Understanding PFAS toxicity through cell culture metabolomics: Current applications and future perspectives

Per- and polyfluoroalkyl substances (PFAS), ubiquitous environmental contaminants, pose significant challenges to ecosystems and human health. While cell cultures have emerged as new approach methodologies (NAMs) in ecotoxicity research, metabolomics is an emerging technique used to characterize the small-molecule metabolites present in cells and to understand their role in various biological processes. Integration of metabolomics with cell cultures, known as cell culture metabolomics, provides a novel and robust tool to unravel the complex molecular responses induced by PFAS exposure. In vitro testing also reduces reliance on animal testing, aligning with ethical and regulatory imperatives. The current review summarizes key findings from recent studies utilizing cell culture metabolomics to investigate PFAS toxicity, highlighting alterations in metabolic pathways, biomarker identification, and the potential linkages between metabolic perturbations. Additionally, the paper discusses different types of cell cultures and metabolomics methods used for studies of environmental contaminants and particularly PFAS. Future perspectives on the combination of metabolomics with other advanced technologies, such as single-cell metabolomics (SCM), imaging mass spectrometry (IMS), extracellular flux analysis (EFA), and multi-omics are also explored, which offers a holistic understanding of environmental contaminants. The synthesis of current knowledge and identification of research gaps provide a foundation for future investigations that aim to elucidate the complexities of PFAS-induced cellular responses and contribute to the development of effective strategies for mitigating their adverse effects on human health.

Flexible molecularly imprinted fiber library for the metabolic analysis of bisphenol F and ecological risk evaluation

Bisphenol F (BPF) has evoked global attentions due to its ubiquity and detrimental effects. Herein, a flexible molecularly imprinted fiber library was firstly proposed for the metabolic analysis of BPF in aquatic ecosystems. The library includes flexible single fibers and fiber arrays to precisely identify BPF and its metabolites with a wide range of polarities. Compared to commercial polyacrylate, the performance increased 11.56-570.98-fold. The adsorption capacity and the LogKow value were positively related. These arrays were used for the acquisition of environmental metabolomics data from aquatic ecosystems. In-depth data analysis showed that risk quotient was lower than 0.76, and bioaccumulation factor was lower than 2000 L/kg. Distribution concentration of BPF and its metabolites changed seasonally, and accumulation in sediment was much larger than that in surface water and hydrobionts. The risk is gradually increasing in sediment, but it does not reach high risk. The likelihood of bioaccumulation of parent compounds was greater than its metabolites. The library can be used in the metabolic diagnosis of pollutants with a broad range of polarities, providing a new method to acquire data for further ecological risk assessment, and offering a revolutionary strategy for environmental metabolomics investigation in aquatic ecosystems.

Evidence of interregional similarity in crayfish metabolomes at reference sites: Progress towards the metabolome as a biomonitoring tool

It has been proposed that biomonitoring may benefit from the use of metabolomics (the study of all small molecules in an organism) to detect sub-lethal organism stress through changes in the metabolite profile (i.e., the metabolome). However, to integrate the metabolome into biomonitoring programs the amount of natural variability among and within populations of indicator taxa must be established prior to generating a reference condition. This study determined variation in the metabolome among ecoregion and stream of origin in the northern crayfish (Faxonius virilis) and if that variation inhibited detection of stressor effects at sites exposed to human activities. We collected crayfish from seven minimally disturbed streams (i.e., reference streams), distributed across three level II ecoregions in central Canada and compared their metabolomes. We found ecoregion and stream origin were poor predictors of crayfish metabolomes. This result suggests crayfish metabolomes were similar, despite differing environmental conditions. Metabolomes of crayfish collected from three stream sites exposed to agricultural activity and municipal wastewater (i.e., test sites) were then compared to the crayfish metabolomes from the seven reference streams. Findings showed that crayfish metabolomes from test sites were strongly differentiated from those at all reference sites. The consistency in the northern crayfish metabolome at the studied reference streams indicates that a single reference condition may effectively detect impacts of human activities across the sampled ecoregions.

