Marine Invertebrate Symbioses: Epigenetic Analysis

Beneath the oceans surface, some species of clams have formed close partnerships with bacteria that help them survive in challenging environments. In lucinid clams, these bacteria mainly reside in the gills and generate energy from hydrogen sulfide through chemosynthesis. This process supplies the clam with nutrients, acting as an internal food source. In return, the clam provides the bacteria with a protected habitat and access to essential chemical compounds, such as sulfide and oxygen, needed for their energy production. This symbiosis has existed for more than 400 million years, making it one of the oldest known animal-microbe partnerships. Yet we still do not understand how such a specific and stable relationship is controlled at the molecular level. Recent work has shown that bacterial products are found throughout the clams body, suggesting that the microbes may influence many organs, not just the gills. At the same time, studies in other animals and plants point to two flexible molecular systems that could help explain this: tiny regulatory molecules called small RNAs and chemical tags on DNA known as epigenetic marks. These tags can switch genes on or off without altering the genetic code itself. They are promising candidates for understanding how the host controls which bacteria are accepted, how the immune system tolerates them, and how the partnership is maintained over a lifetime. However, they have never been studied in lucinid clams. This project focuses on two coastal lucinid clams: Loripes orbiculatus in Europe and Codakia orbicularis in the Caribbean. Both species acquire their bacterial partners from the surrounding seawater, rather than inheriting them from their parents. We hypothesize that these symbionts influence the clams whole body by modifying patterns of small RNAs and DNA chemical marks. These molecular signals likely help clams select specific bacteria, tolerate them without immune activation, and sustain a stable relationship across tissues and developmental stages. More specifically, this project will: Temporarily remove the bacteria from adult L. orbiculatus using antibiotics and then let them reacquire the microbes under controlled conditions. Use advanced sequencing methods to track how small RNAs and DNA modifications change during symbiont loss and reacquisition. Study bacteria-free juvenile C. orbicularis from the Caribbean naturally and compare their molecular patterns with those of symbiotic adults. Apply and refine a non-invasive liquid biopsy approach (similar to a blood test in humans) to monitor these processes over time without harming the animals. By combining DNA and RNA sequencing with these experimental approaches, the project aims to identify epigenetic profiles underlying ancient clam-bacteria symbioses, develop non-lethal methods for studying marine animals, and provide insights relevant to other beneficial microbial partnerships, including those that support healthy coastal ecosystems.