Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France

Abstract

The freshwater pearl mussel Margaritifera margaritifera is one of the most threatened freshwater bivalves worldwide. In this study, we aimed (i) to study the processes by which water quality might affect freshwater mussels in situ and (ii) to provide insights into the ecotoxicological significance of water pollution to natural populations in order to provide necessary information to enhance conservation strategies. M. margaritifera specimens were sampled in two close sites located upstream or downstream from an illegal dumping site. The renal transcriptome of these animals was assembled and gene transcription determined by RNA-seq. Correlations between transcription levels of each single transcript and the bioaccumulation of nine trace metals, age (estimated by sclerochronology), and condition index were determined in order to identify genes likely to respond to a specific factor. Amongst the studied metals, Cr, Zn, Cd, and Ni were the main factors correlated with transcription levels, with effects on translation, apoptosis, immune response, response to stimulus, and transport pathways. However, the main factor explaining changes in gene transcription appeared to be the age of individuals with a negative correlation with the transcription of retrotransposon-related genes. To investigate this effect further, mussels were classified into three age classes. In young, middle-aged and old animals, transcription levels were mainly explained by Cu, Zn and age, respectively. This suggests differences in the molecular responses of this species to metals during its lifetime that must be better assessed in future ecotoxicology studies.

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Acknowledgements

This work was supported by the European Union program LIFE+ Nature (project LIFE13 NAT/FR/000506). We are grateful to all the staff members of the Perigord-Limousin national park for their contribution to this project. We thank the four anonymous reviewers for their careful reading and insightful comments on our work.

Author information

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Authors

Contributions

AB, FP, JT, CK, PG, and MB wrote the manuscript; MB designed the experiment; AB, FP, and CK analyzed the results. JT and JB performed sclerochronological analysis. All authors approved the final version of the manuscript.

Corresponding author

Correspondence to Anthony Bertucci.

Ethics declarations

The collection of M. margaritifera for this study was allowed by the prefectoral decree 60/2008 delivered by the Préfecture de la Dordogne (DIREN Aquitaine) on the 31st of October 2008. In France, no ethical permits are required to carry out research on bivalves. Therefore, all procedures were conducted according to the ethical guidelines of France to ensure ethical appropriateness.

Conflict of interest

The authors declare that they have no competing interests.

Additional information

Responsible editor: Philippe Garrigues

Electronic supplementary material

Online Resource 1

Complete annotation results, including GO terms, of the transcriptome sequenced from M. margaritifera kidney (XLSX 2808 kb)

Online Resource 2

List of genes tested by real-time quantitative PCR. (E: primers efficiency, CV: coefficient of variation for control genes) (XLSX 14 kb)

Online Resource 3

Comparison of expression profiles obtained from RNA-seq and RT-qPCR (PDF 167 kb)

Online Resource 4

List of contigs that varied significantly (FDR ≤ 0.05) between upstream and downstream sites (XLSX 48 kb)

Online Resource 5

Heatmap of sample-to-sample distances computed with the DESeq2 package. Site and year are indicated at the bottom of the figure (Down: downstream, Up: upstream, 09: 2009, 10:2010). The age class is indicated on the right (PDF 122 kb)

Online Resource 6

List of the 11,264 contigs with expression level that correlates with one specific factor based on the FAMT analysis (FDR ≤ 0.01) (XLSX 232 kb)

Online Resource 7

List of contigs belonging to Gene Ontology terms that are enriched in each FAMT categories (r: Pearson correlation coefficient) (XLSX 22 kb)

Online Resource 8

List of contigs belonging to the most represented GO Biological Processes related to Ni, Cd and Pb (r: Pearson correlation coefficient) (XLSX 18 kb)

Online Resource 9

Details of GO enrichment test (FDR ≤ 0.05) for contigs related to Cu in young mussels and list of contigs involved in transport, catalytic activity and fatty acid metabolism (r: Pearson correlation coefficient) (XLSX 52 kb)

Online Resource 10

Principal components analysis (PCA) plot of M. margaritifera digestive glands contamination profile. Variables are represented with black arrows (As and Ni overlap). The two first principal components are plotted with the proportion of variance explained by each component shown on the axis. Symbols correspond either to (A) sampling group or (B) age class (PDF 92 kb)

Online Resource 11

Details of GO enrichment test (FDR ≤ 0.05) for contigs related to Zn in middle-aged mussels and list of contigs involved in gene expression and response to chemical metabolism (r: Pearson correlation coefficient) (XLSX 20 kb)

Online Resource 12

Details of GO enrichment test (FDR ≤ 0.05) for contigs related to Age in old mussels and list of contigs from the GO category “mitochondrion” (r: Pearson correlation coefficient) (XLSX 20 kb)

Online Resource 13

Correlations between the original variables and the Principal Components for the PCA analysis of metal concentrations (XLSX 12 kb)

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Bertucci, A., Pierron, F., Thébault, J. et al. Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France. Environ Sci Pollut Res 24, 27145–27159 (2017). https://doi.org/10.1007/s11356-017-0294-6

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Keywords

  • Freshwater mussel
  • Transcriptomics
  • RNA sequencing
  • Metal pollution
  • Sclerochronology
  • Margaritifera margaritifera
  • In situ study