Logares, RamiroCalafat, AntonioBinsarhan, Mohammad2024-10-212024https://hdl.handle.net/20.500.14154/73269Corals play an essential role in marine environments and their morphological structure provides microbes with different habitat types. In turn, the microbes provide corals with important compounds that contribute to coral fitness and health. Corals have been suggested to hold distinct microbes within the anatomical layer, such as the Skeleton, Surface mucus layer (SML), Tissue, and Gastric cavity. Furthermore, many factors can influence the structure and function of the microbiome, making it more challenging to understand. Coral age, taxonomy, disease, depth zones, and many other abiotic factors could shape coral microbiomes and are responsible for their stability. Disturbances in the relationship's stability between coral hosts and their associated microbes increase the chance of coral infections and bleaching, leading to mortality. Therefore, studying the influence of each factor on the microbiome could lead to a better understanding of the nature and dynamics of this complex system. However, many questions remain regarding how microbes are acquired and function in corals. In this thesis, we explored the coral microbiome and its relationship with two abiotic variables, depth and temperature. High-throughput meta-omics approaches have been used to investigate coral microbiomes. Some limitations may hinder the full benefits of meta-omics; however, these powerful tools open doors for understanding the coral microbiome. Our comprehensive analysis of the Mediterranean Eunicella singularis microbiome revealed significant differences between shallow and mesophotic colonies at both taxonomic and functional levels. While shallow water colonies prominently featured Symbiodinium, essential for coral energy production through photosynthesis, its absence in the mesophotic zone indicates a shift in microbial community structure. In deeper environments, the microbial community exhibited higher abundances of functional genes related to carbohydrate, energy, amino acid, cofactor, and vitamin metabolism. This potentially allows the microbiome to utilize carbon and nitrogen from various sources, such as glutathione, steroids, fatty acids, and aromatic hydrocarbons, which might help sustain coral nutrition through enhanced nutrient availability. Additionally, Metagenome-Assembled Genomes (MAGs) analysis identified microbiome taxa, such as DT-91 (Order Pseudomonadales) and Endozoicomonas, involved in nutrient recycling, vitamin production, and secretion systems, highlighting their role in microbiome fitness. These findings underscore potential microbial adaptation mechanisms to environmental conditions, emphasizing their potential role in facilitating coral resilience and adaptation to different contexts. Further investigations are needed to determine whether these genes are actively expressed in the microbial community and to assess the extent of their influence on both the coral's health and its associated microbiome. Our study of the potential influence of prolonged thermal stress on the cold-water coral D. pertusum revealed a significant impact on the microbiome structure at both taxonomic and functional levels. Metagenomic analyses supported previous research, showing an increase in Rhodobacterales under thermal stress conditions. Moreover, our analyses indicated an increase in the carbon metabolic genes, such as methylotrophy and glycoside hydrolase enzymes, which may destabilize the microbiome and promote the growth of opportunistic pathogenic organisms. Indeed, we found an increase in pathogenic marker genes within the D. pertusum microbiome as temperature increased. Interestingly, the microbial taxa associated with these markers, such as those related to type 1 and 3 secretion systems, also increased in abundance in thermally stressed microbiomes. Additionally, we observed an increase in genes associated with diazotrophic activity, including denitrification and nitrification, which could disrupt the nitrogen cycle balance between the coral and its microbiome, potentially increasing the susceptibility to diseases and mortality. Together, these findings underscore the influence of increasing temperature on the taxonomic and functional structure of the cold-water coral microbiome. However, further research is required to investigate the gene expression profiles associated with formaldehyde assimilation, denitrification, and nitrification. Examining the expression levels of these metabolic pathways would provide deeper insights into their activity and regulation, contributing to a more comprehensive understanding of their roles in the microbiome's response to environmental stressors such as temperature increase.205enCoral healthCoral MicrobiomeMetagenomicsClimate changeMarine ecosystemsThesis