System approaches to elucidate ecosystem functioning constitute an emerging area 
of research within microbial ecology. Such approaches aim at investigating all 
levels of biological information (DNA, RNA, proteins and metabolites) to capture 
the functional interactions occurring in a given ecosystem and track down 
characteristics that could not be accessed by the study of isolated components. 
In this context, the study of the proteins collectively expressed by all the 
microorganisms present within an ecosystem (metaproteomics) is not only crucial 
but can also provide insights into microbial functionality. Overall, the success 
of metaproteomics is closely linked to metagenomics, and with the exponential 
increase in the availability of metagenome sequences, this field of research is 
starting to experience generation of an overwhelming amount of data, which 
requires systematic analysis. Metaproteomics has been employed in very diverse 
environments, and this review discusses the recent advances achieved in the 
context of human biology, soil, marine and freshwater environments as well as 
natural and bioengineered systems.