Winogradsky columns are model microbial ecosystems prepared by adding pond sediment to a clear cylinder with additional supplements and incubated with light. Environmental gradients develop within the column creating diverse niches that allow enrichment of specific bacteria. The enrichment culture can be used to study soil and sediment microbial community structure and function. In this study we used a 16S rRNA gene survey to characterize the microbial community dynamics during Winogradsky column development to determine the rate and extent of change from the source sediment community. Over a period of 60 days, the microbial community changed from the founding pond sediment population: Cyanobacteria, Chloroflexi, Nitrospirae, and Planctomycetes increased in relative abundance over time, while most Proteobacteria decreased in relative abundance. A unique, light-dependent surface biofilm community formed by 60 days that was less diverse and dominated by a few highly abundant bacteria. 67–72% of the surface community was comprised of highly enriched taxa that were rare in the source pond sediment, including the Cyanobacteria Anabaena, a member of the Gemmatimonadetes phylum, and a member of the Chloroflexi class Anaerolinea. This indicates that rare taxa can become abundant under appropriate environmental conditions and supports the hypothesis that rare taxa serve as a microbial seed bank. We also present preliminary findings that suggest that bacteriophages may be active in the Winogradsky community. The dynamics of certain taxa, most notably the Cyanobacteria, showed a bloom-and-decline pattern, consistent with bacteriophage predation as predicted in the kill-the-winner hypothesis. Time-lapse photography also supported the possibility of bacteriophage activity, revealing a pattern of colony clearance similar to formation of viral plaques. The Winogradsky column, a technique developed early in the history of microbial ecology to enrich soil microbes, may therefore be a useful model system to investigate both microbial and viral ecology.
Students are starting to repopulate the campus and the relaxed pace of the summer is being quickly replaced by frenzied preparation for the start of the semester. This semester, I will be teaching the intro to microbiology course that I have taught every year. In the lab, we do some bioinformatics analysis of metagenomic data from a Winogradsky column. A Winogradsky column is a clear cylinder full of pond mud that is used as an enrichment culture to grow bacteria that cant be grown under normal laboratory conditions. To make a Winogradsky column, you collect mud from a pond or riverbank. (For those of us that are used to the cleanliness of working in a sterile hood, that means you have to take off your lab coat, get down on your hands and knees, and scoop up handfuls of goopy stinky slimy stuff from the the edge of a pond. I wear latex gloves.) You then add it to a plexiglass cylinder along with a source of cellulose (I use 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.
Although you can see some changes occurring in the first few days, it takes several weeks or months for it to develop so I always set it up before the semester starts. This year, I had the help of my daughter (age 5) who was eager to get her hands into the gooey muck. We took the mud from the edge of Vassar Lake, a pond on campus. In the pictures you can see the changes that take place over time. The column starts out as grey silt, while the column on the left is 1 year old. The patches of colours are the different communities of bacteria.
(OK, so there is no virology in this post but it sure would be interesting to analyze the viral population of the column in addition to the bacterial population. What is the role of bacteriophages in the community dynamics and nutrient cycling in the Winogradsky column?)