Microorganisms, whether cultured or represented only in environmental DNA samples, constitute the natural resource base of microbial biotechnology. Numerous prokaryotic and fungal genomes have been completely sequenced and the functions of many genes established. For a newly sequenced prokaryotic genome, functions for over 60% of the open reading frames can be provisionally assigned by sequence homology with genes of known function. Knowledge of the ecology, genetics, physiology, and metabolism of thousands of prokaryotes and fungi provides an indispensable complement to the sequence database.

This is an era of explosive growth of analysis and manipulation of microbial genomes as well as of invention of many new, creative ways in which both microorganisms and their genetic endowment are utilized. Microbial biotechnology is riding the crest of the wave of genomics.

The umbrella of microbial biotechnology covers many scientific activities, ranging from production of recombinant human hormones to that of microbial insecticides, from mineral leaching to bioremediation of toxic wastes. In this chapter, we sketch the complex terrain of microbial biotechnology. The purpose of this chapter is to convey the impact, the extraordinary breadth of applications, and the multidisciplinary nature of this technology. The common denominator to the subjects discussed is that in all instances, prokaryotes or fungi provide the indispensable component.