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Quantification of the number of living cells in biofilm or after eradication treatments of biofilm, is problematic for different reasons. We assessed the performance of pre-treatment of DNA, planktonic cells and ex vivo vaginal biofilms of Gardnerella with propidium monoazide (PMAxx) to prevent qPCR-based amplification of DNA from killed cells (viability-qPCR). Standard PMAxx treatment did not completely inactivate free DNA and did not affect living cells. While culture indicated that killing of planktonic cells by heat or by endolysin was complete, viability-qPCR assessed only log reductions of 1.73 and 0.32, respectively. Therefore, we improved the standard protocol by comparing different (combinations of) parameters, such as concentration of PMAxx, and repetition, duration and incubation conditions of treatment. The optimized PMAxx treatment condition for further experiments consisted of three cycles, each of: 15 min incubation on ice with 50 µM PMAxx, followed by 15 min-long light exposure. This protocol was validated for use in vaginal samples from women with bacterial vaginosis. Up to log2.2 reduction of Gardnerella cells after treatment with PM-477 was documented, despite the complex composition of the samples, which might have hampered the activity of PM-477 as well as the quantification of low loads by viability-qPCR.

Potable and urban waters, which is a vital resource, constitute the most basic research area of today. In the current study, a newly optimized co-precipitation method using bismuth(III) hydroxide has been examined for quantitative separation and preconcentration of iron(III), chromium(III), cop-per(II), cobalt(II), mangaNeşe(II), nickel(II), and cadmium(II) ions from water samples. Analytes were co-precipitated and after dissolving analyzed by micro-sample injection system flame atomic absorption spectrophotometry. The influence of variables such as sample volume, sodium hydrox-ide concentration, bismuth(III) concentration, matrix effects, etc. were investigated. The theoretical enrichment factor of the optimized method is 50. The precisions of within-day and intra-day for the analyte elements working real water samples were found in the range of 4.1–4.5. The limit of detections for the analyte elements were in the range of 0.8–9.5 μg/L. The limit of quantification of iron(III), chromium(III), copper(II), cobalt(II), mangaNeşe(II), nickel(II), and cadmium(II) ions were calculated to be 18.0, 21.0, 7.6, 6.8, 13.0, 27.0, and 1.1 μg/L, respectively. The analysis of the BCR-715 standard reference water sample demonstrated the procedure’s accuracy, and the method was successfully applied to two different water samples and nine different plants as a real sample. © 2022 Desalination Publications. All rights reserved.

Magnetic solid-phase extraction was evaluated using polythiophene nanoparticles (Fe3O4@PTh) as the adsorbent for chromium speciation from water samples and total chromium preconcentration from food, biological, and soil samples. Chromium concentrations were determined by microsample injection system – flame atomic absorption spectrometry (MIS-FAAS). Chromium speciation was achieved with selective adsorption of Cr(III) in the presence of Cr(VI) by Fe3O4@PTh from pH 6.5 to 10.0. Total chromium was preconcentrated after the reduction of Cr(VI) to Cr(III). The linear range, detection limit, enrichment factor, and repeatability of the optimized method for Cr(III) in aqueous solution were 4-60 µg L−1, 1.3 µg L−1, 124.7, and 2.2%, respectively. The method was validated by analyzing SPS-WW2 Batch 114, NCS DC 78302 Tibet soil, and LGC7162 strawberry leaves as standard reference materials (SRMs). The results are in good agreement with the certified values. Good recovery, precision, and relative error values were obtained for chromium in real samples by the optimized method.

Radioanalytical methods for the determination of isotopes of Pu, Am and Cm in water samples from nuclear power plants were compared and further developed in a Nordic project (Optimethod) through two intercomparison exercises among Nordic laboratories. With this intercomparison, the analytical performance of some laboratories was improved by modification of the analytical method and adopting new techniques. The obtained results from the two intercomparisons for alpha emitting transuranium isotopes are presented, and the lessons learnt from these intercomparison exercises are discussed. Funding Agencies|University of Helsinki including Helsinki University Central Hospital

The Pisum sativum has been used as a magnetic biocomposite biosorbent for the removal of lead ions from aqueous solutions. These biocomposites were prepared with encapsulated alginate beads into calcium chloride solution, Pisum sativum peel powder and iron (II-III) oxide. Properties of surface and the possible binding sites of the material were evaluated by instrumental analysis using Fourier transform infrared spectroscopy-attenuated total reflection, scanning electron microscope, and X-ray diffraction. Scanning electron microscopy-energy-dispersive X-ray spectroscopy and mapping techniques are also used for evaluation of process. Optimisation of biosorption procedure was done by Plackett-Burman factorial design including parameters such as biocomposite amount, pH, temperature and extraction time. The analytical performance of the biosorption method, application to industrial effluent, the reusability and stability of biosorbent were also investigated. The Pisum sativum magnetic biocomposite adsorbed 90 +/- 4% of lead at the optimum pH value 4 and 125 mg biocomposite amount. The best-fitting isotherm model is Freundlich and theoretical capacity of biosorbent was calculated as 74.05 mg/g. The report of magnetic Pisum sativum biocomposite as a biosorbent may be used as natural renewable resources and reduces the adverse effects on water contaminated for lead.

Yersinia enterocolitica and Yersinia pseudotuberculosis are important zoonotic bacteria causing human enteric yersiniosis commonly reported in Europe. All Y. pseudotuberculosis strains are considered pathogenic, while Y. enterocolitica include both pathogenic and nonpathogenic strains which can be divided into six biotypes (1A, 1B, and 2-5) and about 30 serotypes. The most common types causing yersiniosis in Europe are Y. enterocolitica bioserotypes 4/O:3 and 2/O:9. Strains belonging to biotype 1A are considered as nonpathogenic because they are missing important virulence genes like the attachment-invasion-locus (ail) gene in the chromosome and the virulence plasmid. The role of wild small mammals as a reservoir of enteropathogenic Yersinia spp. is still obscure. In this study, the presence of Yersinia spp. was examined from 1840 wild small mammals, including voles, mice, and shrews, trapped in Finland during a 7-year period. We isolated seven Yersinia species. Y. enterocolitica was the most common species, isolated from 8% of the animals; while most of these isolates represented nonpathogenic biotype 1A, human pathogenic bioserotype 2/O:9 was also isolated from a field vole. Y. pseudotuberculosis of bioserotype 1/O:2 was isolated from two shrews. The ail gene, which is typically only found in the isolates of biotypes 1B and 2-5 associated with yersiniosis, was frequently (23%) detected in the nonpathogenic isolates of biotype 1A and sporadically (6%) in Yersinia kristensenii isolates. Our results suggest that wild small mammals, especially voles, may serve as carriers for ail-positive Y. enterocolitica 1A and Y. kristensenii. We also demonstrate that voles and shrews sporadically excrete pYV-positive Y. enterocolitica 2/O:9 and Y. pseudotuberculosis 1/O:2, respectively, in their feces and, thus, can serve as a contamination source for vegetables by contaminating the soil.

