Chapter 39 : Many Challenges to Classifying Microbial Species

Abstract:

Nature walks aside, studying the natural history of microorganisms is uniquely challenging for a host of reasons, one of which is that there are many different microbial species—or at least groupings that look and act like species. The author saw metagenomic data in the form of genes taken from seawater to identify marine bacteria and was fascinated to discover that although similar genes clustered to form groups, no two were identical. Bacterial and archaeal cells do not pair, recombine gametes, and undergo meiosis. Among others, two observations are critical to understanding the arguments about microbial speciation. The first is the importance of the vast size of microbial populations in nature, and the second is the subtler concept of neutral variation and sequence space. Microbes are the frontier beneath our feet, yet it has taken a long time for Charles Darwin’s ideas to approach their full potential for interpreting microbial diversity. The natural selection is probably very efficient at improving microorganisms to make them nearly ideal machines for reproducing in natural environments, but at the same time the age and size of these populations, the constantly changing environments they must adapt to, and their varied repertoires of DNA acquisition mechanisms make them extraordinarily diverse.