The journal publishes full length research articles as well as brief reports, minireviews, opinion articles and highlights.

The scope of the Journal encompasses the diversity of current research on microbial processes in the environment, microbial communities, interactions and evolution and includes, but is not limited to, the following:

the structure, activities and communal behaviour of microbial communities
microbial community genetics and evolutionary processes
microbial symbioses, microbial interactions and interactions with plants, animals and abiotic factors
microbes in the tree of life, microbial diversification and evolution
microbiomes and holobionts
population biology and clonal structure
microbial metabolic and structural diversity
microbial physiology, growth and survival
primary and secondary metabolism in the environment
microbes and surfaces, adhesion and biofilms
responses to environmental signals and stress factors
modelling and theory development
pollution microbiology
microbial ecology of pathogens
extremophiles and life in extreme and unusual little-explored habitats
element cycles and biogeochemical processes
microbes in a changing world, microbially-influenced global changes
systems biology and computational predictions
evolution and diversity of archaeal and bacterial viruses
new technological developments in microbial ecology and evolution, in particular for the study of activities of microbial communities, non-culturable microorganisms and emerging pathogens
single cell microbial ecology
Interdisciplinary studies of fundamental problems are particularly welcome.