Tag Archives: metagenomics

Published! Paper on the microbial community in Winogradsky columns

Check out the paper in PLoS ONE! 

Ethan Rundell ’13 worked in my lab for two years, his work culminating in first authorship on this paper.


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 IMG_4059layer 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.

Rundell EA, Banta LM, Ward DV, Watts CD, Birren B, Esteban, DJ. (2014) 16S rRNA Gene Survey of Microbial Communities in Winogradsky Columns. PLoS ONE 9(8): e104134. doi:10.1371/journal.pone.0104134


Herpes-Family Viruses are Associated with Stressed Out Corals

Contributed by guest blogger: Ian Heller ‘12

A new review out in the Journal of Experimental Marine Biology and Ecology is causing a rash of media attention regarding the presence of viruses in stressed out coral. However, this media attention, with catchy titles playing at old stigmas against herpes infection in humans, misses the true story told being uncovered in the new field of coral virology. What has the science actually shown?

Coral reefs are hotspots of biodiversity and essential components of the ocean ecosystem. Corals themselves contain an amazingly diverse assembly of different organisms. Tiny organisms like symbiotic algae, fungi bacteria, and archaea are all necessary for healthy coral. Unfortunately, coral reefs are threatened world wide due to rising sea temperatures, acidifying ocean water, and pollution in the form of sewage and fertilizer runoff. These stressors seem linked to an increased incidence of disease in coral, but what pathogens are actually making corals sick?

To investigate whether any viruses were associated with stressed coral, researchers compared the metagenomes of healthy corals and corals grown in water that was too hot, too acidic, too polluted with organic carbon (to simulate sewage stress) or too polluted with plant fertilizer nutrients. Within this “metagenome” is all of the DNA sequences from all of the different algae, bacteria, virus, etc., that are part of each sample, in this case, a coral fragment.

The first step in making such a comparison is sequencing as many of the genes as possible each sample, a feat made feasible by the increasing accessibility of gene sequencing. Next, researchers identify all of the sequences in their samples’ “library” of genes that correspond to viral genes. This means sifting through over 51,000 sequences! To figure out the identify of these sequences, the researchers use a computer algorithm known as BLAST to compared their unknown sequences with known sequences in National Center for Biotechnology Information’s public database of nucleic acid sequences. Then, to find their “viral needles” in the “metagenome haystack”, they use various computational approaches to eliminate non-viral sequences and identify viral sequences. In their results, the researchers found viral sequence from 19 different virus families. Then, when the metagenomes from healthy corals were compared to stressed corals, it was found that the stressed corals had an increased frequency of herpes-virus family sequences.

To confirm that this frequency shift actually corresponded to more herpes genes in stressed corals, the researchers used Real-Time PCR (also know as quatitative PCR) to measure the concentrations of a specific nucleic acid sequence in different corals.  The nucleic acid sequence that was focused on was a herpes virus sequence similar (62% identical) to the thymidylate synthase gene from Saimiriine herpesvirus 2. This experiment showed that indeed, stressed corals tended to have more of this gene in their metagenome than their healthy counterparts.

This study provides an excellent first step into the world of coral virology; it identifies possible candidate viruses that may be contributing to coral illness. However many more questions need to be answered to understand viruses’ role in coral health. For example, few studies have actually observed virus actively hosted by a coral, and none have yet shown that herpes-like viruses can make healthy, unstressed corals sick. The ecological role of viruses may turn out to be surprisingly complex. Some researchers have even proposed that viruses may be necessary for coral survival. Corals host symbiotic algae within their cells, in a mutualism that is a requirement for corals to survive. In order to live inside coral cells, the algae must somehow evade or suppress the corals innate immune response, just as many viruses must do. Will future studies discover a link between the algae infection and virus infection?




Ian Heller is a senior at Vassar, majoring in biology.  He is also good at making puns, and had a hard time choosing a title for this article.  Rejected titles included: Catching herpes from coral sex, Viruses and corals: friends or anemonies?, and Virus in the O.K. Coral.