Whole-transcriptome response to wastewater treatment plant and stormwater effluents in the Asian clam, Corbicula fluminea

Epigenetic changes induced by chronic and acute chromium stress treatments in Arabidopsis thaliana identified by the MSAP-Seq

Chromium (Cr) is an highly toxic metal to plants and causes severe damage to their growth, development, and reproduction. Plant exposure to chronic and acute Cr stress treatments results in significant changes at short time in the gene expression profile and at long time in the genomic DNA methylation profile at a transgenerational level and, consequently, in gene expression. These epigenetic modifications and their implications imposed by the Cr stress are not yet completely known in plants. Herein, were identified the epigenetic changes induced by chronic and acute Cr stress treatments in Arabidopsis thaliana plants using Methylation Sensitive Amplification Polymorphism coupled with next-generation sequencing (MSAP-Seq). First-generation Arabidopsis plants (termed F0 plants) kept under hoagland solution were subjected to Cr stress treatments. For chronic Cr stress, plants were treated through hoagland solution with 2.5 μM Cr during the entire cultivation period until seed harvest. Meanwhile, for acute Cr stress, plants were treated with 5 μM Cr during the first three weeks and returned to unstressful control condition until seed harvest. Seeds from F0 plants were sown and F1 plants were re-submitted to the same Cr stress treatments. The seed germination rate was evaluated from F-2 seeds harvested of F1 plants kept under different Cr stress treatments (0, 10, 20, and 40 μM) compared to the unstressful control condition. These data showed significant changes in the germination rate of F-2 seeds originating from stressed F1 plants compared to F-2 seeds harvested from unstressful control plants. Given this data, F1 plants kept under these chronic and acute Cr stress treatments and unstressful control condition were evaluated for the transgenerational epigenetic modifications using MSAP-Seq. The MSAP-Seq data showed that several genes were modified in their methylation status as a consequence of chronic and acute Cr stress treatment to maintain plant defenses activated. In particular, RNA processing, protein translation, photorespiration, energy production, transmembrane transport, DNA transcription, plant development, and plant resilience were the major biological processes modulated by epigenetic mechanisms identified in F1 plants kept under chronic and acute Cr stress. Therefore, collective data suggested that Arabidopsis plants kept under Cr stress regulate their epigenetic status over generations based on DNA methylation to modulate defense and resilience mechanisms.

Impacts of wastewater effluents and seasonal trends on levels of antipsychotic pharmaceuticals in water and sediments from two cold-region rivers

Most pharmaceuticals are found at trace concentrations in aquatic systems, but their continuous release and potential accumulation can lead to adverse health effects in exposed organisms. Concentrations can vary temporally, driven by variations in discharges of receiving waters, sorption to sediments, and other biotic and abiotic exchange processes. The principal aim of this research was to better understand the occurrence, trends, and dynamics of pharmaceuticals in a cold-climate, riverine environment. To this end, a suite of seven representative antipsychotic pharmaceuticals was measured upstream and downstream of two wastewater treatment plants (WWTPs) in Saskatchewan, Canada, located in the South Saskatchewan River and Wascana Creek, respectively, across three seasons. Concentrations of analytes were in the ng/L range and generally greater downstream of both WWTPs compared to upstream. Some compounds, including the tricyclic antidepressant amitriptyline, which was the most abundant analyte in water and sediment from both sites and across seasons, reached low μg/L concentrations. Data collected from this research effort indicate contamination with antipsychotic pharmaceuticals, with the potential to adversely impact exposed organisms.

PacBio Full-Length and Illumina Transcriptomes of the Gill Reveal the Molecular Response of Corbicula fluminea under Aerial Exposure

Air exposure is a common stress for Corbicula fluminea, an economically important freshwater shellfish consumed in China, during aquaculture and transportation. However, little is known about its molecular responses to air exposure. Therefore, this study used a combination of PacBio full-length and Illumina transcriptomes to investigate its molecular responses to air exposure. A total of 36,772 transcripts were obtained using PacBio sequencing. Structural analysis identified 32,069 coding sequences, 1906 transcription factors, 8873 simple sequence repeats, and 17,815 long non-coding RNAs. Subcellular localization analysis showed that most transcripts were located in the cytoplasm and nucleus. After 96-h of air exposure, 210 differentially expressed genes (DEGs) in the gill were obtained via Illumina sequencing. Among these DEGs, most of the genes related to glycolysis, tricarboxylic acid cycle, lipid metabolism, and amino acid metabolism were upregulated. Additionally, many DEGs associated with immunity, cytoskeleton reorganization, autophagy, and ferroptosis were identified. These findings indicated that metabolic strategy change, immune response, cytoskeleton reconstruction, autophagy, and ferroptosis might be the important mechanisms that C. fluminea use to cope with air exposure. This study will enrich the gene resources of C. fluminea and provide valuable data for studying the molecular mechanisms coping with air exposure in C. fluminea and other freshwater mollusks.

