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Nontargeted screening (NTS) utilizing liquid chromatography electrospray ionization high-resolution mass spectrometry (LC/ESI/HRMS) is increasingly used to identify environmental contaminants. Major differences in the ionization efficiency of compounds in ESI/HRMS result in widely varying responses and complicate quantitative analysis. Despite an increasing number of methods for quantification without authentic standards in NTS, the approaches are evaluated on limited and diverse data sets with varying chemical coverage collected on different instruments, complicating an unbiased comparison. In this interlaboratory comparison, organized by the NORMAN Network, we evaluated the accuracy and performance variability of five quantification approaches across 41 NTS methods from 37 laboratories. Three approaches are based on surrogate standard quantification (parent-transformation product, structurally similar or close eluting) and two on predicted ionization efficiencies (RandFor- IE and MLR- IE ). Shortly, HPLC grade water, tap water, and surface water spiked with 45 compounds at 2 concentration levels were analyzed together with 41 calibrants at 6 known concentrations by the laboratories using in-house NTS workflows. The accuracy of the approaches was evaluated by comparing the estimated and spiked concentrations across quantification approaches, instrumentation, and laboratories. The RandFor- IE approach performed best with a reported mean prediction error of 15× and over 83% of compounds quantified within 10× error. Despite different instrumentation and workflows, the performance was stable across laboratories and did not depend on the complexity of water matrices.

The combination of integrative passive sampling and bioassays is a promising approach for monitoring the toxicity of polar organic contaminants in aquatic environments. However, the design of integrative passive samplers can affect the accumulation of compounds and therewith the bioassay responses. The present study aimed to determine the effects of sampler housing and sorbent type on the number of chemical features accumulated in polar passive samplers and the subsequent bioassay responses to extracts of these samplers. To this end, four integrative passive sampler configurations, resulting from the combination of polar organic chemical integrative sampler (POCIS) and Speedisk housings with hydrophilic-lipophilic balance and hydrophilic divinylbenzene sorbents, were simultaneously exposed at reference and contaminated surface water locations. The passive sampler extracts were subjected to chemical non-target screening and a battery of five bioassays. Extracts from POCIS contained a higher number of chemical features and caused higher bioassay responses in 91% of cases, while the two sorbents accumulated similar numbers of features and caused equally frequent but different bioassay responses. Hence, the passive sampler design critically affected the number of accumulated polar organic contaminants as well as their toxicity, highlighting the importance of passive sampler design for effect-based water quality assessment., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Feature detection plays a crucial role in non-target screening (NTS), requiring careful selection of algorithm parameters to minimize false positive (FP) features. In this study, a stochastic approach was employed to optimize the parameter settings of feature detection algorithms used in processing high-resolution mass spectrometry data. This approach was demonstrated using four open-source algorithms (OpenMS, SAFD, XCMS, and KPIC2) within the patRoon software platform for processing extracts from drinking water samples spiked with 46 per- and polyfluoroalkyl substances (PFAS). The designed method is based on a stochastic strategy involving random sampling from variable space and the use of Pearson correlation to assess the impact of each parameter on the number of detected suspect analytes. Using our approach, the optimized parameters led to improvement in the algorithm performance by increasing suspect hits in case of SAFD and XCMS, and reducing the total number of detected features (i.e., minimizing FP) for OpenMS. These improvements were further validated on three different drinking water samples as test dataset. The optimized parameters resulted in a lower false discovery rate (FDR%) compared to the default parameters, effectively increasing the detection of true positive features. This work also highlights the necessity of algorithm parameter optimization prior to starting the NTS to reduce the complexity of such datasets., (© 2024. The Author(s).)

Using bio-based fertilizer (BBF) in agricultural soil can reduce the dependency on chemical fertilizer and increase sustainability by recycling nutrient-rich side-streams. However, organic contaminants in BBFs may lead to residues in the treated soil. This study assessed the presence of organic contaminants in BBF treated soils, which is essential for evaluating sustainability/risks of BBF use. Soil samples from two field studies amended with 15 BBFs from various sources (agricultural, poultry, veterinary, and sludge) were analyzed. A combination of QuEChERS-based extraction, liquid chromatography quadrupole time of flight mass spectrometry-based (LC-QTOF-MS) quantitative analysis, and an advanced, automated data interpretation workflow was optimized to extract and analyze organic contaminants in BBF-treated agricultural soil. The comprehensive screening of organic contaminants was performed using target analysis and suspect screening. Of the 35 target contaminants, only three contaminants were detected in the BBF-treated soil with concentrations ranging from 0.4 ng g -1 to 28.7 ng g -1 ; out of these three detected contaminants, two were also present in the control soil sample. Suspect screening using patRoon (an R-based open-source software platform) workflows and the NORMAN Priority List resulted in tentative identification of 20 compounds (at level 2 and level 3 confidence level), primarily pharmaceuticals and industrial chemicals, with only one overlapping compound in two experimental sites. The contamination profiles of the soil treated with BBFs sourced from veterinary and sludge were similar, with common pharmaceutical features identified. The suspect screening results suggest that the contaminants found in BBF-treated soil might come from alternative sources other than BBFs., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Bio-based fertilizers (BBFs) have the potential to contain both pesticides and pharmaceutical residues, which may pose a threat to soils, crops, and human health. However, no analytical screening method is available currently to simultaneously analyze a wide range of contaminants in the complex origin-dependent matrices of BBFs. To fill this gap, our study tested and improved an original QuEChERS method (OQM) for simultaneously analyzing 78 pesticides and 18 pharmaceuticals in BBFs of animal, plant, and ashed sewage sludge origin. In spiked recovery experiments, 34-58 pharmaceuticals and pesticides were well recovered (recovery of 70-120%) via OQM at spiking concentrations levels of 10 ng/g and 50 ng/g in these three different types of BBFs. To improve the extraction efficiency further, ultrasonication and end-over-end rotation were added based on OQM, resulting in the improved QuEChERS method (IQM) that could recover 57-79 pesticides and pharmaceuticals, in the range of 70-120%. The detection limits of this method were of 0.16-4.32/0.48-12.97 ng/g, 0.03-11.02/0.10-33.06 ng/g, and 0.06-5.18/0.18-15.54 ng/g for animal, plant, and ash-based BBF, respectively. Finally, the IQM was employed to screen 15 BBF samples of various origins. 15 BBFs contained at least one pesticide or pharmaceutical with ibuprofen being frequently detected in at concentration levels of 4.1-181 ng/g. No compounds were detected in ash-based BBFs., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Yan Dong reports financial support was provided by European Union. Yan Dong reports financial support was provided by Chinese Scholarship Council., (Copyright © 2023. Published by Elsevier B.V.)

