This past June I was able to attend the Marine Ecology and Microbiology class run by Elizabeth Dinsdale and Rob Edwards in Sydney Australia!
During this trip we surveyed two different rocky intertidal zone locations in Sydney Harbor.
At both sites we conducted surveys using transects and quadrats. These surveys helped describe the different organisms and abiotic factors present at each location which was then used to analyze the similarities and differences between the two locations.
At the Bradley’s Head site we also took samples of organism’s associated microbes. To do this we would put our organism of choice in a container and run filtered sea water over them which we would collect and bring back to lab. We used this sample to plate on different media, including marine broth, macconkey agar and TCBS in order to characterize the microbial communities associated with our organism. We also took samples that we would extract DNA from. For these we would run the sample water we had washed over our organisms through a sterivex that would catch the samples DNA in a filter.
All of the students with us were able to extract DNA from there sterivexes using a Modified Column Purification Protocol. Once we had extracted our DNA we then quantified the amount using Qubit.
All these steps lead up to sequencing our extracted DNA. Before doing that we had to complete a library prep. This included fragmenting our DNA, end repair, dA-tailing, adapter ligation, and DNA library purification.
These prepared samples were then sequenced using Nanopore sequencing. In the end all but two of the students ended up with reads that we then analyzed using BLAST.
Along with the lab work we conducted we also got to do many fun activities while in Sydney!
We were able to go to Vivid which is an event that goes on in Sydney where there are lights and projections on all the big buildings and structures downtown, like the Opera House and Sydney Harbor Bridge.
We went snorkeling in Chowder Bay where we were staying and we got to kayak around that area as well!
This two week program was a great opportunity to learn more about sampling, surveying, processing data, and bioinformatics.
I want to thank Elizabeth Dinsdale and Rob Edwards for running this unforgettable program and also thanks to all the students I got to experience it with!