Structure and function of microbial communities

Abstract

Much of our current understanding of microbiology derives from laboratory-based studies of pure cultures, largely motivated by societal needs of improved understanding of the complex physiology of bacteria as relates to pathogenicity, food spoilage, and commercial and medical product development. Such reductionist studies were also used to infer the role of microorganisms in important global and local processes. However, devoid of natural biotic associations, it is increasingly clear that laboratory cultivation conditions do not reflect in situ lifestyles. As Darwin suggested, the primary driver for change is biotic interaction and not changes in the physical/chemical environment. Thus, to provide a more complete understanding of bacteria, it is essential to fully resolve the natural drivers shaping the structure and function of microbial communities. The main thrust of this chapter is to examine the evolutionary, biotic, abiotic, and temporal dimensions that shape microbial communities through time and space. To this end, this chapter strives to integrate the classical with more recently developed methods of inquiry that together are bringing predictive understanding of natural communities of microorganisms.