All posts by Laetitia Wilkins

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.

Personal and professional impressions – Laetitia

I wrote a small piece on my experience of the Marine Microbial Symbiosis workshop #istmobiome in Bocas del Tor on my personal website, as well as a guest blogger for The Research Coordinated Network for Evolution in Changing Seas.

There is a lot cooking right now. Please check in soon again for updates!

Meanwhile in California — Porcelain crab collection for an undergrad project

While David and I went on the urchin/crab collection expedition in Panama earlier this year, we had two undergraduate students from UC Davis starting a project in the Eisen group. Amy Wen and Jolie Lobrutto are interested in learning more about the bacteria that are growing inside urchins and porcelain crabs.

Originally, we planned to bring tissues back from Panama for them to dissect and screen for microbes. However, permit issues prohibited this endeavor. Instead, we decided to focus on urchins and crabs in California. Eric Sanford, a collaborator at UC Davis who is a group leader at Bodega Bay and using urchins as a model species provided us a specimen from the lab and another one from the field. Amy and Jolie dissected them while David and I were lost in Panama.

A few weeks ago I teamed up with Jonathon Stillman, a professor at San Francisco State University & UC Berkeley, and an expert on porcelain crab physiology. He had a collection trip scheduled to look for different species of Porcellanidae at Fort Ross. The tides were low and we were able to collect a good assortment of four different species. Amy and Jolie could not join us because the low tide chart coincided with exams. Nonetheless, they could spare some time to come to the lab and culture bacteria from the new specimens. Amy and Jolie are now experts on the culturing of host-associated bacteria. Soon they will learn how to identify the bugs using Sanger sequencing.

Laetitia and Jonathon looking for porcelain crabs at Fort Ross
Jonathon explains how to identify different species in the field.
Laetitia showing California crabs to Amy and Jolie

We are curious to learn more about which bacteria they found on urchins and porcelain crabs in California!

A few videos of our urchin/crab Panama expedition 2018

Below you can find a few videos from our Panama collection expedition in 2018. Most of the videos were taken during porcelain crab collections.

 

Here in the first video, Alexandra is showing us how to find porcelain crabs in Bocas del Toro at Hospital Point. Note the bad visibility and strong current under water!

 

Here we are looking for porcelain crabs in the mangrove roots, right outside the STRI field station at Bocas del Toro:

 

And I found one!!!

 

Before getting out of the water we decided to quickly look under the boat dock.

 

The following videos were taken on the other side of the isthmus in the Pacific Ocean.

 

This is Playa Hermosa. Porcelain crab heaven!

 

For the end a sequence of snorkeling at Islas Secas:

Urchin/Crab Panama Expedition 2018: Day 18

And this is it. I wrapped everything up today.

On the way to the lab in the morning I bought presents for my family at the Mercado de Artesanias. At the lab I picked the last slow growing colonies and finished my DNA extractions. Alexandra joined me for the last round and I taught her how to use the Zymo DNA Mini Kit. She will continue collecting geminate species and their associated bacteria.

In the late afternoon, Haris quickly came to say goodbye. I felt welcome here and I am grateful for a very productive time.

Finally, in the evening I took the time to meet an old friend and his lovely wife for a good dinner.

Early tomorrow morning I am flying back to California. Once I am back in my office I will edit the video recordings I took during fieldwork and add a few good shots to the photo gallery. Stay tuned!

Urchin/Crab Panama Expedition 2018: Days 16 & 17

No post yesterday because I was doing DNA extractions. I am spending more or less 24h in the lab. The bugs are growing and I became painfully aware of the large sample size of crab tissues we have! I think I can extract DNA out of them all and that keeps me going. During the day I meet other lab rats and during the night cockroaches the size of guinea pigs.

Today I took my first break and went out for lunch with Matthieu Leray. We had a lot to discuss. He is an excellent marine ecologist.

