Temporal and Spatial Distribution of the Microbial Community of Winogradsky Columns

Abstract

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.

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

“…To investigate variability in microbial community development, 100 replicate sediment‐water microcosms (Winogradsky columns) were set up identically. Previous data from multiple experiments in our lab and elsewhere has shown that development of mature Winogradsky column microcosm communities requires 3–4 months, with very few changes in community composition and microcosm function occurring after 12 weeks, while redox potential at all levels in the microcosm declines considerably in the first 10 weeks as cellulose is degraded, then subsequently recovers in the upper water layer while remaining low in the sediment (Pagaling et al ., ; Esteban et al ., ; Supporting Information Fig. S1A).…”

“…Members of the Spirochaetes have been found to associate with Bacteroidetes to enhance cellulose degradation in the rumen (Kudo et al, 1987), and with the Firmicutes species Clostridium thermocellum for cellulose degradation in co-culture (Pohlschroeder et al, 1994) due to their fermentation of the mono-and di-saccharide products of cellulose breakdown. Moreover, Spirochaetes of the genus Treponema were selected in other studies of Winogradsky columns supplemented with cellulose (Esteban et al, 2015). We therefore examined the temporal variation of OTUs mapping to the four phyla Firmicutes, Bacteroidetes, Spirochaetes and Fibrobacteres during microcosm development.…”

“…S1). Dependent on the levels of sulphide present, oxygenic photosynthesis by cyanobacteria and eukaryotic algae may also emerge in the upper layers, and spatial environmental variation within and between microcosms can occur (Pagaling et al, 2014;Esteban et al, 2015;Widder et al, 2016). The different subcommunities of microorganisms which carry out these diverse functions interact with each other and with the abiotic environment to generate an emergent microcosm system; we refer to the total assemblage of organisms in the system as the 'microcosm community'.…”

Carbonate Precipitation in Mixed Cyanobacterial Biofilms Forming Freshwater Microbial Tufa

“…The sediments were used as inoculum for Winogradsky-type ( [39]) columns in order to enrich for cyanobacterial biofilms. Winogradsky columns have been used for diversity and enrichment studies, including that of cyanobacteria ( [40]). The enrichments were used for carbonate precipitation experiments in laboratory.…”

Microbial biospherics: The experimental study of ecosystem function and evolution

“…The early closed systems were complex and undefined (e.g., using unsterilized pond water) and often poorly replicated, and their initial states and outcomes were difficult to quantify even in terms of species composition (12). In contrast to studies of completely closed systems, microcosm experiments continue to play a major role in microbial ecology and evolution, including classical designs, such as chemostats (13), Winogradsky columns (14), batch bioreactors (15), or long-term serial transfer experiments (16). It is to these designs that we envision adding completely closed systems.…”