Around the world, there are some preserved coral collections that could help on the reconstruction of recent coral-symbiont genetic variation and how this variation has evolved since the industrial revolution, when anthropogenic CO₂ emissions started to threaten coral reefs worldwide (Hoegh-Guldberg, 2011). The study of these collections will make it possible to travel back in time and explore recent adaptation of coral symbionts, since there is some evidence and conjecture that coral-dinoflagellate symbiosis change partnerships in response to changing external conditions over ecological and evolutionary timescales. This traveling back in time will allow for the establishment of baselines for host-symbiont associations throughout coral reef ecosystems and studying how stable or variable these associations have been through time, in particular since the outbreak of human industry and its impact on the Earth’s climate, which could be crucial to determine and predict the impact of future mass-bleaching events on these ecosystems. Acquiring such baselines will contribute to modelling approaches estimating the likelihood of coral-symbiont natural and ecosystem-scale adaptation to the predicted scenarios of climate change (Frade et al., 2017).

One collection in particular, the one stored in the Natural History Museum in Vienna, includes a group of Red Sea coral samples collected by the late 19th century, which have been mostly preserved in alcohol. From them, Symbiodiniaceae genetic markers can be extracted, and indeed, this was done by Pedro Frade, my mentor. He extracted Symbiodiniaceae DNA for PCR amplification of the ITS2 subregion of the nuclear ribosomal DNA, since it is an ecological and functionally meaningful marker in Symbiodiniaceae, commonly used for genotyping within this family. This was followed by amplicon-based next-generation sequencing (MiSeq Illumina technology) in order to get ITS2 reads per coral sample for further analysis (my work)....

As a contribution to this, during the six weeks of my PP, my main goal was to perform the complete analysis of the Symbiodiniaceae ITS2 DNA sequences, followed by statistical analysis on the results from the sequence analysis to study the Symbiodiniaceae diversity and a final comparison between the old corals Symbiodiniaceae composition and current Symbiodiniaceae databases in order to provide answers to the previous questions.

After the sequence analysis using the QIIME platform, I spent the last two weeks of my PP working with R to perform statistical analysis in order to obtain the alpha and beta diversity of the Symbiodiniaceae communities (graphs under results).

To compare my final results on Symbiodiniaceae type/species identification with current databases and see if I got similar or compeltely different results I ran the raw sequences against the SymPortal database (see link under Databases) to determine the Symbiodiniaceae composotion of the coral samples (see SymPortal graph under results).

To verify if the Symbiodiniaceae diversity present in the project corals are the same as the ones present in current corals from the Red Sea I had to look for the coral species from my project in databases such as GeoSymbio (see link under Databases) and Santo´s lab (see link under Databases) and look at their Symbiodineaceae species (type) or genus (clade composition).

Moreover, I also BLAST some of the New OTUs obtained from the QIIME analysis (the ones with the higher relative abundance) against the NCBI database to compare and see if they match current species or if I got some potential new ones...

Background photography credits