In vivo environmental metabolomic profiling via a novel microextraction fiber unravels sublethal effects of environmental norfloxacin in gut bacteria

Emerging contaminants (ECs), especially antibiotics, have significantly polluted the environment and threaten the living circumstance of organisms. Environmental metabolomic has emerged to investigate the sublethal effects of ECs. However, lacking noninvasive and real-time sample pretreatment techniques restricts its development in environmental toxicology. Hence, in this study, a real-time and in vivo untargeted analytical technique towards microbial endogenous metabolites was developed via a novel composite solid-phase microextraction (SPME) fiber of ZIF-67 and polystyrene to realize the high-coverage capture of living gut microbial metabolites. To reveal the exposure risks of typical antibiotic - norfloxacin (NFX) to gut bacteria, four representative bacteria were exposed to NFX at environmentally relevant levels. Using the proposed SPME fiber, 70 metabolites were identified to obtain an apparent metabolic separation feature between control and NFX-treated (10 ng/mL) microbial groups, which revealed that the low environmental relevant concentration of NFX would affect normal metabolism of gut bacteria. Additionally, NFX exhibited species-specific toxic effects on microbial growth, especially Escherichia coli displaying a distinct dose-dependent trend. Antioxidative enzymatic activities results demonstrated that beneficial bacteria maintained the state of oxidative stress while symbiotic bacteria suffered from oxidative stress injury under NFX contamination, further corroborating its impact on human intestinal health. This study highlights the suitability of in vivo SPME in the field of metabolite extraction and simultaneously possesses a brilliant application foreground in the environmental metabolomics.

Tomato Cultivar Nyagous Fruit Surface Metabolite Changes during Ripening Affect Salmonella Newport

ABSTRACT

Tomatoes are a valuable crop consumed year-round. Ripe fruit is picked for local sale, whereas tomatoes intended for transit may be harvested at late mature green or breaker stages when fruit firmness preserves quality. In this study, we evaluated Solanum lycopersicum cv. BHN602 association with three Salmonella serotypes and S. lycopersicum cv. Nyagous with Salmonella Newport using fruit at two ripeness stages. Counts of Salmonella Javiana and Typhimurium were higher from red ripe fruit surfaces of BHN602, and counts of Salmonella Newport were higher from ripe Nyagous fruit than from mature green fruit (P < 0.05). Aqueous fruit washes containing fruit surface compounds collected from ripe Nyagous fruit supported more Salmonella Newport growth than green fruit washes (P < 0.05). Growth curve analysis showed that between 2 and 6 h, Salmonella Newport grew at a rate of 0.25 log CFU/h in red fruit wash compared with 0.17 log CFU/h in green fruit wash (P < 0.05). The parallel trend in Salmonella interaction between fruit and wash suggested that surface metabolite differences between unripe and ripe fruit affect Salmonella dynamics. Untargeted phytochemical profiling of tomato fruit surface washes with gas chromatography time-of-flight mass spectrometry showed that ripe fruit had threefold-lower amino acid and fourfold-higher sugar (fructose, glucose, and xylose) levels than green fruit. Green fruit had higher levels of lauric, palmitic, margaric, and arachidic acids, whereas red fruit had more capric acid. The phenolics ferulic, chlorogenic, and vanillic acid, as well as tyrosol, also decreased with ripening. Although limitations of this study preclude conclusions on how specific compounds affect Salmonella, our study highlights the complexity of the plant niche for foodborne pathogens and the importance of understanding the metabolite landscape Salmonella encounters on fresh produce. Fruit surface phytochemical profiling generated testable hypotheses for future studies exploring the differential Salmonella interactions with tomato varieties and fruit at various ripeness stages.

HIGHLIGHTS

Comparison of sub-lethal metabolic perturbations of select legacy and novel perfluorinated alkyl substances (PFAS) in Daphnia magna

Per- and polyfluoroalkyl substances (PFAS) are a class of pollutants of concern due to their ubiquitous presence, persistence, and toxicity in aquatic environments. Legacy PFAS pollutants such as perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) have been more widely studied in aquatic environments. However, replacement PFAS, such as ammonium perfluoro (2-methyl-3-oxahexanoate; GenX) are increasingly being detected with little known information surrounding their toxicity. Here, Daphnia magna, a model organism for freshwater ecotoxicology was used to compare the acute sub-lethal toxicity of PFOS, PFOA, GenX, and PFAS mixtures. Using liquid chromatography with tandem mass spectrometry (LC-MS/MS), the targeted polar metabolic profile extracted from single Daphnia was quantified to investigate perturbations in the exposure groups versus the unexposed organisms. Multivariate statistical analyses demonstrated significant non-monotonic separation in PFOA, GenX, and PFAS mixture exposures. Sub-lethal exposure to concentrations of PFOS did not lead to significant separation in multivariate analyses. Univariate statistics and pathway analyses were used to elucidate the mode of action of PFAS exposure. Exposure to all individual PFAS led to significant perturbations in many amino acids including cysteine, histidine, tryptophan, glycine, and serine. These perturbations are consistent with biochemical pathway disruptions in the pantothenate and Coenzyme A (CoA) biosynthesis, thiamine metabolism, histidine metabolism, and aminoacyl-tRNA biosynthesis pathways. Overall, the collected metabolomic data is consistent with disruptions in energy metabolism and protein synthesis as the primary mode of action of sub-lethal PFAS exposure. Secondary modes of action among individual pollutant exposures demonstrated that the structural properties (carboxylic acid vs. sulfonic acid group) may play a role in the metabolic perturbations observed. Sub-lethal exposure to PFAS mixtures highlighted a mixed response when compared to the individual pollutants (PFOS, PFOA, and GenX). Overall, this study emphasizes the niche capability of environmental metabolomics to differentiate secondary modes of action from metabolic perturbations in both single pollutant and pollutant mixtures within the same chemical class.

