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!

Wrap up of #istmobiome meeting in Panama

Classic beach shot

The last day of the “From model organisms to ecosystems: scaling-up our understanding of host-microbe symbiosis in the sea” #istmobiome meeting in Panama was yesterday.   After a few days of really productive discussions (and awesome field trips!) the last morning was dedicated to outlining a white paper on these topics.  Keep an eye on this space for updates on that process!   It was a great meeting and I wanted to again thank Jarrod, Matt, and Laetititia for all of their working organizing the meeting.  And also to all the folks at STRI who made it possible, both from a scientific and logistical perspective.

In the afternoon we split into various groups… some went fossil hunting, some went surfing, some went looking for lucinid claims (and snorkeling), some flew back to Panama City, and I went fishing (shocker).  Had some good luck out on the reef on the east side of the island.   Those of us that were left went out for a great dinner in the evening.

Miraflores locks on the Panama Canal

Most of the remaining folks left Bocas very early… a couple of people were coming on later flights.  Jonathan, Raquel, and I went to check out the Miraflores locks on the Panama Canal and then head to the airport.   Laetitia stayed in Bocas for more fieldwork.

Panama meeting Day #4

Aaron O’Dea leading fossil class.

Got off to an early start this morning for a 1.25 hour boat ride in the wind, rain, and waves to an amazing fossil site.   This field trip was led by Aaron O’Dea who is a paleontologist with STRI.  I had never looked for fossils before and I have to say it was a blast.  Everyone scrambled around picking things up off the beach (the waves are eroding the site pretty quickly) or pulling things out of the “rock” (more of a compressed sediment).  Not being a marine biologist I didn’t recognize many of the names being thrown around, but there were a lot of really cool looking fossilized (and extinct) corals.  Once the rain and the bugs started to wear us down, we headed partway back for a snorkel at one of the rare sites where there are still Acropora.   This awesome looking coral used to be ubiquitous in the Caribbean but has mostly disappeared (90-95% loss) just since the 1970’s.

Everyone hard at work

The afternoon session was a pair of talks focused on using microbiomes to aid conservation.  Luis Mejia started off with “Biodiversity and Ecology of Plant Microbiomes and its Relevance for Agriculture”.  He showed data and pictures of cacao plants inoculated with endophytes and how they are protected against pathogen damage.  Has done experiments both in the lab and in the field which is pretty awesome.  Moved on to coffee, focusing on the coffee rust fungus.  Did some really comprehensive fungal surveys (ITS) of different coffee species across Panama.  Then a massive amount of work looking for the protective effects of endophytes against the coffee rust fungus.


The second talk was by Raquel Peixoto giving her talk on microbiome manipulation… starting with the mangrove work that was so successful.   She has the most amazing pictures comparing control plots to plots inoculated with beneficial microbes (a consortium of oil degrading bacteria and plant growth promoting bacteria) and the differences are just striking.  Having gotten into mangroves because of oil spills (that killed the mangroves) she wanted to apply the same techniques to corals affected by oil spills… though now her focus is more on corals affected by climate change.  She has had similar success in both protecting corals using beneficial microbes but also in selecting for “super corals” that are more resistant to climate change.  Showed some specific results that the BMCs protect against Vibrio infection of the corals.   Surprising result that some coral colonies, same species and side-by-side in the field… can have quite different microbiomes.  Described an ambitious project to restart the ocean coral reef at Biosphere2… allowing them to measure everything from the beginning.

At the fossil site

Spent a bit of time after the break discussing the use of beneficial microbes in marine conservation… focused mainly on corals, mangroves, and seagrass.

Afterwards we broke out into groups with the goal of discussing “On what taxonomic, phylogenetic, and functional groups should future studies on symbiosis be focusing and why?”   Which turned into:


(caveat, there was a lot of drinking between the discussion and the presentations of the discussions)

Where’s Waldo? Mostly shells but at least one clear fossil.

Group 1:  Which marine taxa should we be focusing on and why?

This group asked more questions; “How do microbiomes enable/enhance survival in unique niches/extreme contexts?”  They talked about toxic sea slugs that have co-evolved with their (specialized) diets.  There’s existing cool work on the system but not microbiome work.  Similar questions with urchins and herbivorous fishes.  The second question was “What are the organizing principles of microbiome assembly?”.   Wondering about the larval stage of organisms and when they acquire their adult microbiomes.  Wanted to consider urchins, sponges, cnidarians, Astrangia, and molluscs for this question.  The last question was “What roles does the host play in the microbiome?”.  For this they wanted to study chemosynthetic organisms, macroalgae, iguana poop, flatworms, and other “simple” systems that are easy to manipulate in the lab/environment.