Complete mitochondrial genome sequence of a brackish water clam Corbicula japonica (Cyrenidae: Bivalvia) collected from an estuary of Gwangyang Bay in Korea

The complete mitochondrial genome of the clam Corbicula japonica is 17,432 bp in length. The sequence consists of 13 protein-coding, 2 ribosomal RNAs, and 22 transfer RNA genes (GenBank accession no. MZ895053). The proportion of base-pairs in C. japonica are A + T (70.5%) and G + C (29.5%). Phylogenetic analysis reveal C. japonica to be sister species to C. fluminea within the monophyletic genus Corbicula, with high support. This study is helpful to the classification of the brackish water clam C. japonica, which is difficult to identify during early development owing to variation of shell morphology.

Using the Daphnia magna Transcriptome to Distinguish Water Source: Wetland and Stormwater Case Studies

A major challenge in ecotoxicology is accurately and sufficiently measuring chemical exposures and biological effects given the presence of complex and dynamic contaminant mixtures in surface waters. It is impractical to quantify all chemicals in such matrices over space and time, and even if it were practical, concomitant biological effects would not be elucidated. Our study examined the performance of the Daphnia magna transcriptome to detect distinct responses across three water sources in Minnesota: laboratory (well) waters, wetland waters, and storm waters. Pyriproxyfen was included as a gene expression and male neonate production positive control to examine whether gene expression resulting from exposure to this well-studied juvenoid hormone analog can be detected in complex matrices. Laboratory-reared (<24 h) D. magna were exposed to a water source and/or pyriproxyfen for 16 days to monitor phenotypic changes or 96 h to examine gene expression responses using Illumina HiSeq 2500 (10 million reads per library, 50-bp paired end [2 × 50]). The results indicated that a unique gene expression profile was produced for each water source. At 119 ng/L pyriproxyfen (~25% effect concentration) for male neonate production, as expected, the Doublesex1 gene was up-regulated. In descending order, gene expression patterns were most discernable with respect to pyriproxyfen exposure status, season of stormwater sample collection, and wetland quality, as indicated by the index of biological integrity. However, the biological implications of the affected genes were not broadly clear given limited genome resources for invertebrates. Our study provides support for the utility of short-term whole-organism transcriptomic testing in D. magna to discern sample type, but highlights the need for further work on invertebrate genomics. Environ Toxicol Chem 2022;41:2107-2123. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Full-Length Transcriptome Sequencing Reveals Tissue-Specific Gene Expression Profile of Mangrove Clam Geloina erosa

Mollusca is the second largest animal phylum and represents one of the most evolutionarily successful animal groups. Geloina erosa, a species of Corbiculidae, plays an important role in mangrove ecology. It is highly adaptable and can withstand environmental pollution and microbial infections. However, there is no reference genome or full-length transcriptome available for G. erosa. This impedes the study of the biological functions of its different tissues because transcriptome research requires reference genome or full-length transcriptome as a reference to improve accuracy. In this study, we applied a combination of Illumina and PacBio single-molecule real-time sequencing technologies to sequence the full-length transcriptomes of G. erosa tissues. Transcriptomes of nine samples obtained from three tissues (hepatopancreas, gill, and muscle) were sequenced using Illumina. Furthermore, we obtained 87,310 full-length reads non-chimeric sequences. After removing redundancy, 22,749 transcripts were obtained. The average Q score of 30 was 94.48%. In total, 271 alternative splicing events were predicted. There were 14,496 complete regions and 3,870 lncRNAs. Differential expression analysis revealed tissue-specific physiological functions. The gills mainly express functions related to filtration, metabolism, identifying pathogens and activating immunity, and neural activity. The hepatopancreas is the main tissue related to metabolism, it also involved in the immune response. The muscle mainly express functions related to muscle movement and control, it contains more energy metabolites that gill and hepatopancreas. Our research provides an important reference for studying the gene expression of G. erosa under various environmental stresses. Moreover, we present a reliable sequence that will provide an excellent foundation for further research on G. erosa.