Assessment of the effectiveness of a novel BioFilm-Membrane BioReactor oil-polluted wastewater treatment technology by applying biomarkers in the mussel Mytilus galloprovincialis

Petrochemical industries and oil refineries are sources of hazardous chemicals into the aquatic environments, and often a leading cause of reduced oxygen availability, thus resulting in adverse effects in biota. This study is an expansion of our previous work on the assessment of the BioFilm-Membrane Bioreactor (BF-MBR) to mitigate the impact of oil-polluted wastewater on marine environments. Specifically, this study evaluated the reduction of selected chemical constituents (hydrocarbons and trace metals) and toxicity related to hypoxia and DNA damage to mussels Mytilus galloprovincialis, before and after treatment of oil-polluted wastewater with the BF-MBR. The application of a multidisciplinary approach provided evidence of the efficiency of BF-MBR to significantly reducing the pollutants load from oily contaminated seawaters. As result, the health status of mussels was preserved by a hypoxic condition due to oily pollutants, as evidenced by the modulation in the gene expression of HIF-1α and PHD and changes in the level of hypotaurine and taurine. Moreover, ameliorative effects in the energy metabolism were also found in mussel gills showing increased levels of glycogen, glucose and ATP, as well as a mitigated genotoxicity was revealed by the Micronucleus and Comet assays. Overall, findings from this study support the use of the BF-MBR as a promising treatment biotechnology to avoid or limiting the compromise of marine environments from oil pollution.

Functional analysis of pristine estuarine marine sediments

Traditional environmental monitoring techniques are well suited to resolving acute exposure effects but lack resolution in determining subtle shifts in ecosystem functions resulting from chronic exposure(s). Surveillance with sensitive omics-based technologies could bridge this gap but, to date, most omics-based environmental studies have focused on previously degraded environments, identifying key metabolic differences resulting from anthropogenic perturbations. Here, we apply omics-based approaches to pristine environments to establish blueprints of microbial functionality within healthy estuarine sediment communities. We collected surface sediments (n = 50) from four pristine estuaries along the Western Cape York Peninsula of Far North Queensland, Australia. Sediment microbiomes were analyzed for 16S rRNA amplicon sequences, central carbon metabolism metabolites and associated secondary metabolites via targeted and untargeted metabolic profiling methods. Multivariate statistical analyses indicated heterogeneity among all the sampled estuaries, however, taxa-function relationships could be established that predicted community metabolism potential. Twenty-four correlated gene-metabolite pathways were identified and used to establish sediment microbial blueprints of essential carbon metabolism and amino acid biosynthesis that were positively correlated with community metabolic function outputs (2-oxisocapraote, tryptophan, histidine citrulline and succinic acid). In addition, an increase in the 125 KEGG genes related to metal homeostasis and metal resistance was observed, although, none of the detected metabolites related to these specific genes upon integration. However, there was a correlation between metal abundance and functional genes related to Fe and Zn metabolism. Our results establish a baseline microbial blueprint for the pristine sediment microbiome, one that drives important ecosystem services and to which future ecosurveillance monitoring can be compared.

Crayfish tissue metabolomes effectively distinguish impacts of wastewater and agriculture in aquatic ecosystems

