Microbial communities that inhabit natural and engineered ecosystems provide essential services for the Earth's life-support system and the human well-being, such as nutrient cycling, protection against diseases or wastewater treatment. The high functional versatility and diversity of microorganisms are the driving forces for upholding ecosystem services and represent a unique resource for novel biotechnological applications. For a stable, secure and sustainable supply of food, feed, energy, materials and chemicals, new microbial community-driven biomanufacturing systems and environmental protection and restoration technologies are developed to achieve a bio-based and environmentally-friendly economy. Microbiome-based therapies also take advantage of emerging strategies to steer microbial ecosystem diversity and functioning. From the agricultural practices to the construction of synthetic microbial factories, the diversity and functionality of microorganisms can be manipulated in natural ecosystems (in situ), in engineered, open ecosystems (ex situ, in vivo) or in confined environments (ex situ, in vitro) for improved applications in medicine, agriculture, bioremediation, and water resource recovery facilities.