The introduction of impressive technologies in the search for life's diversity and activity in soil has led to remarkable new techniques and knowledge concerning the soil microbial community. These have led to finding some important links to function. However, we attest that the general lack of causality found between the many metrics of microbial diversity and populations of soil microbes and function is due, at least in part, to the lack of understanding of the links between microbial populations and dynamics to their physical habitat and attendant moisture conditions. In this opinion paper we explore the importance of this interplay between organism and habitat. Further, as an example of this interplay, we introduce the potential importance of nematode movement and gene transfer in bacterial populations. Highlights: The importance of the physical habitat is highlighted in soil microbiology studies. The interplay between the soil–root–habitat is emphasized. Seeking a functional understanding of biodiversity rather than a ‘biology of numbers and differences’ approach is proposed. The movement of nematodes with respect to horizontal gene transfer is discussed.