Environmental metabolomics has been proposed as a tool for biomonitoring because organisms regulate production or consumption of metabolites in response to environmental conditions. We evaluated the efficacy of the metabolome of three tissues (hepatopancreas, gill, and tail muscle) from the northern crayfish (Faxonius virilis) to detect and differentiate between impacts of human activities (i.e., reference, municipal wastewater, and agriculture). We conducted a reciprocal transfer study exposing crayfish for 1 or 2 weeks in three streams with different amounts and types of human activities in southern Manitoba, Canada. Tissue samples were analyzed using nuclear magnetic resonance spectroscopy to generate a metabolic profile. Findings indicated the gill tissue metabolome best detected and differentiated between human activities. In particular, the gill metabolome was able to rapidly integrate abrupt changes in environmental conditions associated with municipal wastewater activity. In contrast, the tail metabolome best differentiated between crayfish collected at the reference site from those collected at the two impacted sites. Metabolites extracted from hepatopancreas tissue showed limited and inconsistent detection of among site differences. Based on our findings, we conclude that the metabolome of the northern crayfish can be an effective biomonitoring tool, but monitoring purpose will dictate tissue selection. Indeed, we recommend the gill metabolome be used for short-term assays aimed at detecting acute effects, whereas the tail be applied for survey monitoring aimed at detecting deviations in ecological condition at test sites from reference site conditions.

Reproduction stage specific dysregulation of Daphnia magna metabolites as an early indicator of reproductive endocrine disruption

Rapid biomolecular observation in model indicator organisms has been considered as a potential predictor of water pollution from chronic and trace toxicants. This study evaluated the use of Daphnia magna metabolomic measurements as indicators for exposure to reproductive endocrine disruptors by using the model juvenile hormone analogue fenoxycarb. Because D. magna reproduction controls metabolic regulation, the reproduction stage was also carefully considered in metabolic observations and data analysis to examine differences. Comparisons of metabolite abundance regulation between 1 and 12 days of fenoxycarb exposure were performed to investigate the predictability of the sub-chronic (12 days) adverse impacts on reproduction and metabolic regulation based on acute (1 day) metabolic observations. ANOVA-simultaneous component analysis (ASCA) detected reversed patterns in direction of time-course metabolite abundance regulation with fenoxycarb exposure. For example, decreases in the abundances of leucine, asparagine, methionine, and isoleucine which then changed to increases were observed with time during fenoxycarb exposures. The reversed regulation pattern was observed at the last reproduction stage (stage 3), exclusively. Pearson correlation analysis showed that correlations of pairwise metabolites were disrupted with fenoxycarb exposure. Similar to ASCA, data normalization based on the reproduction stage improved the detectability of significant correlations. The disruption on ambient metabolite regulation patterns and pairwise metabolite correlations was consistently observed with both 1 and 12 days of fenoxycarb exposures for sets of select metabolites. The observed regulatory disruptions to these specific metabolites suggest altered oogenesis as the affected metabolites and the specific reproduction stage are related to successful oogenesis. This study demonstrates that D. magna metabolic dysregulation is a predictor of water contamination by endocrine disrupting compounds. The high predictability of sub-chronic (12 days) endocrine disruption was confirmed based on acute (1 day) metabolic observations. Furthermore, integration of the reproduction cycle information in D. magna metabolomics was validated by observing a reproduction stage specific dysregulation in metabolite abundance regulation, which was not observable from the broader data analysis. Consequently, this study confirms the potential for establishing a quantitative relationship between water quality and indicator species metabolic observations. Additionally, it was found that constraining variables relevant to toxicity mechanisms of interest, such as the reproduction stage, is a key consideration for extraction of ecologically meaningful information in environmental metabolomics.

Antioxidant defenses and metabolic responses of blue mussels (Mytilus edulis) exposed to various concentrations of erythromycin

Erythromycin, one of the most widely used macrolide antibiotics, has been detected in various aquatic environments, so erythromycin ecotoxicity should deserve more attention. In this study, blue mussels (Mytilus edulis) were exposed to erythromycin to explore its potential physiological toxicity. After 2d acute and 7d sub-acute exposure to erythromycin, blue mussel glutathione S-transferase (GST) and catalase (CAT) activities were determined with microplate methods and metabolic responses were analyzed using ¹H nuclear magnetic resonance (¹H NMR). The results revealed that GST was approximately 1.6 times higher in exposed mussels at 200 mg/L and higher concentrations. CAT was about 1.9 times higher in exposed mussels at 200 mg/L, indicating that erythromycin exposure led that blue mussels enhanced antioxidant responses. Low doses of erythromycin exposure had a relatively small impact on the metabolism, while high doses of erythromycin exposure (200 and 400 mg/L) disturbed metabolic balance. With the increase of erythromycin concentrations, the individual metabolic differences within the same treatment groups also increased. The significant increase in alanine, glutamate, taurine, glycine and betaine were observed after acute and subacute exposure. Betaine played an important role in protecting antioxidant enzyme activities through adjusting osmotic pressure. The metabolomic results also showed the modes of erythromycin acted on the energy metabolism, osmoregulation, nerve activities and amino acid metabolism. This study highlighted how metabolomics can provide a comprehensive picture of metabolic responses, although significant antioxidant and metabolic responses were observed at high exposure concentrations.

