Soil Microbial Ecology
Arguably, bacteria are the largest genetic reservoir on earth. Over 17,000 biologically active molecules have been allready been detected in cultivated bacteria (Borders 1999; Glasby 1992; Roberts and Higton 1988). Readily cultivatable bacteria, however, only account for a small fraction (maybe 1%) of all bacterial species found in nature. It is therefore commonly assumed that the vast majority of pharmaceutically and industrially important molecules of microbial origin remain to be discovered.
Many biologically active molecules are synthesized by polyketide synthase (PKS) pathways. Polyketides are particularly important as pharmaceuticals (Metsä-Ketelä et al. 1999), including rapamycin (immunosuppressant), erythromycin (antibiotic), lovostatin (anticholesterol drug), and epothilone B (anticancer drug). Particularly prolific producers of polyketides are the actinomycetes, which for decades have yielded novel industrially important products and pharmaceuticals. More recently the rate at which novel antibiotics are introduced into the marketplace has slowed markedly (Metsä-Ketelä et al. 2002; Strohl 2000). Tthis is in part due to a high rate of isolation of previously described strains and molecules (Metsä-Ketelä et al. 2002; Strohl 1997). My postdoctoral research has therefore focused on understanding the ecology and distribution of actinomyctes in soils. At Rutgers Univerity I developed methods that prevent re-investigation of previously described bioactive molecules and to reduce biases introduced by the use of standard cultivation techniques.
Figure 1. TRFLP dendograms used to identify samples with high diverity and unique PKS gene content. Labels indicate the identity of soil samples (NSX) where X = the sample number and NS (1S, 2S, 3S and 4S) indicates the sampling collection site (C) The number of total and unique peaks in the actinomycete specific 16S ribosomal RNA gene TRFLP data (D) The number of total and unique peaks in the KSα TRFLP data.