Metagenomics has provided the discovery of genes and metabolic pathways involved in the degradation of xenobiotics. Some microorganisms can metabolize these compounds, potentiating phytoremediation in association with plant. This study aimed to study the metagenome and the occurrence of atrazine degradation genes in rhizospheric soils of the phytoremediation species Inga striata and Caesalphinea ferrea. The genera of microorganisms predominant in the rhizospheric soils of I. striata and C. ferrea were Mycobacterium, Conexibacter, Bradyrhizobium, Solirubrobacter, Rhodoplanes, Streptomyces, Geothrix, Gaiella, Nitrospira, and Haliangium. The atzD, atzE, and atzF genes were detected in the rhizospheric soils of I. striata and atzE and atzF in the rhizospheric soils of C. ferrea. The rhizodegradation by both tree species accelerates the degradation of atrazine residues, eliminating toxic effects on plants highly sensitive to this herbicide. This is the first report for the species Agrobacterium rhizogenes and Candidatus Muproteobacteria bacterium and Micromonospora genera as atrazine degraders.

2,4,6-Trinitrotoluene (TNT) is a nitroaromatic explosive, highly toxic and mutagenic for organisms. In this study, we report for the first time the screening and isolation of TNT-degrading bacteria from Antarctic environmental samples with potential use as bioremediation agents. Ten TNT-degrading bacterial strains were isolated from Deception Island. Among them, Pseudomonas sp. TNT3 was selected as the best candidate since it showed the highest tolerance, growth, and TNT biotransformation capabilities. Our results showed that TNT biotransformation involves the reduction of the nitro groups. Additionally, Pseudomonas sp. TNT3 was capable of transforming 100 mg/L TNT within 48 h at 28 °C, showing higher biotransformation capability than Pseudomonas putida KT2440, a known TNT-degrading bacterium. Functional annotation of Pseudomonas sp. TNT3 genome revealed a versatile set of molecular functions involved in xenobiotic degradation pathways. Two putative xenobiotic reductases (XenA_TNT3 and XenB_TNT3) were identified by means of homology searches and phylogenetic relationships. These enzymes were also characterized at molecular level using homology modelling and molecular dynamics simulations. Both enzymes share different levels of sequence similarity with other previously described TNT-degrading enzymes and with their closest potential homologues in databases.

Fumonisins (FBs) are mycotoxins that are widely distributed in crops and feed, and ingestion of FBs -contaminated crops is harmful to animal health. Furthermore, it is unknown if Fumonisins B1 (FB1) can cause intestinal toxicity. To investigate FB1-induced intestinal toxicity, mice were treated with 0 or 5 mg/kg FB1 by gavage administration for 42 days. Histopathology indicated that FB1 exposure caused proliferation of intestinal epithelial cells, intestinal villi and epithelial layer shedding, intestinal gland atrophy, and necrosis. Notably, FB1 interfered with nuclear xenobiotic receptors (NXR) homeostasis by regulating the level of aryl hydrocarbon receptor (AHR), constitutive androstane receptor (CAR), pregnane X receptor (PXR) and downstream target genes (CYP450s). Moreover, abnormal expression of inflammatory cytokines (IL-1β, IL-2, IL-4, IL-10, and TNF-α) indicated the occurrence of inflammation. The present study provides new insights regarding the mechanism of FB1-induced intestinal toxicity through activating the NXR system and by triggering inflammatory responses in the intestinal tract in mice.

The fluoride-sensitive indica rice cultivar, IR-64 was subjected to NaF-treatment for 25 days, following which RNA-Seq analysis identified significant up and down regulation of 1,303 and 93 transcripts respectively. Gene ontology (GO) enrichment analysis classified transcripts into groups related to ‘cellular part’, ‘membrane’, ‘catalytic activity’, ‘transporter activity’, ‘binding’, ‘metabolic processes’ and ‘cellular processes’. Analysis of differentially expressed genes (DEGs) revealed fluoride-mediated suppression of abscisic acid (ABA) biosynthesis and signaling. Instead, the gibberellin-dependent pathway and signaling via ABA-independent transcription factors (TFs) was activated. Comparative profiling of selected DEGs in IR-64 and fluoride-tolerant variety, Khitish revealed significant cytoskeletal and nucleosomal remodelling, accompanied with escalated levels of autophagy in stressed IR-64 (unlike that in stressed Khitish). Genes associated with ion, solute and xenobiotic transport were strongly up regulated in stressed IR-64, indicating potential fluoride entry through these channels. On the contrary, genes associated with xenobiotic mobility were suppressed in the tolerant cultivar, which restricted bioaccumulation and translocation of fluoride. Pairwise expression profile analysis between stressed IR-64 and Khitish, supported by extensive statistical modelling predicted that fluoride susceptibility was associated with high expression of genes like amino acid transporter, ABC transporter2, CLCd, MFS monosaccharide transporter, SulfT2.1 and PotT2 while fluoride tolerance with high expression of Sweet11.