International audience; The study of microplastic pollution involves multidisciplinary analyses on a large number of microplastics. Therefore, providing an overview of plastic pollution is time consuming and, despite high throughput analyses, remains a major challenge. The objective of this study is to propose a protocol to determine how many microplastics must be analyzed to give a representative view of the particle size distribution and chemical nature, and calculate the associated margin error. Based on microplastic data from Tara Mediterranean campaign, this approach is explained through different examples. In this particular case, the results show that only 3% of the collected microplastics need to be analyzed to give a precise view on the scale of the North West Mediterranean Basin (error

Plutonium and americium are radionuclides particularly difficult to measure in environmental samples because they are alpha-emitters and therefore necessitate a careful separation before any measurement, either using radiometric methods or ICP-SMS. Recent developments in extraction chromatography resins such as Eichrom (R) TRU and TEVA have resolved many of the analytical problems but drawbacks such as low recovery and spectral interferences still occasionally occur. Here, we report on the use of the new Eichrom (R) DGA resin in association with TEVA resin and high pressure microwave acid leaching for the sequential determination of plutonium and americium in environmental samples. The method results in average recoveries of 83 +/- 15% for plutonium and 73 +/- 22% for americium (n = 60), and a less than 10% deviation from reference values of four IAEA reference materials and three samples from intercomparisons exercises. The method is also suitable for measuring Pu-239 in water samples at the mu Bq/l level, if ICP-SMS is used for the measurement.

Liquid scintillation counting (LSC) is one of the most widely used methods for determining the activity of 241Pu. One of the main challenges of this counting method is the efficiency calibration of the system for the low beta energies of 241Pu (E max = 20.8 keV). In this paper we compare the two most frequently used methods, the CIEMAT/NIST efficiency tracing (CNET) method and the experimental quench correction curve method. Both methods proved to be reliable, and agree within their uncertainties, for the expected quenching conditions of the sources.

Addressing the transmission enigma of the neglected disease Buruli ulcer (BU) is a World Health Organization priority. In Australia, we have observed an association between mosquitoes harboring the causative agent, Mycobacterium ulcerans, and BU. Here we tested a contaminated skin model of BU transmission by dipping the tails from healthy mice in cultures of the causative agent, Mycobacterium ulcerans. Tails were exposed to mosquito (Aedes notoscriptus and Aedes aegypti) blood feeding or punctured with sterile needles. Two of 12 of mice with M. ulcerans contaminated tails exposed to feeding A. notoscriptus mosquitoes developed BU. There were no mice exposed to A. aegypti that developed BU. Eighty-eight percent of mice (21/24) subjected to contaminated tail needle puncture developed BU. Mouse tails coated only in bacteria did not develop disease. A median incubation time of 12 weeks, consistent with data from human infections, was noted. We then specifically tested the M. ulcerans infectious dose-50 (ID50) in this contaminated skin surface infection model with needle puncture and observed an ID50 of 2.6 colony-forming units. We have uncovered a biologically plausible mechanical transmission mode of BU via natural or anthropogenic skin punctures., Author summary Buruli ulcer is a neglected tropical disease caused by infection with Mycobacterium ulcerans. Unfortunately, how people contract this disease is not well understood. Here we show for the first time using experimental infections in mice that a very low dose of M. ulcerans delivered beneath the skin by a minor injury caused by a blood-feeding insect (mosquito) or an experimental needle puncture is sufficient to cause Buruli ulcer. This research provides important laboratory evidence to advance our understanding of Buruli ulcer disease transmission.

International audience; To collect a large data set regarding the occurrence of organic substances in sediment, this study presents the examination of 20 micropollutants, as a national survey. The list of target compounds contains two alkylphenols, three polycyclic aromatic hydrocarbons (PAHs) not commonly included in monitoring programmes, six pesticides or metabolites, five pharmaceutical compounds, two hormones, one UV filter and bisphenol A. The selective and sensitive analytical methods, based on quick, easy, cheap, effective, rugged, and safe (QuEChERS) sample preparation followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) or gas chromatography-time-of-flight mass spectrometry (GC-ToF-MS), allow the quantification at limits comprised between 0.5 and 23 ng/g, depending on the compound. The paper summarizes the analytical results from 154 sampling points. Of the 20 target compounds, 9 were determined at least once, and the sediments contained a maximum of 7 substances. The most frequently detected were PAHs (frequency, 77 %; max., 1,400 ng/g). The pharmaceutical compounds, hormones and pesticides were rarely detected in the samples; the most frequently detected was carbamazepine (frequency, 6 %; max., 31 ng/g). In some cases, the levels of PAHs and bisphenol A exceed the predicted no-effect concentration (PNEC) values.

Phosphorus transport from agricultural land contributes to eutrophication of surface waters. Pipe drain and trench waters from a grassland field on a heavy clay soil in the Netherlands were sampled before and after manure application. Phosphorus speciation was analyzed by physicochemical P fractionation, and the colloidal P fraction in the dissolved fraction (0.45 μm) was analyzed by asymmetric flow field-flow fractionation (AF4) coupled to high-resolution inductively coupled plasma-mass spectrometry and ultraviolet diode array detector. When no manure was applied for almost 7 mo, total P (TP) concentrations were low (21 μmol L), and TP was almost evenly distributed among dissolved reactive P (DRP), dissolved unreactive P (DUP), and particulate P (PP). Total P concentrations increased by a factor of 60 and 4 when rainfall followed shortly after application of cattle slurry or its solid fraction, respectively. Under these conditions, DRP contributed 50% or more to TP. The P speciation within the DUP and PP fractions varied among the different sampling times. Phosphorus associated with dissolved organic matter, probably via cation bridging, comprised a small fraction of DUP at all sampling times. Colloidal P coeluted with clay particles when P application was withheld for almost 7 mo and after application of the solid cattle slurry fraction. At these sampling times, PP correlated well with particulate Fe, Al, and Si, indicating that P is associated with colloidal clay particles. After cattle slurry application, part of DUP was probably present as phospholipids. Physicochemical fractionation combined with AF4 analysis is a promising tool to unravel the speciation of colloidal P in environmental water samples.

Cronobacter spp. involves a group of opportunistic pathogens that cause meningitis in newborns, immunosuppressed individuals with a mortality rate of 50-80%. Seven species like C. sakazakii, C. malonaticus, C. muytjensii, C. turicensis, C. dublinensis, C. universalis, C. condimenti are included in this genus which has been a subject of research especially in the bacteriologic analysis of baby foods. However, since these species were detected also in prepared foodstuffs. The objective of this study was to assert the presence of Cronobacter spp. in foodstuff offered for sale in Turkey. A total of 151 prepared foodstuffs including a variety of spice, flour, instant soup were purchased from different sales points. The presence of Cronobacter spp. were investigated in these samples. Cronobacter suspected isolates which were obtained by microbiological analyses were confirmed by PCR targeted to gyrB gene and were then identified by multiplex PCR. Prevalence of Cronobacter spp was estimated to be 17.88%. Out of 27 Cronobacter spp. isolates obtained, 13(48.1%), 6(22.2%), 5(18.5%), 3(11.1%) belonged to C. sakazakii, C. muytjensii, C. turicensis, C. malonaticus species, respectively. Consequently, the presence of the bacteria in widely consumed foodstuff revealed that Cronobacter spp. is subject to monitoring due to its opportunistic nature in terms of public health concern. İstanbul Üniversitesi - 53226

