Molecular techniques for determining microbial diversity and community structure in natural environments

The ability to quantify the number and kinds of microorganisms within a com munity is fundamental to the understanding of the structure and function of an ecosystem. The simple morphology of most microbes provides few clues fo r their identification and physiological traits are often ambiguous. In add ition, many organisms resist cultivation, which is essential to their chara cterization. Recombinant DNA techniques have provided a means whereby many of the obstacles associated with cultivation and description can be overcom e and subsequently has allowed many new insights into the complexity of nat ural microbial communities. Molecular approaches based on 16S ribosomal RNA (rRNA) sequence analysis allow direct investigation of the community struc ture, diversity, and phylogeny of microorganisms in almost any environment, while quantification of the individual types of microorganisms or entire m icrobial communities may be addressed by nucleic acid hybridization techniq ues. Furthermore, the use of fluorescently labeled population-specific rRNA probes allows microscopic examination of individual cells in complex micro bial assemblages as well as their interactions in situ. In this review, we discuss strategies for characterizing microbial communities without the nee d for cultivation.