Chapter 7 : How To Look, Where To Look

Abstract:

A distinctive feature of microbial communities is that their diversity can be extraordinarily high, not infrequently orders of magnitude greater that the diversity of macrobial ecosystems. The state of "supersaturated coexistence" that defines the coexisting species-limiting resource paradox may be maintained by competition for such resources such that nonequilibrium conditions are generated. The challenge now is to design experiments that can discriminate between these models for supersaturated coexistence, or enable more realistic ones to be formulated. It is increasingly clear that scale effects, both spatial and temporal, are principal determinants of species richness and need to be recognized when attempting to quantify microbial diversity, when addressing basic problems in microbial ecology and microbiogeography, and when maximizing returns from biotechnology search and discovery programs. All too frequently insufficient attention is paid to the design of environment sampling strategies and to evaluating the sampling effort. Despite the spectacular advances in the molecular detection and circumscription of microorganisms and functional genomics, organisms in culture are essential for providing an understanding of microbial interactions, pathogenesis, phenotypic variability, and, in the present context, for delivering biotechnological innovation. Three approaches are presented here: habitat simulation, technological innovation, and taxonomic databases. The success of the molecular detection strategy depends on the quality of the DNA extracted from the environment.