Genome-based and functional differentiation: hallmarks of microbial adaptation, divergence and speciation?

The recent application of high-throughput molecular biology methods to natural microbial communities is profoundly changing our view on the microbial world. In particular, our understanding of microbial population-level differentiation for ecological adaptation that leads to microbial divergence and speciation has been profoundly altered. Numerous processes that underlie microbial differentiation have been identified but determining the relative significance of these processes remains challenging. For example, a major unresolved question is how much of observed genetic heterogeneity is due to neutral versus adaptive processes. Sequence-based and modelling analyses suggest that much of the observed variation is neutral but recent functional omic data suggest that at least some of it is functionally relevant and involved in adaption and divergence. From the limited amount of largely disjointed metagenomic and functional data obtained to date, extensive intra- and inter-system as well as extensive intra- and inter-population differences are apparent. Consequently, it is at present difficult to ascertain specific molecular patterns that define microbial groups that would be congruent with the definition of a microbial species. Concomitant analysis of community genomic complements, transcriptomes, proteomes and metabolomes over relevant spatial and temporal scales in the future will result in detailed molecular descriptions of distinct microbial entities. Such a system-level molecular organismal classification system will need to be solidly grounded in ecological theory, population genetic theory and evolutionary theory, and may be universally applicable to the three domains of life.