This study investigates human exposure to per- and polyfluoroalkyl substances (PFAS) via drinking water and evaluates human health risks. An analytical method for 56 target PFAS, including ultrashort-chain (C2-C3) and branched isomers, was developed. The limit of detection (LOD) ranged from 0.009 to 0.1 ng/L, except for trifluoroacetic-acid and perfluoropropanoic-acid with higher LODs of 35 and 0.24 ng/L, respectively. The method was applied to raw and produced drinking water from 18 Dutch locations, including groundwater or surface water as source, and applied various treatment processes. Ultrashort-chain (300 to 1100 ng/L) followed by the group of perfluoroalkyl-carboxylic-acids (PFCA, ≥C4) (0.4 to 95.1 ng/L) were dominant. PFCA and perfluoroalkyl-sulfonic-acid (≥C4), including precursors, showed significantly higher levels in drinking water produced from surface water. However, no significant difference was found for ultrashort PFAS, indicating the need for groundwater protection. Negative removal of PFAS occasionally observed for advanced treatment indicates desorption and/or degradation of precursors. The proportion of branched isomers was higher in raw and produced drinking water as compared to industrial production. Drinking water produced from surface water, except for a few locations, exceed non-binding provisional guideline values proposed; however, all produced drinking waters met the recent soon-to-be binding drinking-water-directive requirements.

Globally, the reuse of treated sewage effluent for irrigation purposes is increasingly encouraged as a practical solution against the mismatch between the demand for and availability of freshwater resources. The reuse of sewage effluent for sub-surface irrigation (SSI) in agriculture serves the dual purpose of supplying water to crops and diminishing emissions of contaminants of emerging concern (CoECs) into surface water. To investigate such reuse, in a real scale cropland with SSI using sewage effluent, from September 2017 to March 2019 including the extremely dry year 2018, residues were followed of 133 CoECs as related to their physicochemical properties and quantified by liquid chromatography coupled to high-resolution mass spectrometry. Of the 133 target CoECs, 89 were retrieved in the field, most non-detect CoECs have low persistency. During the growing season with sub-surface irrigation, CoECs spread to the shallow groundwater and rhizosphere. Significantly lower concentrations are found between infiltration pipes as compared to directly next to the pipes in shallow groundwater for all persistency-mobility classes. CoECs belonging to the class pm (low persistency and low mobility) or class PM (high persistency and high mobility) class show no change amongst their removal in the rhizosphere and groundwater in a dry versus normal year. CoECs belonging to the class pM (low persistency and high mobility) show high seasonal dynamics in the rhizosphere and shallow groundwater, indicating that these CoECs break down. CoECs of the class Pm (high persistency and low mobility) only significantly build up in the rhizosphere next to infiltration pipes. Climatic conditions with dry summers and precipitation surplus and drainage in winter strongly affect the fate of CoECs. During the dry summer of 2018 infiltrated effluent is hardly diluted, resulting in significantly higher concentrations for the CoECs belonging to the classes pM and Pm. After the extremely dry year of 2018, cumulative concentrations are still significantly higher, while after a normal year during winter precipitation surplus removes CoECs. For all persistency-mobility classes in the shallow groundwater between the pipes, we find significant removal efficiencies. For the rhizosphere between the pipes, we find the same except for Pm. Next to the pipes however we find no significant removal for all classes in both the rhizosphere and shallow groundwater and even significant accumulation for Pm. For this group of persistent moderately hydrophobic CoECs risk characterization ratio's were calculated for the period of time with the highest normalized concentration. None of the single-chemical RCRs are above one and the ΣRCR is also far below one, implying sufficiently safe ambient exposures. Overall the deeper groundwater (7.0-11.8 m below soil surface) has the lowest response to the sub-surface irrigation for all persistency-mobility. When adopting a SSI STP effluent reuse system care must be taken to monitor the CoECs that are (moderately) hydrophobic as these can build up in the SSI system. For the deeper groundwater and for the discharge to the surface water, we find significant removal for the pM and the PM class but not for other classes. In conclusion, relatively high removal efficiencies are shown benefiting the surface waters that would otherwise receive the STP effluent directly., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

