Editorial trend: adverse outcome pathway (AOP) and computational strategy - towards new perspectives in ecotoxicology

The adverse outcome pathway (AOP) has been conceptualized in 2010 as an analytical construct to describe a sequential chain of causal links between key events, from a molecular initiating event leading to an adverse outcome (AO), considering several levels of biological organization. An AOP aims to identify and organize available knowledge about toxic effects of chemicals and drugs, either in ecotoxicology or toxicology, and it can be helpful in both basic and applied research and serve as a decision-making tool in support of regulatory risk assessment. The AOP concept has evolved since its introduction, and recent research in toxicology, based on integrative systems biology and artificial intelligence, gave it a new dimension. This innovative in silico strategy can help to decipher mechanisms of action and AOP and offers new perspectives in AOP development. However, to date, this strategy has not yet been applied to ecotoxicology. In this context, the main objective of this short article is to discuss the relevance and feasibility of transferring this strategy to ecotoxicology. One of the challenges to be discussed is the level of organisation that is relevant to address for the AO (population/community). This strategy also offers many advantages that could be fruitful in ecotoxicology and overcome the lack of time, such as the rapid identification of data available at a time t, or the identification of "data gaps". Finally, this article proposes a step forward with suggested priority topics in ecotoxicology that could benefit from this strategy.

Bioaccumulation and molecular effects of carbamazepine and methylmercury co-exposure in males of Dreissena polymorpha

Dreissena polymorpha is a bivalve promising for biomonitoring in freshwater ecosystems thanks to its abundance and high filtration activity allowing rapid uptake of toxicants and identification of their negative effects. Nonetheless, we still lack knowledge on its molecular responses to stress under realistic scenario, e.g. multi-contamination. Carbamazepine (CBZ) and Hg are ubiquitous pollutants sharing molecular toxicity pathways, e.g. oxidative stress. A previous study in zebra mussels showed their co-exposure to cause more alterations than single exposures, but molecular toxicity pathways remained unidentified. D. polymorpha was exposed 24 h (T24) and 72 h (T72) to CBZ (6.1 ± 0.1 μg L-1), MeHg (430 ± 10 ng L-1) and the co-exposure (6.1 ± 0.1 μg L-1CBZ and 500 ± 10 ng L-1 MeHg) at concentrations representative of polluted areas (~10× EQS). RedOx system at the gene and enzyme level, the proteome and the metabolome were compared. The co-exposure resulted in 108 differential abundant proteins (DAPs), as well as 9 and 10 modulated metabolites at T24 and T72, respectively. The co-exposure specifically modulated DAPs and metabolites involved in neurotransmission, e.g. dopaminergic synapse and GABA. CBZ specifically modulated 46 DAPs involved in calcium signaling pathways and 7 amino acids at T24. MeHg specifically modulated 55 DAPs involved in the cytoskeleton remodeling and hypoxia-induced factor 1 pathway, without altering the metabolome. Single and co-exposures commonly modulated proteins and metabolites involved in energy and amino acid metabolisms, response to stress and development. Concomitantly, lipid peroxidation and antioxidant activities were unchanged, supporting that D. polymorpha tolerated experimental conditions. The co-exposure was confirmed to cause more alterations than single exposures. This was attributed to the combined toxicity of CBZ and MeHg. Altogether, this study underlined the necessity to better characterize molecular toxicity pathways of multi-contamination that are not predictable on responses to single exposures, to better anticipate adverse effects in biota and improve risk assessment.

IMMUNOTOXICITY OF RELEVANT MIXTURES OF PESTICIDES AND METABOLITES ON THP-1 CELLS

Pesticides are used to combat agricultural pests but also trigger side effects on non-target organisms. Particularly, immune system dysregulation is a major concern due to the organism's increased vulnerability to diseases, including cancer development. Macrophages play essential roles in innate and adaptive immunity and can undergo classical (M1) or alternative (M2) activation. The M1 pro-inflammatory phenotype has an antitumor role, while M2 favors tumor promotion. Although previous studies have linked pesticide exposure to immune compromise, macrophage polarization is still poorly studied. Here, we investigated the effects of 72 h-long exposure to the mixture of four pesticides widely used in Brazil (glyphosate, 2,4-D, mancozeb, and atrazine), and their main metabolites (aminomethylphosphonic acid, 2,4-diclorophenol, ethylenethiourea, and desethylatrazine) on human leukemia monocytic THP-1 cell line at concentrations based on the Acceptable Daily Intake (ADI) value established in the country. The data revealed immunotoxicity related to impaired cell metabolism in all exposed groups, decreased cell attachment (Pes: 10^-1; Met: 10^-1; Mix: all concentrations), and disturbance in nitric oxide (NO) levels (Met: 10^-1, 10¹; Mix: all concentrations). The polarization of macrophages towards a more pro-tumor M2-like phenotype was also supported by decreased secretion of the pro-inflammatory cytokine TNF-α (Pes 10⁰, 10¹) and increased IL-8 (Pes 10¹). These outcomes alert about the risk of pesticide exposure in the Brazilian population.

Anaerobic mercury methylators inhabit sinking particles of oxic water columns

Increased concentration of mercury, particularly methylmercury, in the environment is a worldwide concern because of its toxicity in severely exposed humans. Although the formation of methylmercury in oxic water columns has been previously suggested, there is no evidence of the presence of microorganisms able to perform this process, using the hgcAB gene pair (hgc⁺ microorganisms), in such environments. Here we show the prevalence of hgc⁺ microorganisms in sinking particles of the oxic water column of Lake Geneva (Switzerland and France) and its anoxic bottom sediments. Compared to anoxic sediments, sinking particles found in oxic waters exhibited relatively high proportion of hgc⁺genes taxonomically assigned to Firmicutes. In contrast hgc⁺members from Nitrospirae, Chloroflexota and PVC superphylum were prevalent in anoxic sediment while hgc⁺ Desulfobacterota were found in both environments. Altogether, the description of the diversity of putative mercury methylators in the oxic water column expand our understanding on MeHg formation in aquatic environments and at a global scale.

A consensus protocol for the recovery of mercury methylation genes from metagenomes

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-MATE (Hg-cycling Microorganisms in Aquatic and Terrestrial Ecosystems) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on co-assembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a co-assembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

Metabolic, cellular and defense responses to single and co-exposure to carbamazepine and methylmercury in Dreissena polymorpha

Carbamazepine (CBZ) and Hg are widespread and persistent micropollutants in aquatic environments. Both pollutants are known to trigger similar toxicity mechanisms, e.g. reactive oxygen species (ROS) production. Here, their effects were assessed in the zebra mussel Dreissena polymorpha, frequently used as a freshwater model in ecotoxicology and biomonitoring. Single and co-exposures to CBZ (3.9 μg L^-1) and MeHg (280 ng L^-1) were performed for 1 and 7 days. Metabolomics analyses evidenced that the co-exposure was the most disturbing after 7 days, reducing the amount of 25 metabolites involved in protein synthesis, energy metabolism, antioxidant response and osmoregulation, and significantly altering cells and organelles' structure supporting a reduction of functions of gills and digestive glands. CBZ alone after 7 days decreased the amount of α-aminobutyric acid and had a moderate effect on the structure of mitochondria in digestive glands. MeHg alone had no effect on mussels' metabolome, but caused a significant alteration of cells and organelles' structure in gills and digestive glands. Single exposures and the co-exposure increased antioxidant responses vs control in gills and digestive glands, without resulting in lipid peroxidation, suggesting an increased ROS production caused by both pollutants. Data globally supported that a higher number of hyperactive cells compensated cellular alterations in the digestive gland of mussels exposed to CBZ or MeHg alone, while CBZ + MeHg co-exposure overwhelmed this compensation after 7 days. Those effects were unpredictable based on cellular responses to CBZ and MeHg alone, highlighting the need to consider molecular toxicity pathways for a better anticipation of effects of pollutants in biota in complex environmental conditions.