It looks like this trip will work out! This was only possible thanks to a lot of helpful people. I will try to mention a few: There was David Coil who joined me for this adventure. Harilaos Lessios and Jarrod Scott who helped us plan it. Jamie Blair, Jarrod’s esposa who figured out a lot of the logistics. Bill Wcislo and Jonathan Eisen who covered our backs and got us out of the swamp a couple of times. The mysterious customs broker and Paola Galgani who went to talk to the clerks at the airport and who succeeded in releasing the baggage from quarantine. Marcos Ramos, who delivered the suitcases 3min before we had to check-in for our flight to Bocas del Toro. Taisha Parris, Aristoteles Villegas, Laura Geyer, Vilma Fernandez, Urania Gonzales and Plinio Gondola, who handled all the administrative work at the different STRI stations and made me go through the lab security training THREE times.  Deyvis Gonzales and Heather who navigated the STRI boats to our different known and unknown sampling locations. And Alexandra Hiller, my invaluable guide on the porcelain hunt.

At this point, I also want to mention Nino Wilkins and Tania Wyss who worked on the Spanish translations of our CVs, STRI application permit and Panamanian collection permit.  And our respective spouses Isabelle Henry and Donny who took care of our families while we took off.

This is a large group of people that were involved in making this trip happen. And it is just the beginning of the project…

We collected host-associated microbes of urchins and porcelain crabs from both sides of the istmo and made them grow on different media. Now we have to evaluate our results and see if we can increase the catalogue of microbes associated with geminate species.

A few memories taken by Alexandra:

Urchin/Crab Panama Expedition 2018: Day 15

Today we drove from Las Lajas back to Panama City. A very contrasting experience! From nature back into civilization. Alexandra and I talked about science and the next steps of our collaboration. The drive took about 5h and I had some time to think about my personal experience of Panama. It was a very valuable experience to live in Las Lajas and spend time with the local fishermen of Remedios. 

Oropendula nests

Remedios is a small village with its own port and a fish factory. Our captain told us a little bit about his life. He learned how to fish from his father who had learned it from his father. He remembers that there were lots of fish, turtles and sharks in the bay when he was a boy. But now they are all gone. He started to run a transport logistics company because he did not earn enough to support a family as a fisherman anymore. The government put many restrictions on fishing. Some species are protected, others have specific length requirements or can only be caught during a few months of the year. Fishermen don’t always understand these rules and are angry at the environmental offices. He says it is not his fault that all the fish are gone.

The men who are still making a living from fishing sell their products to international companies, such as for example Costco’s. Maria, our host who runs Casa Laguna B&B once drove to Remedios to buy fresh fish for her business. However, that day they were out of fish because the fish had been sold. Trucks pick them up in the morning and by the evening these fish are already in New York. What is an expensive fish at an American restaurant only gave a few cents to the Panamanian fisherman who caught it. This opens my eyes about my own consumerism. Especially in the Bay area of San Francisco where I live you can find high quality food from all over the world. It does not say how much the producer got for it and how many miles it had traveled. There is no information on how much oil was burnt for packaging and transport and in how much waste this resulted. I will try to think twice before I buy groceries when I return. And I will talk to my children about it. Most of the producers are just trying to survive every day. It is the rich consumers who can make the difference by making an educated choice.

Another important point to discuss with my children is our plastic waste. I have seen it every day here in Panama. Even on the remote Islas Secas there is plastic trash. My mom told me that there were no plastic bags at grocery stores when she was a child. Now they are everywhere – in just one generation. In stores, on the beach and in the ocean. This might need a strong re-thinking, too.

These field trips are not only very productive for research. They usually also give me the time and distance to reconsider life and what we are here for.

a bat we found at breakfast
and his little toes

Once we arrived in the city, Alexandra dropped me off at the STRI station on the island of Naos. Here I am now. I will start the first extractions tonight. The centrifuge behind me is begging for it.

Continuing to work with my McGyver science tools!
red colonies…
… that turn into purple when dissolved in DNA/RNA shield!

Urchin/Crab Panama Expedition 2018: Day 14

This is going to be a boring blog post.

2 weeks in Panama already!

