Introduction
Bacterial infections are a major cause of disease outbreaks in fish, leading to reduced productivity in aquaculture. Understanding the molecular responses triggered in the gonads following infection is crucial for improving fish farming practices, optimizing disease control, and identifying the most resilient phenotypes (Caballero-Huertas et al., 2024). This study focuses on two key species: the commercially valuable European sea bass (Dicentrarchus labrax), widely farmed across Europe, and the extensively studied model organism zebrafish (Danio rerio). We investigated epigenomic alterations in both species following bacterial challenge. The epigenomic approach consisted on state-of the arts techniques such as Whole Genome Methylation sequencing (WGMS), microRNA-seq, and RNA-seq .
Methodology
European sea bass and zebrafish were experimentally exposed to bacterial pathogens. In European sea bass, infections were administered via intraperitoneal injection, and gonadal tissues were collected 48 hours post-infection. For zebrafish, exposure occurred through bath immersion. Sequencing libraries were constructed according to standard manufacturer protocols for each specific sequencing technique. Additionally, the expression of selected key microRNAs (miRNAs) was analyzed using the miRCURY LNA SYBR Green PCR Kit.
Results
Bacterial challenge led to substantial alterations in the gonadal epigenome, transcriptome, and miRNome. The most pronounced changes in DNA methylation were observed between male and female samples under the same treatment, with over 88,000 and 105,000 hypermethylated CpG sites, and approximately 3 million and 2.7 million hypomethylated CpG sites, respectively. Transcriptome profiling of European sea bass gonads indicated a higher number of differentially expressed genes (DEGs) in testes compared to ovaries. Four miRNAs were identified in testicular tissue as potential biomarkers of prior infection exposure. In zebrafish, analysis of gonadal miRNA expression revealed sex-dependent differences post-infection, including suppression of reproductive pathways such as oocyte meiosis, and activation of immune-related pathways.
Discussion
As similarly reported by Gelderen et al. (2025a, 2025b ), the sex-specific epigenetic differences observed may underlie the sexually dimorphic responses to infection. These results highlight the significance of incorporating sex as a biological variable in fish immunological and epigenetic research. Although sexual dimorphism is known to modulate immune function across vertebrates, its role in fish immunity remains barely underexplored (Caballero-Huertas et al., 2024). This study enhances our understanding of the sex-driven epigenomic basis in fish, with important implications for aquaculture practices and the development of disease-resistant phenotypes.
References
-Gelderen , T.A. van, et al., (2025). Functional & Integrative Genomics. DOI: 10.1007/s10142-025-01537-w.
-Gelderen, T.A. van, et al., (in press) . BMC Genomics. Preprint DOI: 10.1101/2024.01.24.577069.
-Caballero-Huertas, et al. (2024) . Reviews in Fisheries Science & Aquaculture . DOI: 10.1080/23308249.2024.2390965
Acknowledgements : This study was supported by the Spanish Ministry of Science and Innovation grants 2PID2020-113781RB-I00 “MicroMet” and PID2023-146286OB-I00 “Holosex” , and Aquaexcel 3 TNA project PID27375 “EpInfect ” to LR.