With anthropogenically-driven pressures drastically changing marine coastal ecosystems much international efforts have been focused on its protection. For that reason, Mediterranean states have accepted numerous regional and international contracts. Even though much effort has been given into protection of marine ecosystems by combining and integrating approaches from WFD and MSFD, these tools are still facing many challenges. Within the frame of the MicroLink project we will focus on the anthropogenic pressures effects onto benthic microbial assemblages, fully neglected in the quality legislation protocols. We believed that microbial assemblages could offer potential answer to some of the challenges facing marine protection programmes: (i) challenge of determining effects of multiple pollution pressures on the integrity of the coastal marine ecosystem, (ii) possible improvement of the existing biological indicators pool (iii) potential of applying fast and reliable state-of-the-art approaches to determine structural and functional integrity of marine ecosystems; and (iv) problems associated with assessment of the ecological status of marine sediments. We will tackle the issue by an innovative approach in which we will combine multi-trophic (bacteria, archaea, virus, fungi)/ multilayer approach for studying microbial communities in anthropogenically-impacted vs. reference environments. Microbes dominate marine ecosystems and have pivotal role in biogeochemical cycling and consequently changes exerted on the level of these communities could alter the whole food web, eventually impairing marine ecosystem services. Within this project we intend to focus on an urgent need to define possible contribution and importance of monitoring microbial assemblages in achieving of Good Environmental Status (GES) which could offer us first step toward potential integration of microbial assemblages as indicators of marine environment quality.