Approaches

Some of the most transformative discoveries promising to enable the resolution of this century's grand societal challenges will most likely arise from environmental science and particularly environmental microbiology and biotechnology. Understanding how microbes interact in situ, and how microbial communities respond to envi- ronmental changes remains an enormous challenge for science. Systems biology offers a powerful experimental strategytotackletheexcitingtaskofdecipheringmicrobialinteractions.Inthisframework,entiremicrobialcom- munitiesareconsideredasmetaorganismsandeachlevelofbiologicalinformation (DNA,RNA,proteins andme-tabolites) is investigated along with in situ environmental characteristics. In this way, systems biology can help unravel the interactions between the different parts of an ecosystem ultimately responsible for its emergent properties. Indeed each level of biological information provides a different level of characterisation of the micro- bial communities. Metagenomics, metatranscriptomics, metaproteomics, metabolomics and SIP-omics can be employedtoinvestigatecollectivelymicrobialcommunitystructure,potential,function,activityandinteractions. Omics approaches are enabled by high-throughput 21st century technologies and this review will discuss how their implementation has revolutionised our understanding of microbial communities. © 2014 by Elsevier B.V. on behalf of the Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY 3.0 (http://creativecommons.org/licenses/by/3.0/). Contents intothecarbonandnitrogen fl uxes inmicrobialcommu-nities and inform on microbial interrelationships. Overall omics datasets encompassing metagenomics, metatranscriptomics, metaproteomics, metabolomics and SIP-omics have the potential to provide unprecedent-edaccess tothefunctioningofecosystems.Forthepurposeof this review, the advancement of each omics technology will be discussed.