they may provide appropriate treatment for their patients. The impact of silver application on the wound bioburden needs to be examined carefully to heighten our awareness of any deleterious effects on the healing process, without inducing any unfounded anxieties.

The bacterial response to the chalcogen metalloids Se and Te

Microbial metabolism of inorganics has been the subject of interest since the 1970s when it was recognized that bacteria are involved in the transformation of metal compounds in the environment. This area of research is generally referred to as bioinorganic chemistry or microbial biogeochemistry. Here, we overview the way the chalcogen metalloids Se and Te interact with bacteria. As a topic of considerable interest for basic and applied research, bacterial processing of tellurium and selenium oxyanions has been reviewed a few times over the past 15 years. Oddly, this is the first time these compounds have been considered together and their similarities and differences highlighted. Another aspect touched on for the first time by this review is the bacterial response in cell-cell or cell-surface aggregates (biofilms) against the metalloid oxyanions. Finally, in this review we have attempted to rationalize the considerable amount of literature available on bacterial resistance to the toxic metalloids tellurite and selenite.

Interplay of different transporters in the mediation of divalent heavy metal resistance in Pseudomonas putida KT2440

According to in silico analysis, the genome of Pseudomonas putida KT2440 encodes at least four Zn/Cd/Pb efflux transporters-two P-type ATPases (CadA1 and CadA2) and two czc chemiosmotic transporters (CzcCBA1 and CzcCBA2). In this study we showed that all these transporters are functional, but under laboratory conditions only two of them were involved in the mediation of heavy metal resistance in P. putida KT2440. CadA2 conferred Cd(2+) and Pb(2+) resistance, whereas CzcCBA1 was involved in export of Zn(2+), Cd(2+), and possibly Pb(2+). CadA1, although nonfunctional in P. putida, improved Zn(2+) resistance and slightly improved Cd(2+) resistance when it was expressed in Escherichia coli. CzcCBA2 contributed to Zn resistance of a czcA1-defective P. putida strain or when the CzcA2 subunit was overexpressed in a transporter-deficient strain. It seemed that CzcA2 could complex with CzcC1 and CzcB1 subunits and therefore complement the loss of CzcA1. The CzcCBA2 transporter itself, however, did not function. Expression of cadA1, cadA2, and czcCBA1 was induced by heavy metals, and the expression levels were dependent on the growth medium and growth phase. Expression of cadA2 and czcCBA1 was nonspecific; both genes were induced by Zn(2+), Cd(2+), Pb(2+), Ni(2+), Co(2+), and Hg(2+). On the other hand, remarkably, expression of cadA1 was induced only by Zn(2+). Possible roles of distinct but simultaneously functioning transporters are discussed.

MerR family transcription activators: similar designs, different specificities

Living organisms use metals for a variety of essential functions, and face the problems of how to acquire and regulate the intracellular levels of those metals they need, differentiate between essential and toxic metals, and remove from the cell or detoxify metals that are toxic. In bacteria, cytoplasmic metal ion responsive transcriptional regulators are important in regulating the expression of genes involved in metal ion homeostasis and efflux systems. The MerR family of transcriptional activators are metal sensing regulators that are found in different bacteria and have a common design, but have evolved to recognize and respond to different metals. In this issue of Molecular Microbiology, work by Checa and colleagues describes for the first time a gold-specific MerR family regulator named GolS from Salmonella enterica serovar Typhimurium that controls the production of an efflux pump and a metal chaperone protein that confer resistance to Au salts.

GolS controls the response to gold by the hierarchical induction of Salmonella-specific genes that include a CBA efflux-coding operon

Salmonella employs a specific set of proteins that allows it to detect the presence of gold salts in the environment and to mount the appropriate resistance response. This includes a P-type ATPase, GolT, and a small cytoplasmic metal binding protein, GolB. Their expression is controlled by a MerR-like sensor, GolS, which is highly selective for Au ions. Here, we identify a new GolS-controlled operon named gesABC which codes for a CBA efflux system, and establish its role in Au resistance. GesABC can also mediate drug resistance when induced by Au in a GolS-dependent manner, in a strain deleted in the main drug transporter acrAB. The GolS-controlled transcription of gesABC differs from the other GolS-regulated loci. It is activated by gold, but not induced by copper, even in a strain deleted of the main Cu transporter gene copA, which triggers a substantial GolS-dependent induction of golTS and golB. We demonstrate that the Au-dependent induction of gesABC transcription requires higher GolS levels than for the other members of the gol regulon. This correlates with a divergent GolS operator in the gesABC promoter. We propose that the hierarchical induction within the gol regulon allows Salmonella to cope with Au-contaminated environments.