Hydroxymethylfurfural (HMF) is a plant-based chemical building block that could potentially substitute petroleum-based equivalents, yet ecotoxicological data of this compound is currently limited. In this study, the effects of HMF on the reproduction and survival of Daphnia magna were assessed through validated ecotoxicological tests. The mechanism of toxicity was determined by analysis of transcriptomic responses induced by exposure to different concentrations of HMF using RNA sequencing. HMF exerted toxicity to D. magna with an EC₅₀ for effects on reproduction of 17.2 mg/l. HMF exposure affected molecular pathways including sugar and polysaccharide metabolism, lipid metabolism, general stress metabolism and red blood cell metabolism, although most molecular pathways affected by HMF exposure were dose specific. Hemoglobin genes, however, responded in a sensitive and dose-related manner. No induction of genes involved in the xenobiotic metabolism or oxidative stress metabolism pathway could be observed, which contrasted earlier observations on transcriptional responses of the terrestrial model Folsomia candida exposed to the same compound in a similar dose. We found 4189 orthologue genes between D. magna and F. candida, yet only twenty-one genes of those orthologues were co-regulated in both species. The contrasting transcriptional responses to the same compound exposed at a similar dose between D. magna and F. candida indicates limited overlap in stress responses among soil and aquatic invertebrates. The dose-related expression of hemoglobin provides further support for using hemoglobin expression as a biomarker for general stress responses in daphnids.

3,3′-dichlorobiphenyl (PCB-11) is an emerging PCB congener widely detected in environmental samples and human serum, but its toxicity potential is poorly understood. We assessed the effects of three concentrations of PCB-11 on embryotoxicity and Aryl hydrocarbon receptor (Ahr) pathway interactions in zebrafish embryos (Danio rerio). Wildtype AB or transgenic Tg(gut:GFP) strain zebrafish embryos were exposed to static concentrations of PCB-11 (0, 0.2, 2, or 20 μM) from 24 to 96 h post fertilization (hpf), and gross morphology, Cytochrome P4501a (Cyp1a) activity, and liver development were assessed via microscopy. Ahr interactions were probed via co-exposures with PCB-126 or beta-naphthoflavone (BNF). Embryos exposed to 20 μM PCB-11 were also collected for PCB-11 body burden, qRT-PCR, RNAseq, and histology. Zebrafish exposed to 20 μM PCB-11 absorbed 0.18% PCB-11 per embryo at 28 hpf and 0.61% by 96 hpf, and their media retained 1.36% PCB-11 at 28 hpf and 0.84% at 96 hpf. This concentration did not affect gross morphology, but altered the transcription of xenobiotic metabolism and liver development genes, impeded liver development, and increased hepatocyte vacuole formation. In co-exposures, 20 μM PCB-11 prevented deformities caused by PCB-126 but exacerbated deformities in co-exposures with BNF. This study suggests that PCB-11 can affect liver development, act as a partial agonist/antagonist of the Ahr pathway, and act as an antagonist of Cyp1a activity to modify the toxicity of compounds that interact with the Ahr pathway.

Ingestion of silver nanoparticles (AgNPs) is inevitable linked to their widespread use in food, medicines and other consumer products. However, their effects on human microbiota at non-lethal concentrations remain poorly understood.In this study, the interactions among 1 μg mL−1 AgNPs, the intestinal microbiota, and the probiotic Bacillus subtilis (BS) were tested using in-vitro batch fermentation models inoculated with human fecal matter.Results from metagenomic investigations revealed that the core bacterial community was not affected by the exposure of AgNPs and BS at the later stage of fermentation, while the proportions of rare species changed drastically with the treatments. Furthermore, shifts in the Firmicutes/Bacteriodetes (F/B) ratios were observed after 24 h with an increase in the relative abundance of Firmicutes species and a decrease in Bacteroidetes in all fermentation cultures. The co-exposure to AgNPs and BS led to the lowest F/B ratio.Fluorescent in-situ hybridization analyses indicated that non-lethal concentration of AgNPs negatively affected the relative percentage of Faecalibacterium prausnitzii and Clostridium coccoides/Eubacterium rectales taxa in the fermentation cultures after 24 h. However, exposure to single and combined treatments of AgNPs and BS did not change the overall diversity of the fecal microflora.Functional differences in cell motility, translation, transport, and xenobiotics degradation occurred in AgNPs-treated fermentation cultures but not in AgNPs+BS-treated samples.Compared to the control samples, treated fecal cultures showed no significant statistical differences in terms of short-chain fatty acids profiles, cytotoxic and genotoxic effects on Caco-2 cell monolayers.Overall, AgNPs did not affect the composition and diversity of the core fecal microflora and its metabolic and toxic profiles. This work indicated a chemopreventive role of probiotic on fecal microflora against AgNPs, which were shown by the decrease of F/B ratio and the unaltered state of some key metabolic pathways.