Integrated Genomic and Bioinformatics Approaches to Identify Molecular Links between Endocrine Disruptors and Adverse Outcomes

Exposure to Endocrine Disrupting Chemicals (EDC) has been linked with several adverse outcomes. In this review, we examine EDCs that are pervasive in the environment and are of concern in the context of human, animal, and environmental health. We explore the consequences of EDC exposure on aquatic life, terrestrial animals, and humans. We focus on the exploitation of genomics technologies and in particular whole transcriptome sequencing. Genome-wide analyses using RNAseq provides snap shots of cellular, tissue and whole organism transcriptomes under normal physiological and EDC perturbed conditions. A global view of gene expression provides highly valuable information as it uncovers gene families or more specifically, pathways that are affected by EDC exposures, but also reveals those that are unaffected. Hypotheses about genes with unknown functions can also be formed by comparison of their expression levels with genes of known function. Risk assessment strategies leveraging genomic technologies and the development of toxicology databases are explored. Finally, we review how the Adverse Outcome Pathway (AOP) has exploited this high throughput data to provide a framework for toxicology studies.

Constructing a de novo transcriptome and a reference proteome for the bivalve Scrobicularia plana: Comparative analysis of different assembly strategies and proteomic analysis

Scrobicularia plana is a coastal and estuarine bivalve widely used in ecotoxicological studies. However, the underlying molecular mechanisms for S. plana pollutant responses are hardly known due to the lack of molecular databases. Thus, in this study we present a holistic approach to assess a robust reference transcriptome and proteome of this clam. A mixture of control and metal-exposed individuals was used for mRNA isolation. Four sets of high quality filtered preprocessed reads were generated (two quality scores and two sequenced lengths) and assembled with Mira, Ray and Trinity algorithms. The sixty-four generated assemblies were refined, filtered and evaluated for their proteomic quality. Eight assemblies presented top Detonate scores but one was selected due to its compactness and biological representation, which was generated: (i) from the highest quality dataset (Q20L100), (ii) using Trinity algorithm with all k-mers (AtKa), (iii) removing redundancy by CD-HIT (RR80), and (iv) filtering out poor contigs (F), that was subsequently named Q20L100AtKaRR80F. S. plana proteomic analysis revealed 10,017 peptide groups that corresponded to 2066 proteins with a wide coverage of molecular functions and biological processes, confirming the strength of the database generated.

Effects on the Liver Transcriptome in Baltic Salmon: Contributions of Contamination with Organohalogen Compounds and Origin of Salmon

Hatchery-reared Atlantic salmon (Salmo salar) has been released to support the wild salmon stocks in the Baltic Sea for decades. During their feeding migration, salmon are exposed to organohalogen compounds (OHCs). Here, we investigated the OHC levels and transcriptome profiles in the liver of wild and hatchery-reared salmon collected from the Baltic main basin (BMB), the Bothnian Sea (BS), and the Gulf of Finland (GoF) and examined whether salmon origin and OHC levels contributed to the hepatic transcriptome profiles. There were no differences in the OHC concentrations between wild and reared fish but larger differences between areas. Several transcript levels were associated with non-dioxin-like polychlorinated biphenyls, polybrominated diphenylethers, chlordanes, and dichlorodiphenyltrichloroethane in a concentration-dependent manner. Between wild and reared salmon, lipid metabolism and related signaling pathways were enriched within the BMB and BS, while amino acid metabolism was altered within the GoF. When comparing the different areas, lipid metabolism, environmental stress and cell growth, and death-related pathways were enriched. Class coinertia analysis showed that the covariation in the OHC levels and the transcriptome were significantly similar. These results suggest that the hepatic transcriptomes in wild and hatchery-reared salmon are more affected by the OHC levels rather than the origin of salmon.

Urban ecophysiology: beyond costs, stress and biomarkers

Natural habitats are rapidly declining due to urbanisation, with a concomitant decline in biodiversity in highly urbanised areas. Yet thousands of different species have colonised urban environments. These organisms are exposed to novel urban conditions, which are sometimes beneficial, but most often challenging, such as increased ambient temperature, chemicals, noise and light pollution, dietary alterations and disturbance by humans. Given the fundamental role of physiological responses in coping with such conditions, certain physiological systems such as the redox system, metabolism and hormones are thought to specifically influence organisms' ability to persist and cope with urbanisation. However, these physiological systems often show mixed responses to urbanisation. Does this mean that some individuals, populations or species are resilient to the urban environmental challenges? Or is something missing from our analyses, leading us to erroneous conclusions regarding the impact of urbanisation? To understand the impact of urbanisation, I argue that a more integrated mechanistic and ecological approach is needed, along with experiments, in order to fully understand the physiological responses; without knowledge of their ecological and evolutionary context, physiological measures alone can be misinterpreted. Furthermore, we need to further investigate the causes of and capacity for individual plasticity in order to understand not only the impact of urbanisation, but also species resilience. I argue that abiotic and biotic urban factors can interact (e.g. pollution with micro- and macronutrients) to either constrain or relax individual physiological responses - and, thereby, plasticity - on a temporal and/or spatial scale, which can lead to erroneous conclusions regarding the impact of urbanisation.

