Live map of Global Coral Microbiome Project Sample Photos

A live map of samples collected for the global coral microbiome project is now up on the Vega Thurber lab web page.  Ryan McMinds linked together the more than 3,400 raw sample photos for the project, which are on Flickr, with their overall map coordinates.  (You can also find pretty reef photos and some tourist pics of down time from the expeditions).

The fidelity of GPS and satellite imagery being what it is, I’ve found the map to be useful in getting a broad sense of where samples were taken in relation to broad geographic features, and also the detailed surroundings of each coral.

Reunion GCMP sampling locations
Sampling locations around Isle de la Reunion for the Global Coral Microbiome Project

For example, the proximity of some corals to town is easy to see.

Detail shot of one sampling location from Isle de la Reunion
A more detailed view of samples from the West coast of Isle de la Reunion.

From these local maps we can drill down directly to the corals themselves.


One main theme in the project overall is to share data with the community.  We thought that we’d start by uploading the raw sample photos to Flickr, and organizing them in ways that make them accessible. This also has added benefits for the team, including making photos easier to share within the group.  Coral identification (especially at the species level) is notoriously challenging.  Sharing photos online enables feedback from the community (feel free to drop us a line in the comments) and from collaborators that specialize in coral systematics.  The photos are also linked to sample ids for molecular data, making it easy to look up the surroundings of a particular coral.  Finally, Ryan has  used hierarchies in Light Room to make it easier to manage tags linked to coral taxonomy and location.

We’re looking forward to using tools like these to make our lives easier as we work to characterize the relationships between corals and their microbes.


Coral Sampling in Singapore for the Global Coral Microbiome Project


On my way to Indonesia to speak at the US-Indonesia Kavli Frontiers of Science forum, I’d arranged to stop in Singapore to meet with our collaborator Mónica Medina and Danwei Huang, a talented coral systematist.  We were to dive together to sample corals from a marine preserve an hour’s boat ride south of Singapore.

I arrived at 11:30 pm local time, and we were heading out early in the morning to dive, so I’d had to carefully prepare all of our sampling kits before I left.   After a long shuttle ride out to the Hotel Fragrance Waterfront, I caught a quick rest in a windowless room buried in the center of the building.  The next morning Danwei, Mónica, and Danwei’s student Aden showed up in a university van, and we drove down to the dive boat at the Royal Singapore Yacht Club.

After getting the bulky dry shipper onto the Dolphin Explorer without dropping the whole thing into the water, we cast off and pulled out from the dock. Singapore harbor was a maze of towering supertankers, making the journey out from port feel more like navigating a city block than the ocean.   Singapore is the world’s 2nd busiest container port (after Shanghai, China), processing ~32 million 20′ containers in 2013.  Mónica noted that the density of containers seemed even higher  here than in the Panama canal.

After passing beyond the thicket of supertankers, we motored between many small islands (Pulau), all rocky at the bottom and bristling with deep green jungle on top.  After an hour of catching up with Danwei and Aden about their research and planning our dive, we arrived on site at Pulau Satumu.  Raffles Lighthouse sat perched on the south end of the island, striped in red and white.

It was hot in the boat, so we wasted little time getting ready before getting in to the only slightly cooler water.   The water was thick and green, and we could see bits of trash floating by on the current.  I measured 4.5 meter visibility with the Secchi disk, which was much better than I would have guessed from the surface.

Mónica and I were dive buddies for the sampling, while Danwei and Aden photographed they’re nearby transect and stopped by to help us id corals.  Once we got down the visibility was not too bad, just as the Secchi Disk had indicated, and we didn’t need to use any of the dive lights that we had brought.

Despite some hiccups on the first dive, where we managed to misplace a bright yellow dive bag, we sampled all the corals that we needed (photos here), and were able to move the tissue and skeletal samples to the dry shipper, and preserve the mucus samples in PowerSoil bead tubes.

Thanks to Danwei, Mónica, and Aiden for a successful trip!

Update 10/16/2015:  Added stats on Singapore’s impressive trade volume.

Napkin Diagrams

Growing up, my family rarely ate at a restaurant without leaving remnants of our conversations behind on paper napkins and placemats.  We would draw maps, and graphs, and machines – not all the details but just enough to get across the main idea. So many of the most interesting ideas in science seem to be exchanged informally in the same way.

This blog aims to cover recent developments at the intersection of ecology, evolution and the microbiome.  I’ll focus especially on topics that relate to our work with The Global Coral Microbiome Project, which seeks to understand the evolutionary relationships between corals and their many microbial symbionts. I’m especially interested in sharing new ideas from our work and from the literature in simple and digestable packages. I haven’t blogged much previously, so I’m sure the form of the content will evolve over time.  But the core goal for this blog will be to capture some of the magic of napkin diagrams in online form.

— Edit 10/19/14.  Replaced placeholder text for this entry.