Effects of carbamazepine in aquatic biota

Carbamazepine (CBZ) is one of the most common pharmaceuticals found in the aquatic environment. Here, we reviewed studies in aquatic animals highlighting that CBZ affected ROS homeostasis but also the neuroendocrine system, cell viability, immunity, reproduction, feeding behavior and growth. Notably, the acetylcholinesterase activity was modified by concentrations of the order of ng L^-1 CBZ. At ≥10 μg L^-1, data pointed that CBZ triggered the production of ROS, modifying the activity of antioxidant enzymes and produced a significant cellular stress at concentrations ≥100 μg L^-1. However, the response appeared species-, organ- and time-dependent, and was impacted by different experimental conditions and the origin of animals. In this context, this review discusses the available data and proposes future research priorities.

Subcellular Distribution of Dietary Methyl-Mercury in Gammarus fossarum and Its Impact on the Amphipod Proteome

The transfer of methyl-Hg (MeHg) from food is central for its effects in aquatic animals, but we still lack knowledge concerning its impact on invertebrate primary consumers. In aquatic environments, cell walls of plants are particularly recalcitrant to degradation and as such remain available as a food source for long periods. Here, the impact at the proteomic level of dietary MeHg in Gammarus fossarum was established and linked to subcellular distribution of Hg. Individuals of G. fossarum were fed with MeHg in cell wall or intracellular compartments of Elodea nuttallii. Hg concentrations in subcellular fractions were 2 to 6 times higher in animals fed with cell wall than intracellular compartments. At the higher concentrations tested, the proportion of Hg in metal-sensitive fraction increased from 30.0 ± 6.1 to 41.0 ± 5.7% for individuals fed with intracellular compartment, while biologically detoxified metal fraction increased from 30.0 ± 6.1 to 50.0 ± 2.8% when fed with cell wall compartment. Data suggested that several thresholds of proteomic response are triggered by increased bioaccumulation in each subcellular fraction in correlation with Hg exclusively bound to the metal-sensitive fraction, while the increase of biologically detoxified metal likely had a cost for fitness. Proteomics analysis supported that the different binding sites and speciation in shoots subsequently resulted in different fate and cellular toxicity pathways to consumers. Our data confirmed that Hg bound in cell walls of plants can be assimilated by G. fossarum, which is consistent with its feeding strategy, hence pointing cell walls as a significant source for Hg transfers and toxicity in primary consumers. The high accumulation of Hg in macrophytes makes them a risk for food web transfer in shallow ecosystems. The present results allowed gaining new insights into the effects and uptake mechanisms of MeHg in aquatic primary consumers.

Mercury cycling in freshwater systems - An updated conceptual model

The widely accepted conceptual model of mercury (Hg) cycling in freshwater lakes (atmospheric deposition and runoff of inorganic Hg, methylation in bottom sediments and subsequent bioaccumulation and biomagnification in biota) is practically accepted as common knowledge. There is mounting evidence that the dominant processes that regulate inputs, transformations, and bioavailability of Hg in many lakes may be missing from this picture, and the fixation on the temperate stratified lake archetype is impeding our exploration of understudied, but potentially important sources of methylmercury to freshwater lakes. In this review, the importance of understudied biogeochemical processes and sites of methylmercury production are highlighted, including the complexity of redox transformations of Hg within the lake system itself, the complex assemblage of microbes found in biofilms and periphyton (two vastly understudied important sources of methylmercury in many freshwater ecosystems), and the critical role of autochthonous and allochthonous dissolved organic matter which mediates the net supply of methylmercury from the cellular to catchment scale. A conceptual model of lake Hg in contrasting lakes and catchments is presented, highlighting the importance of the autochthonous and allochthonous supply of dissolved organic matter, bioavailable inorganic mercury and methylmercury and providing a framework for future convergent research at the lab and field scales to establish more mechanistic process-based relationships within and among critical compartments that regulate methylmercury concentrations in freshwater ecosystems.

Biotic formation of methylmercury: A bio-physico-chemical conundrum

Mercury (Hg) is a natural and widespread trace metal, but is considered a priority pollutant, particularly its organic form methylmercury (MMHg), because of human's exposure to MMHg through fish consumption. Pioneering studies showed the methylation of divalent Hg (Hg^II) to MMHg to occur under oxygen-limited conditions and to depend on the activity of anaerobic microorganisms. Recent studies identified the hgcAB gene cluster in microorganisms with the capacity to methylate Hg^II and unveiled a much wider range of species and environmental conditions producing MMHg than previously expected. Here, we review the recent knowledge and approaches used to understand Hg^II-methylation, microbial biodiversity and activity involved in these processes, and we highlight the current limits for predicting MMHg concentrations in the environment. The available data unveil the fact that Hg^II methylation is a bio-physico-chemical conundrum in which the efficiency of biological Hg^II methylation appears to depend chiefly on Hg^II and nutrients availability, the abundance of electron acceptors such as sulfate or iron, the abundance and composition of organic matter as well as the activity and structure of the microbial community. An increased knowledge of the relationship between microbial community composition, physico-chemical conditions, MMHg production, and demethylation is necessary to predict variability in MMHg concentrations across environments.

Effects of cadmium, inorganic mercury and methyl-mercury on the physiology and metabolomic profiles of shoots of the macrophyte Elodea nuttallii

Macrophytes are known to bioaccumulate metals, but a thorough understanding of tolerance strategies and molecular impact of metals in aquatic plants is still lacking. The present study aimed to compare Hg and Cd effects in a representative macrophyte, Elodea nuttallii using physiological endpoints and metabolite profiles in shoots and cytosol. Exposure 24 h to methyl-Hg (30 ng L^-1), inorganic Hg (70 ng L^-1) and Cd (280 μg L^-1) did not affect photosynthesis, or antioxidant enzymes despite the significant accumulation of metals, confirming a sublethal stress level. In shoots, Cd resulted in a higher level of regulation of metabolites than MeHg, while MeHg resulted in the largest number of regulated metabolites and IHg treatment regulated no metabolites significantly. In cytosol, Cd regulated more metabolites than IHg and only arginine, histidine and mannose were reduced by MeHg exposure. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of data suggested that exposure to MeHg resulted in biochemical changes including aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism, nitrogen metabolism, arginine and proline metabolism, cyanoamino acid metabolism, while the treatment of Cd stress caused significant variations in aminoacyl-tRNA biosynthesis and branched-chain amino acids pathways. Data supports an impact of MeHg on N homeostasis, while Cd resulted in an osmotic stress-like pattern and IHg had a low impact. Marked differences in the responses to MeHg and IHg exposure were evidenced, supporting different molecular toxicity pathways and main impact of MeHg on non-soluble compartment, while main impact of IHg was on soluble compartment. Metabolomics was used for the first time in this species and proved to be very useful to confirm and complement recent knowledge gained by transcriptomics and proteomics, highlighting the high interest of multi-omics approaches to identify early impact of environmental pollution.

Towards early-warning gene signature of Chlamydomonas reinhardtii exposed to Hg-containing complex media

The potential of using gene expression signature as a biomarker of toxicants exposure was explored in the microalga Chlamydomonas reinhardtii exposed 2 h to mercury (Hg) as inorganic mercury (IHg) and methyl mercury (MeHg) in presence of copper (Cu) and Suwannee River Humic Acid (SRHA). Total cellular Hg (THg = IHg + MeHg) decreased in presence of SRHA for 0.7 nM IHg and 0.4 nM MeHg, but increased for 70 nM IHg exposure. In mixtures of IHg + MeHg and (IHg or MeHg) + Cu, SRHA decreased THg uptake, except for 0.7 nM IHg + 0.4 nM MeHg which was unchanged (p-value>0.05). In the absence of SRHA, 0.5 μM Cu strongly decreased intracellular THg concentration for 70 nM IHg, while it had no effect for 0.7 nM IHg and 0.4 nM MeHg. The expression of single transcripts was not correlated with measured THg uptake, but a subset of 60 transcripts showed signatures specific to the exposed metal(s) and was congruent with exposure concentration. Notably, the range of fold change values of this subset correlated with THg bioaccumulation with a two-slope pattern in line with [THg]_intra/[THg]_med ratios. Gene expression signature seems a promising approach to complement chemical analyses to assess bioavailability of toxicants in presence of other metals and organic matter.

