Modulation of gene expression in foraminifera exposed to contaminants

Foraminifera are single-celled eukaryotic organisms that are abundant in marine environments. The majority of foraminiferal diversity is found in benthic habitats, and they are known to be present in even highly polluted areas, which has led to a growing interest in their use in biomonitoring. However, there is still a limited understanding of mechanisms underlying benthic foraminifera response to contaminants. In this study, the effects of exposure to two common contaminants in temperate fjords, the antibiotic ciprofloxacin and trace metal copper (Cu), were assessed in one species of benthic foraminifera. This was done through a transcriptome analysis to better understand the genetic response of foraminifera to the contaminants of interest. This study also assessed the change in gene expression to identify potential biomarkers for exposure to the contaminants, which would potentially increase the value of foraminifera as a bioindicator. To identify genes that can be used as potential biomarkers, it is essential that the contaminants exert a measurable effect on the foraminifera. In this study, the effect was measured through a differential gene expression (DE) analysis. Since there are only a few studies on gene expression in benthic foraminifera, the aim of this study was to establish a protocol for mRNA isolation and mRNA sequencing. This was done to secure RNA-seq data of high enough quality to create a transcriptome so a DE analysis could be conducted. If and when differentially expressed genes were detected, a prediction of the function of these genes was made to uncover their potential as biomarkers. This study provides a protocol that produced mRNA of sufficient quality for a de novo transcriptome assembly. Foraminifera exposed to ciprofloxacin and Cu showed significantly differentially expressed genes compared to the control. The function of the differently expressed genes was predicted for a couple of the genes. The function of some of these genes was consistent with studies on other organisms exposed to ciprofloxacin or Cu. More data are needed to support the genes expressed in this study and to support if these genes has a potential as biomarkers. To my knowledge this is the first study to assess the effect on the transcriptome of foraminifera due to the exposure of contaminants.