Novel nickel resistance genes from the rhizosphere metagenome of plants adapted to acid mine drainage

Metal resistance determinants have traditionally been found in cultivated bacteria. To search for genes involved in nickel resistance, we analyzed the bacterial community of the rhizosphere of Erica andevalensis, an endemic heather which grows at the banks of the Tinto River, a naturally metal-enriched and extremely acidic environment in southwestern Spain. 16S rRNA gene sequence analysis of rhizosphere DNA revealed the presence of members of five phylogenetic groups of Bacteria and the two main groups of Archaea mostly associated with sites impacted by acid mine drainage (AMD). The diversity observed and the presence of heavy metals in the rhizosphere led us to construct and screen five different metagenomic libraries hosted in Escherichia coli for searching novel nickel resistance determinants. A total of 13 positive clones were detected and analyzed. Insights about their possible mechanisms of resistance were obtained from cellular nickel content and sequence similarities. Two clones encoded putative ABC transporter components, and a novel mechanism of metal efflux is suggested. In addition, a nickel hyperaccumulation mechanism is proposed for a clone encoding a serine O-acetyltransferase. Five clones encoded proteins similar to well-characterized proteins but not previously reported to be related to nickel resistance, and the remaining six clones encoded hypothetical or conserved hypothetical proteins of uncertain functions. This is the first report documenting nickel resistance genes recovered from the metagenome of an AMD environment.

Pseudomonas fluorescens' view of the periodic table

Growth in a biofilm modulates microbial metal susceptibility, sometimes increasing the ability of microorganisms to withstand toxic metal species by several orders of magnitude. In this study, a high-throughput metal toxicity screen was initiated with the aim of correlating biological toxicity data in planktonic and biofilm cells to the physiochemical properties of metal ions. To this end, Pseudomonas fluorescens ATCC 13525 was grown in the Calgary Biofilm Device (CBD) and biofilms and planktonic cells of this microorganism were exposed to gradient arrays of different metal ions. These arrays included 44 different metals with representative compounds that spanned every group of the periodic table (except for the halogens and noble gases). The minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and minimum biofilm eradication concentration (MBEC) values were obtained after exposing the biofilms to metal ions for 4 h. Using these values, metal ion toxicity was correlated to the following ion-specific physicochemical parameters: standard reduction-oxidation potential, electronegativity, the solubility product of the corresponding metal-sulfide complex, the Pearson softness index, electron density and the covalent index. When the ions were grouped according to outer shell electron structure, we found that heavy metal ions gave the strongest correlations to these parameters and were more toxic on average than the other classes of the ions. Correlations were different for biofilms than for planktonic cells, indicating that chemical mechanisms of metal ion toxicity differ between the two modes of growth. We suggest that biofilms can specifically counter the toxic effects of certain physicochemical parameters, which may contribute to the increased ability of biofilms to withstand metal toxicity.

Zinc in wound healing: theoretical, experimental, and clinical aspects

Zinc is an essential trace element in the human body and its importance in health and disease is appreciated. It serves as a cofactor in numerous transcription factors and enzyme systems including zinc-dependent matrix metalloproteinases that augment autodebridement and keratinocyte migration during wound repair. Zinc confers resistance to epithelial apoptosis through cytoprotection against reactive oxygen species and bacterial toxins possibly through antioxidant activity of the cysteine-rich metallothioneins. Zinc deficiency of hereditary or dietary cause can lead to pathological changes and delayed wound healing. Oral zinc supplementation may be beneficial in treating zinc-deficient leg ulcer patients, but its therapeutic place in surgical patients needs further clarification. Topical administration of zinc appears to be superior to oral therapy due to its action in reducing superinfections and necrotic material via enhanced local defense systems and collagenolytic activity, and the sustained release of zinc ions that stimulates epithelialization of wounds in normozincemic individuals. Zinc oxide in paste bandages (Unna boot) protects and soothes inflamed peri-ulcer skin. Zinc is transported through the skin from these formulations, although the systemic effects seem insignificant. We present here the first comprehensive account of zinc in wound management in relation to current concepts of wound bed preparation and the wound-healing cascade. This review article suggests that topical zinc therapy is underappreciated even though clinical evidence emphasizes its importance in autodebridement, anti-infective action, and promotion of epithelialization.

