Some of Charles Darwin’s most provocative observations in formulating his nascent theory, were of the Galapagos finches, which were broadly similar to the finches on the mainland but had somehow diversified locally, each to its own way of life as determined by conditions on its particular island. Darwin’s insights into the dynamic tensions between geographical dispersal and local adaptation set the stage for 150 years of evolutionary ecology of macrobiota. In microbiology, developing an understanding of microbial speciation has been challenged by historical difficulties in producing a natural history of microorganisms. However, the molecular revolution changed the playing field and we might now be able to produce a first sketch of the rules that determined the microbial origin of species. In this work we propose that, just as for finches in Darwin’s isolated archipelago, the microbiota in geographically isolated habitats vividly display how evolution has played its most astounding tricks. And is in these places were we can ask questions as: How do bacteria speciate? There is increasing evidence for the existence of unique ecosystems dominated by locally adapted microbiota harboring distinct lineages and biological capabilities, much like the macrobiota of Darwin’s Galapagos Islands. As a primary example of such systems, we highlight key discoveries from the Cuatro Cienegas basin, Coahuila, Mexico that challenge some prevailing views in environmental microbiology. For the last eight years we have been conducting research on the community structure of their diverse microbes with population genetic tools on cultivable bacteria, with molecular ecology on non-cultivable bacteria, and with genomics on two keys stone Bacilli specie. 

Results/Conclusions

With all the analysis found an amazing diversity in the site, mostly due to a high differentiation in the microbial composition between different pozas, as well as strong evidences for adaptation at the community and at the genomic level. Here we argue that high microbial endemism requires a combination of geographical isolation, long-term continuity, local adaptation and mechanisms for reducing the intensity of horizontal gene transfer (HGT). We also propose a novel hypothesis that strong P limitation plays an important role in microbial diversification by reducing the intensity of HGT through a variety of pathways.