In the past decades, the intensity and duration of cyanobacterial blooms are increasing due to anthropogenic factors. These phenomena worry drinking water companies and water managers because cyanobacteria produce a diverse range of cyanotoxins, which can cause liver, digestive and neurological diseases. The main exposure routes for humans are the consumption of drinking water that has not been effectively treated and the recreational use of polluted waters. For risk assessment and to conduct studies on large-scale occurrence, the development of reliable but simple, sensitive and cost-effective analytical approaches able to cover a wide range of cyanotoxins is essential. Additionally, the determination of intracellular and extracellular toxins separately is advantageous for risk management. To the best of our knowledge, this is the first time that a method for the multi-class determination of cyanotoxins in fresh water, which is able to separately report intra- and extracellular toxins, meet the criteria of simplicity (not requiring multiple sample preparation procedures or time-consuming steps) and it is based on highly specific high resolution mass spectrometry (potential for wide screening and retrospective analysis). Matrix effects, trueness and precision met general validation criteria for a group of nine cyanotoxins, including anatoxins, cylindrospermopsin and microcystins. Considering a 50 mL sample, the method quantification limits were within the range of 8-45 ng L -1 and 25-129 ng L -1 for intra- and extracellular cyanotoxins, respectively. Anatoxin-a, cylindrospermopsin and some microcystins were found in three out of four Dutch lakes included in the study, at concentrations up to 52 μg L -1 ., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.

Obesity has a serious effect on human health. It relates to metabolic syndrome, including the associated disorders such as type 2 diabetes, heart disease, stroke and hyperemia. The peroxisome proliferator-activated receptors (PPARs) are important receptors to control fat metabolism in the human body. Because of the safety concerns of synthetic drugs targeting PPARs, ligands from natural sources have drawn interest. Earlier, we have found high PPAR activities in extracts from Agaricus bisporus (white button mushroom, WBM). WBM contains a wide range of candidate compounds which could be agonists of PPARs. To identify which compounds are responsible for PPAR activation by WBM extracts, we used fractionation coupled to effect-directed analysis with reporter gene assays specific for all three PPARs for purification and LC/MS-TOF and NMR for compound identification in purified active fractions. Surprisingly, we identified the relatively common dietary fatty acid, linoleic acid, as the main ligand of PPARs in WBM. Possibly, the relatively low levels of linoleic acid in WBM are sufficient and instrumental in inducing its anti-obesogenic effects, avoiding high energy intake and negative health effects associated with high levels of linoleic acid consumption. However, it could not be excluded that a minor relatively potent compound contributes towards PPAR activation, while the anti-obesity effects of WBM may be further enhanced by receptor expression modulating compounds or compounds with completely PPAR unrelated modes of action.

Mass spectrometry based non-target analysis is increasingly adopted in environmental sciences to screen and identify numerous chemicals simultaneously in highly complex samples. However, current data processing software either lack functionality for environmental sciences, solve only part of the workflow, are not openly available and/or are restricted in input data formats. In this paper we present patRoon, a new R based open-source software platform, which provides comprehensive, fully tailored and straightforward non-target analysis workflows. This platform makes the use, evaluation and mixing of well-tested algorithms seamless by harmonizing various common (primarily open) software tools under a consistent interface. In addition, patRoon offers various functionality and strategies to simplify and perform automated processing of complex (environmental) data effectively. patRoon implements several effective optimization strategies to significantly reduce computational times. The ability of patRoon to perform time-efficient and automated non-target data annotation of environmental samples is demonstrated with a simple and reproducible workflow using open-access data of spiked samples from a drinking water treatment plant study. In addition, the ability to easily use, combine and evaluate different algorithms was demonstrated for three commonly used feature finding algorithms. This article, combined with already published works, demonstrate that patRoon helps make comprehensive (environmental) non-target analysis readily accessible to a wider community of researchers.

