MICROBIAL ECOLOGY (BIOL4365) Department of Biology-UPR Mayagüez From Molecular Microbial Ecology Workshop-1999 Sponsor by NSF Center for Microbial Ecology, Michigan State University RIBOSOMAL RNA AS A TOOL IN MICROBIAL ECOLOGY

Traditional techniques. Knowledge of bacterial diversity obtained after more than 100 years of pure culture study is incomplete, and very few of the total number of microbial species are in culture (Torsvik et al., 1995). Until the middle of the last decade enumeration and identification of soil microorganisms hat to rely on phenotypic methods. However, phenotypic methods are restricted to only those bacteria that can be isolated and cultured. Other, maybe completely unsuspected groups, which may be abundant or very active, will not be considered, rendering the emerging picture of the soil microbial community false. Only a small portion of all prokaryotes has so far been cultivated, and the majority of soil bacteria observed microscopically cannot be cultivated. In addition, the selective enrichment culture has severe limitations as an approach to study the community composition of naturally occurring microorganisms (Ard et al., 1992; Amann et. al., 1995). Results with pure culture isolates are not always reproducible due to the variability of phenotypic properties in relation to culture conditions. Furthermore, laboratory cultivation introduces serious bias to community analysis (Boivin-Jahns et al., 1995; Ferris et al., 1996), since the bacterial populations obtained through planting are mainly dependent on the isolation media used (Sørheim et al., 1989), as well as on purification and maintenance procedures. Since nutrient-rich media are used the selection might be biased towards copiotrophic bacteria rather than dominant community members. In addition, properties of microbes ex situ may differ, because they lack the interaction among populations or with the natural environment, or change their physiological state as a result of adaptation to the changed environment. Consequently, in situ diversity and community structure are unlikely to be represented by collections of natural isolates.