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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.

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.

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.