Microbial biogeography: the end of the ubiquitous dispersal hypothesis?

Ken Timmis is a difficult scientist to refuse when he asks you a favour. In his capacity as senior editor of the Environmental Microbiology journal, he asked me to write a research highlight on the paper by Ryšánek and colleagues (2014), which I had originally reviewed and made one of those very rare (for me) recommendations to ‘accept as is’. In the paper, the authors examined the continental-scale spatial distributions of a single lineage of terrestrial protists within the genus Klebsormidium; using rbcL sequences to screen the isolated strains, which they asserted would provide better resolution than an internal transcribed spacer (ITS) targeted approach (Ryšánek et al., 2014). Interestingly, from a natural history perspective, they identified novel genotypes from the 190 Klebsormidium colonies isolated from their samples. In addition, and particularly fascinating to me, the authors presented strong evidence for both cosmopolitism and endemicity in terms of the biogeographical distribution across the Klebsormidium genotypes. Below, I set out a brief potted history on the rise of microbial biogeography in order to provide context on how this work, in my view, significantly contributes to our growing knowledge on this important fundamental subject. It is now widely accepted that to better understand the ecology of microorganisms (inclusive of archaea, bacteria, fungi, and protists) and their roles in ecosystem functioning could be achieved if traditional ecological theories can be applied to microorganisms (Carbonero et al., 2014). The great promise is that this would help us better understand and predict changes in the natural environment, would allow improved manipulation of agricultural and engineered systems, and would give improved protection of human health. It would be fair to state that the adoption and adaptation of ecological theory in microbial ecology began to really gain momentum from the middle of the last decade (Prosser et al., 2007). A particular emphasis is placed on ‘adaptation’, as it would be naïve to ever lose sight of/or ignore the fact that the biology of animals and plants, of which traditional ecology is almost exclusively based upon, are different from that of microorganisms. Moreover, even the biology of different microorganisms can be staggeringly different, and assuming equivalence based on microscopic body size is similarly naïve. On this critical point, Carbonero and colleagues (2014) stated that due to differences in scale and physiologies between macroorganisms and microorganisms [and indeed between types of microorganisms (my addendum)], there will be principles of ecology that are difficult to reconcile between traditional and microbial ecology. Therefore, this represents a substantial challenge to the worthwhile cause of developing an inclusive ecology. From a fundamental perspective, the growing acceptance and incorporation of traditional ecological principles and theory into microbial ecological research over the last 10 years has started to move us away from what Prosser and colleagues (2007) opined was the accumulation of situation-bound statements that are of limited predictive ability, offering few insights. Indeed, this was exemplified at the time by an anonymous referee’s quote published in this journal, ‘There is no apparent study concept other than “we went out to the campus pond one day and took 2 samples for sequencing” ’, and found they were different [my addendum] (Anon, 2006). The interest in translating principles and theories from traditional ecology to microbial ecology has largely centred on the question of microbial biogeography. As a basic definition, ‘biogeography is the study of the distribution of biodiversity over space and time. It aims to reveal where organisms live, at what abundance, and why?’ (Hughes Martiny et al., 2006). An initial grounding on the subject of microbial biogeography can be gained from the review and analysis papers by Jennifer Martiny and colleagues (Hughes Martiny et al., 2006; Hanson et al., 2012). *For correspondence. E-mail cjvdg@ceh.ac.uk; Tel. (+44)