Comparative study of Cu uptake and early transcriptome responses in the green microalga Chlamydomonas reinhardtii and the macrophyte Elodea nuttallii

Microalgae are widely used as representative primary producers in ecotoxicology, while macrophytes are much less studied. Here we compared the bioavailability and cellular toxicity pathways of 2 h-exposure to 10^-6 mol L^-1 Cu in the macrophyte Elodea nuttallii and the green microalga Chlamydomonas reinhardtii. Uptake rate was similar but faster in the algae than in the macrophyte, while RNA-Sequencing revealed a similar number of regulated genes. Early-regulated genes were congruent with expected adverse outcome pathways for Cu with Gene Ontology terms including gene regulation, energy metabolism, transport, cell processes, stress, antioxidant metabolism and development. However, the gene regulation level was higher in E. nuttallii than in C. reinhardtii and several categories were more represented in the macrophyte than in the microalga. Moreover, several categories including oxidative pentose phosphate pathway (OPP), nitrate metabolism and metal handling were only found for E. nuttallii, whereas categories such as cell motility, polyamine metabolism, mitochondrial electron transport and tricarboxylic acid cycle (TCA) were unique to C. reinhardtii. These differences were attributed to morphological and metabolic differences and highlighted dissimilarities between a sessile and a mobile species. Our results highlight the efficiency of transcriptomics to assess early molecular responses in biota, and the importance of studying more aquatic plants for a better understanding on the impact and fate of environmental contaminants.

Molecular Effects, Speciation, and Competition of Inorganic and Methyl Mercury in the Aquatic Plant Elodea nuttallii

Mercury (Hg) remains hazardous in aquatic environments because of its biomagnification in food webs. Nonetheless, Hg uptake and impact in primary producers is still poorly understood. Here, we compared the cellular toxicity of inorganic and methyl Hg (IHg and MeHg, respectively) in the aquatic plant Elodea nuttallii. IHg and MeHg regulated contigs involved in similar categories (e.g., energy metabolism, development, transport, secondary metabolism), but MeHg regulated more contigs, supporting a higher molecular impact than IHg. At the organism level, MeHg induced antioxidants, while IHg decreased chlorophyll content. The uptake of Hg and expression of a subset of contigs was subsequently studied in complex media. Measured uptake pointed to a contrasted impact of cell walls and copper (Cu) on IHg and MeHg. Using a speciation modeling, differences in uptake were attributed to the differences in affinities of IHg and MeHg to organic matter in relation to Cu speciation. We also identified a distinct gene expression signature for IHg, MeHg, and Cu, further supporting different molecular toxicity of these trace elements. Our data provided fundamental knowledge on IHg and MeHg uptake in a key aquatic primary producer and confirmed the potential of transcriptomics to assess Hg exposure in environmentally realistic systems.

Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases

Microbial mercury (Hg) methylation in sediments can result in bioaccumulation of the neurotoxin methylmercury (MMHg) in aquatic food webs. Recently, the discovery of the gene hgcA, required for Hg methylation, revealed that the diversity of Hg methylators is much broader than previously thought. However, little is known about the identity of Hg-methylating microbial organisms and the environmental factors controlling their activity and distribution in lakes. Here, we combined high-throughput sequencing of 16S rRNA and hgcA genes with the chemical characterization of sediments impacted by a waste water treatment plant that releases significant amounts of organic matter and iron. Our results highlight that the ferruginous geochemical conditions prevailing at 1–2 cm depth are conducive to MMHg formation and that the Hg-methylating guild is composed of iron and sulfur-transforming bacteria, syntrophs, and methanogens. Deltaproteobacteria, notably Geobacteraceae, dominated the hgcA carrying communities, while sulfate reducers constituted only a minor component, despite being considered the main Hg methylators in many anoxic aquatic environments. Because iron is widely applied in waste water treatment, the importance of Geobacteraceae for Hg methylation and the complexity of Hg-methylating communities reported here are likely to occur worldwide in sediments impacted by waste water treatment plant discharges and in iron-rich sediments in general.

Effects of two-hour exposure to environmental and high concentrations of methylmercury on the transcriptome of the macrophyte Elodea nuttallii

The effects of two methylmercury (CH₃Hg⁺, MeHg) concentrations, representative of environmental level and extreme contamination, were investigated on the macrophyte Elodea nuttallii during a 2h-exposure combining transcriptomic (RNA-Seq), physiological endpoints (pigment contents, activity of anti-oxidative stress enzymes) and bioaccumulation. Exposure to MeHg induced the up- and down-regulation of numerous genes (4389 and 16853 for 10ngL^-1 and 10μgL^-1 MeHg exposure, respectively) involved in sugar, amino acid and secondary metabolism (e.g. cinnamic acid, flavonoids) at both concentrations. Genes coding for photosynthesis, membrane integrity, metal homeostasis, water transport and anti-oxidative enzymes were additionally up- and down-regulated at the higher concentration. At the physiological level, exposure to both MeHg concentrations resulted in a strong increase of anthocyanin content in shoots. Chlorophyll content and antioxidant enzyme activities were unchanged. The data suggest that the macrophyte was able to efficiently cope with the stress resulting from MeHg exposure, possibly by using anthocyanin as anti-oxidant and S-rich amino acids (such as cysteine and methionine) as chelators. Transcriptomics analysis enabled gaining novel insights on molecular effects of MeHg in primary producers, which are one of the main entry pathway of hazardous MeHg in aquatic food webs.

Transcriptomic approach for assessment of the impact on microalga and macrophyte of in-situ exposure in river sites contaminated by chlor-alkali plant effluents

Water quality degradation is a worldwide problem, but risk evaluation of chronic pollution in-situ is still a challenge. The present study aimed to evaluate the potential of transcriptomic analyses in representative aquatic primary producers to assess the impact of environmental pollution in-situ: the microalga Chlamydomonas reinhardtii and the macrophyte Elodea nuttallii were exposed 2 h in the Babeni Reservoir of the Olt River impacted by chlor-alkali plant effluent release resulting in increased concentrations of Hg and NaCl in receiving water. The response at the transcriptomic level was strong, resulting in up to 5485, and 8700 dysregulated genes (DG) for the microalga and for the macrophyte exposed in the most contaminated site, respectively. Transcriptomic response was congruent with the concentrations of Hg and NaCl in the water of the impacted reservoir. Genes involved in development, energy metabolism, lipid metabolism, nutrition, and RedOx homeostasis were dysregulated during in-situ exposure of both organisms. In addition, genes involved in the cell motility of C. reinhardtii and development of the cell wall of E. nuttallii were affected. DG were in line with adverse outcome pathways and transcriptomic studies reported after exposure to high concentrations of Hg and NaCl under controlled conditions in the laboratory. Transcriptomic response provided a sensitive measurement of the exposure as well as hints on the tolerance mechanisms of environmental pollution, and is thus promising as an early-warning tool to assess water quality degradation.

Trophic fate of inorganic and methyl-mercury in a macrophyte-chironomid food chain

Dietary transfer of mercury (Hg) is central for its effects on higher trophic animals, nonetheless, its driving parameters and characteristics are not well understood. Here we measured Hg species transfer (uptake) from the macrophyte Elodea nuttallii -mimicking tissues incorporation in sediments after decay- to Chironomus riparius. Methyl-Hg (MMHg) was more transferable than inorganic Hg (IHg) from plant's intracellular and cell wall compartments. After 10-d-long exposure, MMHg was predominantly found in MMHg form in the cytosolic compartment (S) of chironomids, while IHg showed similar concentrations in S and insoluble debris (P) compartments. After cessation of Hg species exposure (depuration), only MMHg resulted in a bioaccumulation factor >1. Toxicokinetics modelling indicated a demethylation of MMHg in the S fraction and its concomitant storage in the P fraction as IHg during both uptake and depuration, revealing an elimination and detoxification mechanism. Our data support that MMHg is more transferable than IHg to sensitive subcellular targets as well as bioavailable fraction in chironomids, in line with field studies showing higher MMHg transfer than IHg in food webs. Hence our data point out macrophytes as a potential Hg source to benthic food webs to be considered for enhancing aquatic environment protection during phytoremediation programs.

