The Pearl River Estuary (PRE) is the largest estuary in southern China and under high metal stress. In the present study, we employed an integrated method of transcriptomics and proteomics to investigate the ecotoxicological effects of trace metals on the Hong Kong oyster Crassostrea hongkongensis. Three oyster populations with distinct spatial distributions of metals were sampled, including the Control (Station QA, the lowest metal levels), the High Cd (Station JZ, the highest Cd), and the High Zn–Cu–Cr–Ni (Station LFS, with the highest levels of zinc, copper, chromium, and nickel). Dominant metals in oysters were differentiated by principal component analysis (PCA), and theirgene and protein profiles were studied using RNA-seq and iTRAQ techniques. Of the 2250 proteins identified at both protein and RNA levels, 70 proteins exhibited differential expressions in response to metal stress in oysters from the two contaminated stations. There were 8 proteins altered at both stations, with the potential effects on mitochondria and endoplasmic reticulum by Ag. The genotoxicity, including impaired DNA replication and transcription, was specifically observed in the High Cd oysters with the dominating influence of Cd. The structural components (cytoskeleton and chromosome-associated proteins) were impaired by the over-accumulated Cu, Zn, Cr, and Ni at Station LFS. However, enhanced tRNA biogenesis and exosome activity might help the oysters to alleviate the toxicities resulting from their exposure to these metals. Our study provided comprehensive information on the molecular changes in oysters at both protein and RNA levels in responding to multi-levels of trace metal stress.

The complexation with extracellular polymeric substances (EPS) greatly reduces the toxicity of heavy metals towards organisms in the environment. However, the molecular mechanism of EPS−metal complexation remains unclear owing to the limitation of precise analysis for key fractions and functionalities in EPS that associate with metals. Herein, we explored the EPS−Cd (II) complexation by fluorescence excitation emission matrix coupled with parallel factor (EEM−PARAFAC), two-dimensional Fourier transform infrared correlation spectroscopy (2D-FTIR−COS) and X-ray photoelectron spectroscopy (XPS), attempting to explain the mechanisms of EPS in alleviating Cd (II) toxicity toward a green alga Chlorella vulgaris (C. vulgaris). When the algal EPS were removed, the cell internalizations of Cd (II), growth inhibition rate and chlorophyll autofluorescence increased, but the surface adsorption and esterase activities decreased, indicating that the sorption of Cd (II) by EPS was crucial in alleviating the algal toxicity. Moreover, the complexation with proteins in EPS controlled the sorption of Cd (II) to algal EPS, resulting in the chemical static quenching of the proteins fluorescence by 47.69 ± 2.37%. Additionally, the complexing capability of the main functionalities, COO⁻ and C–OH in proteins with Cd (II) was stronger than that of C–O(H) and C–O–C in polysaccharides or C–OH in the humus-related substances. Oxygen atom in protein carboxyl C–O might be the key site of EPS−Cd (II) complexation, supported by the modified Ryan−Weber complexation model and the obvious shift of oxygen valence-electron signal. These findings provide deep insights into understanding the interaction of EPS with heavy metals in aquatic environment.

Cadmium (Cd) is an important heavy metal pollutant in the Bohai Sea. Mitochondria are recognized as the key target for Cd toxicity. However, mitochondrial responses to Cd have not been fully investigated in marine fishes. In this study, the mitochondrial responses were characterized in gills of juvenile flounder Paralichthys olivaceus treated with two environmentally relevant concentrations (5 and 50 μg/L) of Cd for 14 days by determination of mitochondrial membrane potential (MMP), observation of mitochondrial morphology and quantitative proteomic analysis. Both Cd treatments significantly decreased MMPs of mitochondria from flounder gills. Mitochondrial morphologies were altered in Cd-treated flounder samples, indicated by more and smaller mitochondria. iTRAQ-based proteomic analysis indicated that a total of 128 proteins were differentially expressed in both Cd treatments. These proteins were basically involved in various biological processes in gill mitochondria, including mitochondrial morphology and import, tricarboxylic acid (TCA) cycle, oxidative phosphorylation (OXPHOS), primary bile acid biosynthesis, stress resistance and apoptosis. These results indicated that dynamic regulations of energy homeostasis, cholesterol metabolism, stress resistance, apoptosis, and mitochondrial morphology in gill mitochondria might play significant roles in response to Cd toxicity. Overall, this study provided a global view on mitochondrial toxicity of Cd in flounder gills using iTRAQ-based proteomics.

