Bacteria are diverse and ubiquitous in the environment. They are found virtually everywhere; many places that you would expect, and many that may be surprising. New technologies are permitting us to identify and characterize new bacterial species at an astonishing rate. Understanding the diversity and identity of bacterial species in different environments is critical in understanding the role of bacteria in environmental processes and in disease. In my lab, we are using metagenomics and metatranscriptomics to investigate microbial diversity and gene expression in Winogradsky columns and in Catskill Mountain soils.
Sergei Winogradsky, a Russian microbiologist in the late 1800′s and early 1900′s, was instrumental in establishing the basis for microbial physiology and microbial ecology. He was the first to describe chemoautotrophs. In addition, he described the role of nitrifying bacteria in the nitrogen cycle and the microbial oxidation of various sulfur compounds.
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 metabolites, different microbes will thrive and create their own niche. Bacterial growth is seen as changes in colour from the original grey-brown mud to a rich pallet of reds and greens. The colored zones that we can expect are due primarily to photosynthetic microbes. In the upper, aerobic layers, we can expect photosynthetic eukaryotic microbes; in the lower, anoxic layers, we can expect purple and green, photosynthetic bacteria. These photosynthetic bacteria utilize various sulfur sources as electron donors for photosynthesis. The vast majority of these microorganisms cannot be cultured independently under normal laboratory conditions.
I am interested in understanding how the conditions within the Winogradsky column influence microbial diversity and to identify the major metabolic activities of microorganisms in the column. In my lab and in my microbiology class we are analyzing metagenome and metatranscriptome data from Winogradsky columns.