Metabolite biomarkers of chlorothalonil exposure in earthworms, coelomic fluid, and coelomocytes

Earthworm (Eisenia fetida) metabolomics is a useful indicator of toxicant exposure. Extracts of whole earthworms are most commonly used to measure metabolic perturbations, in addition to coelomic fluid which has been used on a more limited basis. Coelomocytes are free moving cells found within earthworm coelomic fluid, and the potential of this compartment has not been evaluated for its utility in earthworm metabolomics. In this study, earthworms were exposed to 18.5 and 37.0 mg/kg chlorothalonil, a commonly used fungicide that targets glutathione. The metabolic impacts of a 14-day chlorothalonil exposure were assessed using ¹H NMR and targeted LC-MS measurements of earthworm, coelomic fluid, and coelomocyte extracts. Coelomic fluid was identified as the most sensitive matrix for measuring the effects of chlorothalonil exposure, where an increase in glutamine levels was the only biomarker observed at both doses. At the high dose, multiblocked-orthogonal partial least squares-discriminant analysis (MB-OPLS-DA) supported increased N-acetylserine and ophthalmic acid levels as additional biomarkers of exposure in coelomic fluid. These perturbations may indicate increased oxidative stress, although no changes in glutathione were observed in any matrix.

Using metabolomics to assess the sub-lethal effects of zinc and boscalid on an estuarine polychaete worm over time

INTRODUCTION

Zinc is a heavy metal commonly detected in urban estuaries around Australia. Boscalid is a fungicide found in estuaries, both in water and sediment, it enters the system predominantly through agricultural run-off. Zinc is persistent while boscalid breaks down, with a half-life of 108 days. Both contaminants are widely distributed and their effects on ecosystems are not well understood.

OBJECTIVES

The aim of this study was to determine the metabolite changes in Simplisetia aequisetis (an estuarine polychaete) following laboratory exposure to a sub-lethal concentration of zinc or boscalid over a 2-week period.

METHODS

Individuals were collected at six time points over a 2-week period. Whole polychaete metabolites were extracted and quantified using a multi-platform approach. Polar metabolites were detected using a semi-targeted GC-MS analysis and amine containing compounds were analysed using a targeted LC-MS analysis. Total lipid energy content was also analysed for Simplisetia aequisetis.

RESULTS

The pathways that responded to zinc and boscalid exposure were alanine, aspartate and glutamate metabolism (AAG); glycine, serine and threonine metabolism (GST) and metabolites associated with the tricarboxylic acid cycle (TCA). Results showed that changes in total abundance of some metabolites could be detected as early as 24-h exposure. Changes were detected in the metabolites before commonly used total lipid energy assays identified effects.

CONCLUSION

A multi-platform approach provided a holistic overview of the metabolomic response to contaminants in polychaetes. This approach shows promise to be used in biomonitoring programs to provide early diagnostic indicators of contamination and exposure.

Evaluating sub-lethal stress from Roundup® exposure in Artemia franciscana using 1H NMR and GC-MS

Global salinization trends present an urgent need for methods to monitor aquatic ecosystem health and characterize known and emerging stressors for water bodies that are becoming increasingly saline. Environmental metabolomics methods that combine quantitative measurements of metabolite levels and multivariate statistical analysis are powerful tools for ascertaining biological impacts and identifying potential biomarkers of exposure. We propose the use of the saltwater aquatic crustacean, Artemia franciscana, as a model organism for environmental metabolomics in saltwater ecosystems. Artemia are a good choice for ecotoxicity assays and metabolomics analysis because they have a short life cycle, their hemolymph is rich in metabolites and they tolerate a wide salinity range. In this work we explore the potential of Artemia franciscana for environmental metabolomics through exposure to the broad-spectrum herbicide, glyphosate. The LC50 for a 48 h exposure of Roundup® was determined to be 237 ± 23 ppm glyphosate in the Roundup® formulation. Artemia cysts were hatched and exposed to sub-lethal glyphosate concentrations of 1.00, 10.0, 50.0, or 100 ppm glyphosate in Roundup®. We profiled 48 h old Artemia extracts using 1H NMR and GC-MS. Dose-dependent metabolic perturbation was evident for several metabolites using univariate and multivariate analyses. Metabolites significantly affected by Roundup® exposure included aspartate, formate, betaine, glucose, tyrosine, phenylalanine, gadusol, and isopropylamine. Biochemical pathway analysis with the KEGG database suggests impairment of carbohydrate and energy metabolism, folate-mediated one-carbon metabolism, Artemia molting and development, and microbial metabolism.

