Using Metagenomics to Investigate Microbial Diversity part of Teaching Genomics at Small Colleges:Genomics Instructional Units Minicollection
Using Winogradsky columns, a soil enrichment culture, students explore microbial diversity through metagenomics. The Winogradsky column is a complex community of interacting microorganisms. In a community such as is present in soil, we know there is an abundance of bacteria but we don't really know the true extent of the diversity and composition of the microbial community. Culture based-techniques are limited to analysis of the bacteria that grow in the lab, and most bacteria don't grow under normal lab conditions. Therefore, we need non-culture based techniques to investigate the diversity of this community. In this module, students investigate the microbial diversity in distinct layers of the Winogradsky column using high throughput sequencing of 16s rRNA sequences. Students extract genomic DNA from the Winogradsky column, the 16s rRNA genes are amplified by PCR, and the products are sequenced. The obtained sequences are then classified and analyzed using bioinformatics tools, and metabolic activities in the different regions of the columns are inferred from the species present. To make a Winogradsky column, mud is collected from a pond or riverbank and added to a plexiglass cylinder along with a source of cellulose, such as leaf litter, and additional sulfate to promote enrichment for microorganisms involved in the sulfur cycle. Over a period of months, layers of microorganisms requiring a range of environmental conditions develop in distinct niches with distinct populations participating in diverse metabolic activities. As various metabolites in the column are used, byproducts are produced, and the environment in the column changes. As a result of changing concentrations of oxygen, hydrogen sulfide, and variations in other metabolites, different microbes will thrive in their own niche. Bacterial growth is seen as changes in color from the original grey-brown mud to a rich pallet of reds and greens. The colored zones are due primarily to phototrophic microbes. In the upper, aerobic layers, we can expect photosynthetic eukaryotic microbes; in the lower, anoxic layers, we can expect purple and green, phototrophic bacteria. These phototrophic bacteria utilize various sulfur sources as electron donors for photolysis. The vast majority of these microorganisms cannot be cultured independently under normal laboratory conditions.