The use of biosensors for environmental monitoring

Microarray analysis of a microbe-mineral interaction

The weathering of volcanic minerals makes a significant contribution to the global silicate weathering budget, influencing carbon dioxide drawdown and long-term climate control. Basalt rocks may account for over 30% of the global carbon dioxide drawdown in silicate weathering. Micro-organisms are known to play a role in rock weathering yet the genomics and genetics of biological rock weathering are unknown. We apply DNA microarray technology to determine putative genes involved in weathering using the heavy metal-resistant organism, Cupriavidus metallidurans CH34; in particular we investigate the sequestering of iron. The results show that the bacterium does not depend on siderophores. Instead, the up-regulation of porins and transporters which are employed concomitantly with genes associated with biofilm formation suggests that novel passive and active iron uptake systems are involved. We hypothesize that these mechanisms induce rock weathering by changes in chemical equilibrium at the microbe-mineral interface, reducing the saturation state of iron. We also demonstrate that low concentrations of metals in the basalt induce heavy metal-resistant genes. Some of the earliest environments on the Earth were volcanic. Therefore, these results not only elucidate the mechanisms by which micro-organisms might have sequestered nutrients on the early Earth but also provide an explanation for the evolution of multiple heavy metal resistance genes long before the creation of contaminated industrial biotopes by human activity.

A simple and highly repeatable colorimetric toxicity assay method using 2,6-dichlorophenolindophenol as the redox color indicator and whole eukaryote cells

A simple and highly reproducible toxicity assay method was studied by employing 2,6-dichlorophenolindophenol (DCIP) as a redox color indicator, baker's yeast Saccharomyces cerevisiae, and a thermostable three-consecutive-stir unit. The absorbance of DCIP was decreased by increasing the metabolism activity of S. cerevisiae to intake glucose as an organic substance. By optimizing the measurement conditions, we obtained highly sensitive responses to glucose between 0.75 and 30 mg/L (eight points, n = 3) with an incubation time of the reaction mixture of 10 min at 30 degrees C. An excellent value of 1.15% was obtained as the average of the repeatability from eight points. Next, for the characterization of this method, we investigated the influence on the colorimetric response of dissolved substances, such as inorganic ions and surfactants, in natural water. Furthermore, the colorimetric responses to several toxicants were examined using Cu2+, Mn2+, Zn2+, Cr3+, and Fe3+ as heavy-metal ions and simazine as an agricultural chemical. As a result, notable colorimetric responses were obtained for Cu2+ and Mn2+ at several concentrations, and the results were compared with those obtained using river water as a real sample. In the stability test, responses to 30 mg/L glucose were obtained for 28 days when the yeast cell suspension was stored at 4 degrees C (response reduction, 43.9%; average of the relative standard deviation for nine testing days, 22.7%; average of repeatability, 1.01%).

New concept for a toxicity assay based on multiple indexes from the wave shape of damped metabolic oscillation induced in living yeast cells (part II): application to analytical toxicology

An ideal toxicity assay should utilize multiple indexes obtained from transient changes of metabolic activities. Here, we demonstrate the possibility for a novel toxicity bioassay using the damped glycolytic oscillation phenomenon occurring in starved yeast cells. In a previous study, the phenomenon was characterized in detail. Under optimum conditions to induce the phenomenon, the wave shapes of the damped glycolytic oscillations were changed by the instantaneous addition of both glucose and chemicals and by changing the chemical concentration. We estimated the changes in the oscillation wave shapes as six indexes, i.e., the number of wave cycles, maximum amplitude, oscillation frequency, attenuation coefficient, initial peak height, and non-steady-state time. These index changes were obtained from several kinds of chemicals. The chemicals, especially those for acids (0.01-100 mM HCl and 0.01-50 mM citric acid), bases (0.001-50 mM KOH), heavy metal ions (1-1,000 mg L(-1); Cu(2+), Pb(2+), Cd(2+), Hg(2+)), respiratory inhibitors (3-500 mg L(-1) NaN(3)), dissolved oxygen removers (10-300 mg L(-1) NaSO(3)), surfactants (10-200 mg L(-1) benzalkonium chloride), and aldehyde (10-1,000 mg L(-1) acetaldehyde), showed characteristic patterns depending on each chemical and its concentration. These significant results demonstrate the possibilities of new methods for both toxicity qualification and quantification.

