MODERN METHODS IN SUBSURFACE MICROBIOLOGY - IN-SITU IDENTIFICATION OFMICROORGANISMS WITH NUCLEIC-ACID PROBES

Like many other parts of microbial ecology, subsurface microbiology ha s entered the molecular age. As one example of various powerful molecu lar techniques, fluorescently labeled rRNA-targeted nucleic acid probe s today allow an in situ identification of individual microbial cells in their natural habitats, The technique relies on the specific hybrid ization of the nucleic acid probes to the naturally amplified intracel lular rRNA. Fluorescently labeled, rRNA-targeted oligonucleotide probe s are perfect tools for many areas of microbial ecology since they can monitor specific populations in environmental samples based on consta nt genotypic features and not on variable phenotypic features like mor phology. In case of immobilized communities like biofilms, exact spati al distributions of microorganisms can be analyzed on a micrometer sca le. Recent technical improvements have increased the number of potenti al applications considerably. Today, better fluorescent dyes enable id entification of routinely more than 50% of the cells even in oligotrop hic aquatic samples in which the visualization of small cells with low numbers of ribosomes had been problematic. This compares favorably wi th the usually less than 1% of microorganisms which can be characteriz ed based on cultivation-dependent methods.