In this paper, we investigated the possible presence of endocrine disrupting chemicals (EDCs) based on measuring the total estrogenic and androgenic activity in human milk samples. We used specific bioassays for analysis of the endocrine activity of estrogens and estrogen-like EDCs and androgens and androgen-like EDCs and developed a separation method to evaluate the contribution from natural hormones in comparison to that of EDCs to total endocrine activities. We extracted ten random samples originating from the Norwegian HUMIS biobank of human milk and analyzed their agonistic or antagonistic activity using the ERα- and AR CALUX® bioassays. The study showed antagonistic activity towards the androgen receptor in 8 out of 10 of the assessed human milk samples, while 2 out of 10 samples showed agonistic activity for the ERα. Further investigations demonstrated anti-androgenic activity in the polar fraction of 9 out of 10 samples while no apolar extracts scored positive. The culprit chemicals causing the measured antagonistic activity in AR CALUX was investigated through liquid chromatography fractionation coupled to bioanalysis and non-target screening involving UHPLC-Q-TOF-MS/MS, using a pooled polar extract. The analysis revealed that the measured anti-androgenic biological activity could not be explained by the presence of endogenous hormones nor their metabolites. We have demonstrated that human milk of Norwegian mothers contained anti-androgenic activity which is most likely associated with the presence of anthropogenic polar EDCs without direct interferences from natural sex hormones. These findings warrant a larger scale investigation into endocrine biological activity in human milk, as well as exploring the chemical sources of the activity and their potential effects on health of the developing infant., (Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Source zones containing tar, a dense non-aqueous phase liquid (DNAPL), can contaminate groundwater for centuries. A common occurrence of tar is at former Pintsch gas factories. Little is known about the composition and fate of contaminants dissolving from Pintsch gas tar DNAPL. In this study, we determined the composition and water-soluble characteristics of mobile aromatic hydrocarbons and their biodegradation metabolites in the DNAPL contaminated groundwater at a former Pintsch gas tar plant. We assessed the factors that determine the fate of observed groundwater contaminants. Measured values of density (1.03-1.06 kg/m 3 ) and viscosity (18.6-39.4 cP) were found to be relatively low compared to common coal tars. Analysis showed that unlike common coal tars phenanthrene is the primary component rather than naphthalene. Moreover, it was found that Pintsch gas tar contains a relatively high amount of light molecular aromatic hydrocarbon compounds, such as benzene, toluene, ethylbenzene and xylenes (BTEX). Less commonly reported components, such as styrene, ethyltoluenes, di-ethylbenzene, 1,2,4,5-tetramethylbenzene, were also detected in water extracts from Pintsch gas tar. Moreover, 46 relatively hydrophilic metabolites were found within the tar samples. Metabolites present within the tar suggest biodegradation of mobile aromatic Pintsch gas tar compounds occurred near the DNAPL. Based on eleven detected suspect metabolites, a novel anaerobic biodegradation pathway is proposed for indene. Overall, our findings indicate that Pintsch gas tar has higher invasive and higher flux properties than most coal tars due to its relatively low density, low viscosity and, high content of water-soluble compounds. The partitioning of contaminants from multi-component DNAPL into the aqueous phase and re-dissolution of their slightly less hydrophobic metabolites back from the aqueous phase into the DNAPL is feasible and demonstrates the complexity of assessing degradation processes within a source zone., Competing Interests: Declaration of competing interest We wish to confirm that there are no known conflicts of interest associated with this publication and there has been no significant financial support for this work that could have influenced its outcome., (Crown Copyright © 2020. Published by Elsevier B.V. All rights reserved.)

The desalination and reuse of discharged cooling tower water (CTW) as feed water for the cooling tower could lower the industrial fresh water withdrawal. A potential pre-treatment method before CTW desalination is the use of constructed wetlands (CWs). Biodegradation is an important removal mechanism in CWs. In the present study, the impact of the biocides 2,2-dibromo-2-cyanoacetamide (DBNPA) and glutaraldehyde on the biodegradation process by CW microorganisms was quantified in batch experiments in which benzoic acid was incubated with realistic CTW biocide concentrations. DBNPA had a stronger negative impact on the biodegradation than glutaraldehyde. The combination of DBNPA and glutaraldehyde had a lower impact on the biodegradation than DBNPA alone. UHPLC-qTOF-MS/MS non-target screening combined with data-analysis script 'patRoon' revealed two mechanisms behind this low impact. Firstly, the presence of glutaraldehyde resulted in increased DBNPA transformation to the less toxic transformation product 2-bromo-2-cyanoacetamide (MBNPA) and newly discovered 2,2-dibromopropanediamide. Secondly, the interaction between glutaraldehyde and DBNPA resulted in the formation of new products that were less toxic than DBNPA. The environmental fate and toxicity of these products are still unknown. Nevertheless, their formation can have important implications for the simultaneous use of the biocides DBNPA and glutaraldehyde for a wide array of applications., Competing Interests: Declaration of Competing Interest The authors declare that there are no conflicts of interest., (Copyright © 2019 Elsevier B.V. All rights reserved.)

The application of biochar as a soil amendment can increase concentrations of soil organic matter, especially water-extractable organic substances. Due to their mobility and reactivity, more studies are needed to address the potential impact of biochar water-extractable substances (BWES) on the sorption of herbicides in agricultural soils that are periodically flooded. Two paddy soils (100 and 700 years of paddy soil development), unamended or amended with raw (BC) or washed biochar (BCW), were used to test the influence of BWES on the sorption behavior of the herbicides azimsulfuron (AZ) and penoxsulam (PE). The adsorption of AZ to biochar was much stronger than that to the soils, and it was adsorbed to a much larger extent to BC than to BCW. The depletion of polar groups in the BWES from the washed biochar reduced AZ adsorption but had no effect on PE adsorption. The adsorption of AZ increased when the younger soil (P100) was amended with BC and decreased when it was amended with BCW. In P700, which has lower dissolved organic carbon (DOC) content than P100, the adsorption of AZ increased regardless of whether biochar was raw or washed. The adsorption of PE slightly decreased when P100 was amended with BC or BCW and slightly increased when P700 was amended with BC or BCW. In order to evaluate compositional differences in the biochar and BWES before and after the washing treatment, we performed solid-state 13 C NMR spectroscopy of BC and BCW, and high resolution mass spectrometry of BWES. Our observations stress the importance of proper consideration of soil and biochar properties before their incorporation into paddy soils, since biochar may reduce or increase the mobility of AZ and PE depending on soil properties and time of application., (Copyright © 2019. Published by Elsevier B.V.)

