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May the clams be with you

It feels like we just came back from the workshop in Panama. Time has been flying like never before. Is that normal in January? I have spent most of it in the laboratory, extracting DNA from clam gills. Matt introduced me to Gustav Paulay at the Florida Museum of Natural History. Gustav studies biodiversity on coral reefs and Pacific islands. He regularly organizes large-scale taxonomic surveys but he also tests hypotheses about the past census of biodiversity on earth before human activities using paleontological, ecological, and phylogenetic tools. Matt and Gustav have collaborated extensively in the past. I reached out ot Gustav to ask for more lucinid clam gills to complement our collections of closely related host species on both sides of the isthmus. I hit the jackpot! Only a few days after I had returned from Panama, we received a package from Amanda Bemis, Gustav’s collaborator at the museum with very precious clam gills, carefully preserved in ethanol. The extractions went well, hopefully we can start sequencing soon!

Lucinid bivalves from the wet collections of the Florida Museum

I caught fire. Motivated by the kindness of Gustav and Mandy, I reached out to many museums across the country with presumed collections: Oregon State University, the Cal Academy of Sciences, The Natural History Museum of Los Angeles, UC Santa Barbara, Harvard, and eventually also the Smithsonian collections in D.C. Many passionate emails. Most of them responded. Material Transfer Agreements to sign. Bothering Jonathan to be responsible. And many, many more nights in the laboratory extracting DNA from clam gills.

The largest specimen so far!
From a Galapagos expedition more than 50 years ago!

 

 

 

 

 

 

 

The DNA integrity of our fresh clams from Bocas del Toro in December 2018 is far better than any of the museum specimens stored in 70-100% ethanol. The expensive Zymo buffer did a brilliant job of shielding our DNA. RNAlater looked weak in comparison. Museum specimens resulted in high concentrations but very degraded DNA. However, it looks like some of them will fill some important gaps of sampling with regard to the genomic information of the lucinid chemosymbionts.

While I am writing this, Matt and Jarrod are traveling to Coiba accompanied by a visiting Master student – Jade Sourisse, two interns – Catalina Rodriguez and Helio Quintero, and two expert taxonomists from Brazil – Arthur Anker and Paulo Pachelle. They are taking advantage of extremely low tides during this time of the year. This trip is part of our big effort this year to finalize the collection of samples. They will look for snapping shrimp, sea urchins, reef fish, and lucinid bivalves. Jarrod even contacted Aaron O’Dea who generously offered equipment to dig for sediment with fossils and lucinid bivalves. Oh, I wish I could be there right now!

Check out this video from Wyatt Toure who took their field course on Coiba a few weeks ago!

I am sitting here in Davis and taking a fieldwork safety training and learning how to teach a seminar in marine microbial ecology. After my official transfer to UC Davis, I am taking advantage of the resources that are provided for international expeditions, including survival training, a satellite phone, and international health care. The latter includes free vaccinations and malaria prevention. If everything works out, we will soon travel to Costa Rica and dig for more clams. When I go out in the evening to look at the moon, I think of Matt and Jarrod further down south along the Pacific coastline looking at the same moon. Stay safe on Coiba!

On a brighter note, team Davis is welcoming a new undergraduate researcher, Ipek Yasmin Meric. Yasmin has worked the last two weeks in the lab and helped me dissect clam gills and extract DNA. She also supported me mentally through the more or less useful/necessary/laborious RNA removal treatments and several rounds of running gels and normalizations. It is a pleasure to have her around. We hope to see some sequences soon.

Yasmin dissecting gills from museum specimens.

Welcome to the Isthmus Microbiome Project

Welcome to the blog for the Isthmus Microbiome Project, a collaboration between UC Davis and the Smithsonian Tropical Research Institute (STRI) in Panama. The full title of the project is pretty descriptive “Evolution of Microbiomes in Shallow-water Marine Organisms Split by the Isthmus of Panama in the Western Atlantic vs Eastern Pacific Oceans”.

Preliminary work has begun on the project, mostly by Jarrod Scott, a postdoc at STRI who has been collecting sea urchin samples from both the Pacific and Caribbean sides of Panama.  This part of the project is being done in collaboration with Hariloas Lessios, an urchin researcher at STRI. Laetitia Wilkins, a postdoc in the Eisen lab at UC Davis went down to Panama in August and helped with urchin collections and dissections. See a sample from her fieldwork here.  While there she struck up a collaboration with Alexandra Hiller, a crab researcher at STRI and will be focusing her part of the project on crabs.

In late January 2018, myself (David Coil) and Laetitia will be heading down to Panama for a 2-3 week collection and bacterial culturing trip.  We’ll be trying to collect multiple species of urchin and crabs from both sides of the isthmus and culture microbes from every sample.  In addition Laetitia will be collecting a number of crab samples for subsequent amplicon/metagenomic analysis.   Stay tuned for blog post from the road!