Chemotaxis and behavioral physiology of not-yet-cultivated microbes

Chemotaxis assays provide a rapid and efficient means of (1) studying the chemotactic behavior of microorganisms in complex samples and (2) identifying potential growth substrates and generating inocula for subsequent isolation trials. The chemotaxis method thus complements the set of techniques currently available for the investigation of not-yet-cultured microbes. Although restricted to motile and chemotactically active microorganisms, a considerable fraction of species can be covered with this technique, particularly in bacterioplankton communities. Several formats of the chemotaxis assay have been developed. Capillaries are loaded with solutions of test compounds and are inserted in small microscopic chambers, in bottles containing culture suspensions, or incubated directly in situ. The latter two techniques are also suitable for experiments with anaerobic bacteria. In flat rectangular glass capillaries, the accumulating microorganisms can be observed directly by light microscopy in a dark field. Afterward, the chemotactically active bacteria can be identified by analyses of their 16S rRNA gene fragments. The method has been used to identify an essential carbon compound required for the growth of previously unculturable phototrophic consortia. This knowledge proved essential for the subsequent successful enrichment of these bacterial associations. Furthermore, it has been shown that different not-yet-cultured members of aerobic lake water bacterioplankton communities are chemotactically active and attracted by different carbon compounds.