The synergistic cooperation of microbial cells and their extracellular polymeric substances (EPS) in biofilms is critical for the biofilm’s resistance to heavy metals and the migration and transformation of heavy metals. However, the effects of different components of biofilms have not been fully understood. In this study, the spatial distribution and speciation of copper in the colloidal EPS, capsular EPS, cell walls and membranes, and intracellular fraction of unsaturated Pseudomonas putida (P. putida) CZ1 biofilms were fully determined at the subcellular level. It was found that 60–67% of copper was located in the extracellular fraction of biofilms, with 44.7–42.3% in the capsular EPS. In addition, there was 15.5–20.1% and 17.2–21.2% of copper found in the cell walls and membranes or the intracellular fraction, respectively. Moreover, an X-ray absorption fine structure spectra analysis revealed that copper was primarily bound by carboxyl-, phosphate-, and hydrosulfide-like ligands within the extracellular polymeric matrix, cell walls and membranes, and intracellular fraction, respectively. In addition, macromolecule quantification, fourier-transform infrared spectroscopy spectra and sulfur K-edge x-ray absorption near edge structure analysis further showed the carboxyl-rich acidic polysaccharides in EPS, phospholipids in cell walls and cell membranes, and thiol-rich intracellular proteins were involved in binding of copper in the different components of biofilm. The full understanding of the distribution and chemical species of heavy metals in biofilms not only promotes a deep understanding of the interaction mechanisms between biofilms and heavy metals, but also contributes to the development of effective biofilm-based heavy metal pollution remediation technologies.

Hydrogen gas (H₂) has been shown as an important factor in plant tolerance to abiotic stresses, but the underlying mechanisms remain unclear. In the present study, the effects of H₂ and its interaction with nitric oxide (NO) on alleviating cadmium (Cd) stress in Brassica campestris seedlings were investigated. NO donor (SNP) or hydrogen-rich water (HRW) treatment showed a significant improvement in growth of Cd-stressed seedlings. Cd treatment upregulated both endogenous NO and H₂ (36% and 66%, respectively), and the increase of H₂ was prior to NO increase. When treated with NO scavenger (PTIO) or NO biosynthesis enzyme inhibitors (L-NAME and Gln), HRW-induced alleviation under Cd stress was prevented. Under Cd stress, HRW pretreatment significantly enhanced the NO accumulation, and together up-regulated the activity of NR (nitrate reductase) and expression of NR. HRW induced lower reactive oxygen species (ROS), higher AsA content, enhanced activity of POD (peroxidase) and SOD (superoxide dismutase) in seedling roots were inhibited by PTIO, L-NAME and Gln. Through proteomic analysis, the level of 29 proteins were changed in response to H₂ and NO-induced amelioration of Cd stress. Nearly half of them were involved in oxidation-reduction processes (about 20%) or antioxidant enzymes (approximately 20%). These results strongly indicate that in Cd-stressed seedlings, pretreatment with HRW induces the accumulation of H₂ (biosynthesized or permeated), which further stimulates the biosynthesis of NO through the NR pathway. Finally, H₂ and NO together enhance the antioxidant capabilities of seedlings in response to Cd toxicity.

Dibenzofuran (DBF) derivatives have caused serious environmental problems, especially those produced by paper pulp bleaching and incineration processes. Prominent for its resilient mutagenicity and toxicity, DBF poses a major challenge to human health. In the present study, a new strain of Pseudomonas aeruginosa, FA-HZ1, with high DBF-degrading activity was isolated and identified. The determined optimum conditions for cell growth of strain FA-HZ1 were a temperature of 30 °C, pH 5.0, rotation rate of 200 rpm and 0.1 mM DBF as a carbon source. The biochemical and physiological features as well as usage of different carbon sources by FA-HZ1 were studied. The new strain was positive for arginine double hydrolase, gelatinase and citric acid, while it was negative for urease and lysine decarboxylase. It could utilize citric acid as its sole carbon source, but was negative for indole and H2S production. Intermediates of DBF 1,2-dihydroxy-1,2-dihydrodibenzofuran, 1,2-dihydroxydibenzofuran, 2-hydroxy-4-(3′-oxo-3′H-benzofuran-2′-yliden)but-2-enoic acid, 2,3-dihydroxybenzofuran, 2-oxo-2-(2′-hydrophenyl)lactic acid, and 2-hydroxy-2-(2′-hydroxyphenyl)acetic acid were detected and identified through liquid chromatography-mass analyses. FA-HZ1 metabolizes DBF by both the angular and lateral dioxygenation pathways. The genomic study identified 158 genes that were involved in the catabolism of aromatic compounds. To identify the key genes responsible for DBF degradation, a proteomic study was performed. A total of 1459 proteins were identified in strain FA-HZ1, of which 100 were up-regulated and 104 were down-regulated. A novel enzyme “HZ6359 dioxygenase”, was amplified and expressed in pET-28a in E. coli BL21(DE3). The recombinant plasmid was successfully constructed, and was used for further experiments to verify its function. In addition, the strain FA-HZ1 can also degrade halogenated analogues such as 2, 8-dibromo dibenzofuran and 4-(4-bromophenyl) dibenzofuran. Undoubtedly, the isolation and characterization of new strain and the designed pathways is significant, as it could lead to the development of cost-effective and alternative remediation strategies. The degradation pathway of DBF by P. aeruginosa FA-HZ1 is a promising tool of biotechnological and environmental significance.

