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. 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, 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. This is in part due to a high rate of isolation of previously described strains and molecules. My postdoctoral research was therefore focused on understanding the ecology and distribution of actinomyctes in soils. At Rutgers Univerity I developed culture independent methodologies for screening soils and isolates for the presence of novel PKS gene-clusters.
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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. |
References:
Wawrik, B., D. Kutliev, U. A. Abdivasievna, J. J. Kukor, G. J. Zylstra, and L. Kerkhof. 2007. Biogeography of actinomycete communities and type II polyketide synthase genes in soils collected in New Jersey and Central Asia. Applied and Environmental Microbiology 73:2982-9.
Wawrik, B., L. J. Kerkhof, J. J. Kukor, and G. J. Zylstra. 2005. Effect of different carbon sources on community composition of bacterial enrichments from soil. Applied and Environmental Microbiology 71:6776-83.
Wawrik, B., L. J. Kerkhof, G. J. Zylstra, and J. J. Kukor. 2005. Identification of unique type II polyketide synthase genes in soil. Applied and Environmental Microbiology 71:2232-8.
Wawrik, B., T. Doolotkeldieva, D. Kutliev, L. J. Kerkhof, G. J. Zylstra, and J. J. Kukor. Prospecting Uncultured Microbial Biodiversity. Annals of the Missouri Botanical Gardens.