Several needs in the context of the water-energy-food nexus will become more prominent in the next decades. It is crucial to delineate these challenges and to find opportunities for innovative microbial technologies in the framework of sustainability and climate change. Here, we focus on four key issues, that is the imbalance in the nitrogen cycle, the diffuse emission of methane, the necessity for carbon capture and the deterioration of freshwater reserves. We suggest a set of microbial technologies to deal with each of these issues, such as (i) the production of microbial protein as food and feed, (ii) the control of methanogenic archaea and better use of methanotrophic consortia, (iii) the avoidance of nitrification and (iv) the upgrading of CO2 to microbial bioproducts. The central message is that instead of using crude methods to exploit microorganisms for degradations, the potentials of the microbiomes should be used to create processes and products that fit the demands of the cyclic market economy
