Back to the basics: The need for ecophysiological insights to enhance our understanding of microbial behaviour in the rhizosphere

Microorganisms exhibit an astonishing diversity and wide genetic variability even within species, in particular with respect to their metabolic pathways and host-interactive capabilities. The mosaic genomes that encode these capacities are accountable for the abilities of environmental microbes to survive and thrive in highly complex systems such as soil and the rhizosphere. Whereas credits are to be given to traditional microbiology studies, e.g. with rhizobia and their interaction with the plant, an explosive enhancement of our understanding of the plant-microorganism interactive system has been recently achieved by the broad application of the molecular toolbox, in particular high-throughput sequencing (HTS) technologies. The latter have allowed to access thousands to millions of microbial phylotypes and functions at relatively low cost and effort. While such techniques have improved the accessibility of the taxonomic and functional diversity of rhizosphere and soil microbial communities, detailed insights into organismal ecology and physiology (reflecting the behaviour of populations of cells) within the community in the natural environment are still required. In this review, we first examine the current 'state-of-the-art' of rhizosphere ecology studies and what HTS strategies have added to our understanding of the system. We posit that our capacity to develop and test refined ecological hypotheses is hindered if we solely depend on deep-sequencing methods. Plant-soil-microorganism systems represent one of the most intriguing 'playgrounds' for assessments of ecological theories, since they offer a myriad of ways to investigate ecological interactions (i.e. intra- and inter-specifically), physiological and behavioural traits. In addition, the evolutionary processes that lead to innovation in the microbiota are likely prominent in the rhizosphere. Thus, there is a perceived need to shift our attention from the HTS studies, that extensively map the local microbiota in an overall fashion, to studies focusing on as-yet-unaddressed fundamental questions about the plant-soil microbiota system. Such a paradigm shift will certainly assist us in the unravelling of the building blocks of rhizosphere (and soil) microbial communities, as well as form a basis for targeted manipulation of these in their natural settings