Exposure history and adaptation of the inoculum to chemicals have been shown to influence the outcome of ready biodegradability tests. However, there is a lack of information about the mechanisms involved in microbial adaptation and the implication thereof for the tests. In the present study, we investigated the impact of a long-term exposure to N-methylpiperazine (NMP) and 4-chloroaniline (4CA) of an activated sludge microbial community using chemostat systems. The objective was to characterize the influence of adaptation to the chemicals on an enhanced biodegradation testing, following the OECD 310 guideline. Cultures were used to inoculate the enhanced biodegradability tests, in batch, before and after exposure to each chemical independently in chemostat culture. Composition and diversity of the microbial communities were characterised by 16s rRNA gene amplicon sequencing. Using freshly sampled activated sludge, NMP was not degraded within the 28 d frame of the test while 4CA was completely eliminated. However, after one month of exposure, the community exposed to NMP was adapted and could completely degrade it. This result was in complete contrast with that from the culture exposed for 3 months to 4CA. Long term incubation in the chemostat system led to a progressive loss of the initial biodegradation capacity of the community, as a consequence of the loss of key degrading microorganisms. This study highlights the potential of chemostat systems to induce adaptation to a specific chemical, ultimately resulting in its biodegradation. At the same time, one should be critical of these observations as the dynamics of a microbial community are difficult to maintain in chemostat, as the loss of 4CA biodegradation capacity demonstrates., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Metformin (MET) is a pharmaceutical product mostly biotransformed in the environment to a transformation product, guanylurea (GUA). In ready biodegradability tests (RBTs), however, contrasting results have been observed for metformin. The objective of this study was to measure the biodegradation of MET and GUA in RBTs, using activated sludge from the local wastewater treatment plant, either directly or after pre-exposure to MET, in a chemostat. The activated sludge community was cultivated in chemostats, in presence or absence of MET, for a period of nine months, and was used in RBT after one, three and nine months. The results of this study showed that the original activated sludge was able to completely remove MET (15 mg/l) and the newly produced GUA (50% of C 0MET ) under the test conditions. Inoculation of the chemostat led to a rapid shift in the community composition and abundance. The community exposed to 1.5 mg/l of MET was still able to completely consume MET in the RBTs after one-month exposure, but three- and nine-months exposure resulted in reduced removal of MET in the RBTs. The ability of the activated sludge community to degrade MET and GUA is the result of environmental exposure to these chemicals as well as of conditions that could not be reproduced in the laboratory system. A MET-degrading strain belonging to the genus Aminobacter has been isolated from the chemostat community. This strain was able to completely consume 15 mg/l of MET within three days in the test. However, community analysis revealed that the fluctuation in relative abundance of this genus (<1%) could not be correlated to the fluctuation in biodegradation capacity of the chemostat community., (Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.)

Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system. Metabolomics studies involve sophisticated analytical techniques such as mass spectrometry and nuclear magnetic resonance spectroscopy, and generate large amounts of high-dimensional and complex experimental data. Open source processing and analysis tools are of major interest in light of innovative, open and reproducible science. The scientific community has developed a wide range of open source software, providing freely available advanced processing and analysis approaches. The programming and statistics environment R has emerged as one of the most popular environments to process and analyse Metabolomics datasets. A major benefit of such an environment is the possibility of connecting different tools into more complex workflows. Combining reusable data processing R scripts with the experimental data thus allows for open, reproducible research. This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation and identification, and biochemical network and pathway analysis. Multifunctional workflows, possible user interfaces and integration into workflow management systems are also reviewed. In total, this review summarises more than two hundred metabolomics specific packages primarily available on CRAN, Bioconductor and GitHub.

The presence of perfluoroalkyl substances (PFASs) in sediments and groundwater on the Maltese Islands is reported here for the first time. Sediments and soil samples were collected from 24 sites and groundwater was collected from 10 boreholes. PFASs were extracted from water and solid samples using solid phase extraction. The extracts were then analysed using ultra performance liquid chromatography coupled to mass spectrometry in tandem (UPLC-MS/MS). All sediment, soil and groundwater samples were contaminated with at least one PFAS. PFOS (

The historic emissions of polar micropollutants in a natural drinking water source were investigated by nontarget screening with high-resolution mass spectrometry and open cheminformatics tools. The study area consisted of a riverbank filtration transect fed by the river Lek, a branch of the lower Rhine, and exhibiting up to 60-year travel time. More than 18,000 profiles were detected. Hierarchical clustering revealed that 43% of the 15 most populated clusters were characterized by intensity trends with maxima in the 1990s, reflecting intensified human activities, wastewater treatment plant upgrades and regulation in the Rhine riparian countries. Tentative structure annotation was performed using automated in silico fragmentation. Candidate structures retrieved from ChemSpider were scored based on the fit of the in silico fragments to the experimental tandem mass spectra, similarity to openly accessible accurate mass spectra, associated metadata, and presence in a suspect list. Sixty-seven unique structures (72 over both ionization modes) were tentatively identified, 25 of which were confirmed and included contaminants so far unknown to occur in bank filtrate or in natural waters at all, such as tetramethylsulfamide. This study demonstrates that many classes of hydrophilic organics enter riverbank filtration systems, persisting and migrating for decades if biogeochemical conditions are stable.