Plasmids pMOL28 and pMOL30 of Cupriavidus metallidurans are specialized in the maximal viable response to heavy metals

We fully annotated two large plasmids, pMOL28 (164 open reading frames [ORFs]; 171,459 bp) and pMOL30 (247 ORFs; 233,720 bp), in the genome of Cupriavidus metallidurans CH34. pMOL28 contains a backbone of maintenance and transfer genes resembling those found in plasmid pSym of C. taiwanensis and plasmid pHG1 of C. eutrophus, suggesting that they belong to a new class of plasmids. Genes involved in resistance to the heavy metals Co(II), Cr(VI), Hg(II), and Ni(II) are concentrated in a 34-kb region on pMOL28, and genes involved in resistance to Ag(I), Cd(II), Co(II), Cu(II), Hg(II), Pb(II), and Zn(II) occur in a 132-kb region on pMOL30. We identified three putative genomic islands containing metal resistance operons flanked by mobile genetic elements, one on pMOL28 and two on pMOL30. Transcriptomic analysis using quantitative PCR and microarrays revealed metal-mediated up-regulation of 83 genes on pMOL28 and 143 genes on pMOL30 that coded for all known heavy metal resistance proteins, some new heavy metal resistance proteins (czcJ, mmrQ, and pbrU), membrane proteins, truncated transposases, conjugative transfer proteins, and many unknown proteins. Five genes on each plasmid were down-regulated; for one of them, chrI localized on pMOL28, the down-regulation occurred in the presence of five cations. We observed multiple cross-responses (induction of specific metal resistance by other metals), suggesting that the cellular defense of C. metallidurans against heavy metal stress involves various regulons and probably has multiple stages, including a more general response and a more metal-specific response.

Differential gene expressions in arbuscular mycorrhizal-colonized tomato grown under heavy metal stress

When tomato was grown in either "Breinigerberg" soil, which has a high content of Zn and of other heavy metals or in non-polluted soil enriched with up to 1 mM CdCl2, plants colonized with the arbuscular mycorrhizal fungus (AMF) Glomus intraradices grew distinctly better than non-mycorrhizal controls. An analysis of differential mRNA transcript formations was performed on several plant genes coding for products potentially involved in heavy metal tolerance. Northern blot analyses indicated that the mRNA from either roots or leaves was not differentially expressed in the case of LePCS1 (coding for phytochelatin synthase), Lemt1, Lemt3 and Lemt4 (for metallothioneins) or LeNramp2 (for a broad range heavy metal transporter) in both mycorrhizal and non-mycorrhizal plants, grown either with or without heavy metals. In contrast, Lemt2 was strongly expressed only in non-AMF-colonized roots, and only after growth in the Breinigerberg soil or in the presence of high CdCl2-concentrations. AMF colonization distinctly reduced the level of Lemt2 transcripts. This was also the case for the root specific LeNramp1 transporter, however, only after growth in the Breinigerberg soil, but not under Cd-stress. Likewise, the levels of LeNramp3 transcripts were reduced by the AMF colonization in roots, but not in leaves. Quantitative Real-Time RT-PCR-experiments performed with Lemt2, LeNramp1 and LeNramp3 largely corroborated the Northern analysis data. In situ hybridization experiments with Lemt2 and LeNramp1 showed that both genes were strongly expressed throughout the plant cells in non-colonized roots, whereas colonized roots revealed only few signals restricted to some parenchyma cells. All the data suggest that the transcript levels of some, but not all genes of the Nramp or mt family are elevated under heavy metal stress. AMF colonization results in a down-regulation of these genes, presumably due to the fact that the content of heavy metals is lower in mycorrhizal than in non-colonized roots. A suppression subtractive hybridization (SSH) Library from hyphae of the AMF G. intraradices grown in high versus low Zn++ provided none of the genes which were down-regulated at the plant side (mt or Nramp genes). In contrast, several gene sequences coding for enzymes potentially catalysing the detoxification of reactive oxygen species were found. Thus the fungal cells in the symbiosis may primarily have to cope with the heavy metal-induced oxidative stress.

