In situ and Ex situ Conservation of Commercial Tropical Trees - ITTO

467Nucleic Acid Based-methodsThe three most commonly used methods above produce non-repeatable results,since the outcome data is qualitative and only enables comparative analysis.As a result, no precise taxonomic descriptions would be available. Moreover,the system only measures the metabolically active components. In the case ofPFLA measurements, the microbial components that exist in the minutepopulation may not be detected. Likewise, it is not possible to create a universalstandard of data to be compared, since the measurements are inter-laboratorydependent.With the advent of molecular biology, various nucleic acid based-methodshave been available to ecologists. For their appropriate application, the choiceof methods should be based on the nature and capabilities of each method.While starting from the same materials (DNA extract from environmentalsamples), the target and the resolution of the analysis would be different. Box2 summarizes the various nucleic acid-based techniques that are commonlyused to study molecular microbial ecology.Box 2Table 1. Molecular methods used to examine soil microbial diversitymethods16S rRNA gene sequence analysisin-situ hybridisationDNA-RNA re-association kineticsARDRAPCR amplification or expression cloningBAC librariesFlow cytometryRNA dot of slot blotSSCP%GC contentT-RFLPDGGE or TGGECommentsCloning required; provides identification of members ofcommunityRequire certain probes; labour intensiveProvides a global view of genetic complexity of sampleMore useful for simple communities; useful forcomparative analysisFunctional diversity targetPermanent archive of genetic information from sampledenvironment; phylogenetic and functional diversityEnumeration micro-organismsRepresentation of metabolically active members of acommunityComparative analysisGlobal view of community diversityComparative analysisUsed to monitor enrichment, comparative analysisAbbreviation: ARDRA, amplified ribosomal DNA restriction analysis, BAC, bacterial artificialchromosome; DGGE, denaturing-gradient gel electrophoresis; SSCP, single-strand conformationalpolymorphisms; TGGE, temperature-gradient gel electrophoresis; T-RFLP, terminal-restrictionfragment-lengthpolymorphisms.(Source: Rondon et al. 1999)