Prokaryotic Symbionts of Termite Gut Flagellates: Phylogenetic and Metabolic Implications of a Tripartite Symbiosis Andreas Brune, Ulrich Stingl 1 Introduction The symbiotic associations of termites with their gut microorganisms have been studied for almost a century. While the earlier work had focused on the intestinal protozoa of lower termites and their role in digestion, the more recent investigations have been directed mainly at the prokaryotic gut micro- organisms, their metabolic activities, and the structure and function of the bacterial and archaeal populations. In addition, the application of microsensor techniques has revealed the unexpected dynamics of the physiochemical gut conditions and given the first indications of the spatial organization of the major microbial activities, which has led to the recognition that the gut pro- vides a variety of different microhabitats for its microbiota. The most important habitats for the prokaryotes in the hindgut of lower termites are provided by the intestinal protozoa. Although it is long known that the gut flagellates are intimately associated with prokaryotes, the signifi- cance of this phenomenon has not been fully appreciated. The difficulties surrounding cultivation of the protozoa and the complete absence of pure cultures of the prokaryotic symbionts so far allowed merely a morphological description of the different associations. Their exact nature and the possible benefits for the partners are mostly in the dark. However, with the advent of molecular biology tools and the resulting new possibilities, the interest in the symbiotic associations between prokaryotes and termite gut flagellates has been renewed. A definitive classification of these associations into the different categories of symbiosis, such as mutualism, parasitism, or commensalism, would require a level of understanding that remains to be reached. This chapter will therefore use the term symbiosis in its broader definition, as it was originally coined by Anton de Bary (1878), which comprises all kinds of associations between dif- ferent species. A. Brune Max Planck Institute for Terrestrial Microbiology, Marburg, Germany U. Stingl Springer-Verlag Berlin Heidelberg 2005 © Progress in Molecular and Subcellular Biology Jörg Overmann (Ed.) Molecular Basis of Symbiosis Department of Microbiology, Oregon State University, Corvallis, Or., USA