Isolation and Cultivation of Bacteria

Isolation and cultivation of microorganisms enables in combination with cultivation-independent methods comprehensive research on ecology and function of microbes. The availability of cultures provides opportunities for ecophysiological experiments, enables high-quality genome research and represents a mandatory prerequisite for the description of new taxa of prokaryotes. Unfortunately, access to microorganism by cultivation methods is still quite limited, and the majority of the microbial diversity remains uncultured so far. This chapter discusses the potential reasons for this lack in cultivability and reviews advances in cultivation methods for prokaryotes. Detailed analysis of the media and methods used by taxonomists for isolation of bacterial strains used for description of >1000 new species revealed that the description of new taxa in the ranks of species and genera is currently not methodically limited. On the other hand, isolation of strains enabling the description of taxa representing higher ranks is obviously strongly limited by the currently applied methods. Consequently, different cultivation strategies are required according to the scientific goals of the respective research. While taxonomists interested in the description of new species affiliated with any genus or family can isolate new strains suitable for this task by using standard cultivation methods and media, ecologists interested in cultivation of model organisms appearing in natural systems with high cell numbers, as well as taxonomists interested in isolation of strains representing new higher ranking taxa like orders, classes and phyla, should rather use high-throughput non-standard methods in combination with optimized screening protocols.