Illuminating the detection chain of bacterial bioreporters

Engineering bacteria for measuring chemicals of environmental or toxicological concern (bioreporter bacteria) has grown slowly into a mature research area. Despite many potential advantages, current bioreporters do not perform well enough to comply with environmental detection standards. Basically, the reasons for this are the lack of engineering principles in the detection chain in the bioreporters. Here, we dissect critical steps in the detection chain and illustrate how bioreporter design could be improved by mutagenizing specificity and selectivity of the sensing and regulatory proteins, by newer expression strategies and application of different signalling networks. Furthermore, we describe how redesigning bioreporter assays with respect to pollutant transport into the cells and application of other detection devices can decrease detection limits and increase the speed of detection.

Chemical speciation and toxicity of metals assessed by three bioluminescence-based assays using marine organisms

Metal toxicity is a function of the biology of the target organism and the chemical speciation of the metal. The toxicity of 11 metals was assessed with three cell-based bioassays based on marine organisms: the bacterium Photobacterium phosphoreum of the Microtox bioassay, an environmental strain of P. phosphoreum, and photocytes isolated from the brittlestar Ophiopsila californica. Metal speciation was calculated for three commonly used media: NaCl-based Microtox bioassay medium, artificial seawater glycerol, and artificial seawater. Decreased bioluminescence was considered a proxy for cell toxicity. In all three assays the elements Cd and Hg exhibited similar speciation as well as similar toxicity profiles. The element Cu was toxic in all three assays despite different metal speciation for the P. phosphoreum bioassay. The element Ag was toxic to both bacterial strains but not to photocytes despite a similar chemical speciation for all three assays. In general, the Microtox bioassay was sensitive to all metals (except Pb), whereas the photocytes were the least sensitive to the metals. The heightened response of the Microtox bioassay probably resulted from a combination of the limited complexing power of the medium and the greater sensitivity of the bacterial strain.

Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: towards a catalogue of metal-responsive genes

Ralstonia metallidurans, formerly known as Alcaligenes eutrophus and thereafter as Ralstonia eutropha, is a beta-Proteobacterium colonizing industrial sediments, soils or wastes with a high content of heavy metals. The type strain CH34 carries two large plasmids (pMOL28 and pMOL30) bearing a variety of genes for metal resistance. A chronological overview describes the progress made in the knowledge of the plasmid-borne metal resistance mechanisms, the genetics of R. metallidurans CH34 and its taxonomy, and the applications of this strain in the fields of environmental remediation and microbial ecology. Recently, the sequence draft of the genome of R. metallidurans has become available. This allowed a comparison of these preliminary data with the published genome data of the plant pathogen Ralstonia solanacearum, which harbors a megaplasmid (of 2.1 Mb) carrying some metal resistance genes that are similar to those found in R. metallidurans CH34. In addition, a first inventory of metal resistance genes and operons across these two organisms could be made. This inventory, which partly relied on the use of proteomic approaches, revealed the presence of numerous loci not only on the large plasmids pMOL28 and pMOL30 but also on the chromosome. It suggests that metal-resistant Ralstonia, through evolution, are particularly well adapted to the harsh environments typically created by extreme anthropogenic situations or biotopes.

