Patterns, Processes and Mechanisms in Microbial Ecology: Contributions from the 'Omics'

Abstract

The complexity of interactions among microorganisms and of microorganisms with their environment and with other organisms is becoming increasingly understood by microbial ecology researchers, helped by the development of 'meta-omics' methods such as metagenomics, metatranscriptomics, metaproteomics, metametabolomics and other related techniques. As in any ecological framework, the concepts of pattern, process and mechanism are of primary importance to the microbial ecology context. The observation and description of ecological patterns are not enough and there is a need to seek the processes and mechanisms that may explain the occurrence of these patterns. However, as there is some confusion about the meaning and importance of these concepts in microbial ecology studies, some operative definitions and considerations to help microbial ecology researchers to become acquainted with these ecological concepts are provided in this chapter. A brief account of the contributions from the 'meta-omics' to the identification and understanding of patterns, processes and mechanisms in microbial ecology is also provided. This chapter is focused on the community and biogeographical levels of soil microbiomes studied using some of the 'meta-omics' methods, as much of the recent work has been performed at these ecological levels and in this habitat.