Microbial Ecology Biogeography: An Emerging Cornerstone for Understanding Prokaryotic Diversity, Ecology, and Evolution Alban Ramette and James M. Tiedje Center for Microbial Ecology, Michigan State University, 540 Plant and Soil Sciences Building, East Lansing, MI 48824-1325, USA Received: 17 January 2005 / Accepted: 25 May 2005 / Online publication: 8 November 2006 Abstract New questions about microbial ecology and diversity combined with significant improvement in the resolving power of molecular tools have helped the reemergence of the field of prokaryotic biogeography. Here, we show that biogeography may constitute a cornerstone ap- proach to study diversity patterns at different taxonomic levels in the prokaryotic world. Fundamental processes leading to the formation of biogeographic patterns are examined in an evolutionary and ecological context. Based on different evolutionary scenarios, biogeographic patterns are thus posited to consist of dramatic range expansion or regression events that would be the results of evolutionary and ecological forces at play at the genotype level. The deterministic or random nature of those underlying processes is, however, questioned in light of recent surveys. Such scenarios led us to predict the existence of particular genes whose presence or polymorphism would be associated with cosmopolitan taxa. Furthermore, several conceptual and methodolog- ical pitfalls that could hamper future developments of the field are identified, and future approaches and new lines of investigation are suggested. Introduction Prokaryotic biogeography can be defined as the science that documents the spatial distribution of prokaryotic taxa in the environment at local, regional, and continen- tal scales. In a broader sense, this discipline examines variation of microbial features (e.g., genetic, phenotypic, physiological) at different spatial scales, between distantly located sampling sites or along large environmental gradients. Its scope also encompasses the understanding of the processes generating and maintaining those dis- tribution patterns. The ultimate goals are to propose and evaluate theories regarding the creation and evo- lution of such diversity patterns in the environment. Not surprisingly, this definition is identical to the one already existing for eukaryotic organisms [41], and this also may explain why current conceptual approaches share high similarities with the ones already described for eukaryotes. The study of microbial biogeography may offer promising benefits to many research areas. Examples of application may be foreseen in the global epidemiology of human, animal, and plant pathogens; in the moni- toring of the fate of inoculated biocontrol or bioreme- diation agents when applied at large scale; or in the identification of geographic areas where those beneficial bacteria thrive in the environment. More generally, this field will undoubtedly improve our understanding of the global microbial diversity and of the evolutionary forces shaping it. Interest in studying spatial patterns of prokaryotes has its origin back to the beginning of the 20th century when scientists began to question the existence of dif- ferent bacteria at distantly located sites [3, 5]. Microbial biogeography has recently gained renewed interest in the microbial ecology community because of new questions about microbial diversity and the availability of power- ful molecular tools to describe diversity, especially at the genotype level (e.g., [43, 48, 68]). Thus, an increasing number of studies have been published on this topic as applied to different bacterial groups in terrestrial or marine ecosystems. Biogeographic patterns associated with bacterial diversity have been reviewed elsewhere [27, 29]. The aims of this article were (1) to summarize the knowledge gained from studies about prokaryotic bioge- Correspondence to: Alban Ramette at present address: Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany; E-mail: aramette@mpi-bremen.de DOI: 10.1007/s00248-005-5010-2 & Volume 53, 197–207 (2007) & * Springer Science + Business Media, Inc. 2006 197