- © The Mineralogical Society Of America
Small variations in phenotypic characteristics (the length or shape of a bird’s beak or the color of its plumage, the timing of flowering in plants, the level of resistance to disease) have been used as markers to trace evolutionary processes in macroorganisms since Darwin’s Origin of Species (Darwin 1859). Until recently, microbiologists have had difficulty recognizing evolutionary processes in natural microbial populations because phenotypic characters and adaptations unique to certain populations have been virtually impossible to identify at the individual scale. High-resolution molecular techniques, such as multi-locus sequence analysis and environmental genomics, today provide the means to survey microheterogeneity in natural microbial systems. Already these molecular surveys have uncovered fine-scale patterns of diversity within populations previously thought to be homogeneous (Palenik 1994; Palys et al. 1997; Schleper et al. 1998; Whitaker et al. 2003; Acinas et al. 2004; Papke et al. 2004; Tyson et al. 2004; Venter et al. 2004; Thompson et al. 2005) and are beginning to provide clues to evolutionary mechanisms through which diversity is generated and maintained at this scale.
Coming in the wake of studies that assessed microbial diversity through amplification and sequencing of single genes (particularly 16S rRNA) (Pace 1997), high resolution molecular tools have revealed a microbial world that is much more vast and far more complex than anyone had anticipated. How do we make sense of this diversity? What can it tell us about how microbial ecosystems are structured and how they function in their geochemical contexts? Is biodiversity consistently partitioned into species, and are species the most ecologically relevant units of diversity in microbial systems? Can we monitor diversity to determine how changes in environmental conditions shape communities and drive the evolution of new functions? The answers to these questions will in part result …