Coastal ecosystems are considered buffer zones for the discharge of land-derived nutrients without accounting for potential negative side effects. Hence, there is an urgent need to better understand the ecological assembly and dynamics of the microorganisms that are involved in nitrogen (N) cycling in such systems. Here, we employed two complementary methodological approaches (i.e., shotgun metagenomics and quantitative PCR) to examine the distribution and abundance of selected microbial genes involved in N transformations. We used soil samples collected along a well-established pristine salt marsh soil chronosequence that spans over a century of ecosystem development at the island of Schiermonnikoog, The Netherlands. Across the examined soil successional stages, the structure of the populations of genes involved in N cycling processes was strongly related to (shifts in the) soil nitrogen levels (i.e., [Formula: see text], [Formula: see text]), salinity and pH (explaining 73.8% of the total variation, R (2) = 0.71). Quantification of the genes used as proxies for N fixation, nitrification and denitrification revealed clear successional signatures that corroborated the taxonomic assignments obtained by metagenomics. Notably, we found strong evidence for niche partitioning, as revealed by the abundance and distribution of marker genes for nitrification (ammonia-oxidizing bacteria and archaea) and denitrification (nitrite reductase nirK, nirS and nitrous oxide reductase nosZ clades I and II). This was supported by a distinct correlation between these genes and soil physico-chemical properties, such as soil physical structure, pH, salinity, organic matter, total N, [Formula: see text], [Formula: see text] and [Formula: see text], across four seasonal samplings. Overall, this study sheds light on the successional trajectories of microbial N cycle genes along a naturally developing salt marsh ecosystem. The data obtained serve as a foundation to guide the formulation of ecological models that aim to effectively monitor and manage pristine and impacted salt marsh areas. Such models should account for the ecology as well as the historical contingency of N cycling communities.

Selenium (Se) is of key importance to human health with a very narrow concentration range of optimal dietary intake. Due to the inherent analytical challenge linked with the low natural abundance, information on precise and accurate Se speciation in deficient environments is hardly existent. This study presents a novel approach to determine Se species-specifically at ultratraces, by online coupling of a preconcentration (trap) column to an ion chromatography inductively coupled plasma mass spectrometry (IC-ICP-MS) system. It is demonstrated that with this robust and work/time efficient method, the predominant selenium oxyanions, selenite (Se(IV)) and selenate (Se(VI)), can be quantified down to 7.3 and 8.3 picogram total Se, respectively, in an overall analytical time of 420 s, only. The applicability for environmental samples was proven on pristine volcanic ashes collected from seven different volcanoes. The high sensitivity of the novel approach allowed to determine speciation in samples that were strongly depleted in total selenium (0.05 mg kg(-1) Se) with only minor fractions of Se mobilized (i.e., less than 10% of the total selenium was leached in 10 out of 12 samples). The studied samples showed considerate differences in selenium speciation, with selenite and selenate co-occurring in most samples. The fact that the studied sample leachates had a wide range of pH (3.78-9.55) and major anion/cation composition underlines the versatility and wide potential application range of the method presented.

Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. Its physicochemical properties affect microbial distributions inside the soil matrix, metagenome extraction and its subsequent analyses. To better understand the bias inherent to soil metagenome 'processing', we focus on soil physicochemical properties and their effects on the perceived bacterial distribution. In the light of this information, each step of soil metagenome processing is then discussed, with an emphasis on strategies for optimal soil sampling. Then, the interaction of cells and DNA with the soil matrix and the consequences for microbial DNA extraction are examined. Soil DNA extraction methods are compared and the veracity of the microbial profiles obtained is discussed. Finally, soil metagenomic sequence analysis and exploitation methods are reviewed.

Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. Its physicochemical properties affect microbial distributions inside the soil matrix, metagenome extraction and its subsequent analyses. To better understand the bias inherent to soil metagenome 'processing', we focus on soil physicochemical properties and their effects on the perceived bacterial distribution. In the light of this information, each step of soil metagenome processing is then discussed, with an emphasis on strategies for optimal soil sampling. Then, the interaction of cells and DNA with the soil matrix and the consequences for microbial DNA extraction are examined. Soil DNA extraction methods are compared and the veracity of the microbial profiles obtained is discussed. Finally, soil metagenomic sequence analysis and exploitation methods are reviewed.

Medically important bacteria can persist in surface waters longer than was previously thought, by activating specific survival strategies and, thus, may represent a further threat to human health, in that they are non-detectable by the traditional culture methods currently used for the evaluation of microbiological quality. Combining microbial physiology, microbial biochemistry, microbial genetics, microbial ecology and molecular biology techniques allow us to achieve more accurate detection of human pathogens located in natural environments external to the human body.

Compost and digestate are important recycling fertilizers and have beneficial effects on soil parameters. However, they can contain significant amounts of organic pollutants. Here, the first comprehensive data set on dibenzo-p-dioxins and -furans (PCDD/F), dioxin-like polychlorinated biphenyls (DL-PCB), brominated flame retardants, perfluorinated alkyl substances (PFAS), pesticides, phthalates, nonylphenol and chlorinated paraffins (CP) in source-separated compost and digestate from Switzerland is presented (n = 3-18). The median summation 17PCDD/F and summation 12DL-PCB concentrations were at 3.2 ng I-TEQ kg(-1)dry weight (dw) and 3.0 ng WHO-TEQ kg(-1)dw, respectively. Brominated diphenyl ether 209 (BDE 209) accounted for 72% of the total polyBDE content (10 microg kg(-1)dw). Hexabromocyclododecane (HBCD) and tetrabromobisphenol A (TBBPA) levels were at 100 and 0.51 microg kg(-1)dw, respectively. PFAS were identified for the first time in compost and digestate (median concentration 6.3 microg kg(-1)dw, summation 21compounds). Out of 269 pesticides analysed, 30 fungicides, 14 herbicides, eight insecticides and one acaricide were detected. Di-(2-ethylhexyl)phthalate (DEHP) median concentration accounted for 280 microg kg(-1)dw and nonylphenol was below the detection limit of 1 mg kg(-1)dw. The sum of short and medium chain CP was between 90 and 390 microg kg(-1)dw. The concentrations observed were at or above the levels found in background soils, which are the main recipient of compost and digestate. Where actually applied, compost can contribute considerably to the total input of organic pollutants to the soil. However, on a total Swiss agricultural area base, inputs seem to be limited.

