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

466Most useful microbial secondary metabolites come from microorganismsthat inhabit soils, especially actinomycetes taxa, Bacillus spp., mycobacteria,and pseudomonads (Kobinata & Osada et al. 1998, Rondon et al. 1999a).However, most microbes in nature have not yet been discovered, either byusing culture-based approaches or by culture-independent techniques. Thediversity of soil microbes is still largely unexplored, and it is suggested to bemuch greater than was thought before (Rondon et al. 2000).Approaches for assessing soil microbial diversityThere has been a long history of trying to measure the richness and diversity ofthe soil microbial community in a given environment. The main obstacle is thefact that soil microbial communities are characterised by complex componentsthat cannot be cultivated using conventional plate-culture. A gram of soil maycontain more than 5,000 different taxa of microorganisms, and most of them(more than 95%) are viable but not culturable (Torsvik et al. 1990 & 1994).Improved laboratory media that are specific to a particular microorganism havebeen available, but again, the target organism is limited. Several methods basedon physiological characteristics, especially by detecting catabolizing ability ofseveral known compounds, have been used to overcome inherent constraintsduring cultivation of unknown groups of organisms, such as Biology system(Zak et al. 1994) and Catabolic Response Profile (CRP) (Degens & Harris1997, Degens 1997, 1998, 1999). Even though both approaches were useful for‘fingerprinting’ soil microbial diversity among different land-uses (Winding 1994,Degens and Vojuodic-Vukovic 1999), little information was available to interpretthese ‘values of diversity’. Moreover, the outcome of these methods was limitedto the compounds used during the test. Nonetheless, these are the only simplemethods that are currently available to examine functional diversity, wheregenetic diversity is directly linked to physiological traits.Fatty acid pattern of microbial phospholipids and lipopolysaccharides(PFLAs) is yet another method used to fingerprint soil microbial diversity. Themethod is based on the fact that the composition of total microbial fatty acids istaxonomically specific. Classification of soil microorganisms therefore couldbe conducted by subdividing the fatty acids according to their chain structure,degree of saturation, and substitution by specific ‘signaturePFLAs’ (Zelles etal. 1992, Zelles & Bai 1993). Despite high resolution, it is difficult to interpretdiversity as revealed by this approach.