Microbial biogeography?

Until quite recently microbial biogeography has existed more as a ‘statistically improbable phrase’ than a field of study. For example, biogeography is accorded but two pages in the otherwise exhaustive text on microbial diversity by Ogunseitan (2005). Likewise microbes can be completely missing from current discussions of biogeography (e.g. Lomolino & Heaney, 2004). A conceptual prejudice was that there is no microbial biogeography as microorganisms are easily dispersed: the famous ‘all microbes are everywhere, the environment selects’. This may seem curious to nonmicrobiologists. Most would agree that dispersal ability may dilute the impact of vicariance events but in and of itself does not obliterate all distributional patterns in time and space; witness those of birds and butterflies. The attitude of microbial ecologists was also quite likely a self-defence mechanism, a reaction to an inability to begin to grapple with the subject because of problems which existed in simply counting organisms in natural samples of soil or water and the limited number of morphological characters that distinguish species and genera (Fig. 1). However, tools have changed and so have the perceptions of microbial ecologists. Discussions of whether all species are everywhere or not have given way to the realization that indeed many, if not most, protist species appear to be very widely distributed. However, these ‘species’, distinguished via morphology, probably do not correspond with interbreeding populations. Cryptic species, forms genetically distinct but morphologically similar, appear to be common. Intriguingly, genetically distinct populations occur among more or less continuously distributed species, such as the dinoflagellate ‘species complex’ of Alexandrium tamarense, some of which are toxic. The toxicity of the dinoflagellate population appears to be a quite variable character, unpredictable from phylogeny (Uwe et al., 2003). Thus, for protists, it appears that all ‘morpho-types’ may be everywhere but not all genotypes. The mechanisms maintaining genetic isolation among protists are obscure. The sequencing of DNA from natural samples is showing not only new groups but also unexpectedly high species richness. For example, Countway et al. (2005) obtained surprising results by using sophisticated molecular techniques to analyse samples from a very simple experiment with seawater. A single seawater sample was distributed into a set of 4-L bottles. DNA was collected from two bottles at the start of the experiment, then from three bottles after 24 h and again after 72 h from the last three bottles. The DNA in the seawater obtained from time zero, after 24 h and after 72 h was cloned and sequenced, thus allowing estimation of species abundance. Sampling with time allowed the experimenters to exploit the fact that placing microbial populations in bottles alters the composition of the population. Thus, species in low, difficult to detect concentrations often become more abundant with time in ‘bottled water’. Species composition did change with time and a total of 165 species or phylotypes of protists were found. Statistical estimators of sampling error suggested that about 300 protist species were present in the original 32 L of seawater. As for prokaryotes, molecular tools allow us to distinguish bacteria from one another on a genetic basis, rather than relying on their abilities to use a particular substrate or show a particular colony type – characteristics requiring cultivation of the organisms. Thus, using sequence data, an entire new kingdom of life, the archaebacteria, was discovered. The first application of molecular approaches, sequencing sections of ribosomal RNA, also reinforced the idea that all bacteria were everywhere. The strain SAR