Background Current sequencing technology enables taxonomic profiling of microbial ecosystems at high resolution and depth by using the 16S rRNA gene as a phylogenetic marker. Taxonomic assignation of newly acquired data is based on sequence comparisons with comprehensive reference databases to find consensus taxonomy for representative sequences. Nevertheless, even with well-characterised ecosystems like the human intestinal microbiota it is challenging to assign genus and species level taxonomy to 16S rRNA amplicon reads. A part of the explanation may lie in the sheer size of the search space where competition from a multitude of highly similar sequences may not allow reliable assignation at low taxonomic levels. However, when studying a particular environment such as the human intestine, it can be argued that a reference database comprising only sequences that are native to the environment would be sufficient, effectively reducing the search space. Results We constructed a 16S rRNA gene database based on high-quality sequences specific for human intestinal microbiota, resulting in curated data set consisting of 2473 unique prokaryotic species-like groups and their taxonomic lineages, and compared its performance against the Greengenes and Silva databases. The results showed that regardless of used assignment algorithm, our database improved taxonomic assignation of 16S rRNA sequencing data by enabling significantly higher species and genus level assignation rate while preserving taxonomic diversity and demanding less computational resources. Conclusion The curated human intestinal 16S rRNA gene taxonomic database of about 2500 species-like groups described here provides a practical solution for significantly improved taxonomic assignment for phylogenetic studies of the human intestinal microbiota. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2265-y) contains supplementary material, which is available to authorized users.

tmoA and related genes encode the alpha-subunit of the hydroxylase component of the major group (subgroup 1 of subfamily 2) of bacterial multicomponent mono-oxygenase enzyme complexes involved in aerobic benzene, toluene, ethylbenzene and xylene (BTEX) degradation. A PCR-denaturing gradient gel electrophoresis (DGGE) method was developed to assess the diversity of tmoA-like gene sequences in environmental samples using a newly designed moderately degenerate primer set suitable for that purpose. In 35 BTEX-degrading bacterial strains isolated from a hydrocarbon polluted aquifer, tmoA-like genes were only detected in two o-xylene degraders and were identical to the touA gene of Pseudomonas stutzeri OX1. The diversity of tmoA-like genes was examined in DNA extracts from contaminated and non-contaminated subsurface samples at a site containing a BTEX-contaminated groundwater plume. Differences in DGGE patterns were observed between strongly contaminated, less contaminated and non-contaminated samples and between different depths, suggesting that the diversity of tmoA-like genes was determined by environmental conditions including the contamination level. Phylogenetic analysis of the protein sequences deduced from the amplified amplicons showed that the diversity of TmoA-analogues in the environment is larger than suggested from described TmoA-analogues from cultured isolates, which was translated in the DGGE patterns. Although different positions on the DGGE gel can correspond to closely related TmoA-proteins, relationships could be noticed between the position of tmoA-like amplicons in the DGGE profile and the phylogenetic position of the deduced protein sequence.

tmoA and related genes encode the alpha-subunit of the hydroxylase component of the major group (subgroup 1 of subfamily 2) of bacterial multicomponent mono-oxygenase enzyme complexes involved in aerobic benzene, toluene, ethylbenzene and xylene (BTEX) degradation. A PCR-denaturing gradient gel electrophoresis (DGGE) method was developed to assess the diversity of tmoA-like gene sequences in environmental samples using a newly designed moderately degenerate primer set suitable for that purpose. In 35 BTEX-degrading bacterial strains isolated from a hydrocarbon polluted aquifer, tmoA-like genes were only detected in two o-xylene degraders and were identical to the touA gene of Pseudomonas stutzeri OX1. The diversity of tmoA-like genes was examined in DNA extracts from contaminated and non-contaminated subsurface samples at a site containing a BTEX-contaminated groundwater plume. Differences in DGGE patterns were observed between strongly contaminated, less contaminated and non-contaminated samples and between different depths, suggesting that the diversity of tmoA-like genes was determined by environmental conditions including the contamination level. Phylogenetic analysis of the protein sequences deduced from the amplified amplicons showed that the diversity of TmoA-analogues in the environment is larger than suggested from described TmoA-analogues from cultured isolates, which was translated in the DGGE patterns. Although different positions on the DGGE gel can correspond to closely related TmoA-proteins, relationships could be noticed between the position of tmoA-like amplicons in the DGGE profile and the phylogenetic position of the deduced protein sequence.

The genotypic diversity of antibiotic-producing Pseudomonas spp. provides an enormous resource for identifying strains that are highly rhizosphere competent and superior for biological control of plant diseases. In this study, a simple and rapid method was developed to determine the presence and genotypic diversity of 2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas strains in rhizosphere samples. Denaturing gradient gel electrophoresis (DGGE) of 350-bp fragments of phlD , a key gene involved in DAPG biosynthesis, allowed discrimination between genotypically different phlD + reference strains and indigenous isolates. DGGE analysis of the phlD fragments provided a level of discrimination between phlD + genotypes that was higher than the level obtained by currently used techniques and enabled detection of specific phlD + genotypes directly in rhizosphere samples with a detection limit of approximately 5 × 10 3 CFU/g of root. DGGE also allowed simultaneous detection of multiple phlD + genotypes present in mixtures in rhizosphere samples. DGGE analysis of 184 indigenous phlD + isolates obtained from the rhizospheres of wheat, sugar beet, and potato plants resulted in the identification of seven phlD + genotypes, five of which were not described previously based on sequence and phylogenetic analyses. Subsequent bioassays demonstrated that eight genotypically different phlD + genotypes differed substantially in the ability to colonize the rhizosphere of sugar beet seedlings. Collectively, these results demonstrated that DGGE analysis of the phlD gene allows identification of new genotypic groups of specific antibiotic-producing Pseudomonas with different abilities to colonize the rhizosphere of sugar beet seedlings.

Detection of Salmonella by bacteriologic methods is known to be time consuming. Therefore, we have developed a real-time probe-specific polymerase chain reaction (PCR) to rapidly detect Salmonella invA gene-based PCR products from chicken feces and carcasses by a fluorescence resonance energy transfer assay. The sensitivity and the specificity of this system were determined as 3 colony-forming units ml(-1) and 100%, respectively. Overnight tetrathionate broth enrichment cultures of chicken feces and carcass samples were used in template preparation for PCR. Also, a standard bacteriology was performed (National Poultry Improvement Plan-U.S. Department of Agriculture, Bacteriological Analytical Manual-Food and Drug Administration Center for Food Safety and Applied Nutrition) for confirmation. Seventy-two cloacal swab, 147 intestine, and 50 carcass (neck) samples were examined. Thirteen (8.8%) and 25 (17%) of the intestinal samples were found to harbor Salmonella by bacteriology and PCR, respectively. Forty-five of 50 (90%) carcass samples were Salmonella positive by both methods. Salmonella was not detected from cloacal swab samples. Results indicate that this assay has the potential for use in routine monitoring and detection of Salmonella in infected flocks and carcasses.

Bacillus anthracis, the causative agent of anthrax, is a zoonotic pathogen that is relatively common throughout the world and may cause life threatening diseases in animals and humans. There are many PCR-based assays in use for the detection of B. anthracis. While most of the developed assays rely on unique markers present on virulence plasmids pXO1 and pXO2, relatively few assays incorporate chromosomal DNA markers due to the close relatedness of B. anthracis to the B. cereus group strains. For the detection of chromosomal DNA, different genes have been used, such as BA813, rpoB, gyrA, plcR, S-layer, and prophage-lambda. Following a review of the literature, an in silico analysis of all signature sequences reported for identification of B. anthracis was conducted. Published primer and probe sequences were compared for specificity against 134 available Bacillus spp. genomes. Although many of the chromosomal targets evaluated are claimed to be specific to B. anthracis, cross-reactions with closely related B. cereus and B. thuringiensis strains were often observed. Of the 35 investigated PCR assays, only 4 were 100% specific for the B. anthracis chromosome. An interlaboratory ring trial among five European laboratories was then performed to evaluate six assays, including the WHO recommended procedures, using a collection of 90 Bacillus strains. Three assays performed adequately, yielding no false positive or negative results. All three assays target chromosomal markers located within the lambdaBa03 prophage region (PL3, BA5345, and BA5357). Detection limit was further assessed for one of these highly specific assays.

Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution. Published version

Two types of biological tests were employed for monitoring the toxicological profile of sediment cores in the Three Gorges Reservoir (TGR), China. In the present study, sediments collected in June 2010 from TGR were analyzed for estrogen receptor (ER)- and aryl hydrocarbon receptor (AhR)-mediated activities. The estrogenic activity was assessed using a rapid yeast estrogen bioassay, based on the expression of a green fluorescent reporter protein. Weak anti-estrogenic activity was detected in sediments from an area close to the dam of the reservoir, and weak estrogenic activities ranging from 0.3 to 1 ng 17β-estradiol (E2) equivalents (EQ) g(-1) dry weight sediment (dw) were detected in sediments from the Wanzhou to Guojiaba areas. In the upstream areas Wanzhou and Wushan, sediments demonstrated additive effects in co-administration of 1 nM E2 in the yeast test system, while sediments from the downstream Badong and Guojiaba areas showed estrogenic activities which seemed to be more than additive (synergistic activity). There was an increasing tendency in estrogenic activity from upstream of TGR to downstream, while this tendency terminated and converted into anti-estrogenic activity in the area close to the dam. The AhR activity was detected employing rat hepatoma cell line (H4IIE). EROD activities were found homogenously distributed in sediments in TGR ranging from 200 to 311 pg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) EQ g(-1) dw for total AhR agonists and from 45 to 76 pg TCDD EQ g(-1) dw for more persistent AhR agonists. The known AhR agonists polycyclic aromatic hydrocarbon, polychlorinated biphenyl, and PCDD/F only explained up to 8 % of the more persistent AhR agonist activity in the samples, which suggests that unidentified AhR-active compounds represented a great proportion of the TCDD EQ in sediments from TGR. These findings of estrogenic potential and dioxin-like activity in TGR sediments provide possible weight-of-evidence of potential ecotoxicological causes for the declines in fish populations which have been observed during the past decades in TGR.

Sample preparation is critical in relation to analysis time, sample throughput and therefore analysis costs. Due to recent advances in liquid chromatography-mass spectrometry (LC-MS) instrumentation, the detection of many compounds within one run became possible, and methods for the simultaneous analysis of different compound groups were developed. To be able to analyze compounds with different physical and chemical properties simultaneously, generic, non-selective sample-preparation procedures are applied. The most frequently reported generic sample-preparation methods are a solvent extraction only, solid-phase extraction and a Quick, Easy, Cheap, Effective, Rugged, and Safe (QuEChERS) approach. These multi-analyte methods – sometimes including more than 150 different compounds – are of much interest for analytical laboratories due to their reduction in costs. A clear drawback of generic sample-preparation procedures is the occurrence of abundant matrix effects, which compromise detection limits, quantitative aspects, method selectivity and maintenance frequency. In contrast to the trend towards non-selective sample preparation, an opposite trend towards more selective sample-preparation methods is expected to be able to confirm the identity of compounds unambiguously (e.g., stereoisomers). This review gives an overview of generic sample-preparation procedures in the analysis of veterinary drug residues in products of animal origin using LC-MS as the detection technique and an outlook towards expected future trends.

International audience; Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. Its physicochemical properties affect microbial distributions inside the soil matrix, metagenome extraction and its subsequent analyses. To better understand the bias inherent to soil metagenome 'processing', we focus on soil physicochemical properties and their effects on the perceived bacterial distribution. In the light of this information, each step of soil metagenome processing is then discussed, with an emphasis on strategies for optimal soil sampling. Then, the interaction of cells and DNA with the soil matrix and the consequences for microbial DNA extraction are examined. Soil DNA extraction methods are compared and the veracity of the microbial profiles obtained is discussed. Finally, soil metagenomic sequence analysis and exploitation methods are reviewed.

The availability of novel and advanced molecular methods based on soil nucleic acids has revolutionized our studies of the microbiota of soil. In particular, our understanding of the daunting diversity of soil microbes has grown to maturity, opening up a new box of challenging research questions about microbial functioning and interactions. We here review recent developments in, as well as the state-of-the-art of, the molecular methods applied to soil, and discuss a few salient cases in which they have enhanced our understanding of the soil microbiota and its functioning. In particular, we place a focus on the interface between soil fungal hyphae and the corresponding non-fungal-affected soil, i.e., the mycosphere. This selective environment may reduce the diversity of its inhabitants, allowing an improved picture of their ecology and functioning via molecular techniques. We present arguments for the contention that, to investigate testable hypotheses, a polyphasic approach is needed, in which work on the basis of molecular approaches such as metagenomics and metatranscriptomics is coupled to that based on culturable organisms. Thus, advances in our understanding of local functioning and adaptation of bacterial mycosphere inhabitants will be fostered by combined metagenomics/metatranscriptomics and cultivation-based approaches. (C) 2010 Elsevier Masson SAS. All rights reserved.

Four quantification methods for short-chain chlorinated paraffins (SCCPs) or polychlorinated alkanes (PCAs) using gas chromatography electron capture negative ionisation low resolution mass spectrometry (GC-ECNI-LRMS) were investigated. The method based on visual comparison of congener group patterns of external standards used for quantification and fish samples was very sensitive for the choice of the quantification standard. Two other methods used the existing relation of the response factors with the chlorine content of SCCP mixtures for quantification. Results from the three methods above deviated from nominal values less than 20%. This was ~50% when individual PCA standards were applied for quantification of SCCPs. The deviation is probably caused by the fact that only C10 carbon chain length standards with 5-9 chlorine atoms could be used. However, quantification using individual PCA standards is a promising method provided more standards will become commercially available. The clear advantage is that the standards are defined, which makes quantification comparable between different laboratories. Application of all four quantification methods to the analysis of four different fish samples gave results that agreed with the median values within ±40%. © 2011 Taylor & Francis.

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Reyss, J. L. Riotte, J. Freydier, R. 2 ELSEVIER SCIENCE BV AMSTERDAM MAR CHEM; We report vertical profiles of radium-226 (Ra-226) concentrations determined in seawater and suspended particles collected in the North-West Pacific using Multi Collector-Inductively Coupled Plasma Mass Spectrometry (MC-ICP-MS). Dissolved Ra-226 concentrations were determined in small size water samples (between 110 and 250 ml volume) with a precision usually better than 5% (internal error, two standard error, 2 sigma(m)) using a chemical protocol slightly modified compared to previous studies that provides a chemical recovery of 90%. The Ra-226 activities thus obtained are in good agreement with the Ra-226 activities determined using low-background gamma spectrometry. In this work, we report the first Ra-226 activities determined in marine suspended particles using MC-ICP-MS. We thus show that this method is very useful to determine Ra-226 concentrations in suspended particles that have been poorly studied up to now because they display very low Ra-226 activities (i.e. two orders of magnitude lower than the Ra-226 activity in seawater). Such a sensitive method can thus be used to build high-resolution vertical profiles of dissolved and particulate Ra-226 activities, which would allow us to better understand the impact of biology on the oceanic Ra cycle. (C) 2011 Elsevier B.V. All rights reserved.

