Soil metaproteomics as a tool for monitoring functional microbial communities: promises and challenges

Abstract

Soil is a complex and dynamic network of different biological processes linked in an intricate manner to facilitate effective ecosystem functioning. Microbial diversity and its functioning are crucial to effective ecosystem working and its sustenance. Metagenomic studies undertaken to-date have illustrated the tremendous diversity of both culturable and unculturable microbiome in specific ecosystems, but their exact role in ecosystem functioning needs to be addressed. This can be undertaken by studying the protein repertoire in the ecosystem, which are the direct and undeviating key players in the ongoing metabolic processes. Metaproteomics, an emerging science, tries to snapshot the entire proteins present in a specific environment at a particular time interval. It links the phylogeny and functionality of soil microorganisms, describing not only at the level of the individual dominant organism, but also at the community level, therefore, profiling microbial enzymes may be a sensitive indicator of the soil ecosystem. With the emergence of high-performance mass spectrometry, the approach to mine these functional complex soil microbiomes became feasible; however, it is hindered by the presence of innumerable interfering molecules present in the soil samples. This review focuses on recent developments in soil metaproteomics, particularly, in terms of protein extraction methodologies and mass spectrometry-based measurements, as well as their applications in soil based approaches to decipher the underlying processes responsible for differential functioning in diverse environments.