16S rRNA Gene Survey of Microbial Communities in Winogradsky Columns

Abstract

A Winogradsky column is a clear glass or plastic column filled with enriched sediment. Over time, microbial communities in the sediment grow in a stratified ecosystem with an oxic top layer and anoxic sub-surface layers. Winogradsky columns have been used extensively to demonstrate microbial nutrient cycling and metabolic diversity in undergraduate microbiology labs. In this study, we used high-throughput 16s rRNA gene sequencing to investigate the microbial diversity of Winogradsky columns. Specifically, we tested the impact of sediment source, supplemental cellulose source, and depth within the column, on microbial community structure. We found that the Winogradsky columns were highly diverse communities but are dominated by three phyla: Proteobacteria, Bacteroidetes, and Firmicutes. The community is structured by a founding population dependent on the source of sediment used to prepare the columns and is differentiated by depth within the column. Numerous biomarkers were identified distinguishing sample depth, including Cyanobacteria, Alphaproteobacteria, and Betaproteobacteria as biomarkers of the soil-water interface, and Clostridia as a biomarker of the deepest depth. Supplemental cellulose source impacted community structure but less strongly than depth and sediment source. In columns dominated by Firmicutes, the family Peptococcaceae was the most abundant sulfate reducer, while in columns abundant in Proteobacteria, several Deltaproteobacteria families, including Desulfobacteraceae, were found, showing that different taxonomic groups carry out sulfur cycling in different columns. This study brings this historical method for enrichment culture of chemolithotrophs and other soil bacteria into the modern era of microbiology and demonstrates the potential of the Winogradsky column as a model system for investigating the effect of environmental variables on soil microbial communities.

Assembly of microbial communities in replicate nutrient‐cycling model ecosystems follows divergent trajectories, leading to alternate stable states

“…After 16 weeks the composition had again changed strikingly, with a resurgence in Proteobacteria (27 ± 9%) and Bacteroidetes (10 ± 7%), the emergence of Spirochaetes (10 ± 8%) and variable persistence of Firmicutes (35 ± 19%). These observations are similar to those of previous studies on Winogradsky column ecology which showed that Proteobacteria , Bacteroidetes and Firmicutes were the dominant phyla (Rundell et al ., ; Abbasian et al ., ), though the overall community composition was source sediment‐dependent (Pagaling et al ., ; Rundell et al ., ).…”

“…This makes it possible to perform replicate experiments on a scale that would be impossible for animals or plants. Here, we exploited these attributes to make a direct test of the reproducibility of microbial ecosystem development, using nutrient-cycling microcosms (Winogradsky columns) made from freshwater pond sediment and water (Rundell et al, 2014;Abbasian et al, 2015). The microbiology of the Winogradsky column is wellunderstood, with the key stages in its initial development being driven by anaerobic cellulose degradation and subsequent sulphate reduction (Rogan et al, 2005).…”

Effect of storage temperature on bacterial diversity in chicken skin

“…Microbial community heat map analysis (Rundell et al . ) and multiple‐sample similarity tree construction (weighted FastUnifrac) (Lozupone and Knight ) were used to compare differences and similarities between the three bacterial community structures (Fig. a).…”

“…This analysis confirmed that the bacterial communities were most similar between T25 and T37, as indicated by the T25 and T37 samples clustered together, while T4 was separate from the two other samples. Microbial community heat map analysis (Rundell et al 2014) and multiple-sample similarity tree construction (weighted FastUnifrac) (Lozupone and Knight 2005) were used to compare differences and similarities between the three bacterial community structures (Fig. 9a).…”

Cultivation of Bacteria From Aplysina aerophoba: Effects of Oxygen and Nutrient Gradients

“…Secondly, we explore the use of -omics data in defining nutrients and cultivation conditions for Poribacteria and the addition of a sponge derived antibiotic (aeroplysinin-1). Lastly, we describe the first attempts to enrich a complex microbial community maintaining at least some metabolic interactions of the sponge microbiome in a stratified cultivation system based on the Winogradsky-column approach (Madigan et al, 2014;Rundell et al, 2014) and within Liquid-Solid cultures.…”