To achieve a better understanding of the ecological significance of Archaea in relation to petroleum contamination, we examined the composition of archaeal communities in anoxic coastal marine infralittoral sediments and their response to simulated petroleum contamination. Sediments were collected at an experimental site, and half were mixed with oil. Control and oiled sediments were then reworked into PVC cores that were inserted into the sediment at their sampling site at 20 m water depth. After 503 d of in situ incubation, molecular and statistical analyses clearly showed that petroleum contamination induced significant shifts in the composition of archaeal communities inhabiting these anoxic sediments. Overall, contamination led to a significant decrease in diversity. Control sediments were dominated by Crenarchaeota, whereas in oiled sediments,Euryarchaeota became dominant, as attested by the particular contribution of Methanococcoides, Methanosarcina, and Methanolobus sequences. Methanogens could be indirectly related to the degradation of the added hydrocarbons by participating in syntrophic consortia with hydrocarbon-degrading acetogenic bacteria. In addition, the abundance of anaerobic methane-oxidizing Archaea sequences in oiled sediments could indicate that anaerobic oxidation of methane (AOM) occurs at the depth selected for the analyses. Further studies undertaken to quantify vertical distribution of AOM, methanogenic activity, and their potential causative Archaea would help to enhance understanding of this complex petroleum-contaminated sedimentary system.

Abstract Molecular taxonomy is one of the most promising yet challenging fields of biology. Molecular markers such as nuclear and mitochondrial genes are being used in a variety of studies surveying marine nematode taxa. Sequences from more than 600 species have been deposited to date in online databases. These barcode sequences are assigned to 150 nominal species from 104 genera. There are 41 species assigned to Enoplea and 109 species to Chromadorea. Morphology-based surveys are greatly limited by processing speed, while barcoding approaches for nematodes are hampered by difficulties in matching sequence data with morphology-based taxonomy. DNA barcoding is a promising approach because some genes contain variable regions that are useful to discriminate species boundaries, discover cryptic species, quantify biodiversity and analyse phylogeny. We advocate a combination of several approaches in studies of molecular taxonomy, DNA barcoding and conventional taxonomy as a necessary step to enhance the knowledge of biodiversity of marine nematodes.

Culture-independent molecular methods based on the amplification, cloning and sequencing of small-subunit ribosomal RNA genes (SSU rDNAs) are powerful tools to study the diversity of microorganisms. Despite so, the eukaryotic microbial diversity of many ecosystems, including peatlands has not yet received much attention. We analysed the eukaryotic diversity by molecular surveys in water from the centre of a pristine Sphagnum-dominated peatland in the Jura Mountains of Switzerland during a complete seasonal cycle. The clone libraries constructed from five different temporal samplings revealed a high diversity of protists with representatives of all major eukaryotic phyla. In addition, four sequence types could not be assigned to any known high-level eukaryotic taxon but branched together with a rather good statistic support, raising the possibility of a novel, deep branching eukaryotic clade. The analysis of seasonal patterns of phylotypes showed a clear change in the eukaryotic communities between the warm period (late spring and summer) and the cold period (autumn and winter). Chrysophytes dominated the samples in the cold period while testate amoebae (Arcellinida and Euglyphida) and a few other groups peaked in summer. A few phylotypes (such as a cryptomonad and a perkinsid) were abundant at given sampling times and then almost disappeared, suggesting bloom-like dynamics. (C) 2010 Published by Elsevier GmbH.

In this study three major types of preconcentration methods based upon different principles (cation exchange, physical absorption and hydrophobic extraction) were evaluated and optimized for the extraction and determination of three highly toxic heavy metals namely Cd, Ph and Sn by graphite furnace and hybrid generation atomic absorption spectrometry in real samples. The optimum analytical condition were examined and the analytical features of each method were revealed and compared. Detection limit: as low as 0.003-0.025 mu g L(-1) for Cd(2+), 0.05-0.10 mu g L(-1) for Pb(2+) and 0.1-0.25 mu g L(-1) for Sn(4+) depending on the extraction method were obtained with RSD values between 3.08% and 6.11%. A preliminary assessment of the pollution status of three important natural ecosystems in Epirus region (NW Greece) was performed and some early conclusions were drawn and discussed. (C) 2008 Published by Elsevier B.V. J Hazard Mater

Waste streams from industrial processes such as metal smelting or mining contain high concentrations of sulfate and metals with low pH. Dissimilatory sulfate reduction carried out by sulfate-reducing bacteria (SRB) at low pH can combine sulfate reduction with metal-sulfide precipitation and thus open possibilities for selective metal recovery. This study investigates the microbial diversity and population changes of a single-stage sulfidogenic gas-lift bioreactor treating synthetic zinc-rich waste water at pH 5.5 by denaturing gradient gel electrophoresis of 16S rRNA gene fragments and quantitative polymerase chain reaction. The results indicate the presence of a diverse range of phylogenetic groups with the predominant microbial populations belonging to the Desulfovibrionaceae from delta-Proteobacteria. Desulfovibrio desulfuricans-like populations were the most abundant among the SRB during the three stable phases of varying sulfide and zinc concentrations and increased from 13% to 54% of the total bacterial populations over time. The second largest group was Desulfovibrio marrakechensis-like SRB that increased from 1% to about 10% with decreasing sulfide concentrations. Desulfovibrio aminophilus-like populations were the only SRB to decrease in numbers with decreasing sulfide concentrations. However, their population was

The screening of ingredients in municipal wastewater samples was studied, by reverse-phase high-performance liquid chromatography (RP-HPLC) implemented with a ultraviolet (UV)-diode array detector, in an effort to establish a quick screening method for finding the main UV-absorbing components of the wastewater that enters the biological treatment plant. For the purposes of direct comparison of the chromatograms obtained, a single sample taken from the inlet of municipal biological treatment plant was used for all experimental tests and the optimal elution conditions were established by detailed investigation through isocratic and gradient elution techniques. The optimal column resolution was reached by testing a broad range of capacity and selectivity factor values. The criterion used for validating the complete separation of solutes was based on the spectral purity of eluted chromatogram peaks and on the stability of retention time of a peak in real-time chromatograms taken at different wavelengths during the elution process. From this research work, it was found that the overall chromatogram peak pattern was sensitive to the mobile phase composition and solvent system but under fixed elution conditions, the pattern of the major peaks was stable and depended on the composition of the wastewater sample. By testing different types of elution modes, it was found that the best column resolution was obtained under programmed isocratic-gradient elution using a binary mobile phase. Finally, a relatively high column resolution method is reported for fragmentation of municipal wastewater samples. Water and Environment Journal

tmoA and related genes encode the alpha-subunit of the hydroxylase component of the major group (subgroup 1 of subfamily 2) of bacterial multicomponent mono-oxygenase enzyme complexes involved in aerobic benzene, toluene, ethylbenzene and xylene (BTEX) degradation. A PCR-denaturing gradient gel electrophoresis (DGGE) method was developed to assess the diversity of tmoA-like gene sequences in environmental samples using a newly designed moderately degenerate primer set suitable for that purpose. In 35 BTEX-degrading bacterial strains isolated from a hydrocarbon polluted aquifer, tmoA-like genes were only detected in two o-xylene degraders and were identical to the touA gene of Pseudomonas stutzeri OX1. The diversity of tmoA-like genes was examined in DNA extracts from contaminated and non-contaminated subsurface samples at a site containing a BTEX-contaminated groundwater plume. Differences in DGGE patterns were observed between strongly contaminated, less contaminated and non-contaminated samples and between different depths, suggesting that the diversity of tmoA-like genes was determined by environmental conditions including the contamination level. Phylogenetic analysis of the protein sequences deduced from the amplified amplicons showed that the diversity of TmoA-analogues in the environment is larger than suggested from described TmoA-analogues from cultured isolates, which was translated in the DGGE patterns. Although different positions on the DGGE gel can correspond to closely related TmoA-proteins, relationships could be noticed between the position of tmoA-like amplicons in the DGGE profile and the phylogenetic position of the deduced protein sequence.