Mercury speciation in Pinus nigra barks from Monte Amiata (Italy): An X-ray absorption spectroscopy study

This study determined, by means of X-ray absorption near-edge structure (XANES) spectroscopy, the speciation of mercury (Hg) in black pine (Pinus nigra) barks from Monte Amiata, that were previously shown to contain exceptionally high (up to some mg kg^-1) Hg contents because of the proximity to the former Hg mines and roasting plants. Linear fit combination (LCF) analysis of the experimental spectra compared to a large set of reference compounds showed that all spectra can be fitted by only four species: β-HgS (metacinnabar), Hg-cysteine, Hg bound to tannic acid, and Hg⁰. The first two are more widespread, whereas the last two occur in one sample only; the contribution of organic species is higher in deeper layers of barks than in the outermost ones. We interpret these results to suggest that, during interaction of barks with airborne Hg, the metal is initially mechanically captured at the bark surface as particulate, or physically adsorbed as gaseous species, but eventually a stable chemical bond is established with organic ligands of the substrate. As a consequence, we suggest that deep bark Hg may be a good proxy for long term time-integrated exposure, while surface bark Hg is more important for recording short term events near Hg point sources.

Biofilm composition in the Olt River (Romania) reservoirs impacted by a chlor-alkali production plant

Freshwater biofilms can be useful indicators of water quality and offer the possibility to assess contaminant effects at the community level. The present field study examines the effects of chlor-alkali plant effluents on the community composition of biofilms grown in the Olt River (Romania) reservoirs. The relationship between ambient water quality variables and community composition alterations was explored. Amplicon sequencing revealed a significant modification of the composition of microalgal, bacterial and fungal communities in the biofilms collected in the impacted reservoirs in comparison with those living in the uncontaminated control reservoir. The abundance corrected Simpson index showed lower richness and diversity in biofilms collected in the impacted reservoirs than in the control reservoir. The biofilm bacterial communities of the impacted reservoirs were characterized by the contaminant-tolerant Cyanobacteria and Bacteroidetes, whereas microalgal communities were predominantly composed of Bacillariophyta and fungal communities of Lecanoromycetes and Paraglomycetes. A principal component analysis revealed that major contaminants present in the waste water of the chlor-alkali production plant, i.e. Na⁺, Ca²⁺, Cl^- and Hg, were correlated with the alteration of biofilm community composition in the impacted reservoirs. However, the biofilm composition was also influenced by water quality variables such as NO₃^-, SO₄^2-, DOC and Zn from unknown sources. The results of the present study imply that, even when below the environmental quality standards, typical contaminants of chlor-alkali plant releases may affect biofilm composition and that their impacts on the microbial biodiversity might be currently overlooked.

Influence of chemical speciation and biofilm composition on mercury accumulation by freshwater biofilms

Mercury (Hg) is a pollutant of high concern for aquatic systems due to the biomagnification of its methylated form along the food chain. However, in contrast to other metals, gaining knowledge of its bioavailable forms for aquatic microorganisms remains challenging, making Hg risk assessment difficult. Ubiquitous and sessile freshwater biofilms are well known to accumulate and to transform Hg present in their ambient environment. The present study thus aims to evaluate whether non-extractable (proxy of intracellular) Hg accumulated by biofilms could be a good indicator of Hg bioavailability for microorganisms in freshwater. To that end, the link between Hg concentration and speciation, as well as biofilm composition (percentage of abiotic, biotic, chlorophyll and phycocyanin-fractions and abundance of dsrA, gcs, merA and hgcA bacterial genes) and biofilm Hg accumulation was examined. The studied biofilms were grown on artificial substrata in four reservoirs along the Olt River (Romania), which was contaminated by Hg coming from chlor-alkali plant effluents. The 0.45 μm-filterable Hg concentrations in ambient waters were measured and inorganic IHg speciation was modelled. Biofilms were analyzed for their non-extractable IHg and methylmercury (MeHg) contents as well as for their composition. The non-extractable IHg content was related, but not significantly, to the concentration of total IHg (r² = 0.88, p = 0.061) whereas a significant correlation was found with the predicted IHg concentration that is not bound to dissolved organic matter (r² = 0.95, p = 0.027), despite its extremely low concentrations (10^-25 M), showing a limitation of the thermodynamic Hg modelling to predict Hg bioavailability. The studied biofilms were different in biomass and composition and a principal component analysis showed that the non-extractable IHg content correlated with the abundance of the merA and hgcA genes, while MeHg accumulation was only linked with the abundance of the rRNA 16S gene. The present study suggests that non-extractable IHg concentrations in biofilms are a useful proxy of IHg bioavailable forms in waters whereas the hgcA and merA genes are good biomarkers of both biofilm IHg exposure and bioavailability.

The class III peroxidase PRX17 is a direct target of the MADS-box transcription factor AGAMOUS-LIKE15 (AGL15) and participates in lignified tissue formation

Several physiological functions have been attributed to class III peroxidases (PRXs) in plants, but the in planta role of most members of this family still remains undetermined. Here, we report the first functional characterization of PRX17 (At2g22420), one of the 73 members of this family in Arabidopsis thaliana. Localization of PRX17 was examined by transient expression in Nicotiana benthamiana. Loss- and gain-of-function mutants in A. thaliana were studied. Regulation at the gene and protein levels was analyzed using β-glucuronidase (GUS) activity, quantitative reverse transcriptase (qRT)-PCR, zymography, and chromatin immunoprecipitation. Phenotypes were characterized including lignin and xylan contents. PRX17 was expressed in various tissues, including vascular tissues, and PRX17 was localized to the cell wall. In prx17, the lignin content was reduced in the stem and siliques and bolting was delayed, while the opposite phenotype was observed in 35S:PRX17 plants, together with a significant increase of lignin and xylan immunofluorescence signal. Finally, we demonstrated that the transcription factor AGAMOUS-LIKE15 (AGL15) binds to the PRX17 promoter and regulates PRX17 expression level. This converging set of structural, transcriptomic and physiological data suggests that PRX17, under the control of AGL15, contributes to developmental programs by playing an essential role in regulating age-dependent lignified tissue formation, including changes in cell wall properties.

Role of cellular compartmentalization in the trophic transfer of mercury species in a freshwater plant-crustacean food chain

Mercury (Hg) represents an important risk for human health through the food webs contamination. Macrophytes bioaccumulate Hg and play a role in Hg transfer to food webs in shallow aquatic ecosystems. Nevertheless, the compartmentalization of Hg within macrophytes, notably major accumulation in the cell wall and its impact on trophic transfer to primary consumers are overlooked. The present work focusses on the trophic transfer of inorganic Hg (IHg) and monomethyl-Hg (MMHg) from the intracellular and cell wall compartments of the macrophyte Elodea nuttallii - considered a good candidate for phytoremediation - to the crustacean Gammarus fossarum. The results demonstrated that Hg accumulated in both compartments was trophically bioavailable to gammarids. Besides IHg from both compartments were similarly transferred to G. fossarum, while for MMHg, uptake rates were ∼2.5-fold higher in G. fossarum fed with the cell wall vs the intracellular compartment. During the depuration phase, Hg concentrations in G. fossarum varied insignificantly suggesting that both IHg and MMHg were strongly bound to biological ligands in the crustacean. Our data imply that cell walls have to be considered as an important source of Hg to consumers in freshwater food webs when developing procedures for enhancing aquatic environment protection during phytoremediation programs.