Today was not much different from yesterday with the exception that I finished lab work early: at 21:30 already! We started at 6:30, spent most of the day collecting at Islas Secas and came back in the afternoon for dissecting crabs and culturing bacteria. Most of the dilutions are growing well! Even the ones in the anaerobic chambers.

Alexandra and I decided to drive back to Panama City tomorrow morning. We collected a lot. I just typed 228 samples for microbiome analysis into the google sheet, including 13 different porcelain crab species and three different tissues. At the moment there are 45 plates harboring tissue samples for bacteria and 50 bacterial cultures in glycerol. This means that I will have to finish a lot of lab work during the next couple of days. Every extra day counts. I am looking forward to enjoying the luxury that comes with a real molecular genetic laboratory at the STRI facility in Naos.

Last evening of doing lab work at the Casa Laguna B&B

 

Urchin/Crab Panama Expedition 2018: Day 13

Another long day. Maybe the longest so far. We had to leave the hostel at 6:30. Our host’s mother extra got up and brewed us some strong Italian coffee. Such a lovely lady!

We hired a local fisherman to bring us out to the Archipelago de Islas Secas. The boat ride took almost 1.5h: first down a river along the mangroves and then out into the open ocean. We tried hard to spot a crocodile but they hid too well. Here at the Pacific side of the isthmus we depend on the tides. We can only find porcelain crabs during deep low tides. This gives us around 2h to find the crabs! The marine life around Islas Secas is amazing! I needed a lot of self discipline not to get distracted by the schools of fish passing by and the moray eels looking out of their holes. What a pity that David was not with us. I was accompanied by some large beauties. I worked with my full commitment, regardless of scratches and waves. For the first hour I did not find anything. However, then I figured it out and started finding them.

On the way back to the fisherman’s village we noticed some huge houses and development in the area. This place is unique with regard to its pristine nature and wilderness. People live in small villages in colorful houses. Life is simple and sufficient. Many families have chickens, a few cows and pigs. However, now it looks like they are selling their land to turn it into cash. Many buyers are rich international investors who want to develop the area, build large hotels and make money with all-inclusive resorts. Moreover, there is a law in Panama that makes it easier to get a residence permit if you buy real estate. This is not a good development for the local flora and fauna, including humans.

Like yesterday, I immediately started processing samples and culturing bacteria when we came back to the hostel. I only took a quick break for the sunset at the longest beach in Panama, 5min by (bare-) foot from the hostel.

Sunset at Las Lajas

The bugs are growing well. I hope I can isolate them successfully.

I was particularly pleased to find P. haigae today, named after Janet Haig a pioneer in porcelain crab research! As a tribute I will browse in the Reports of the Lund University Chile Expedition 1948-49 (link). In this report, Haig describes crustaceans that they found during their expedition (titles in Swedish, text in English and Spanish). I wonder how collection permits were regulated in South America during that time.

Urchin/Crab Panama Expedition: Day 12

After a rich breakfast we drove to Playa Hermosa to check out some classic tide pools. Right on time, at low tide, we started searching. And we found! A lot. Two hours later we were both smiling and feeling accomplished. I guessed four different species in my little collection tank. Without a break we drove straight to the port to meet a fisherman who will bring us to las Islas Secas tomorrow morning. Google map on Alexandra’s iPhone was confused and led us for 10km on a dirt road through several cattle gates and private properties until we hit a pig transport. The driver yelled at us to turn around. With a bit of luck we finally ended up in the right village and talked to the fisherman and his buddies. Apparently it is going to be very rough tomorrow. Better no breakfast…

Back at the hostel I started making dilution streaks of our cultures, sampling them for DNA extractions and storing them for long-term in glycerol. This was followed by dissections of the new crabs and incubations of their fresh tissues. We are far from done tonight. Some species are so similar that Alexandra has to use a microscope and count the hairs on their legs to figure out who they are. This takes time!

Labwork in my hotel room…

I am going back to dissecting little porcelain crabs now…

Ready for dissections