Thirsty in the field? Have a rock hammer?

Group 2: What resources, tools, and products should we be attempting to generate?

This group talked about what resources you need to start a microbiome project.  For example if your question was about chemosymbionts you might start with 16S, FISH, metagenomics, TEM, etc.  What processes are you interested in?  How broad do you want to sample?   How much do you want to look at?  Need to understand the biology of your system (life history, know your organism, conservation, evolutionary significance).   Boiled it down into two big questions; “How to move into a new system?” and “How to combine ongoing research into a new project?”.   Gave an example they called the “Marine Foundational Microbiome Project”.  Wanted to consider seagrass, kelp, coral, sponges, and mangroves… some cross the marine terrestrial ecosystems and are all foundational species.  They finished talking about tools and projects.   What level of resolution do you want to examine the microbiome with?  Products to consider; host genome/transcriptome, population genetics, diversification, keep samples (storage), range, ecology, phenotypes, time series, be operationally straightforward.   Actually need first; field guide, support/incentive for isolating and describing new species, new cultures, export permits, link 16S read to habitat.  Their moonshot idea is a new buffer that would perfectly preserve DNA indefinitely without freezing.

Trying to get to the next good one.

Group 3: What experimental approaches should be used?

The group that I was in focused on experimentation.  Discussed common garden ARMs to examine succession and resilience (functional shifts, evolutionary relationships/convergence related to host microbiome).  Also considered the dynamics of microbiomes over time and space in hosts/habitats (e.g. across gradients).  Talked some about experiments to track sources of microbes across seascapes (e.g. fish, birds, abiotics sources, boats, etc.).  Considered manipulations… what variables are interesting to manipulate?  Then of course we can manipulates the microbiomes themselves.  We spent a lot of time talking about large-scale moonshot style mesocosm experiments.   For example having mangroves, seagrass, and corals in a giant set of controlled conditions… with and without microbiome manipulations.   Especially cool under changing ambient temperature.  One of my favorite topics was a proposal by Allen Herre about a giant experiment that’s going to happen anyway… where a new road is going to be built out to the Bocas del Toro Province.   Previous work in Panama has shown this is associated with big changes in the marine environment.   This would be an opportunity for a large scale “manipulation” experiment.  A lot of potential for cool research without having to bear the cost of the manipulation.  Thought about multiple generation experiments under controlled conditions (e.g. using organisms from both sides of the isthmus) and looking at microbiome data.   Our last topic was seagrass restorations using the probiotic models presented by Raquel and Luis earlier today.

Panama meeting day #4

Raquel presenting the summary of the “what is a healthy microbiome?” discussion.

Discussion day!   After I took a nice jungle hike this morning we had another good breakfast and then convened in the classroom for some really amazing discussions.   We split into two big groups today.   The first group was supposed to discuss  “What is a healthy microbiome? Does microbial diversity matter for the host? Are more microbes better? Or fewer beneficial symbionts?”.  We had a great discussion about these topics, our group contained a nice mix of microbiome folks and community ecologists.   We started off saying that it was basically impossible to define a healthy microbiome, but in the end we did come up with some possible parameters to consider (e.g. stability, resilience to pathogens, correlated with host/ecosystem health).   A large part of the discussion was about diversity (is it always good?, what does it even mean?, how do we define it?) and how to actually measure “health” of either an ecosystem, a host, or a microbiome.

Jungle trail on station

The second group was tasked with “How to identify the tipping point from symbiosis to dysbiosis in host-associated microbiomes?“.  They started with the same conclusions that health is difficult to define and subjective.   They described a continuum from “stable/similar/symbiosis” via “in flux” to “dissimilar/variable/dysbiosis”.  Emphasized the need to draw on existing ecological theory to explore and quantify this concept of tipping points.   Key points here would be community assembly, resilience, hysteresis, and feedback loops.

After another delicious lunch, we came back to the classroom for the next set of discussions.   This time there were three groups, tasked with the following topics:

  • 2C: How do we go from describing the variation to deciphering what is driving it?
  • 2D: A null model for microbial communities
  • 2E: Monitoring host-microbe interactions: can we identify model systems or hosts to monitor (e.g., host-microbiomes with cosmopolitan distribution)?

