Prokaryotic Diversity

As in most other environments, phylogenetic analysis of the 16S rRNA genes of the prokaryotes in the hindgut of several termites has revealed an enormous diversity of the intestinal microbiota (see Brune 2005 for a review). The majority of clones in bacterial clone libraries of several species in the genus Reticu-litermes bears less than 90% sequence similarity to those of known, cultivated microorganisms. Clones in the so-called Termite Group 1 (Ohkuma and Kudo 1996; Hongoh et al. 2003; Yang et al. 2005) even represent a new bacterial phylum, the 'Endomicrobia' (Stingl et al. 2005), which contains no cultivated representatives and apparently consists exclusively of endosymbionts of termite gut protozoa (see (8).4.2.2.). The fact that most clones recovered in these studies fall within lineages consisting exclusively of clones obtained from the hindgut of termites, with the closest relatives of a given clone usually stemming from the most closely related termite (Yang et al. 2005), indicates that most of the prokaryotes in termite guts are specific for and also restricted to this particular habitat.

A number of prokaryotes from termite guts have been isolated in pure culture. Many of the isolates are unique to the termite gut habitat and catalyze key activities in hindgut metabolism, e.g., methanogenesis, reductive aceto-genesis, nitrogen fixation, or uric acid fermentation (e.g., Breznak 1994; Leadbetter and Breznak 1996; Leadbetter et al. 1998, 1999; Lilburn et al. 2001; Boga et al. 2003; Graber et al. 2004). Also, oxygen reduction by anaerobic bacteria, such as lactic acid bacteria (Tholen et al. 1997; Bauer et al. 2000), homoacetogenic bacteria (Boga and Brune 2003), and sulfate-reducing bacteria (Kuhnigk et al. 1996; Fröhlich et al. 1999), emerges as a potentially important activity (see above).

Although the characterization of the isolates has provided valuable information on metabolic properties and other physiological features relevant for the colonization of this particular habitat, there are still enormous discrepancies between the phylogenetic groups dominating the clone libraries and the species recovered by cultivation, indicating the presence of a strong cultivation bias (Breznak 2000; Brune 2005). To date, there is not a single isolate representing the prokaryotes associated with the gut flagellates. In general, the lack of knowledge on the individual components of the prokaryotic microbiota and their metabolic capacities and activities in situ still make it difficult to define the essential functions and understand the complex interactions.

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