Currently developed sequencing and other high throughput technologies enable us to explore the role of microorganisms in the environment. Here environmental microbiome is defined as the collection of microbial genomes in a particular environment

and the environmental microbiome research (or environmental microbiomics) aims to understand the biodiversity

composition

structure

function

interaction

evolution and dynamics of microbial communities as well as their linkages with environmental drivers and ecosystem functioning. This review is focused on environmental microbiomes from soil

water and air. Firstly

the current advanced sequencing technologies and associated tools for environmental microbiome data analysis are reviewed

then the current research progress in environmental microbiomes were summarized with foci on addressing key scientific questions in microbial ecology and environmental science. This review proposes key scientific questions

and highlights the importance of our understanding of microbial functions and underlying mechanisms in future environmental microbiome studies.