A method for the trace analysis of polar micropollutants (MPs) by direct injection of surface water and groundwater was validated with ultrahigh-performance liquid chromatography using a core-shell biphenyl stationary phase coupled to time-of-flight high-resolution mass spectrometry. The validation was successfully conducted with 33 polar MPs representative for several classes of emerging contaminants. Identification and quantification were achieved by semi-automated processing of full-scan and data-independent acquisition MS/MS spectra. In most cases good linearity (R 2 ≥ 0.99), recovery (75% to 125%) and intra-day (RSD < 20%) and inter-day precision (RSD < 10%) values were observed. Detection limits of 9 to 83 ng/L and 9 to 93 ng/L could be achieved in riverbank filtrate and surface water, respectively. A solid-phase extraction was additionally validated to screen samples from full-scale reverse osmosis drinking water treatment at sub-ng/L levels and overall satisfactory analytical performance parameters were observed for RBF and reverse osmosis permeate. Applicability of the direct injection method is shown for surface water and riverbank filtrate samples from an actual drinking water source. Several targets linkable to incomplete removal in wastewater treatment and farming activities were detected and quantified in concentrations between 28 ng/L for saccharine in riverbank filtrate and up to 1 μg/L for acesulfame in surface water. The solid phase extraction method applied to samples from full-scale reverse osmosis drinking water treatment plant led to quantification of 8 targets between 6 and 57 ng/L in the feed water, whereas only diglyme was detected and quantified in reverse osmosis permeate. Our study shows that combining the chromatographic resolution of biphenyl stationary phase with the performance of time-of-flight high-resolution tandem mass spectrometry resulted in a fast, accurate and robust method to monitor polar MPs in source waters by direct injection with high efficiency., (Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.)

The isolation of microorganisms from soil impacted by xenobiotic chemicals and exposing them in the laboratory to the contaminant can provide important information about their response to the contaminants. The purpose of this study was to isolate bacteria from soil with historical application of herbicides and to evaluate their potential to degrade diuron. The isolation media contained either glucose or diuron as carbon source. A total of 400 bacteria were isolated, with 68% being Gram-positive and 32% Gram-negative. Most isolates showed potential to degrade between 10 and 30% diuron after five days of cultivation; however Stenotrophomonas acidophila TD4.7 and Bacillus cereus TD4.31 were able to degrade 87% and 68%, respectively. The degradation of diuron resulted in the formation of the metabolites DCPMU, DCPU, DCA, 3,4-CAC, 4-CA, 4-CAC and aniline. Based on these results it was proposed that Pseudomonas aeruginosa TD2.3, Stenotrophomonas acidaminiphila TD4.7, B. cereus TD4.31 and Alcaligenes faecalis TG 4.48, act on 3,4-DCA and 4-CA by alkylation and dealkylation while Micrococcus luteus and Achromobacter sp follow dehalogenation directly to aniline. Growth on aniline as sole carbon source demonstrates the capacity of strains to open the aromatic ring. In conclusion, the results show that the role of microorganisms in the degradation of xenobiotics in the environment depends on their own metabolism and also on their synergistic interactions.

The presence of perfluoroalkyl substances (PFASs) in rain water on the Maltese Islands is reported here for the first time and an extensive survey of these substances in surface water also reported. The Maltese archipelago lies at the centre of the Mediterranean Sea and consists of three main inhabited islands: Malta, Gozo and Comino. Surface water was collected from 41 valleys during the months of February and March 2015 at the peak of the wet season. Rain water was collected during the months of December 2014, February, August, September and October 2015. PFASs were extracted from the water samples using solid phase extraction and the extracts were then analysed using ultra performance liquid chromatography coupled to mass spectrometry in tandem (UPLC-MS/MS). All surface and rain water samples were contaminated with at least one PFAS. PFOS (

Carbon-based nanomaterials, such as C 60 fullerenes, are expected to accumulate in soil due to direct release and deposition from the atmosphere. However, little is known about the environmental fate of these nanoparticles which may be susceptible to photochemical and microbial degradation. In the present work, C 60 was incubated for a period of 28 days and irradiated with UVA light. Three experiments were carried out where the fullerenes were either spiked onto a glass surface or added to quartz sand or sandy soil samples. At specific time intervals the samples were extracted and analysed by liquid chromatography coupled to UV or high resolution mass spectrometric (HRMS) detection. The fullerenes were degraded in all the treatments and the decay followed a pseudo-first-order rate law. In absence of a solid matrix, the half-life (t 1⁄2 ) of the C 60 was 13.1 days, with an overall degradation of 45.1% that was accompanied by the formation of functionalized C 60 -like structures. Furthermore, mass spectrometric analysis highlighted the presence of a large number of transformation products that were not directly related to the irradiation and presented opened cage and oxidized structures. When C 60 was spiked into solid matrices the degradation occurred at a faster rate (t 1⁄2 of 4.5 and 0.8 days for quartz sand and sandy soil, respectively). Minor but consistent losses were found in the non-irradiated samples, presumably due to biotic or chemical processes occurring in these samples. The results of this study suggest that light-mediated transformation of the fullerenes will occur in the environment., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

The study of not only main flame retardants but also of related degradation products or impurities has gained attention in the last years and is relevant to assess the safety of our consumer products and the emission of potential contaminants into the environment. In this study, we show that plastics casings of electric/electronic devices containing TBBPA contain also a complex mixture of related brominated chemicals. These compounds were most probably coming from impurities, byproducts, or degradation products of TBBPA and TBBPA derivatives. A total of 14 brominated compounds were identified based on accurate mass measurements (formulas and tentative structures proposed). The formulas (or number of bromine elements) for 19 other brominated compounds of minor intensity are also provided. A new script for the recognition of halogenated compounds based on combining a simplified isotope pattern and mass defect cluster analysis was developed in R for the screening. The identified compounds could be relevant from an environmental and industrial point of view.

