Title : Microbial Diversity - Exploration of Natural Ecosystems and Microbiomes Authors :

Microorganisms are the pillars of life on Earth. Over billions of years, they have evolved into every conceivable niche on the planet. Microbes reshaped the oceans and atmosphere and gave rise to conditions conducive to multicellular organisms. Only in the past decade have we started to peer deeply into the microbial cosmos, and what we have found is amazing. Microbial ecosystems behave, in many ways, like large-scale ecosystems, although there are important exceptions. We review recent advances in our understanding of how microbial diversity is distributed across environments, how microbes influence the ecosystems in which they live, and how these nano-machines might be harnessed to advance our understanding of the natural world. The turn of the 21 century saw the rise of a new kind of natural historian, focused on the invisible life that permeates our planet [1]. Unlike earlier naturalists, like Alexander von Humboldt or Alfred Russell Wallace, who documented the “...endless forms most beautiful...”, recognized by Darwin as the fruits of natural selection, these new explorers confronted a strange and unfathomably vast world of imperceptible single-celled organisms [2]. This world was largely inaccessible and underestimated prior to the advent of molecular fingerprinting and high-throughput sequencing technologies, which now allow us to circumvent culture-based approaches [2,3]. The excitement in this new era of exploration is palpable, as molecular toolsets help crack open the microbial “dark matter” [4] responsible for driving global biogeochemical cycles [5], maintaining the health of multicellular organisms [6], and ensuring the longevity of our ~3.8 billion-year-old biosphere [7]. At first, each sequencing survey seemed like another Voyage of the Beagle. However, unlike Victorian naturalists, microbial ecologists had the tools of modern genetics and molecular biology at their fingertips. Consequently, the transition from a descriptive phase to a more quantitative, mechanistic understanding of how diverse microbial communities assemble, fluctuate through time, and achieve biological and ecological functionality was rapid. Although microbial ecology is still a young field with many unanswered questions, we explore recent advances in our understanding of how natural environments shape and maintain microbial diversity over time and space, and how the diversity of microbial communities influences the environment. We briefly discuss how microbial ecology fits into the larger body of established theory underlying traditional ecology. Finally, we look