Characterization of sediment toxicity in Shanghai Harbor using toxicity tests and digital gene expression analysis based on clams Ruditapes phillipinarum.

In the present study, chemical analysis of contaminants (three classes of organic pollutants and seven metals) and elutriate toxicity test were adopted to evaluate the potential environmental hazards of dredged sediment samples from five sites (SS1-5) along Huangpu River Channel (Shanghai Harbor, China). The metal Pb, Cu, Cr, Zn and the organic pollutants including total hexachlorocyclohexane (HCHs) and total dichlorodiphenyltrichloroethane (DDTs) in the five samples exceeded the threshold for effects level (TEL) to varying degrees. The probable effect concentration quotients (QPECm) of contaminants from the five dredged samples were all above 0.25, which means potential toxicity risks. Elutriate toxicity tests using medaka fish (Oryzias melastigma) and manila clam (Ruditapes philippinarum) showed that SS2 caused mortality to both species and SS1 caused mortality to fish. To explore the molecular biomarkers that may reflect the toxic effects, differential expressed genes were identified by RNA-Seq-based transcriptome profiling from the survived clams exposed to the two polluted elutriates (SS1, SS2). In clams exposed to SS1 and SS2 elutriate, 368 and 860 differential expressed genes (DEGs) were up-regulated, 199 and 1304 genes were down-regulated, respectively. Fourteen DEGs were selected from the enriched pathways that reflect cytotoxicity and responses to xenobiotics for the following quantitative real time PCR analysis. The transcriptomic profiling and the selected gene's expression patterns from clams exposed to SS1 and SS2 showed significant differences with the non-contaminated and control groups. Using the expression data of the selected gene battery in Factor Analysis allowed the discrimination between contaminated and non-contaminated sites and may reflect an influence gradient of sites. The development of the assay of these molecular biomarkers may provide a rapid and high-throughput tool for the quality assessment of the dredging sediments.

Data on characterization of dredging sediment of Safi harbour - Morocco.

This data article reports the geotechnical (the water content, the specific density, the Atterberg limits, the methylene blue value and the grain size distribution), chemical (the content of organic matter and calcium carbonate) and mineralogical characteristics of sediments dredged in Safi harbour (Morocco). Samples are collected in seven point (P1, P2, P3, P4, P5, P6 and P7) of two zones of port (the channel zone and the basin zone), placed in opaque drums and kept in a cold room protected from light. Then the homogeneous samples are mixed. We note S1 the mixture of P1, P2 and P3 correspond to the basin zone of the port and S2 the mixture of P4, P5, P6 and P6 correspond to the channel zone of the port.