Molecular tools for the study of microbiomes associated with marine animal forests

<ns3:p>The central role played by microbes as driving forces of biogeochemical cycles, as well as the second genome of most organisms, has reinforced the necessity to study this unseen majority. Their relationships with Marine Animal Forests (MAFs) have been proven essential for maintaining these ecosystems in the face of ongoing climate change, driving key processes such as nutrient cycling, pathogen control, and resistance and resilience to anthropogenic perturbations. In MAFs, diverse microorganisms – viruses, archaea, bacteria, fungi, and protists - have been shown to occupy different compartments and act as symbionts, parasites, or pathogens, depending on the environmental conditions. They are also vulnerable to change, which can result in impacts on the MAF functioning. In this chapter, we present omics techniques that can be used for a better understanding of the distribution, ecological roles, and interactions between MAFs and their associated microbiomes. The chapter explores themes ranging from sampling design and field procedures to analysis, aiming to provide a set of tools that can be used in a standardized manner to facilitate comparative studies and contribute to the protection, management, and restoration of these ecosystems.</ns3:p>