Role of Settling Particles on Mercury Methylation in the Oxic Water Column of Freshwater Systems

As the methylation of inorganic mercury to neurotoxic methylmercury has been attributed to the activity of anaerobic bacteria, the formation of methylmercury in the oxic water column of marine ecosystems has puzzled scientists over the past years. Here we show for the first time that methylmercury can be produced in particles sinking through oxygenated water column of lakes. Total mercury and methylmercury concentrations were measured in the settling particles and in surface sediments of the largest freshwater lake in Western Europe (Lake Geneva). While total mercury concentration differences between sediments and settling particles were not significant, methylmercury concentrations were about ten-fold greater in settling particles. Methylmercury demethylation rate constants (k_d) were of similar magnitude in both compartments. In contrast, mercury methylation rate constants (k_m) were one order of magnitude greater in settling particles. The net potential for methylmercury formation, assessed by the ratio between the two rate constants (k_m k_d^-1), was therefore up to ten fold greater in settling particles, denoting that in situ transformations likely contributed to the high methylmercury concentration found in settling particles. Mercury methylation was inhibited (∼80%) in settling particles amended with molybdate, demonstrating the prominent role of biological sulfate-reduction in the process.

Elodea nuttallii exposure to mercury exposure under enhanced ultraviolet radiation: Effects on bioaccumulation, transcriptome, pigment content and oxidative stress

The hypothesis that increased UV radiation result in co-tolerance to Hg toxicity in aquatic plants was studied at the physiological and transcriptomic level in Elodea nuttallii. At the transcriptomic level, combined exposure to UV+Hg enhanced the stress response in comparison with single treatments, affecting the expression level of transcripts involved in energy metabolism, lipid metabolism, nutrition, and redox homeostasis. Single and combined UV and Hg treatments dysregulated different genes but with similar functions, suggesting a fine regulation of the plant to stresses triggered by Hg, UV and their combination but lack of co-tolerance. At the physiological level, UV+Hg treatment reduced chlorophyll content and depleted antioxidative compounds such as anthocyanin and GSH/GSSG in E. nuttallii. Nonetheless, combined exposure to UV+Hg resulted in about 30% reduction of Hg accumulation into shoots vs exposure to Hg alone, which was congruent with the level of expression of several transporter genes, as well as the UV effect on Hg bioavailability in water. The findings of the present work underlined the importance of performing experimentation under environmentally realistic conditions and to consider the interplay between contaminants and environmental variables such as light that might have confounding effects to better understand and anticipate the effects of multiple stressors in aquatic environment.

Environmental quality assessment of reservoirs impacted by Hg from chlor-alkali technologies: case study of a recovery

Mercury (Hg) pollution legacy of chlor-alkali plants will be an important issue in the next decades with the planned phase out of Hg-based electrodes by 2025 within the Minamata convention. In such a context, the present study aimed to examine the extent of Hg contamination in the reservoirs surrounding the Oltchim plant and to evaluate the possible improvement of the environmental quality since the closure of its chlor-alkali unit. This plant is the largest chlor-alkali plant in Romania, which partly switched to Hg-free technology in 1999 and definitely stopped the use of Hg electrolysis in May 2012. Total Hg (THg) and methylmercury (CH₃Hg) concentrations were found to decrease in the surface waters and sediments of the reservoirs receiving the effluents of the chlor-alkali platform since the closure of Hg units. Hence, calculated risk quotients (RQ) indicated no adverse effect of Hg for aquatic organisms from the ambient water exposure. RQ of Hg in sediments were mostly all higher than 1, showing important risks for benthic organisms. However, ecotoxicity testing of water and sediments suggest possible impact of other contaminants and their mixtures. Hg hotspots were found in soils around the platform with RQ values much higher than 1. Finally, THg and CH₃Hg concentrations in fish were below the food safety limit set by the WHO, which contrasts with previous measurements made in 2007 revealing that 92 % of the studied fish were of high risk of consumption. Discontinuing the use of Hg electrodes greatly improved the surrounding environment of chlor-alkali plants within the following years and led to the decrease environmental exposure to Hg through fish consumption. However, sediment and soil still remained highly contaminated and problematic for the river reservoir management. The results of this ecological risk assessment study have important implications for the evaluation of the benefits as well as limits of the Minamata Convention implementation.

Transcriptomic and Physiological Responses of the Green Microalga Chlamydomonas reinhardtii during Short-Term Exposure to Subnanomolar Methylmercury Concentrations

The effects of short-term exposure to subnanomolar methyl-mercury (MeHg) concentrations, representative of contaminated environments, on the microalga Chlamydomonas reinhardtii were assessed using both physiological end points and gene expression analysis. MeHg bioaccumulated and induced significant increase of the photosynthesis efficiency, while the algal growth, oxidative stress, and chlorophyll fluorescence were unaffected. At the molecular level, MeHg significantly dysregulated the expression of genes involved in motility, energy metabolism, lipid metabolism, metal transport, and antioxidant enzymes. Data suggest that the cells were able to cope with subnanomolar MeHg exposure, but this tolerance resulted in a significant cost to the cell energy and reserve metabolism as well as ample changes in the nutrition and motility of C. reinhardtii. The present results allowed gaining new insights on the effects and uptake mechanisms of MeHg at subnanomolar concentrations in aquatic primary producers.

Dendrochemical assessment of mercury releases from a pond and dredged-sediment landfill impacted by a chlor-alkali plant

Although current Hg emissions from industrial activities may be accurately monitored, evidence of past releases to the atmosphere must rely on one or more environmental proxies. We used Hg concentrations in tree cores collected from poplars and willows to investigate the historical changes of Hg emissions from a dredged sediment landfill and compared them to a nearby control location. Our results demonstrated the potential value of using dendrochemistry to record historical Hg emissions from past industrial activities.

Persistent Hg contamination and occurrence of Hg-methylating transcript (hgcA) downstream of a chlor-alkali plant in the Olt River (Romania)

Chlor-alkali plants using mercury (Hg) cell technology are acute point sources of Hg pollution in the aquatic environment. While there have been recent efforts to reduce the use of Hg cells, some of the emitted Hg can be transformed to neurotoxic methylmercury (MeHg). Here, we aimed (i) to study the dispersion of Hg in four reservoirs located downstream of a chlor-alkali plant along the Olt River (Romania) and (ii) to track the activity of bacterial functional genes involved in Hg methylation. Total Hg (THg) concentrations in water and sediments decreased successively from the initial reservoir to downstream reservoirs. Suspended fine size particles and seston appeared to be responsible for the transport of THg into downstream reservoirs, while macrophytes reflected the local bioavailability of Hg. The concentration and proportion of MeHg were correlated with THg, but were not correlated with bacterial activity in sediments, while the abundance of hgcA transcript correlated with organic matter and Cl(-) concentration, indicating the importance of Hg bioavailability in sediments for Hg methylation. Our data clearly highlights the importance of considering Hg contamination as a legacy pollutant since there is a high risk of continued Hg accumulation in food webs long after Hg-cell phase out.

Effects of copper-oxide nanoparticles, dissolved copper and ultraviolet radiation on copper bioaccumulation, photosynthesis and oxidative stress in the aquatic macrophyte Elodea nuttallii

In this study, the uptake and sub-toxic effects of CuO nanoparticles (CuO-NPs), dissolved Cu(II) alone or in combination with UV radiation on the aquatic macrophyte Elodea nuttallii were studied. Emphasis was on Cu accumulation, growth, photosynthesis and the oxidative stress related enzymes peroxidase (POD) and superoxide dismutase (SOD). The results showed stronger Cu accumulation in plants exposed to 10 mg L(-1) CuO-NPs, corresponding to 1.4-2 mg L(-1) dissolved Cu(II), than to 256 μg L(-1) Cu(II). However, the ratio between the accumulated Cu and dissolved Cu in CuO treatments was lower than in Cu(II) treatments. Additional UV exposure increased accumulation in both treatments, with the effect being stronger for Cu accumulation from CuO-NPs than for dissolved Cu(II). Photosynthetic capacity was strongly reduced by UV treatment, whereas remained unaffected by Cu(II) or CuO-NP treatments. Similarly, the increase of SOD activity was more pronounced in the UV treatments. On the other hand, POD activity enhancement was strongest in the plants exposed to CuO-NPs for 24 h. Expression of the copper transporter COPT1 as revealed by RT-qPCR was inhibited by Cu(II) and CuO-NP treatment, limiting the uptake of excess Cu into the cells. Overall, the combined exposure of E. nuttallii to UV radiation with CuO-NPs or Cu(II) has a higher impact than exposure to CuO-NPs or Cu(II) alone. The results imply that heavy pollution of natural water with CuO-NPs or dissolved Cu might have stronger effects in combination with natural UV irradiation on organisms in situ.

