Of Microbes and Maps

Biogeography is the study of the spatial and temporal distribution of organisms. Anyone who has ever had a visit to the zoo or natural history museum has taken a crash course in biogeography. Jaguars hangout in Central and South American rain forests, and cheetahs cruise African savannas. Badass dinosaurs roamed the earth millions of years ago. The field of biogeography is centuries old, and its hypotheses and theories are foundational to the contemporary fields of ecology, evolution, zoology, botany, geology, and geography.

While patterns of biogeography are governed by a multitude of variables and forces, we can boil it down to a few key ecological and evolutionary processes. Rates of dispersal, colonization, and diversification (i.e. speciation and extinction) ultimately create these patterns. The big question is, are there universal rules that dictate the formation and maintenance of biogeography across all domains of life? Sometimes it seems that microbes dance to the beat of their own drum when it comes to ecological and evolutionary theory. But maybe we need to develop the appropriate tools and approaches to ask the right questions.

For microbial biogeographers, the standing hypothesis for nearly a century has been the frequently cited, but often mistranslated, Bass Becking hypothesis, “Everything is everywhere, but the environment selects.” In other words, microbes are ubiquitously dispersed and filtered across habitats. The patterns of biogeography we observe result from the environment selecting a specific community from a global microbial pool that is locally adapted to particular conditions. In support of this is a microbe’s small size, large population, and ability to withstand unfavorable conditions through dormancy strategies. An alternative hypothesis is that patterns of biogeography arise due to dispersal limitation and subsequent diversification processes, like genetic drift and local adaptation. How do we test for dispersal limitation? Well, it requires a serious consideration of scale.

We’ve found microbial life practically everywhere we’ve looked. We know that coarse environmental variables like pH influence microbial community structure (for more info, check out the publications of the Fierer and Knight labs). However, these surveys are generally conducted at broad phylogenetic scales, using 16S rRNA gene sequences to bin microbes into units of diversity or species (the canonical unit being ≥97% 16S rRNA identity), across environmental gradients. Diversification of 16S rRNA genes takes millions of years, approximately 1% divergence/50 million years! To put that into perspective, the last common ancestor of all primates is estimated at 81.7 Mya. That is a lot of time for dispersal and diversification to create patterns of biogeography in monkeys, apes, and humans. When we assess microbial biogeography using a 97% 16S rRNA identity cutoff, we are obscuring the genetic and ecological diversity accumulated over 100 million years of evolution.

Microbes are everywhere, but when we increase our taxonomic resolution, do we see limits to dispersal? To rigorously test if dispersal limitation can influence patterns of microbial biogeography, we need to narrow our phylogenetic focus. We need to study populations of closely related microbes sampled across appropriate environmental, spatial, and temporal scales. Easier said than done. This is the approach I am using for my research on Streptomyces biogeography. In the coming weeks I’d like to expand this discussion on the processes creating patterns of microbial biogeography by diving into the literature. For an excellent review on the current status of microbial biogeography research, check out this article by Hanson and others. That’s all for now, cheers!



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