Per- and polyfluoroalkyl substances (PFASs) are a large group of chemicals and can be detected in environmental and human samples all over the world. Toxicity of existing and emerging PFASs will be a long-term source of concern. This study aimed to investigate structure-dependent inhibitory effects of 14 PFASs towards the activity of 11 UDP-glucuronosyltransferase (UGT) isoforms. In vitro UGTs-catalyzed glucuronidation of 4-methylumbelliferone (4-MU) was employed to determine the inhibition of PFASs towards different UGT isoforms. All the PFASs showed <75% of inhibition or stimulation effects on UGT1A3, UGT1A7, UGT1A9, UGT2B4, UGT2B7 and UGT2B17. However, PFASs showed broad inhibition on the activity of UGT1A1 and UGT1A8. The activity of UGT1A1 was inhibited by 98.8%, 98%, 79.9%, 77.1%, and 76.9% at 100 μmoL/L of perfluorodecanoic acid (PFDA), perfluorooctanesulfonic acid potassium salt (PFOS), perfluorotetradecanoic acid (PFTA), perfluorooctanoic acid (PFOA) and perfluorododecanoic acid (PFDoA), respectively. UGT1A8 was inhibited by 97.6%, 94.8%, 86.3%, 83.4% and 77.1% by PFDA, PFTA, perfluorooctadecanoic acid (PFOcDA), PFDoA and PFOS, respectively. Additionally, PFDA significantly inhibited UGT1A6 and UGT1A10 by 96.8% and 91.6%, respectively. PFDoA inhibited the activity of UGT2B15 by 88.2%. PFDA and PFOS exhibited competitive inhibition towards UGT1A1, and PFDA and PFTA showed competitive inhibition towards UGT1A8. The inhibition kinetic parameter (Kᵢ) were 3.15, 1.73, 13.15 and 20.21 μmoL/L for PFDA-1A1, PFOS-1A1, PFDA-1A8 and PFTA-1A8, respectively. The values were calculated to be 0.3 μmoL/L and 1.3 μmoL/L for the in vivo inhibition of PFDA towards UGT1A1-and UGT1A8-catalyzed metabolism of substances, and 0.2 μmoL/L and 2.0 μmoL/L for the inhibition of PFOS towards UGT1A1 and the inhibition of PFTA towards UGT1A8, respectively. Molecular docking indicated that hydrogen bonds and hydrophobic interactions contributed to the interaction between PFASs and UGT isoforms. In conclusion, exposure to PFASs might inhibit the activity of UGTs to disturb metabolism of endogenous compounds and xenobiotics. The structure-related effects of PFASs on UGTs would be very important for risk assessment of PFASs.

Various crustaceans are farmed using aquaculture, and food deprivation or fasting can occur due to changing of environmental or management strategies. However, the molecular mechanisms underlying responses to starvation in crustaceans remain unclear. To address this, 12 hepatopancreas transcriptomes were compared for oriental river prawn (Macrobrachium nipponense) from four fasting stages (0, 7, 14 and 21 d). Gene Ontology functional annotation and Kyoto Encyclopaedia of Genes and Genomes pathway enrichment analysis of differentially expressed genes were subsequently performed. During the early stages of starvation (0–7 d), drug metabolism via the cytochrome P450 pathway and metabolism of xenobiotics by the cytochrome P450 pathway were enriched, suggesting that they metabolised compounds generated under starvation stress. As starvation proceeded (7–14 d), the retinol (vitamin A) metabolism pathway was activated, based on three up-regulated genes (CYP3, ADH and UGT), along with the two p450 pathways. Meanwhile, vitamin A was gradually consumed. As acute starvation was reached (14–21 d), vitamin A deficiency decreased the mRNA expression levels of IGF-I that is involved in the mTOR signalling pathway, which ultimately affected the growth and development of M. nipponense. Our results implicate drug/xenobiotic metabolism by cytochrome P450s in adaptation to starvation stress. Furthermore, metabolic cascades (CYP and retinol pathways) and growth (mTOR signalling) pathways are clearly triggered in crustaceans during starvation. The findings expand our understanding of the genes associated with hepatopancreas functioning in M. nipponense, and the underlying molecular mechanisms that govern the responses of crustaceans to starvation stress.

Microplastics are well-documented pollutants in the marine environment that result from production or fragmentation of larger plastic items. The knowledge about the direct effects of microplastics on immunity, including fish, is still very limited. We investigated the in vitro effects of microplastics [polyvinylchloride (PVC) and polyethylene (PE)] on gilthead seabream (Sparus aurata) and European sea bass (Dicentrarchus labrax) head-kidney leucocytes (HKLs). After 1 and 24 h of exposure of HKLs with 0 (control), 1, 10 and 100 mg mL⁻¹ MPs in a rotatory system, cell viability, innate immune parameters (phagocytic, respiratory burst and peroxidase activities) and the expression of genes related to inflammation (il1b), oxidative stress (nrf2, prdx3), metabolism of xenobiotics (cyp1a1, mta) and cell apoptosis (casp3) were studied. Microplastics failed to affect the cell viability of HKLs. In addition, they provoke very few significant effects on the main cellular innate immune activities, as decrease on phagocytosis or increase in the respiratory burst of HKLs with the highest dose of microplastics tested. Furthermore, microplastics failed to affect the expression of the selected genes on sea bass or seabream, except the nrf2 which was up-regulated in seabream HKLs incubated with the highest doses. Present results seem to suggest that continue exposure of fish to PVC or PE microplastics could impair fish immune parameters probably due to the oxidative stress produced in the fish leucocytes.