Human exposure to mercury in artisanal small-scale gold mining areas of Kedougou region, Senegal, as a function of occupational activity and fish consumption

We investigated mercury (Hg) exposure of food web and humans in the region of Kedougou, Senegal, where Hg is used for gold amalgamation in artisanal small-scale gold mining (ASGM). For this purpose, total mercury (THg) concentration was determined in eight fish species and two shellfish species from Gambia River and in human hair from 111 volunteers of different age and sex, living in urban locations (Kedougou and Samekouta) or in ASGM areas (Tinkoto and Bantako). THg concentrations in fish samples range from 0.03 to 0.51 mg kg(-1) wet weight (ww) and 0.5 to 1.05 mg kg(-1) ww for shellfish. THg concentrations in fish are below the WHO guideline of 0.5 mg kg(-1) ww, whereas 100 % of shellfish are above this safety guideline. In the entire set of fish and shellfish samples, we documented a decrease of THg concentrations with increasing selenium to mercury (Se:Hg) ratio suggesting a protection of Se against Hg. However, local population consuming fish from the Gambia River in the two ASGM areas have higher THg concentrations (median = 1.45 and 1.5 mg kg(-1) at Bantako and Tinkoto) in hair than those from others localities (median = 0.42 and 0.32 mg kg(-1) at Kedougou town and Samekouta) who have diverse diets. At ASGM sites, about 30 % of the local population present Hg concentrations in hair exceeding 1 mg kg(-1), defined as the reference concentration of Hg in hair. We also evidence a higher exposure of women to Hg in the Tinkoto ASGM site due to the traditional distribution of daily tasks where women are more involved in the burning of amalgams. The discrepancy between the calculated moderate exposure through fish consumption and the high Hg concentrations measured in hair suggest that fish consumption is not the only source of Hg exposure and that further studies should focus on direct exposure to elemental Hg of population living at ASGM sites.

Antagonistic and synergistic effects of light irradiation on the effects of copper on Chlamydomonas reinhardtii

The present study showed the important role of light intensity and spectral composition on Cu uptake and effects on green alga Chlamydomonas reinhardtii. High-intenisty light (HL) increased cellular Cu concentrations, but mitigated the Cu-induced decrease in chlorophyll fluorescence, oxidative stress and lipid peroxidation at high Cu concentrations, indicating that Cu and HL interact in an antagonistic manner. HL up-regulated the transcription of genes involved in the antioxidant response in C. reinhardtii and thus reduced the oxidative stress upon exposure to Cu and HL. Combined exposure to Cu and UVBR resulted in an increase of cellular Cu contents and caused severe oxidative damage to the cells. The observed effects were higher than the sum of the effects corresponding to exposure to UVBR or Cu alone suggesting a synergistic interaction.

Effects of macrophytes on the fate of mercury in aquatic systems

Vegetated and shallow areas such as wetlands and salt marshes, as well as freshwater lakes and rivers, have been identified as hotspots for Hg methylation. The presence of aquatic macrophytes, the predominant primary producers in shallow waters, plays an important but still poorly understood role in the fate of Hg in these environments. The present review focuses on the influences of macrophytes on Hg speciation and distribution in sediments, the rhizosphere, and the water column; on Hg transformation; and on Hg release to the environment, including transfer to the trophic web. Future research will require an improved understanding of the mechanisms and the factors controlling these aspects as well as a broader general view. Thus, the main gaps in knowledge are also discussed.

Extremely elevated methyl mercury levels in water, sediment and organisms in a Romanian reservoir affected by release of mercury from a chlor-alkali plant

We examined mercury (Hg) biogeochemistry and biomagnification in the Babeni Reservoir, a system strongly affected by the release of Hg from a chlor-alkali plant. Total mercury (THg) concentrations in river water reached 88 ng L(-1) but decreased rapidly in the reservoir (to 9 ng L(-1)). In contrast, monomethylmercury (MMHg) concentrations increased from the upstream part of the reservoir to the central part (0.7 ng L(-1)), suggesting high methylation within the reservoir. Moreover, vertical water column profiles of THg and MMHg indicated that Hg methylation mainly occurred deep in the water column and at the sediment-water interface. The discharge of Hg from a chlor-alkali plant in Valcea region caused the highest MMHg concentrations ever found in non-piscivorous fish worldwide. MMHg concentrations and bioconcentration factors (BCF) of plankton and macrophytes revealed that the highest biomagnification of MMHg takes place in primary producers.

Physiological and proteomic changes suggest an important role of cell walls in the high tolerance to metals of Elodea nuttallii

Macrophytes bioaccumulate metals, the suggestion being made that they be considered for phytoremediation. However, a thorough understanding of the mechanisms of metal tolerance in these plants is necessary to allow full optimization of this approach. The present study was undertaken to gain insight into Hg and Cd accumulation and their effects in a representative macrophyte, Elodea nuttallii. Exposure to methyl-Hg (23 ng dm(-3)) had no significant effect while inorganic Hg (70 ng dm(-3)) and Cd (281 μg dm(-3)) affected root growth but did not affect shoots growth, photosynthesis, or antioxidant enzymes. Phytochelatins were confirmed as having a role in Cd tolerance in this plant while Hg tolerance seems to rely on different mechanisms. Histology and subcellular distribution revealed a localized increase in lignification, and an increased proportion of metal accumulation in cell wall over time. Proteomics further suggested that E. nuttallii was able to efficiently adapt its energy sources and the structure of its cells during Hg and Cd exposure. Storage in cell walls to protect cellular machinery is certainly predominant at environmental concentrations of metals in this plant resulting in a high tolerance highlighted by the absence of toxicity symptoms in shoots despite the significant accumulation of metals.

Analysis of the Elodea nuttallii transcriptome in response to mercury and cadmium pollution: development of sensitive tools for rapid ecotoxicological testing

Toxic metals polluting aquatic ecosystems are taken up by inhabitants and accumulate in the food web, affecting species at all trophic levels. It is therefore important to have good tools to assess the level of risk represented by toxic metals in the environment. Macrophytes are potential organisms for the identification of metal-responsive biomarkers but are still underrepresented in ecotoxicology. In the present study, we used next-generation sequencing to investigate the transcriptomic response of Elodea nuttallii exposed to enhanced concentrations of Hg and Cd. We de novo assembled more than 60 000 contigs, of which we found 170 to be regulated dose-dependently by Hg and 212 by Cd. Functional analysis showed that these genes were notably related to energy and metal homeostasis. Expression analysis using nCounter of a subset of genes showed that the gene expression pattern was able to assess toxic metal exposure in complex environmental samples and was more sensitive than other end points (e.g., bioaccumulation, photosynthesis, etc.). In conclusion, we demonstrate the feasibility of using gene expression signatures for the assessment of environmental contamination, using an organism without previous genetic information. This is of interest to ecotoxicology in a wider sense given the possibility to develop specific and sensitive bioassays.