Fullerenes are carbon based nanoparticles that may enter the environment as a consequence of both natural processes and human activities. Although little is known about the presence of these chemicals in the environment, recent studies suggested that soil may act as a sink. The aim of the present work was to investigate the presence of fullerenes in soils collected in The Netherlands. Samples (n = 91) were taken from 6 locations and analyzed using a new developed LC-QTOF-MS method. The locations included highly trafficked and industrialized as well as urban and natural areas. In general, C 60 was the most abundant fullerene found in the environment, detected in almost a half of the samples and at concentrations in the range of ng/kg. Other fullerenes such as C 70 and an unknown structure containing a C 60 cage were detected to a lower extent. The highest concentrations were found in the proximity of combustion sites such as a coal power plant and an incinerator, suggesting that the nanoparticles were unintentionally produced during combustions processes and reached the soil through atmospheric deposition. Consistent with other recent studies, these results show that fullerenes are widely present in the environment and that the main route for their entrance may be due to human activities. These data will be helpful in the understanding of the distribution of fullerenes in the environment and for the study of their behavior and fate in soil., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Amino acids are an important and highly dynamic fraction of organic N in soils and their determination in soil without derivatization is challenging due to the difficulties in separation and detection of trace amounts of these polar analytes. In the present work, we developed an analytical method to quantify 20 free amino acids in aqueous soil extracts without derivatization. The method employed hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) technique combined with a cation exchange solid phase extraction (SPE). Four stable isotope labelled amino acids were used as internal standards to improve the method performance. Good separation of 20 underivatized amino acids was achieved within 12min. The limit of detection (LODs) and limit of quantification (LOQs) were in the range of 13-384ngg(-1) and 43-1267ngg(-1) (dry soil basis), respectively. The results showed that overall recoveries with high precision were obtained for the extracted free amino acids from ten different soils. The overall recoveries of 18 amino acids were similar for the ten soils used, which differed substantially in organic C content and in other properties as soil texture and pH. For most of the amino acids, the average recoveries from soil extracts were between 74% and 117%, with the exception of Met (31%), Pro (52%) and Arg (68%). Variability was within acceptable limits (relative standard deviations were between 4% and 13%), with the exception of Met (relative standard deviation=90%) and Arg (relative standard deviation=53%). Thus the proposed method with high throughout and high analyte specificity shows great promise for consistent analysis of free amino acids extracted from soils and offers new horizons for the analysis of amino acids in terrestrial and aquatic ecosystem., (Copyright © 2016 Elsevier B.V. All rights reserved.)

The increasing production of fullerenes likely means a release of these chemicals in the environment. Since soils and sediments are expected to act as a sink, analytical tools are needed to assess the presence of fullerenes in these matrices. In the present work, a method was developed for the determination of fullerenes at environmental relevant levels employing Ultra High Performance Liquid Chromatograph coupled with High Resolution Mass Spectrometry (UHPLC-HRMS). Chromatographic separation was achieved with a core-shell biphenyl stationary phase that provided fast analysis with complete baseline separation. Ion Booster Electro Spray Ionization (IB-ESI) resulted in higher ionization efficiency and was much less susceptible to adduct formation in comparison with standard ESI, whereas Quadrupole Time of Flight (QTOF) MS granted high resolution mass spectra used for accurate identification. The Instrumental method limits of detection (ILoD) and quantification (ILoQ) were 6 and 20 fg, respectively, for C60 and 12 and 39 fg, respectively, for C70. Matrix effects related to co-extractants were systematically investigated in soil and sediments extracts through standard addition method (SAM) and monitoring the signal response during the chromatographic run of these samples. Consequently, minor chromatographic modifications were necessary for the analysis of matrices with high organic carbon content. The method limit of detection (MLoD)ranged from 84 pg/kg to 335 pg/kg, whereas limit of quantification (MLoQ) ranged from 279 pg/kg to 1.1 ng/kg. Furthermore, the method was successfully applied for the analysis of functionalized fullerenes (i.e. methanofullerenes). To the best of our knowledge, this is the first analytical method for the analysis of fullerenes in soils and sediments that employ core-shell biphenyl stationary phase as well as IB-ESI-QTOF MS hyphenated with UHPLC., (Copyright © 2016 Elsevier B.V. All rights reserved.)

High resolution mass spectrometry (HRMS) was successfully applied to elucidate the structure of a polyfluorinated polyether (PFPE)-based formulation. The mass spectrum generated from direct injection into the MS was examined by identifying the different repeating units manually and with the aid of an instrument data processor. Highly accurate mass spectral data enabled the calculation of higher-order mass defects. The different plots of MW and the nth-order mass defects (up to n = 3) could aid in assessing the structure of the different repeating units and estimating their absolute and relative number per molecule. The three major repeating units were -C2H4O-, -C2F4O-, and -CF2O-. Tandem MS was used to identify the end groups that appeared to be phosphates, as well as the possible distribution of the repeating units. Reversed-phase HPLC separated of the polymer molecules on the basis of number of nonpolar repeating units. The elucidated structure resembles the structure in the published manufacturer technical data. This analytical approach to the characterization of a PFPE-based formulation can serve as a guide in analyzing not just other PFPE-based formulations but also other fluorinated and non-fluorinated polymers. The information from MS is essential in studying the physico-chemical properties of PFPEs and can help in assessing the risks they pose to the environment and to human health. Graphical Abstract ᅟ.