From years 2000 to 2003, Salmonella was investigated from a total of 1785 samples comprised of chicken intestinal samples, cloacal swabs, drag swabs, litter samples and chick dust samples collected from 191 poultry breeding flocks belonging to 15 different chicken breeding stock companies in the Marmara region, Turkey by a SYBR green-based real-time polymerase chain reaction (SGBRT-PCR), by a probe-specific real-time polymerase chain reaction (PSRT-PCR) and by standardized bacteriology as described in the manual of National Poultry Improvement Plan and Auxillary Provisions, United States Department of Agriculture. Between January 2000 and July 2001, Salmonella was detected at the rates of 5.87% and 4.10% out of a total of 1242 samples by SGBRT-PCR and bacteriology, respectively. From July 2001 until December 2003, Salmonella was found at rates of 11.42% and 5.52% from a total of 543 samples by PSRT-PCR and bacteriology, respectively. The dominant Salmonella serovar was determined as Salmonella enterica subsp. enterica Serovar Enteritidis ( S. Enteritidis), while serogroup C1 and C2 in 2001 and serogroup E1 in 2002 were isolated as additional serovars. As a conclusion, S. Enteritidis seems to be the major problem in poultry breeding flocks in Turkey, and both of the real-time polymerase chain reaction methods were found more sensitive than standard bacteriology for the detection of Salmonella from poultry samples.

The use of ionic surfactant supramolecular aggregates is described, as means for accomplishing the concentration of analytes with different polarities using the same extraction pattern. The proposed method is based on the phase separation of an anionic surfactant through the formation of perplexed lamellar phases, allowing for the extraction of hydrated metal cations by complexation and metal-chelates by hydrophobic interactions. The data suggest that both extraction and phase separation are controlled by the presence of ionic surfactant as a function of the degree of phase divergence from the lamellar to bilayer phase. This again is determined by the composition of the phase-forming parameters, these are the surfactant concentration, the kind and amount of metallic counterparts and ionic strength. On the basis of these findings, the proposed method was successfully applied to the determination of metal species in natural waters. The limits of detection were easily brought down to the low microgram per liter levels by simply preconcentrating 10 mL of sample volume in the presence of at least 0.45% (w/v) of anionic surfactant. The method provided extraction recoveries higher than 94.0% with standard deviations well below 7.0%. (c) 2005 Elsevier B.V. All rights reserved. Analytica Chimica Acta

Eight new primer sets were designed for PCR detection of (i) mono-oxygenase and dioxygenase gene sequences involved in initial attack of bacterial aerobic BTEX degradation and of (ii) catechol 2,3-dioxygenase gene sequences responsible for metacleavage of the aromatic ring. The new primer sets allowed detection of the corresponding genotypes in soil with a detection limit Of 10(3)-10(4) or 10(5)-10(6) gene copies g(-1) soil, assuming one copy of the gene per cell. The primer sets were used in PCR to assess the distribution of the catabolic genes in BTEX degrading bacterial strains and DNA extracts isolated from soils sampled from different locations and depths (vadose, capillary fringe and saturated zone) within a BTEX contaminated site. In both soil DNA and the isolates, tmoA-, xylM- and xylE1-like genes were the most frequently recovered BTEX catabolic genes. xylM and xylE1 were only recovered from material from the contaminated samples while tmoA was detected in material from both the contaminated and non-contaminated samples. The isolates, mainly obtained from the contaminated locations, belonged to the Actinobacteria or Proteobacteria (mainly Pseudomonas). The ability to degrade benzene was the most common BTEX degradation phenotype among them and its distribution was largely congruent with the distribution of the tmoA-like genotype. The presence of tmoA and xylM genes in phylogenetically distant strains indicated the occurrence of horizontal transfer of BTEX catabolic genes in the aquifer. Overall, these results show spatial variation in the composition of the BTEX degradation genes and hence in the type of BTEX degradation activity and pathway, at the examined site. They indicate that bacteria carrying specific pathways and primarily carrying tmoA/xylM/xylE1 genotypes, are being selected upon BTEX contamination. (c) 2005 Elsevier B.V. All rights reserved.

International audience; The ubiquitous presence of alkylphenol ethoxylates in the environment as well as concern for endocrine disruption effects in biota caused by their degradation products (such as octyl- and nonylphenol) has raised interest in the environmental fate of these compounds. As part of an effort to model their behavior in a subestuary of the Chesapeake Bay, a quantitative method for the analysis of octyl- and nonylphenol, and their ethoxylates (1−5) in water and sediment was developed. Extraction procedures are based on solid-phase extraction techniques. Identification and quantitation of the analytes is done by liquid chromatography coupled to tandem mass spectrometry. Instrument detection limits for the compounds ranged from 0.1 to 9 pg injected on column, which allowed method detection limits of 0.04−3 ng/L in water and 0.2−13 ng/g of dry weight in sediment. The method was used to analyze water and sediment from the Back River, MD, where concentrations for the individual compounds ranged from

Heterocyclic polyaromatic compounds, including dinaphthofurans, 2-(2-naphthalenyl)benzothiophene, methylated chrysene, and benz[a]anthracene, were identified and confirmed as major cytochrome P4501A (CYP1A)-inducing compounds in a contaminated sediment close to the industrial site of Bitterfeld (Germany). Identification was achieved by the application of an effect-directed fractionation and analysis approach. This approach comprised the combination of a rainbow trout liver cell line (RTL-W1) bioassay to select for CYP1A-inducing effects by measuring 7-ethoxyresorufin-O-deethylase activity, a multistep fractionation procedure, and various methods of chemical characterization. The identified nonpriority pollutants were found to be significantly more potent than the reference compound, benzo[a]pyrene, and among the most potent polycyclic inducers known. On the basis of the history of industrial activity at the contaminated site, the heterocyclic compounds identified in this study are thought to stem from 2-naphthol production. 2-Naphthol is one of the most high-tonnage products of the aniline dye industry in general, thereby indicating the potential environmental relevance of the identified heterocyclic aromatic compounds. To date, however, no or very little knowledge exists about their occurrence, fate, and biological effects.

