It would seem justified to assert that, so far, no revision of the Darwinian paradigm has become necessary as a consequence of the spectacular discoveries of molecular biology. But there is something else that has indeed affected our understanding of the living world: that is its immense diversity.
Ernst Mayr (2004)
DNA sequencing continues to reveal new species that could not be found with conventional methods. Nowhere is this more true than in the microbial world where the sequence-based estimates of species in a gram of soil commonly run into the thousands (Gans et al., 2005; Roesch et al., 2007). Only a fraction of these species would typically be identified by culture-based methods, revealing that the majority of microbial species will not grow in current laboratory conditions (Hugenholtz et al., 1998). This realization, along with the rapidly decreasing cost of DNA sequencing, has led to an impressive effort to identify and catalog microbial diversity across a wide range of environments. These environments include soil, which is often considered one of the most diverse environments, but also range out to marine environments including the open ocean (Yooseph et al., 2007), the massive microbial mats that form stromatolites (Baumgartner et al., 2009) (Fig. 7.1C), and hydrothermal vents where large numbers of rare species have been found (Sogin et al., 2006).
The survey of microbial life is also looking inward to the species that live in and on humans, as exemplified by the concept of the human micro-biome. Numerous projects are under way to catalog genetic diversity in areas including the skin, the oral cavity, and the intestine (Dethlefsen et al., 2006; Ley et al., 2006a). Whereas intestinal communities have been found to be quite similar across humans as compared with other mammals (Ley et al., 2008), different people often carry different sets of micro-bial species, underlining the complexity of intestinal ecology (Guarner and Malagelada, 2003; Eckburg et al., 2005; Dethlefsen et al., 2006). The composition of the gut microbiota has also been found to have important implications for health and has been linked to a range of diseases including obesity, inflammatory bowel disease, and colonic cancer (Guarner and Malagelada, 2003; McGarr et al., 2005; Dethlefsen et al., 2006; Ley et al., 2006b; Manichanh et al., 2006).
Recognition of the vast diversity within microbial communities has occurred alongside another realization about microbial life: the importance of social interactions. It is now accepted that many phenotypes of one cell influence the ability of surrounding cells to divide and survive, which are social traits in an evolutionary sense (Crespi, 2001; West et