GCMP: Visit to Penn State and First look at Australia Data



We recently had a great trip to Penn State, where we visited with Mónica Medina  and her group. Ryan McMinds, Becky Vega Thurber and I headed out there to work with Mónica’s group on the Global Coral Microbiome Project (GCMP).  Mónica, Joe Pollock, and the whole lab were amazing hosts. We stayed in Mónica’s house and had the chance to spend some time with her lovely tia and wonderful daughters.

The overall project aims to understand the microbes living on reef-building corals, which are thought to play key roles in corals’ resistance or vulnerability to environmental stressors like climate change and algal competition.  We are working with the Earth Microbiome Project to assess bacterial diversity in a large global collection of coral samples. In the meantime, we are moving forward with a subset of samples collected in Australia.

For this project, we have enough preliminary data from our previous work and the literature on coral microbiomes to form fairly specific hypotheses.  So we decided to be fairly formal about framing our key hypotheses, the testable predictions for each hypothesis, and planning ahead of time many of the specific analyses we’d do to test those predictions.

Some of the key questions we’re trying to address include:

  • How do different ‘habitats’ within a coral, such as mucus vs. tissue vs. skeleton differ in microbial community?  We predicted that the microbial community in the coral surface mucus layer (SML), which is a key interface between the coral and its environment, will be more strongly influenced by local environmental factors than the microbial community within coral tissues. We predicted that the tissue community would be more driven by the evolutionary history of the coral.
  • Have distantly related corals with similar life-history strategies converged on similar microbiomes?  We are testing a number of concrete predictions in this area for features ranging from the abundance of microbial antibiotic production pathways (we predict there will be more in stress-resistant corals) to the extent of inter-individual variability in different types of corals.
  • Can we identify clear cases of co-evolution between corals and their microbes?  A key prediction of the coral holobiont theory is corals and their bacteria are symbiotic partners that have co-evolved over long periods of time.  This is a challenging idea to test, but our sampling scheme was designed to have enough power to try to address these questions.  We’re first assessing what bacteria, archaea and Symbiodinium lineages are found in most or all of our coral specimens, and will then move on to evolutionary analyses of these groups. 

These are just a few of the ideas we’re kicking around at the moment. Any of these predictions may very well be incorrect, and we’re happy to find that out – mostly we’re excited to have data in hand, and grateful to the large network of coral scientists that helped us get to the point where we can start testing these predictions in a more  definitive way than previously possible. The results from some of these evolutionary and ecological questions will help to inform model-building in later stages of the project, where we are going to test whether incorporating information on microbial diversity can improve models of which coral species are vulnerable to disease and bleaching.

During our visit, we worked with Joe Pollock to start analyzing DNA sequence data for this project, and with Styles Smith to connect these data to ongoing bacterial genome sequencing efforts. Having everyone in the same room proved to be very useful for advancing the project rapidly. We now have Symbiodinium (ITS2)  data for most of these samples, and bacterial/archaeal  (16S rRNA gene) data for all of them. Although long OTU-picking and beta-diversity runs ate up the first few days, we were able to summarize this sample set into some nice tables for publication; conduct basic quality-control, OTU picking, and core diversity analyses; revise our taxonomic annotations of Symbiodinium diversity (more on this later); set up our organizational system; and got a preliminary look at what the data are telling us about our four or five of our key predictions.

Right now we’re working on a Dropbox model, with standardized folders (input/output/procedure subfolders) for different sub-analyses, and using IPython notebooks  or bash scripts to record analysis procedures.  So far this is working fairly well, although it helps being in the same place to rapidly coordinate what’s happening in each folder, especially if multiple people are contributing to the same analysis. Disambiguating those types of synchronous contributions is a place where a more formal version management system like GitHub could be advantageous.  For example the Earth Microbiome Project is coordinating their analysis in this way (see here). We may still go there, but for now the team is small and connected enough that we might avoid the overhead.

In any case, many thanks to everyone in Mónica’s group for a great visit. As this analysis matures,  I’ll try to write more on approaches we’re taking to connect our microbiological data to coral functional traits and life-history strategies.


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