Mercury bioaccumulation in the aquatic plant Elodea nuttallii in the field and in microcosm: accumulation in shoots from the water might involve copper transporters

Previous studies suggest that macrophytes might participate in bioaccumulation and biomagnification of toxic mercury (Hg) in aquatic environment. Hg bioaccumulation and uptake mechanisms in macrophytes need therefore to be studied. Amongst several macrophytes collected in an Hg contaminated reservoir in Romania, Elodea nuttallii showed a high organic and inorganic Hg accumulation and was then further studied in the laboratory. Tolerance and accumulation of Hg of this plant was also high in the microcosm. Basipetal transport of inorganic Hg was predominant, whereas acropetal transport of methyl-Hg was observed with apparently negligible methylation or demethylation in planta. Hg concentrations were higher in roots>leaves>stems and in top>middle>bottom of shoots. In shoots, more than 60% Hg was found intracellularly where it is believed to be highly available to predators. Accumulation in shoots was highly reduced by cold, death and by competition with Cu(+). Hg in E. nuttallii shoots seems to mainly originate from the water column, but methyl-Hg could also be remobilized from the sediments and might drive in part its entry in the food web. At the cellular level, uptake of Hg into the cell sap of shoots seems linked to the metabolism and to copper transporters. The present work highlights an important breakthrough in our understanding of Hg accumulation and biomagnifications: the remobilization of methyl-Hg from sediments to aquatic plants and differences in uptake mechanisms of inorganic and methyl-Hg in a macrophyte.

Effect of Elodea nuttallii roots on bacterial communities and MMHg proportion in a Hg polluted sediment

The objective of this study was to assess the effect of a rooted macrophyte Elodea nuttallii on rhizosphere bacterial communities in Hg contaminated sediments. Specimens of E. nuttallii were exposed to sediments from the Hg contaminated Babeni reservoir (Olt River, Romania) in our microcosm. Plants were allowed to grow for two months until they occupied the entirety of the sediments. Total Hg and MMHg were analysed in sediments where an increased MMHg percentage of the total Hg in pore water of rhizosphere sediments was found. E. nuttallii roots also significantly changed the bacterial community structure in rhizosphere sediments compared to bulk sediments. Deltaproteobacteria dominated the rhizosphere bacterial community where members of Geobacteraceae within the Desulfuromonadales and Desulfobacteraceae were identified. Two bacterial operational taxonomic units (OTUs) which were phylogenetically related to sulfate-reducing bacteria (SRB) became abundant in the rhizosphere. We suggest that these phylotypes could be potentially methylating bacteria and might be responsible for the higher MMHg percentage of the total Hg in rhizosphere sediments. However, SRB were not significantly favoured in rhizosphere sediments as shown by qPCR. Our findings support the hypothesis that rooted macrophytes created a microenvironment favorable for Hg methylation. The presence of E. nuttallii in Hg contaminated sediments should therefore not be overlooked.

Transcriptome analysis of various flower and silique development stages indicates a set of class III peroxidase genes potentially involved in pod shattering in Arabidopsis thaliana

BACKGROUND

Plant class III peroxidases exist as a large multigenic family involved in numerous functions suggesting a functional specialization of each gene. However, few genes have been linked with a specific function. Consequently total peroxidase activity is still used in numerous studies although its relevance is questionable. Transcriptome analysis seems to be a promising tool to overcome the difficulties associated with the study of this family. Nevertheless available microarrays are not completely reliable for this purpose. We therefore used a macroarray dedicated to the 73 class III peroxidase genes of A. thaliana to identify genes potentially involved in flower and fruit development.

RESULTS

The observed increase of total peroxidase activity during development was actually correlated with the induction of only a few class III peroxidase genes which supports the existence of a functional specialization of these proteins. We identified peroxidase genes that are predominantly expressed in one development stage and are probable components of the complex gene networks involved in the reproductive phase. An attempt has been made to gain insight into plausible functions of these genes by collecting and analyzing the expression data of different studies in plants. Peroxidase activity was additionally observed in situ in the silique dehiscence zone known to be involved in pod shattering. Because treatment with a peroxidase inhibitor delayed pod shattering, we subsequently studied mutants of transcription factors (TF) controlling this mechanism. Three peroxidases genes -AtPrx13, AtPrx30 and AtPrx55- were altered by the TFs involved in pod shatter.

CONCLUSIONS

Our data illustrated the problems caused by linking only an increase in total peroxidase activity to any specific development stage or function. The activity or involvement of specific class III peroxidase genes needs to be assessed. Several genes identified in our study had not been linked to any particular development stage or function until now. Notably AtPrx13, which is one of the peroxidase genes not present on commercially available microarrays. A systematic survey of class III peroxidase genes expression is necessary to reveal specific class III peroxidase gene functions and the regulation and evolution of this key multifunctional enzyme family. The approach used in this study highlights key individual genes that merit further investigation.

An anionic class III peroxidase from zucchini may regulate hypocotyl elongation through its auxin oxidase activity

The high number of peroxidase genes explains the description of numerous physiological functions and the fact that the in planta function of a single isoform has never been characterized yet. We analyzed in transgenic Arabidopsis thaliana the localization of a zucchini isoperoxidase (APRX), previously purified thanks to its pectin binding ability. We confirmed that the protein is localized near the cell wall, mainly produced in the elongation area of the hypocotyls and respond to exogenous auxin. In addition, the ectopic overexpression of APRX induced changes in growth pattern and a significant reduction of endogenous indole-3-acetic acid (IAA) level. In agreement with these observations APRX showed an elevated in vitro auxin oxidase activity. We propose that APRX participates in the negative feedback regulation of auxin level and consequently terminates the hypocotyl elongation process.

Specific functions of individual class III peroxidase genes

In higher plants, class III peroxidases exist as large multigene families (e.g. 73 genes in Arabidopsis thaliana). The diversity of processes catalysed by peroxidases as well as the large number of their genes suggests the possibility of a functional specialization of each isoform. In addition, the fact that peroxidase promoter sequences are very divergent and that protein sequences contain both highly conserved domains and variable regions supports this hypothesis. However, two difficulties are associated with the study of the function of specific peroxidase genes: (i) the modification of the expression of a single peroxidase gene often results in no visible mutant phenotype, because it is compensated by redundant genes; and (ii) peroxidases show low substrate specificity in vitro resulting in an unreliable indication of peroxidase specific activity unless complementary data are available. The generalization of molecular biology approaches such as whole transcriptome analysis and recombinant DNA combined with biochemical approaches provide unprecedented tools for overcoming these difficulties. This review highlights progress made with these new techniques for identifying the specific function of individual class III peroxidase genes taking as an example the model plant A. thaliana, as well as discussing some other plants.

PeroxiBase: the peroxidase database

Peroxidases (EC 1.11.1.x), which are encoded by small or large multigenic families, are involved in several important physiological and developmental processes. Analyzing their evolution and their distribution among various phyla could certainly help to elucidate the mystery of their extremely widespread and diversified presence in almost all living organisms. PeroxiBase was originally created for the exhaustive collection of class III peroxidase sequences from plants (Bakalovic, N., Passardi, F., et al., 2006. PeroxiBase: a class III plant peroxidase database. Phytochemistry 67, 534-539). The extension of the class III peroxidase database to all proteins capable to reduce peroxide molecules appears as a necessity. Our database contains haem and non-haem peroxidase sequences originated from annotated or not correctly annotated sequences deposited in the main repositories such as GenBank or UniProt KnowledgeBase. This new database will allow obtaining a global overview of the evolution the protein families and superfamilies capable of peroxidase reaction. In this rapidly growing field, there is a need for continual updates and corrections of the peroxidase protein sequences. Following the lack of unified nomenclature, we also introduced a unique abbreviation for each different family of peroxidases. This paper thus aims to report the evolution of the PeroxiBase database, which is freely accessible through a web server (http://peroxibase.isb-sib.ch). In addition to new categories of peroxidases, new specific tools have been created to facilitate query, classification and submission of peroxidase sequences.

