With the benefit of hindsight, the last 20 years in microbial ecology will probably be referred to as the census period that dramatically changed our perception of biodiversity within the three domains of life. Bacteria and archaea are no longer viewed as groups of peculiar and morphologically simple organisms that show relatively little diversification despite their long evolutionary history, but have now been recognized to harbour a perplexing number of novel phylogenetic lineages (Rappé & Giovannoni, 2003). Current estimates assume that the number of prokaryotic species ranges in the millions and thus vastly exceeds the fewer than 10 000 described prokaryotic species that have been isolated to date in pure culture (Curtis et al., 2002). This dramatic paradigm shift was only made possible by the development of cultivation-independent molecular approaches for surveying microbial diversity in nature. Whilst it is now evident that most prokaryotes cannot be cultured easily, due to their living in complex communities and their intimate metabolic links with both their abiotic and biotic environments, the powerful arsenal of techniques at our disposal enables us to see beyond the ‘cultured few’ and gain valuable insights into the realm of uncultured microorganisms (Wagner, 2004). It is now relatively straightforward to determine the species richness of natural microbial communities by comparative sequence analysis of environmentally retrieved 16S rRNA gene sequences (Olsen et al., 1986; Schloss & Handelsman, 2004).
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