Lipidomics for wildlife disease etiology and biomarker discovery: a case study of pansteatitis outbreak in South Africa

INTRODUCTION

Lipidomics is an emerging field with great promise for biomarker and mechanistic studies due to lipids diverse biological roles. Clinical research applying lipidomics is drastically increasing, with research methods and tools developed for clinical applications equally promising for wildlife studies.

OBJECTIVES

Limited research to date has applied lipidomics, especially of the intact lipidome, to wildlife studies. Therefore, we examine the application of lipidomics for in situ studies on Mozambique tilapia (Oreochromis mossambicus) in Loskop Dam, South Africa. Wide-scale mortality events of aquatic life associated with an environmentally-derived inflammatory disease, pansteatitis, have occurred in this area.

METHODS

The lipidome of adipose tissue (n = 31) and plasma (n = 51) from tilapia collected from Loskop Dam were characterized using state of the art liquid chromatography coupled to high-resolution tandem mass spectrometry.

RESULTS

Lipid profiles reflected pansteatitis severity and were significantly different between diseased and healthy individuals. Over 13 classes of lipids associated with inflammation, cell death, and/or oxidative damage were upregulated in pansteatitis-affected adipose tissue, including ether-lipids, short-chained triglyceride oxidation products, sphingolipids, and acylcarnitines. Ceramides showed a 1000-fold increase in the most affected adipose tissues and were sensitive to disease severity. In plasma, triglycerides were found to be downregulated in pansteatitis-affected tilapia.

CONCLUSION

Intact lipidomics provided useful mechanistic data and possible biomarkers of pansteatitis. Lipids pointed to upregulated inflammatory pathways, and ceramides serve as promising biomarker candidates for pansteatitis. As comprehensive coverage of the lipidome aids in the elucidation of possible disease mechanisms, application of lipidomics could be applied to the understanding of other environmentally-derived inflammatory conditions, such as those caused by obesogens.

Metabolomics approaches for the discrimination of disease suppressive soils for Rhizoctonia solani AG8 in cereal crops using 1H NMR and LC-MS

The suppression of soilborne crop pathogens such as Rhizoctonia solani AG8 may offer a sustainable and enduring method for disease control, though soils with these properties are difficult to identify. In this study, we analysed the soil metabolic profiles of suppressive and non-suppressive soils over 2 years of cereal production. We collected bulk and rhizosphere soil at different cropping stages and subjected soil extracts to liquid chromatography-mass spectrometry (LC-MS) and proton nuclear magnetic resonance spectroscopy (¹H NMR) analyses. Community analyses of suppressive and non-suppressive soils using principal component analyses and predictive modelling of LC-MS and NMR datasets respectively, revealed distinct biochemical profiles for the two soil types with clustering based on suppressiveness and cropping stage. NMR spectra revealed the suppressive soils to be more abundant in sugar molecules than non-suppressive soils, which were more abundant in lipids and terpenes. LC-MS features that were significantly more abundant in the suppressive soil were identified and assessed as potential biomarkers for disease suppression. The structures of a potential class of LC-MS biomarkers were elucidated using accurate mass data and MS fragmentation spectrum information. The most abundant compound found in association with suppressive soils was confirmed to be a macrocarpal, which is an antimicrobial secondary metabolite. Our study has demonstrated the utility of environmental metabolomics for the study of disease suppressive soils, resulting in the discovery of a macrocarpal biomarker for R. solani AG8 suppressive soil which can be further studied functionally in association with suppression pot trials and microbial isolation studies.

Evaluation of Daphnia magna metabolic responses to organic contaminant exposure with and without dissolved organic matter using 1H nuclear magnetic resonance (NMR)-based metabolomics

