Untangling the complex geographic and evolutionary patterns of microbes

The tiny size of microorganisms belies their extraordinary complexity. In spite of their size, most microbes have several thousand genes that encode a wide range of metabolic and cellular functions, some acquired from distant relatives through the process of lateral gene transfer (LGT). The spread of antibiotic resistance and adaptation to challenging environments such as polluted sites are particularly compelling examples of the impact of microbial LGT on society. One consequence of LGT is that building a Tree of Life to understand the evolution of microorganisms may be impossible or a meaningless exercise, since so much genetic information has been shared between distant lineages. The first part of my proposed research will address this question, by using new criteria to assemble trees that are more resistant to the effects of LGT, and by developing phylogenetic network approaches that can effectively show both vertical (parent-to-offspring) and lateral connections. A key objective of this work will be to replace the canonical Tree of Life with a network that is understandable in spite of its increased complexity. Microbes rarely act alone: instead they are commonly found in communities containing anywhere from a handful of different species in extreme environments, to hundreds or potentially thousands in our gut, in soil, and in the sea. The membership of a microbial community can determine its function; for example, different communities are associated with different clinical outcomes in various types of microbial disease. We have developed GenGIS, a geographic information system that lets a user test hypotheses about the relationship between microbial community structure and potential influencing factors using user-proposed geographic gradients. The second part of this proposal will extend GenGIS to evaluate all possible simple gradients and a large subset of more-complex ones, to relate patterns of dispersal to geographic and environmental factors. Microbes make all other life on Earth possible, and our approaches will help to understand critical influencing and risk factors that can lead to changes in these fundamental communities.