Algal aquaculture is developing exponentially worldwide, with multiple applications in the food, chemical and pharmaceutical industries. Current research in algal biotechnology mostly focuses on metabolite discovery, aquaculture yield improvement and engineering bottlenecks. However, agronomical experience shows that controlling the interaction of land crops with mutualistic or pathogenic microbes is most critical to successful production. Likewise, controlling the microbial flora associated with algae (the 'algal microbiome') is emerging as the biggest biological challenge for their increased usage. Bacteria can control the morphogenesis of algae, while others are indispensable to algal survival. Pathogens are causing devastating diseases, the impact of which worsens with the intensification of aquaculture practices. Thus, the overarching aim of ALFF is to train 15 ESRs (researchers and technologists) within a multinational consortium, whilst bringing a scientific step-change in our understanding of these interactions, leading to the development of superior mass algal cultivation and biocontrol strategies. ALFF tackles: 1) the identification, taxonomy and utilisation of naturally-occurring algal symbionts and pathogens; 2) inter- and intra-species signalling and chemical ecology in aquaculture, natural environment and simplified systems (i.e. axenic cultures +/- symbionts); 3) and harnesses state of the art genomics, molecular, and biochemical techniques to characterise these interactions. A highly interdisciplinary team underpins an ambitious theoretical, field, hands-on training and research program. With the support of high profile institutions, ALFF foresees an exceptionally broad range of dissemination and outreach initiatives to help policy makers and the general public better understand the opportunities and issues relating to the sustainable use of our aquatic freshwater and marine resources, within and beyond the EU.