Chlorantraniliprole (CAP) is a newly developed, widely applied insecticide. In the aquatic environment, several transformation products are formed under natural conditions, one by dehydration and others by photoinduced degradation. Data on aquatic ecotoxicity of CAP can mainly be found in registration and regulatory evaluation reports. Moreover, the toxicity of its transformation products and especially effects upon chronic exposure remain completely unknown. Hence, our aim was to investigate the acute and chronic toxicity of CAP and its transformation products to the daphnid Daphnia magna. The results showed that CAP is extremely toxic to D. magna, with an acute and chronic LC50 of 9.4 and 3.7 μg/L, respectively. No effects on daphnid reproduction were observed, but the impact on daphnid survival also affected population growth rate, with an EC50 of 3.5 μg/L. In contrast, no negative effects of the two main degradation products were observed. The present study demonstrated a high sensitivity of nontarget microcrustaceans to CAP. However, the actual risk of CAP in water diminishes with its spontaneous or light-induced degradation into two transformation products, showing no toxicity to the daphnids in the present study.

Halogen-free flame retardants (HFFRs), such as the aromatic organophosphorus flame retardants (OPFRs) triphenyl phosphate (TPHP), resorcinol bis(diphenylphosphate) (PBDPP) and bisphenol A bis(diphenylphosphate) (BPA-BDPP) have been proposed as potential replacements for brominated flame retardants in polymers and textiles. Although these OPFRs are already marketed, their environmental fate and effects are poorly characterised. The aim of this study was therefore to determine the mineralisation and primary biodegradation of these OPFRs by activated sludge. Mineralisation was monitored by measuring CO2 production by means of GC analysis, whereas primary biodegradation was monitored by LC-MS/MS analysis of the OPFRs and their potential metabolites. TPHP was biodegraded and mineralised most rapidly and achieved the requirement for ready biodegradability (60% of theoretical maximum mineralisation). Primary biodegradation was also rapid for PBDPP, but 60% mineralisation was not achieved within the time of the test, suggesting that transformation products of PBDPP may accumulate. Primary degradation of BPA-BDPP was very slow and very low CO2 production was also observed. Based on these results, TPHP and to a lesser extent PBDPP appear to be suitable replacements for the more environmentally persistent brominated flame retardants., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

There is a tendency to substitute frequently used, but relatively hazardous brominated flame retardants (BFRs) with halogen-free flame retardants (HFFRs). Consequently, information on the persistence, bioaccumulation and toxicity (PBT) of these HFFRs is urgently needed, but large data gaps and inconsistencies exist. Therefore, in the present study the toxicity of a wide range of HFFRs to the water flea Daphnia magna was investigated. Our results revealed that four HFFRs were showing no effect at their Sw (saturated water concentration) and three had a low toxicity (EC50>10 mg L(-1)), suggesting that these compounds are not hazardous. Antimony trioxide had a moderate toxicity (EC50=3.01 mg L(-1), 95% CL: 2.76-3.25) and triphenyl phosphate and the brominated reference compound tetra bromobisphenol A were highly toxic to D. magna (EC50=0.55 mg L(-1), 95% CL: 0.53-0.55 and EC50=0.60 mg L(-1), 95% CL: 0.24-0.97 respectively). Aluminum trihydroxide and bisphenol A bis(diphenyl phosphate) caused limited mortality at Sw (26 and 25% respectively) and have a low solubility (<10 mg L(-1)). Hence, increased toxicity of these compounds may be observed when for instance decreasing pH could increase solubility. By testing all compounds under identical conditions we provided missing insights in the environmental hazards of new generation flame retardants and propose as best candidates for BFR replacements: APP, ALPI, DOPO, MHO, MPP, ZHS and ZS., (© 2013 Elsevier B.V. All rights reserved.)

The lower gastrointestinal tract is a major mucosal site of HIV entry and initial infection. Thus, the induction of strong cellular immune responses at this mucosal site will be an important feature of an effective HIV vaccine. We have used a novel prime-boost vaccination approach to induce immune responses at mucosal sites. Orally delivered recombinant Clostridium perfringens expressing HIV-1 gag (Cp-Gag) was evaluated for induction of HIV-1 Gag specific T cell responses in a prime-boost model with intranasal inoculation of HIV-1 virus like particles (VLP). HIV-1 specific cellular immune responses in both the effector (Lamina propria) and inductive sites (Peyer's patches) of the gastrointestinal (GI) tract were significantly higher in mice immunized using Cp-Gag and VLPs in a prime-boost approach compared to mice immunized with either Cp-Gag or VLPs alone. Such cellular immune response was found to be mediated by both CD8(+) and CD4(+) T cells. Such a strong mucosal immune response could be very useful in developing a mucosal vaccine against HIV-1.

Clostridium perfringens is a normal bacterial flora of the small and large intestines of humans and other animals. The current study investigates the potential use of a noncytotoxic C. perfringens as an oral vaccine vehicle for expression and intestinal delivery of a large amount of SIV antigens. Here we report the construction of a recombinant C. perfringens vaccine vector expressing high levels of SIV p27 during sporulation. Following oral administration of this recombinant C. perfringens vaccine vector to mice, large amounts of intact p27 protein were detected in the terminal ileum where the majority of Peyer's Patches (PPs) are located. Furthermore, dendritic cells (DCs) beneath the mucosal surface in the PPs were able to capture SIV p27 antigen, when PPs were exposed to C. perfringens expressing SIV p27 antigen. In addition, uptake of C. perfringens was able to induce maturation of mouse DCs. These results support the potential use of C. perfringens as an oral SIV/HIV vaccine vector.