Microorganisms of untold diversity are usually members of complex communities that dominate every corner of our biosphere. They orchestrate key processes in geochemical cycling, biodegradation and in the protection of entire ecosystems from major environmental shifts. Within the oceans, nominal cell counts greater than 105/ml predict an estimated 3.6 x 1029 microbial cells with cellular carbon of ~3 x 1017 grams. Given the enormous number of microbes and their vast metabolic diversity, the accumulation of mutations during the past 3.5 billion years should have led to very high levels of genetic and phenotypic variation. A mere 30 years ago, Woese introduced the first and only meaningful molecular paradigm for defining relationships between microbial taxa. With advances in molecular techniques, it soon became evident that microbial diversity is at least 100 times greater than estimates based upon traditional cultivation-dependent surveys.
However the sequencing of full-length ribosomal RNAs or other conserved gene families rarely informs us about the relative population numbers for different kinds of microbes. Understanding microbial ecological processes such as biogeography and ecosystem function requires information about population structures including measures of richness and evenness. The recent introduction of massively parallel sequencing technology offers a means to simultaneously measure evenness and richness of microbial populations. Through the collection of large numbers of hypervariable regions in small subunit ribosomal RNAs we have been able to generate highly resolved profiles of microbial population structures for communities under different ecological constraints. We have discovered a spectacular wealth of previously unknown diversity. A relatively small number of different populations dominate all samples, but thousands of low-abundance populations account for most of the observed phylogenetic diversity. This "rare biosphere" is very ancient and may represent a nearly inexhaustible source of genomic innovation. Members of the rare biosphere are highly divergent from each other and at different times in earth's history may have had a profound impact on shaping planetary processes.
