Microbial diversity in the era of genomics

Summary

THE CONTINUING SAGA OF THE MICROBIAL SPECIES

Fundamental to the assessment of global microbial diversity is understanding the unit of measurement of diversity, namely the microbial species. Historically, definition of a microbial species has been accomplished by employing relatively crude methods based on laboratory culture. Limitations of both the methods and the philosophical construct underpinning the species definition for micro-organisms have been elaborately detailed by Woese (2004), who pointed out the fallacies of the ‘concept of a bacterium’ that led to the inclusion of all bacteria (as then understood) within the single grouping of ‘prokaryotes’, with a shared ‘prokaryotic’ organization evolved ultimately from a common prokaryotic ancestor (Stanier & van Niel, 1962; Stanier et al., 1957, 1963). Woese (2004) tracks the history of the ‘prokaryote–eukaryote’ dichotomy to the protozoologist Edouard Chatton (1938), whose reasoning was that, just as nucleated cells represented a monolithic grouping structurally and phylogenetically, non-nucleated cells (bacteria) also do so. Woese (2004) provides an eloquent explanation for the lack of philosophical understanding impelled by, on the one hand, technological advance and, on the other, ‘fundamentalist reductionism’ (the reductionism of 19th century classical physics), namely the view that living systems can be completely understood in terms of the properties of their constituent parts. The unfortunate aspect of fundamentalist reductionism is that it ignores the notion of emergent properties. The definition of a ‘micro-organism’ is, in itself, elusive.