Soil bacterial community analysis using high-throughput sequencing and metagenomics is unraveling an enormous contingent of species that are present in low numbers and may vary at a small (< cm) scale. The functional significance of the rare microorganisms both in terms of overall ecosystem function and its resilience is yet to be fully answered. We can begin to address this question by a suite of methods. Innovative culturing methods allow us to access some members of this group, meta-transcriptomics and -proteomics can indicate of activity of some, and stable isotope probing and other substrate-linked markers can indicate particular groups that are active. A second phase of this topic is conceptual, including what are the spatial patterns of rare members – patchy or uniform, are rare members basically a refugia, which of those detected are alive (e.g. VBNC), do some have regulatory properties that are more responsive with minimal stimulus, how much of a response is stochastic (chance-based) and finally, are the valued ecofunctions few but dispersed among millions of taxa? Examples will be used to illustrate the known and unknown.