Abstract
Below every step we take there is groundwater. Out-competing rivers, lakes and wetlands in terms of water quantity and quality, shallow aquifers are an essential reservoir of freshwater for the human population. At the same time, they represent the largest freshwater biome on earth, forming a responsive but vulnerable interface between the highly dynamic surface aquatic and terrestrial ecosystems and the environmentally static deeper zones of the subsurface. Shallow aquifers are home to a vast phylogenetic and functional microbial diversity, regularly surpassing those of surface environments. Predominantly colonized by microorganisms, key drivers of community composition and biogeochemical cycles are the hydrogeological settings, availability of energy and prevailing redox conditions, as well as climate and local to regional anthropogenic activities. Although there is steadily growing knowledge on microbial biodiversity and their potential functions, quantitative data on active key processes, such as carbon cycling, are scarce. We do have a very incomplete idea of the abundances and distribution of viruses, protists and fungi and their ecological role in groundwater. In this Review, we discuss current and future pressures to shallow groundwater ecosystems in terms of microbial community dynamics particularly in light of global and climate change, that is, groundwater pollution and warming.