Arabidopsis mgd mutants with reduced monogalactosyldiacylglycerol contents are hypersensitive to aluminium stress

Aluminium (Al) is a key element that plays a major role in inhibiting plant growth and productivity under acidic soils. While lipids may be involved in plant tolerance/sensitivity to Al, the role of monogalactosyldiacylglycerol (MGDG) in Al response remains unknown. In this study, Arabidopsis MGDG synthase (AtMGD) mutants (mgd1, mgd2 and mgd3) and wild-type (Col-0) plants were treated with AlCl₃; the effect of aluminium on root growth, aluminium distribution, plasma membrane integrity, lipid peroxidation, hydrogen peroxide content and membrane lipid compositions were analysed. Under Al stress, mgd mutants exhibited a more severe root growth inhibition, plasma membrane integrity damage and lipid peroxidation compared to Col-0. Al accumulation in root tips showed no difference between Col-0 and mutants under Al stress. Lipid analysis demonstrated that under Al treatment the MGDG content in all plants and MGDG/DGDG (digalactosyldiacylglycerol) remarkably reduced, especially in mutants impairing the stability and permeability of the plasma membrane. These results indicate that the Arabidopsis mgd mutants are hypersensitive to Al stress due to the reduction in MGDG content, and this is of great significance in the discovery of effective measures for plants to inhibit aluminium toxicity.

Corbicula fluminea: A sentinel species for urban Rare Earth Element origin

The increase in the global population, coupled with growing consumption of Rare Earth Elements (REEs), has led to increasing transfer of these emerging contaminants into the environment, particularly through the effluents from wastewater treatment plants (WWTP). The objectives of this study were to determine the geochemical quality of a French river subject to strong urban pressure (the Jalle River in the Bordeaux area) and to examine the bioavailability of natural and anthropogenic REEs in a model species of freshwater bivalve, the Asian clam Corbicula fluminea. To this end, two fractions (dissolved and total) of the water from the Jalle River were sampled and the bivalves were exposed by in situ caging during a three-month monitoring period. The REE patterns obtained showed the presence of Gadolinium (Gd) anomalies in the dissolved and total fractions as well as in Corbicula fluminea. The apparent bioavailability of natural REEs was in the following order for the dissolved fraction: Medium REEs (MREEs) > Light REEs (LREEs) > Heavy REEs (HREEs) and for the particulate fraction: MREEs > LREEs = HREEs. These results highlight the importance of the particulate fraction in the study of the bioavailability of REEs in bivalves. An increase of anthropogenic Gd (Gd_anth) was observed in the dissolved fraction between the upstream site (3.4 ng.L^-1) and the WWTP Downstream site (48.4 ng.L^-1). The Gd anomaly observed in the water was also observed in Corbicula fluminea with a significant increase in the bioaccumulation of Gd_anth, from 1.5 ± 1 ng.g_DW^-1 upstream to 4.1 ± 0.7 ng.g_DW^-1 downstream of the WWTP effluents, thus confirming the enhanced bioavailability of medical-origin Gd to freshwater bivalves. This study strongly suggests that Corbicula fluminea can be used as a sentinel species in the monitoring of Gd contamination of medical origin. It would thus appear important to consider the potential entry of this contaminant into the human food chain via other, commercially exploited bivalve species.

Changes in the gene expression profile of Arabidopsis thaliana under chromium stress