Previous studies have shown that contaminant toxicity to target organisms is altered by the presence of dissolved organic matter (DOM). Contaminants can bind to DOM and this may alter the bioavailability and subsequent toxicity of the contaminants. However, molecular-level techniques are needed to more closely evaluate the impact of DOM on the sub-lethal biochemical responses to emerging contaminants. To investigate how DOM may alter the metabolic response to organic contaminant exposure, ¹H nuclear magnetic resonance (NMR)-based metabolomics was used to investigate how the metabolome of Daphnia magna changes when Suwannee River DOM (5 mg organic carbon/L) is included in the acute exposure of four contaminants with varying hydrophobicity. Sub-lethal concentrations of the hydrophobic contaminant 17α-ethynylestradiol (EE2), the relatively more polar compounds carbamazepine and imidacloprid, or the anionic contaminant perfluorooctane sulfonate (PFOS) were used. A 48-h exposure to DOM alone had a minor impact on the metabolome of D. magna. There were significant increases in amino acids from EE2 exposure which were reduced in the presence of DOM, suggesting that DOM may alleviate the sub-lethal metabolic response from EE2 exposure through sorption and a reduction in freely dissolved EE2. The metabolome was relatively unaltered with exposure to carbamazepine and imidacloprid in the presence of DOM which is likely because these contaminants are water soluble and did not strongly interact with DOM. PFOS exposure resulted in a more significant metabolic response with DOM suggesting that DOM enhanced the uptake and bioavailability of PFOS in D. magna. As such, the presence of DOM should be considered when determining sensitive molecular-level changes in organisms to sub-lethal organic contaminant exposure.

Metabolomic responses to sublethal contaminant exposure in neonate and adult Daphnia magna

The use of consumer products and pharmaceuticals that act as contaminants entering waterways through runoff and wastewater effluents alters aquatic ecosystem health. Traditional toxicological endpoints may underestimate the toxicity of contaminants, as lethal concentrations are often orders of magnitude higher than those found within freshwater ecosystems. While newer techniques examine the metabolic responses of sublethal contaminant exposure, there has been no direct comparison with ontogeny in Daphnia. It was hypothesized that Daphnia magna would have distinct metabolic changes after 3 different sublethal contaminant exposures, because of differences in the toxic mode of action and ontogeny. To test this hypothesis, the proton nuclear magnetic resonance metabolomic profiles were measured in D. magna aged day 0 and 18 after exposure to 28% of the lethal concentration of 50% of organisms tested (LC50) of atrazine, propranolol, and perfluorooctanesulfonic acid (PFOS) for 48 h. Principal component analysis revealed significant separation of contaminants from the control daphnids in both neonates and adults exposed to propranolol and PFOS. In contrast, atrazine exposure caused separation from the controls in only the adult D. magna. Minimal ontogenetic changes in the targeted metabolites were seen after exposure to propranolol. For both atrazine and PFOS exposures ontogeny exhibited unique changes in the targeted metabolites. These results indicate that, depending on the contaminant studied, neonates and adults respond uniquely to sublethal contaminant exposure. Environ Toxicol Chem 2017;36:938-946. © 2016 SETAC.

Significance of metabolite extraction method for evaluating sulfamethazine toxicity in adult zebrafish using metabolomics

Recently, environmental metabolomics has been introduced as a next generation environmental toxicity method which helps in evaluating toxicity of bioactive compounds to non-target organisms. In general, efficient metabolite extraction from target cells is one of the keys to success to better understand the effects of toxic substances to organisms. In this regard, the aim of this study is (1) to compare two sample extraction methods in terms of abundance and quality of metabolites and (2) investigate how this could lead to difference in data interpretation using pathway analysis. For this purpose, the antibiotic sulfamethazine and zebrafish (Danio rerio) were selected as model toxic substance and target organism, respectively. The zebrafish was exposed to four different sulfamethazine concentrations (0, 10, 30, and 50mg/L) for 72h. Metabolites were extracted using two different methods (Bligh and Dyer and solid-phase extraction). A total of 13,538 and 12,469 features were detected using quadrupole time-of-flight liquid chromatography mass spectrometry (QTOF LC-MS). Of these metabolites, 4278 (Bligh and Dyer) and 332 (solid phase extraction) were found to be significant after false discovery rate adjustment at a significance threshold of 0.01. Metlin and KEGG pathway analysis showed comprehensive information from fish samples extracted using Bligh and Dyer compared to solid phase extraction. This study shows that proper selection of sample extraction method is critically important for interpreting and analyzing the toxicity data of organisms when metabolomics is applied.

Omics technologies and their applications to evaluate metal toxicity in mice M. spretus as a bioindicator

Metals are important components of living organisms since many biological functions critically depend on their interaction with some metal in the cell. However, human activities have increased toxic metal levels in the terrestrial and aquatic ecosystems affecting living organisms. The impact of metals on cellular metabolism and global homeostasis has been traditionally assessed in free-living organisms by using conventional biomarkers; however, to obtain a global vision of metal toxicity mechanisms and the responses that metals elicit in the organisms, new analytical methodologies are needed. We review the use of omics approaches to assess the response of living organisms under metal stress illustrating the possibilities of different methodologies on the basis of our previous results. Most of this research has been based on free-living mice Mus spretus, a conventional bioindicator used to monitor metal pollution in Doñana National Park (DNP) (SW Spain), which is an important European biological reserve for migrating birds affected by agricultural, mining and industrial activities. The benefits of using omic techniques such as heterologous microarrays, proteomics methodologies (2-DE, iTRAQ®), metallomics, ionomics or metabolomics has been remarked; however, the complexity of these areas requires the integration of omics to achieve a comprehensive assessment of their environmental status. This article is part of a Special Issue entitled: Environmental and structural proteomics.