A microbial biosensor to predict bioavailable nickel in soil and its transfer to plants

Ralstonia eutropha strain AE2515 was constructed and optimised to serve as a whole-cell biosensor for the detection of bioavailable concentrations of Ni2+ and Co2+ in soil samples. Strain AE2515 is a Ralstonia eutropha CH34 derivative containing pMOL1550, in which the cnrYXH regulatory genes are transcriptionally fused to the bioluminescent luxCDABE reporter system. Strain AE2515 was standardised for its specific responses to Co2+ and Ni2+. The detection limits for AE2515 were 0.1 microM Ni2+ and 9 microM Co2+, respectively. The signal to noise (S/N) bioluminescence response and the metal cation concentration could be linearly correlated: for Ni2+ this was applicable within the range 0.1-60 microM, and between 9 and 400 microM for Co2+. The AE2515 biosensor strain was found to be highly selective for nickel and cobalt: no induction was observed with Zn(II), Cd(II), Mn(II), Cu(III) and Cr(VI). In mixed metal solutions, the bioluminescent response always corresponded to the nickel concentrations. Only in the presence of high concentrations of Co2+ (2 mM), the sensitivity to nickel was reduced due to metal toxicity. AE2515 was used to quantify the metal bioavailability in various nickel-enriched soils, which had been treated with additives for in situ metal immobilisation. The data obtained with strain AE2515 confirmed that the bioavailability of nickel was greatly reduced following the treatment of the soils with the additives beringite and steel shots. Furthermore, the data were found to correlate linearly with those on the biological accumulation of Ni2+ in specific parts of important agricultural crops, such as maize and potato. Therefore, the test can be used to assess the potential transfer of nickel to organisms of higher trophic levels, in this case maize and potato plants grown on nickel-enriched soils, and the potential risk of transfer of these elements to the food chain.

Quantification of bacterial lead resistance via activity assays

The level of microbial resistance to heavy metals is an important issue for the microbial ecology of heavy metal-contaminated habitats. However, assays based upon growth in nutrient media will overestimate the resistance level due to metal ion interactions with inorganic and organic components. The analysis of Pb-resistant bacteria isolated from soils containing up to 38 mmol total Pb x kg(-1) indicated that PYT80B medium which did not contain inorganic salts, contained low amounts of organic matter, and was buffered with a molecule that did not interact with metal ions (2-N-morpholinoethanesulfonic acid (MES)) provided the lowest estimates of lead resistance. However, better results were obtained by assaying metabolic activity (aerobic respiration) of resting cells suspended in 10 mM MES. By this criterion, 50% inhibition of Arthrobacter JS7 was found at 37 microM Pb(NO3)2. The effects of Pb+2 concentrations upon respiration of resting cells and growth rate in PYT80B medium were similar. The activity assay also showed that metal resistance was induced to higher levels when Arthrobacter JS7 was grown in the presence of Pb.

Colloidal gold filtrates as metal substrates for surface-enhanced infrared absorption spectroscopy

A new method for obtaining surface-enhanced infrared absorption (SEIRA) spectra of antibodies and antibody/antigen complexes has been developed. Antibodies attached to colloidal gold particles and then collected by filtration onto porous polyethylene membranes show enhanced spectral bands at 1080 and 990 cm-1 regardless of the antibody specificity. Attachment of a model antigen, glucose oxidase, to its specific antibody/colloid complex prior to collection produces enhanced bands at 1540, 1395, and 1250 cm-1. Similarly, when the antigen Salmonella is attached to its specific antibody/colloid complex prior to collection, a new enhanced band is observed at 1015 cm-1. Similarities and differences of the SEIRA spectra obtained on gold colloid are compared to previous work on gold films.

Immunoassays based on surface-enhanced infrared absorption spectroscopy

A new type of biosensor for pathogens has been developed. The sensor produces spectral fingerprints of biological systems by using surface-enhanced infrared absorption (SEIRA) spectroscopy. Antibodies were immobilized onto a 10-nm-thick film of gold which had been previously deposited on a Si wafer. SEIRA spectra of the antibodies measured in the external reflection mode exhibited two new bands at 1085 and 990 cm-1. These new bands were observed with p-polarized radiation but were absent with s-polarized radiation. The spectrum of water on the surface of the sensor was observed under both directions of polarization. The sensor was first tested with a model system consisting of glucose oxidase (GOX) and the antibodies for glucose oxidase (anti-GOX). In addition to the bands due to the anti-GOX at 1085 and 990 cm-1, new bands were observed at 1397, 1275, and 930 cm-1 when the GOX antigens were present. The same type of sensor was prepared for Salmonella (SAL) by immobilizing antibodies for Salmonella (anti-SAL) on a gold-surfaced Si water. The SEIRA spectra for anti-SAL antibodies were very similar to those for anti-GOX, with bands at 1085 and 990 cm-1; however, a sharp new band was observed at 1045 cm-1 after the sensor was exposed to the SAL antigens. In addition to specific new bands due to antigens, both GOX and SAL sensors exhibited changes in the regions of water absorptions at approximately 3500 and 850 cm-1 when the antigens were present.