Based on previous studies and preliminary test results, 200 μM was used as the test concentration of chromium (Cr), and changes in the gene expression profile of Arabidopsis thaliana in response to 24-h treatments of Cr(III) and Cr(VI) were analyzed using the Arabidopsis ATH1 Genome Array. The results were as follows. There were 238 upregulated genes and 858 downregulated genes in response to treatments with Cr(III) and Cr(VI). For Cr(III) and Cr(VI) treatments, there were 185 and 587 specifically upregulated genes as well as 220 and 956 specifically downregulated genes, respectively. Among the common differentially expressed genes (DEGs), the expression levels of genes involved in redox, secondary metabolism, and energy metabolism processes were significantly downregulated, while those of genes related to the stress response, photosynthesis, and sulfur metabolism were significantly upregulated. These findings indicated that Cr seriously affected the normal activities of A. thaliana cells. Some genes associated with stress and regulation were upregulated to adapt to the stress caused by Cr. Among the unique DEGs, the expression levels of genes involved in indole-3-acetic acid (IAA) regulatory pathway were significantly increased in response to Cr(III) treatment; the expression levels of genes involved in the abscisic acid (ABA) regulation pathway and carotenoid synthesis were significantly increased following Cr(VI) treatment. These results revealed some differences in response to Cr(III) and Cr(VI) in A. thaliana.

Transcriptomic analysis of HepG2 cells exposed to fractionated wastewater effluents suggested humic substances as potential inducer of whole effluent toxicity

We performed a transcriptome-based bioassay (TSB assay) using human hepatoma HepG2 cells to evaluate the potential toxicity of whole wastewater effluents from two membrane bioreactors (MBRs) and a conventional activated sludge process (AS). The biologically active agent(s) in the wastewater effluents were characterized based on expression of the marker genes (i.e., CYP1A1, AKR1B10, GCLM and GPX2) selected by DNA microarray analysis, after the wastewater effluent samples were concentrated by a reverse osmosis (RO) membrane and further fractionated by various manipulations. The qPCR assay of marker genes demonstrated that the induction of CYP1A1 and GPX2 was mitigated after passing through C18 and chelate columns. In addition, clear induction of CYP1A1 was observed in the smallest size fraction with 1 k Da or smaller organic molecules in all the tested effluents. These results together with the water quality data of the fractionated samples suggested that responsible constituents for potentially adverse and abnormal transcriptomic responses in HepG2 could have hydrophobic nature and act with metal-dissolved organic matter (DOM) complexes in 1 k Da or smaller size fraction. Although DOM is known to play two contradictory roles as a protector and an inducer of toxicants, our present study indicated the DOM in wastewater effluent, particularly humic substances with acidic nature, functioned as a toxicity inducer of residual chemicals in the effluents. This study provided a new insight into the nature of "toxic unknowns" in the wastewater effluents, which should be monitored whole through the reclamation process and prioritized for removal.

Transcriptome analysis of response mechanism to ammonia stress in Asian clam (Corbicula fluminea)

Corbicula fluminea is highly sensitive to ammonia, and its response mechanism to ammonia stress is unclear. In this study, C. fluminea was exposed to different levels of ammonia (control group, 10 mg/L, and 25 mg/L) for 24 h and 48 h. A comparative analysis of transcriptome sequencing (RNA-seq) of C. fluminea digestive gland showed that the expression of 6742 genes (11.54%) was significantly affected by ammonia stress. The TLR, NF-κB, FOXO, and apoptotic signaling pathways were involved in the regulation. The differential expression of 14 genes was confirmed by real-time PCR. In summary, the response mechanism of C. fluminea digestive gland under ammonia stress may be different from that of oxidative stress in marine vertebrates. Also, the NMDAR-mediated pathway may not be the main mechanism in the response to ammonia stress in C. fluminea. The present study is a preliminary study for further investigation into ammonia toxicity in shellfish.

The Shock Effect of Inorganic Suspended Solids in Surface Runoff on Wastewater Treatment Plant Performance

Previous studies on the water quality of surface runoff often focused on the chemical oxygen demand (COD), nitrogen, phosphorus, and total suspended solid (TSS), but little is known in terms of the inorganic suspended solids (ISS). This research investigated the effects of ISS carried by surface runoff on the treatment efficiency of the pretreatment facilities and the ratio of mixed liquor volatile suspended solid to mixed liquor suspended solid (MLVSS/MLSS) of the activated sludge in a wastewater treatment plant (WWTP) with the anaerobic-anoxic-oxic (AAO) process in Chongqing city, China. The results showed that the surface runoff had a long-lasting impact on the grit removal capacity of the grit chamber, affecting the normal operation after the rainfall. In contrast, the primary sedimentation tank showed strong impact resistance with higher removal rates of COD, TSS, and ISS. Nonetheless, the primary settling tank aggravates the removal of organic carbon in sewage during rainfall, having a negative impact on subsequent biological treatment. The ISS in the surface runoff could increase the sludge concentration and decrease the MLVSS/MLSS ratio. After repeated surface runoff impact, the MLVSS/MLSS ratio in the activated sludge would drop below even 0.3, interrupting the normal operation of WWTP.