BIOLOGICAL SIGNIFICANCE

This work presents new contributions in the study of environmental metal pollution in terrestrial ecosystems using Mus spretus mice as bioindicator in Doñana National Park (SW Spain) and surroundings. In addition, it has been demonstrated that the integration of omics multi-analytical approaches provides a very suitable approach for the study of the biological response and metal interactions in exposed and free-living mice (Mus musculus and Mus spretus, respectively) under metal pollution.

Liquid chromatography time of flight mass spectrometry based environmental metabolomics for the analysis of Pseudomonas putida Bacteria in potable water

Water supply biofilms have the potential to harbour waterborne diseases, accelerate corrosion, and contribute to the formation of tuberculation in metallic pipes. One particular species of bacteria known to be found in the water supply networks is Pseudomonas sp., with the presence of Pseudomonas putida being isolated to iron pipe tubercles. Current methods for detecting and analysis pipe biofilms are time consuming and expensive. The application of metabolomics techniques could provide an alternative method for assessing biofilm risk more efficiently based on bacterial activity. As such, this paper investigates the application of metabolomic techniques and provides a proof-of-concept application using liquid chromatography coupled with time-of-flight mass spectrometry (LC-ToF-MS) to three biologically independent P. putida samples, across five different growth conditions exposed to solid and soluble iron (Fe). Analysis of the samples in +ESI and -ESI mode yielded 887 and 1789 metabolite features, respectively. Chemometric analysis of the +ESI and -ESI data identified 34 and 39 significant metabolite features, respectively, where features were considered significant if the fold change was greater than 2 and obtained a p-value less than 0.05. Metabolite features were subsequently identified according to the Metabolomics Standard Initiative (MSI) Chemical Analysis Workgroup using analytical standards and standard online LC-MS databases. Possible markers for P. putida growth, with and without being exposed to solid and soluble Fe, were identified from a diverse range of different chemical classes of metabolites including nucleobases, nucleosides, dipeptides, tripeptides, amino acids, fatty acids, sugars, and phospholipids.

Impact of environmental pollution on caged mussels Mytilus galloprovincialis using NMR-based metabolomics

Metabolic responses to environmental pollution, mainly related to Hg and PAHs, were investigated in mussels. Specimens of Mytilus galloprovincialis, sedentary filter-feeders, were caged in anthropogenic-impacted and reference sites along the Augusta coastline (Sicily, Italy). The gills, mainly involved in nutrient uptake, digestion and gas exchange, were selected as target organ being the first organ to be affected by pollutants. Severe alterations in gill tissue were observed in mussels from the industrial area compared with control, while gill metabolic profiles, obtained by (1)H NMR spectroscopy and analyzed by multivariate statistics, exhibited significant changes in amino acids, energy metabolites, osmolytes and neurotransmitters. Overall, the morphological changes and metabolic disturbance detected in gill tissues may suggest that the mussels transplanted to the contaminated field site were suffering from adverse environmental condition. The concurrent morphological and metabolomic investigations as applied here result effective in assessing the environmental influences on health status of aquatic organisms.

Metabolomics in plant environmental physiology

Changes in plant metabolism are at the heart of plant developmental processes, underpinning many of the ways in which plants respond to the environment. As such, the comprehensive study of plant metabolism, or metabolomics, is highly valuable in identifying phenotypic effects of abiotic and biotic stresses on plants. When study is in reference to analysing samples that are relevant to environmental or ecologically based hypotheses, it is termed 'environmental metabolomics'. The emergence of environmental metabolomics as one of the latest of the omics technologies has been one of the most critically important recent developments in plant physiology. Its applications broach the entire landscape of plant ecology, from the understanding of plant plasticity and adaptation through to community composition and even genetic modification in crops. The multitude of novel studies published utilizing metabolomics methods employ a variety of techniques, from the initial stages of tissue sampling, through to sample preservation, transportation, and analysis. This review introduces the concept and applications of plant environmental metabolomics as an ecologically important investigative tool. It examines the main techniques used in situ within field sites, with particular reference to sampling and processing, and those more appropriate for use in laboratory-based settings with emphasis on secondary metabolite analysis.