Cadmium tolerance and hyperaccumulation by Thlaspi caerulescens populations grown in hydroponics are related to plant uptake characteristics in the field

In order to fully understand the hyperaccumulation process and to increase the potential of plants for phytoextraction purposes, there is a need for more investigation of hyperaccumulating species or populations. Five Swiss populations of Thlaspi caerulescens J. & C. Presl originating from non-metalliferous but naturally Cd-rich soils (1.1-9.2 mg Cd kg^-1) were compared with Ganges and Prayon populations and a non-accumulating species, Thlaspi perfoliatum (L.) F.K. Meyer, for their tolerance (shoot and root dry weight and root length) and Cd hyperaccumulation in hydroponics (0, 1, 5, 10, 20 and 50 μm Cd). In the field, the Swiss populations accumulated Zn and clearly hyperaccumulated Cd (up to 505 mg Cd kg^-1 dry weight). The general response was significantly different between populations but in general an increasing Cd concentration in solution led to a decrease in dry weight production and an increase in Cd concentration in shoots. The shoot dry weight was a more discriminating parameter for tolerance than root dry weight and total root length. The Swiss populations behaved similarly to the Ganges population but differently from the Prayon population. Cadmium concentrations in shoots were above 100 mg kg^-1 when plants were grown in 1 μm Cd, except for the Prayon population and T. perfoliatum. In addition, as 1 μm Cd did not induce any visible toxicity symptoms, it was found to be adequate to test Cd hyperaccumulation. However, the most striking feature was the positive linear relationship observed between the transfer factor (TF) calculated in the field and the response of a population to increasing Cd concentrations in solution, indicating that plant uptake in the field had an influence on the plant response in solution.

PeroxiBase: a class III plant peroxidase database

Class III plant peroxidases (EC 1.11.1.7), which are encoded by multigenic families in land plants, are involved in several important physiological and developmental processes. Their varied functions are not yet clearly determined, but their characterization will certainly lead to a better understanding of plant growth, differentiation and interaction with the environment, and hence to many exciting applications. Since there is currently no central database for plant peroxidase sequences and many plant sequences are not deposited in the EMBL/GenBank/DDBJ repository or the UniProt KnowledgeBase, this prevents researchers from easily accessing all peroxidase sequences. Furthermore, gene expression data are poorly covered and annotations are inconsistent. In this rapidly moving field, there is a need for continual updating and correction of the peroxidase superfamily in plants. Moreover, consolidating information about peroxidases will allow for comparison of peroxidases between species and thus significantly help making correlations of function, structure or phylogeny. We report a new database (PeroxiBase) accessible through a web server with specific tools dedicated to facilitate query, classification and submission of peroxidase sequences. Recent developments in the field of plant peroxidase are also mentioned.

Peroxidases have more functions than a Swiss army knife

Plant peroxidases (class III peroxidases) are present in all land plants. They are members of a large multigenic family. Probably due to this high number of isoforms, and to a very heterogeneous regulation of their expression, plant peroxidases are involved in a broad range of physiological processes all along the plant life cycle. Due to two possible catalytic cycles, peroxidative and hydroxylic, peroxidases can generate reactive oxygen species (ROS) (*OH, HOO*), polymerise cell wall compounds, and regulate H2O2 levels. By modulating their activity and expression following internal and external stimuli, peroxidases are prevalent at every stage of plant growth, including the demands that the plant meets in stressful conditions. These multifunctional enzymes can build a rigid wall or produce ROS to make it more flexible; they can prevent biological and chemical attacks by raising physical barriers or by counterattacking with a large production of ROS; they can be involved in a more peaceful symbiosis. They are finally present from the first hours of a plant's life until its last moments. Although some functions look paradoxical, the whole process is probably regulated by a fine-tuning that has yet to be elucidated. This review will discuss the factors that can influence this delicate balance.

Distribution of cadmium in leaves of Thlaspi caerulescens

Knowledge of the intracellular distribution of Cd in leaves is necessary in order to understand the mechanisms of hyperaccumulation in Thlaspi caerulescens. Ganges and Prayon, two ecotypes accumulating Cd to different levels, were grown in nutrient medium containing varying concentrations (0, 5, 10, 50, and 100 microM) of Cd. Several different approaches were combined in this study to (i) validate the results obtained by a specific method and (ii) establish the link between observations and measurements performed at different scales. In both ecotypes, Cd, localized by autoradiography, was found mainly at the edges of the leaves, but also in points of higher concentration spread over the whole limb surface. This localization was clearly correlated with the necrotic spots observed on Prayon leaves. Scanning electron microscopy coupled with energy dispersive X-ray microanalysis (cryo-SEM-EDXMA) and tissue fractionation (apoplasm, cell walls, mesophyll protoplasts, and lower epidermis) showed that Cd had similar patterns of distribution in leaf cells of both ecotypes. Cadmium was found both inside the cells and in the cell walls, mainly in the large epidermal cells but also in small epidermal cells. All the methods used agreed well and the results indicated that metal storage in the plants studied involves more than one compartment and that Cd is stored principally in the less metabolically active parts of leaf cells.

Hyperaccumulation of cadmium and zinc in Thlaspi caerulescens and Arabidopsis halleri at the leaf cellular level

Vacuolar compartmentalization or cell wall binding in leaves could play a major role in hyperaccumulation of heavy metals. However, little is known about the physiology of intracellular cadmium (Cd) sequestration in plants. We investigated the role of the leaf cells in allocating metal in hyperaccumulating plants by measuring short-term (109)Cd and (65)Zn uptake in mesophyll protoplasts of Thlaspi caerulescens "Ganges" and Arabidopsis halleri, both hyperaccumulators of zinc (Zn) and Cd, and T. caerulescens "Prayon," accumulating Cd at a lower degree. The effects of low temperature, several divalent cations, and pre-exposure of the plants to metals were investigated. There was no significant difference between the Michaelis-Menten kinetic constants of the three plants. It indicates that differences in metal uptake cannot be explained by different constitutive transport capacities at the leaf protoplast level and that plasma and vacuole membranes of mesophyll cells are not responsible for the differences observed in heavy metal allocation. This suggests the existence of regulation mechanisms before the plasma membrane of leaf mesophyll protoplasts. However, pre-exposure of the plants to Cd induced an increase in Cd accumulation in protoplasts of "Ganges," whereas it decreased Cd accumulation in A. halleri protoplasts, indicating that Cd-permeable transport proteins are differentially regulated. The experiment with competitors has shown that probably more than one single transport system is carrying Cd in parallel into the cell and that in T. caerulescens "Prayon," Cd could be transported by a Zn and Ca pathway, whereas in "Ganges," Cd could be transported mainly by other pathways.

The C-terminal domains of the GABA(b) receptor subunits mediate intracellular trafficking but are not required for receptor signaling

GABA(B) receptors are G-protein-coupled receptors that mediate slow synaptic inhibition in the brain and spinal cord. These receptors are heterodimers assembled from GABA(B1) and GABA(B2) subunits, neither of which is capable of producing functional GABA(B) receptors on homomeric expression. GABA(B1,) although able to bind GABA, is retained within the endoplasmic reticulum (ER) when expressed alone. In contrast, GABA(B2) is able to access the cell surface when expressed alone but does not couple efficiently to the appropriate effector systems or produce any detectable GABA-binding sites. In the present study, we have constructed chimeric and truncated GABA(B1) and GABA(B2) subunits to explore further GABA(B) receptor signaling and assembly. Removal of the entire C-terminal intracellular domain of GABA(B1) results in plasma membrane expression without the production of a functional GABA(B) receptor. However, coexpression of this truncated GABA(B1) subunit with either GABA(B2) or a truncated GABA(B2) subunit in which the C terminal has also been removed is capable of functional signaling via G-proteins. In contrast, transferring the entire C-terminal tail of GABA(B1) to GABA(B2) leads to the ER retention of the GABA(B2) subunit when expressed alone. These results indicate that the C terminal of GABA(B1) mediates the ER retention of this protein and that neither of the C-terminal tails of GABA(B1) or GABA(B2) is an absolute requirement for functional coupling of heteromeric receptors. Furthermore although GABA(B1) is capable of producing GABA-binding sites, GABA(B2) is of central importance in the functional coupling of heteromeric GABA(B) receptors to G-proteins and the subsequent activation of effector systems.