Bioluminescence-based assays for detection and characterization of bacteria and chemicals in clinical laboratories

OBJECTIVES

To survey recent advances in the application of bioluminescence to public health problems. The usefulness of bacterial (lux) and eucaryotic (luc) luciferase genes is presented, along with several examples that demonstrate their value as "reporters" of many endpoints of clinical concern.

CONCLUSIONS

The development of new technologies for monitoring biological and chemical contaminants is in continuous progress. Recent excitement in this area has come from the use of genes encoding enzymes for bioluminescence as reporter systems. Applications of the recombinant luciferase reporter phage concept now provide a sensitive approach for bacterial detection, their viability, and sensitivity to antimicrobial agents. Moreover, a number of fusions of the lux and luc genes to stress inducible genes in different bacteria can allow a real-time measurement of gene expression and determination of cellular viability, and also constitute a new tool to detect toxic chemicals and their bioavailability.

The czc operon of Alcaligenes eutrophus CH34: from resistance mechanism to the removal of heavy metals

The plasmid-borne czc operon ensures for resistance to Cd2+, Zn2+ and Co2+ ions through a tricomponent export pathway and is associated to various conjugative plasmids of A. eutrophus strains isolated from metal-contaminated industrial areas. The czc region of pMOL30 was reassessed especially for the segments located upstream and downstream the structural genes czc CBA. In cultures grown with high concentrations of heavy metals, czc-mediated efflux of cations is followed by a process of metal bioprecipitation. These observations led to the development of bioreactors designed for the removal of heavy metals from polluted effluents.

Plasmids for heavy metal resistance in Alcaligenes eutrophus CH34: mechanisms and applications

Alcaligenes eutrophus CH34 is the main representative of a group of strongly related strains (mostly facultative chemolithotrophs) that are well adapted to environments containing high levels of heavy metals. It harbors the megaplasmids pMOL28 and pMOL30 which carry resistance determinants to Co2+, Ni2+, CrO(4)2-, Hg2+, Tl+, Cd2+, Cu2+ and Zn2+. Among the best characterized determinants are the cnr operon (resistance to Co, Ni) on pMOL28 and the czc operon on pMOL30 (resistance to Co, Cd and Zn). Although the two systems reveal a significant degree of amino acid similarity in the structural genes, the regulation of the operons is different. The resistance mechanism in both cases is based on efflux. The efflux mechanism leads to a pH increase outside of the cytoplasmic membrane. Metals are sequestered from the external medium through the bioprecipitation of metal carbonates formed in the saturated zone around the cell. This latter phenomenon can be exploited in bioreactors designed to remove metals from effluents. The bacteria are immobilized on composite membranes in a continuous tubular membrane reactor (CTMR). The effluent continuously circulates through the intertubular space, while the external surface of the tubes is in contact with the growth medium. Metal crystals are eventually removed by the effluent stream and collected on a glass bead column. The system has been applied to effluents containing Cd, Zn, Co, Ni and Cu. By introducing catabolic plasmids involved in the aerobic degradation of PCBs and 2,4-D into metal-resistant A. eutrophus strains, the application range was widened to include effluents polluted with both organic and inorganic substances. Biosensors have been developed which are based on the fusion of genes induced by metals to a reporter system, the lux operon of Vibrio fischeri. Bacterial luciferases produce light through the oxidation of fatty aldehydes. The gene fusions are useful both for the study of regulatory genes and for the determination of heavy metal concentrations in the environment.