Isolation and characterization of four gram-positive nickel-tolerant microorganisms from contaminated sediments

Microbial communities from riparian sediments contaminated with high levels of Ni and U were examined for metal-tolerant microorganisms. Isolation of four aerobic Ni-tolerant, Gram-positive heterotrophic bacteria indicated selection pressure from Ni. These isolates were identified as Arthrobacter oxydans NR-1, Streptomyces galbus NR-2, Streptomyces aureofaciens NR-3, and Kitasatospora cystarginea NR-4 based on partial 16S rDNA sequences. A functional gene microarray containing gene probes for functions associated with biogeochemical cycling, metal homeostasis, and organic contaminant degradation showed little overlap among the four isolates. Fifteen of the genes were detected in all four isolates with only two of these related to metal resistance, specifically to tellurium. Each of the four isolates also displayed resistance to at least one of six antibiotics tested, with resistance to kanamycin, gentamycin, and ciprofloxacin observed in at least two of the isolates. Further characterization of S. aureofaciens NR-3 and K. cystarginea NR-4 demonstrated that both isolates expressed Ni tolerance constitutively. In addition, both were able to grow in higher concentrations of Ni at pH 6 as compared with pH 7 (42.6 and 8.5 mM Ni at pH 6 and 7, respectively). Tolerance to Cd, Co, and Zn was also examined in these two isolates; a similar pH-dependent metal tolerance was observed when grown with Co and Zn. Neither isolate was tolerant to Cd. These findings suggest that Ni is exerting a selection pressure at this site for metal-resistant actinomycetes.

The isolation and initial characterization of mercury resistant chemolithotrophic thermophilic bacteria from mercury rich geothermal springs

Mercury rich geothermal springs are likely environments where mercury resistance is critical to microbial life and where microbe-mercury interactions may have evolved. Eleven facultative thermophilic and chemolithoautotrophic, thiosulfate oxidizing bacteria were isolated from thiosulfate enrichments of biofilms from mercury rich hot sulfidic springs in Mount Amiata, Italy. Some strains were highly resistant to mercury (>or=200 muM HgCl(2)) regardless of its presence or absence during primary enrichments, and three reduced ionic mercury to its elemental form. The gene encoding for the mercuric reductase enzyme (MerA), was amplified by PCR from seven strains. However, one highly resistant strain did not reduce mercury nor carried merA, suggesting an alternative resistance mechanism. All strains were members of the order Bacillales and were most closely related to previously described thermophiles belonging to the Firmicutes. Phylogenetic analyses clustered the MerA of the isolates in two supported novel nodes within the Firmicutes lineage and a comparison with the 16S rRNA gene tree suggested at least one case of horizontal gene transfer. Overall, the results show that the thermophilic thiosulfate oxidizing isolates were adapted to life in presence of mercury mostly, but not exclusively, by possessing MerA. These findings suggest that reduction of mercury by chemolithotrophic thermophilic bacteria may mobilize mercury from sulfur and iron deposits in geothermal environments.

Dominance of sphingomonads in a copper-exposed biofilm community for groundwater treatment

The structure, biological activity and microbial biodiversity of a biofilm used for the removal of copper from groundwater were studied and compared with those of a biofilm grown under copper-free conditions. A laboratory-scale submerged fixed biofilter was fed with groundwater (2.3 l h(-1)) artificially polluted with Cu(II) (15 mg l(-1)) and amended with sucrose (150 mg l(-1)) as carbon source. Between 73 and 90 % of the Cu(II) was removed from water during long-term operation (over 200 days). The biofilm was a complex ecosystem, consisting of eukaryotic and prokaryotic micro-organisms. Scanning electron microscopy revealed marked structural changes in the biofilm induced by Cu(II), compared to the biofilm grown in absence of the heavy metal. Analysis of cell-bound extracellular polymeric substances (EPS) demonstrated a significant modification of the composition of cell envelopes in response to Cu(II). Transmission electron microscopy and energy-dispersive X-ray microanalysis (EDX) showed that copper bioaccumulated in the EPS matrix by becoming bound to phosphates and/or silicates, whereas copper accumulated only intracytoplasmically in cells of eukaryotic microbes. Cu(II) also decreased sucrose consumption, ATP content and alkaline phosphatase activity of the biofilm. A detailed study of the bacterial community composition was conducted by 16S rRNA-based temperature gradient gel electrophoresis (TGGE) profiling, which showed spatial and temporal stability of the species diversity of copper-exposed biofilms during biofilter operation. PCR reamplification and sequencing of 14 TGGE bands showed the prevalence of alphaproteobacteria, with most sequences (78 %) affiliated to the Sphingomonadaceae. The major cultivable colony type in plate counts of the copper-exposed biofilm was also identified as that of Sphingomonas sp. These data confirm a major role of these organisms in the composition of the Cu(II)-removing community.