Mycelial biomass estimates in soils are usually obtained by measuring total hyphal length or by measuring the amount of fungal-specific biomarkers such as ergosterol and phospholipid fatty acids (PLFAs). These methods determine the biomass of the fungal community as a whole and do not allow species-specific identification. Molecular methods based on the extraction of total soil DNA and the use of genes as biomarkers enable identification of mycelia directly from the environment. Three molecular techniques were compared to determine the most reliable method for determining the biomass of individual fungal species in soil. The growth of extramatrical mycelium of two ectomycorrhizal (EM) fungal species (Suillus bovinus and Paxillus involutus) in soil was monitored by denaturing gradient gel electrophoresis, a cloning technique and real-time quantitative polymerase chain reaction, and the results were compared with those obtained with hyphal length determination and PLFA analysis. The molecular methods enabled identification and relative quantification of both species separately in an environment with several fungal species present and showed consistent results. Amounts of target DNA per gram soil were used to quantitatively compare soil samples. Increasing amounts of S. bovinus DNA and decreasing amounts of P. involutus DNA were detected over time in an environment containing a more complex community. This work demonstrates that molecular methods provide tools to determine the biomass of individual fungal species in soil. (C) 2003 Published by Elsevier B.V. on behalf of the Federation of European Microbiological Societies.

Molecular identification techniques based on total DNA extraction provide a unique tool for identification of mycelium in soil. Using molecular identification techniques, the ectomycorrhizal (EM) fungal community under coniferous vegetation was analyzed. Soil samples were taken at different depths from four horizons of a podzol profile. A basidiomycete-specific primer pair (ITS1F-ITS4B) was used to amplify fungal internal transcribed spacer (ITS) sequences from total DNA extracts of the soil horizons. Amplified basidiomycete DNA was cloned and sequenced, and a selection of the obtained clones was analyzed phylogenetically. Based on sequence similarity, the fungal clone sequences were sorted into 25 different fungal groups, or operational taxonomic units (OTUs). Out of 25 basidiomycete OTUs, 7 OTUs showed high nucleotide homology (≥99%) with known EM fungal sequences and 16 were found exclusively in the mineral soil. The taxonomic positions of six OTUs remained unclear. OTU sequences were compared to sequences from morphotyped EM root tips collected from the same sites. Of the 25 OTUs, 10 OTUs had ≥98% sequence similarity with these EM root tip sequences. The present study demonstrates the use of molecular techniques to identify EM hyphae in various soil types. This approach differs from the conventional method of EM root tip identification and provides a novel approach to examine EM fungal communities in soil.

A method has been developed for the simultaneous determination of traces of Fe(III) and Fe(II) in water by on-line coupling of spectrophotometry with flame atomic absorption spectrometry (FAAS). The method involves cloud-point extraction (CPE) of both species with ammonium pyrrolidinecarbodithioate (APDC) under standard conditions, which facilitates the in situ complexation and extraction of both species. Differentiation of the oxidation states of iron is achieved by using mathematical equations to overcome the interference of Fe(Ill) in the spectrophotometric determination of Fe(Il) when they are both present in the same solution. In this manner the time-consuming and labor-intensive steps of preoxidation of Fe(II) or reduction of Fe(III) are eliminated. By preconcentrating a 10-mL sample solution detection limits as low as 7 mug L-1, were obtained after a single-step extraction procedure. The relative standard deviation (n=4, 30 mug L-1) was 2.6% and 1.8% for spectrophotometry and FAAS, respectively. Recoveries in the range of 96-105% were obtained by analysis of spiked real samples. The method was further verified by analyzing a certified reference material (IMEP-9); for this the recovery was 98.5%. Anal Bioanal Chem

This report describes a rapid detection procedure for salmonellae from chicken feces by the combination of tetrathionate primary enrichment (preenrichment [PE])-bacterial lysis-capillary PCR and capillary gel electrophoresis. Pure Salmonella enterica serovar Enteritidis 64K was reisolated and detected by capillary PCR after buffered peptone water and nutrient broth, tetrathionate broth base Hajna (TTBH), and tetrathionate broth (TTB) preenrichments. When the same culture was mixed with intestinal homogenate, bacteriological reisolation and capillary PCR detection was achieved only by TTBH and TTB preenrichments. Capillary gel electrophoresis revealed that a Salmonella genus-specific 281-bp PCR product was detected when Salmonella strains but not non- Salmonella strains were tested. The detection limit of capillary PCR with whole-cell DNA extracted from pure Salmonella enterica serovars Enteritidis 64K, Typhimurium LT2-CIP60-62, and Gallinarum 64K was 3, 3, and 9 CFU ml −1 , respectively. The detection limit of capillary PCR from whole-cell DNA extracted from intestinal homogenate artificially contaminated with the same three strains was 3, 3, and 7 CFU ml −1 , respectively. We compared the results of the capillary PCR and bacteriological examination from the natural samples. Thirty-five of 53 naturally contaminated samples produced a specific PCR product. In 9 of the 35 PCR-positive samples, Salmonella could not be detected bacteriologically either by PE or a primary and delayed secondary enrichment (DSE) combination. In the 18 PCR-negative samples, 4 samples were found to harbor Salmonella by both PE and DSE and 14 samples were positive after DSE. Fifty-three additional intestinal homogenate samples, which were negative by their PE and DSE in bacteriological examination, were found to be also negative by their PCRs. The total time required to detect Salmonella with the capillary PCR method we used was approximately 20 h. If samples are from clinically diseased birds, the total time for PCR and detection is reduced to 2 h since the 18-h PE is not required. These results indicate that TTB enrichment, bacterial lysis, and genus-specific capillary PCR combined with capillary gel electrophoresis constitute a sensitive and selective procedure which has the potential to rapidly identify Salmonella -infected flocks.

This study develops a method for solid phase microextraction (SPME) of ten widespread herbicides from water. The selected herbicides belong to different chemical groups are EPTC, molinate, propachlor, trifluralin, atrazine, propazine, terbuthylazine, prometryne, alachlor. Their determination was carried out by gas chromatography with flame thermionic and mass spectrometric detection. To perform the SPME, two types of fibre have been assayed: Carbowax-divinylbenzene (CW-DVB) of 65 mum thickness and polydimethylsiloxane-divinylbenzene (PDMS-DVB) of 65 mum thickness. The main factors affecting the SPME process such as pH, ionic strength, methanol content, memory effect, stirring rate and adsorption-time profile were studied. The method was applied to spiked natural waters such as ground water, sea water, lake water and river water in a concentration range of 0.1 to 10 mug/L. Limits of detection with each of the detectors were determined to be 1 - 20 ng/L in PDMS-DVB and 2-20 ng/L. CW-DVB fibres. The recoveries of herbicides compared to distilled water were in relatively high levels 78.3-127.3 % and the average r(2) values of the calibration curves were above 0.99 for all the analytes. The SPME conditions were finally optimized in order to obtain maximum sensitivity and samples were applied for the trace-level determination in river water samples originating from Ioannina region (Greece). International Journal of Environmental Analytical Chemistry

This study is part of a more extensive research program to characterize pollution in two different lagoons in Italy using a multitrial biomarker approach in combination with residue analysis. It looks at levels of 2,3,7,8-chlorinated PCDDs and PCDFs in crabs and sediments from several locations in the Venice and Orbetello Lagoons, both affected by various types of pollution. The PCDD/F levels found in crabs and sediment from Venice and Orbetello Lagoons varied between sampling sites: the highest being from Porto Marghera harbor, a part of the Venice Lagoon characterized by high industrial impact. Principal Component Analysis was used to identify groups of similar sediment samples which can be correlated to possible sources of contamination. Four different sediment fingerprint patterns were recognized in the two-dimensional space formed by the two principal components which were mainly formed by a combination of highly chlorinated PCDDs and PCDFs.