The release of hexavalent chromium [Cr(VI)] into water bodies poses a major threat to the environment and human health. However, studies of the biological response to Cr(VI) are limited. In this study, a toxic bacterial mechanism of Cr(VI) was investigated using Pannonibacter phragmitetus BB (hereafter BB), which was isolated from chromate slag. The maximum Cr(VI) concentrations with respect to the resistance and reduction by BB are 4000 mg L−1 and 2500 mg L−1, respectively. In the BB genome, more genes responsible for Cr(VI) resistance and reduction are observed compared with other P. phragmitetus strains. A total of 361 proteins were upregulated to respond to Cr(VI) exposure, including enzymes for Cr(VI) uptake, intracellular reduction, ROS detoxification, DNA repair, and Cr(VI) efflux and proteins associated with novel mechanisms involving extracellular reduction mediated by electron transfer, quorum sensing, and chemotaxis. Based on metabolomic analysis, 174 metabolites were identified. Most of the upregulated metabolites are involved in amino acid, glucose, lipid, and energy metabolisms. The results show that Cr(VI) induces metabolite production, while metabolites promote Cr(VI) reduction. Overall, multi-enzyme expression and metabolite production by BB contribute to its high ability to resist/reduce Cr(VI). This study provides details supporting the theory of Cr(VI) reduction and a theoretical basis for the efficient bioremoval of Cr(VI) from the environment.

Iron-bearing clays are ubiquitously distributed as mineral dusts in the atmosphere. Bromophenols were reported as the major products from thermal decomposition of the widely used brominated flame retardants (BFRs). However, little information is available for the reactivity of iron associated with mineral dusts to interact with the atmospheric bromophenols and the subsequent toxic effects. Herein, three common clay minerals (montmorillonite, illite and kaolinite) were used to simulate mineral dusts, and the reactions with gaseous 2-bromophenol were systematically investigated under environmentally relevant atmospheric conditions. Our results demonstrate that structural Fe(III) in montmorillonite and Fe(III) from iron oxide in illite mediated the dimerization of 2-bromophenol to form hydroxylated polybrominated biphenyl and hydroxylated polybrominated diphenyl ether. The surface reaction is favored to occur at moisture environment, since water molecules formed complex with 2-bromophenol and the reaction intermediates via hydrogen bond to significantly lower the reaction energy and promote the dimerization reaction. More importantly, the formed dioxin-like products on clay mineral dust increased the toxicity of the particles to A549 lung cell by decreasing cell survival and damaging cellular membrane and proteins. The results of this study indicate that not only mineral dust itself but also the associated surface reaction should be fully considered to accurately evaluate the toxic effect of mineral dust on human health.

Microplastics (MPs) are now one of the major environmental problems due to the large amount released in aquatic and terrestrial ecosystems, as well as their diffuse sources and potential impacts on organisms and human health. Still the molecular and cellular targets of microplastics’ toxicity have not yet been identified and their mechanism of actions in aquatic organisms are largely unknown. In order to partially fill this gap, we used a mass spectrometry based functional proteomics to evaluate the modulation of protein profiling in zebra mussel (Dreissena polymorpha), one of the most useful freshwater biological model. Mussels were exposed for 6 days in static conditions to two different microplastic mixtures, composed by two types of virgin polystyrene microbeads (size = 1 and 10 μm) each one. The mixture at the lowest concentration contained 5 × 105 MP/L of 1 μm and 5 × 105 MP/L of 10 μm, while the higher one was arranged with 2 × 106 MP/L of 1 μm and 2 × 106 MP/L of 10 μm.Proteomics’ analyses of gills showed the complete lack of proteins’ modulation after the exposure to the low-concentrated mixture, while even 78 proteins were differentially modulated after the exposure to the high-concentrated one, suggesting the presence of an effect-threshold. The modulated proteins belong to 5 different classes mainly involved in the structure and function of ribosomes, energy metabolism, cellular trafficking, RNA-binding and cytoskeleton, all related to the response against the oxidative stress.

During the last years, declines in honey bee colonies are being registered worldwide. Cholinergic pesticides and their extensive use have been correlated to the decline of pollinators and there is evidence that pesticides act as neuroendocrine disruptors affecting the metabolism of neuropeptides. However, there is a big absence of studies with quantitative results correlating the effect of pesticide exposure with changes on neuropeptides insects, and most of them are conducted under laboratory conditions, typically with individual active ingredients. In this study, we present an analytical workflow to evaluate pesticide effects on honey bees through the analysis of (neuro)peptides. The workflow consists of a rapid extraction method and liquid chromatography with triple quadrupole for preselected neuropeptides. For non-target analysis, high resolution mass spectrometry, multivariate analysis and automatic identification of discriminated peptides using a specific software and protein sequence databases. The analytical method was applied to the analysis of target and non-target (neuro)peptides in honey bees with low and high content of a wide range of pesticides to which have been exposed in field conditions. Our findings show that the identification frequency of target neuropeptides decreases significantly in honey bees with high concentration of pesticides (pesticide concentrations ≥ 500 μg kg⁻¹) in comparison with the honey bees with low content of pesticides (pesticide concentrations ≤ 20 μg kg⁻¹). Moreover, the principal component analysis in non-target search shows a clear distinction between peptide concentration in honey bees with high level of pesticides and honey bees with low level. The use of high resolution mass spectrometry has allowed the identification of 25 non-redundant peptides responsible for discrimination between the two groups, derived from 18 precursor proteins.