I got to hang out with the “deciphering drivers” group.  We spend the first third of the discussion trying to come up with general principles to describe drivers of community structure (e.g. biotic factors, host traits, abiotic factors, chance).   The rest of the time was spent listing the various specific drivers that we thought, at a minimum, should be described or at least considered in a marine microbiome study.   Examples of host traits to consider were genotype, age, life history, lifestyle, population/demography, transmission mode, compartmentalization, and diet.  Example of environmental traits included temperature, salinity, electron donors/acceptors, niche-specific co-variants (very broad!), stoichiometry, community structure/ecology, sampling context, light, natural history of the site, and location.

Coconuts to palms

The second group talked about null models.  This is a tough one for me to summarize since I have no ecology or stats in my background.  They talked about how we use null models without knowing it when we do statistical tests, but they might not be the right model for the hypotheses we want to test.   They went through the idea of building a model and what do you need for that (adding terms to the null model).   They then slid into a list of considerations before starting an experiment (replicates, physical environment, sampling potential for broader community etc.).   Last was tossing ideas around about other cool things we could do in this system.  Discussed artificial systems, pooling all the neighbors for microbiome context, enrichment protocols, and bottom-up versus top-down controls on the microbiome.

Anemones (by Jonathan Eisen)

The last group talked about monitoring approaches for the microbiome and potential model systems.  Defined monitoring as observational studies, across either space or time.  Model systems would contain well-defined taxa with known relationships between the host and the microbiome.  Emphasized that model systems require the ability to manipulate experimentally.  Asked about what the impact of the microbiome on the host effect on ecosystem services might be.  Spend the second half of their time trying to figure out what is the low-hanging fruit in the marine microbiome world.   Included bioblitzes, doing work in places where environmentally rich context exists, unique systems (e.g. powerplants), reciprocal transplants, herbivorous fishes, and coral restoration.

Dinner! (some kind of jack)

Had a nice long break, during which I was able to take a cab to the end of the road, walk out on a reef, catch a few fish, clean one for dinner, then take a cab back.  In 70 minutes!  Once we got rolling we did lightning talks (<5 minutes) by various participants.

-Matt LeRay talked about marine symbioses and showed a cool video of examples.

-Tiago Pereira talked about his work on various systems including his current work on marine nematodes.  Particularly interested in spatial-temporal variation in natural systems.   Focused at the moment on marine and terrestrial nematode microbiomes.

-Bob Thacker talked about his work on sponge microbiomes here at Bocas del Toro.  Every species has a very distinct microbiome.

-Jarrod Scott talked about some of the IstmoBiome work at Bocas del Toro and Isla Coiba.  Described a summary of the metagenomic data generated from their water samples at both locations over time.   Have ~140 MAGs (metagenome assembled genomes).

-Lizzy Wilbanks talked about her research interests… having come to microbiome research from a chemistry background.  Interested in ecophyisology, bacterial metabolism, biogeochemical cycles, interactions between species, how do ecological/evolutionary interactions shape microbial symbioses.

-Doug Rasher talked about his work on apparently disparate systems, but which operate on similar fundamental operating principles.  Went into more detail about herbivory on coral reefs and the effect that has on interactions between corals and algae.  Presented some results from a collaboration with Jarrod on fish gut microbiomes.

-Maggie Sogin works on gutless worms found seagrass beds and nearby sediments on Elba Island.  As the name implies, they have no guts… and have symbionts below the cuticle.  They hypothesize that the worms actually digest the symbionts directly which is pretty awesome.  She is working on the flow of sugar through the system via metagenomics and metabolomics.

I missed the next two talks (Ben Yuen and Becky Vega-Thurber) after an unscheduled change in the plan.  Sorry Becky and Ben!

-Then Koty Sharp talked about her work on Astrangia poculata (a hard coral).  She studies the microbiome and how it changes over time (seasonality is a major driver).

And evening off!  Some discussion about hitting the bars in town but we’ll see… I’ll post this now just in case.

Here’s the tweets from the day:

Panama meeting day #3

Invertebrate show and tell in the lab

Had a good social evening last night, including Jonathan playing with the ROV in the pool at the bar.   Started off the second morning with a short talk by Jonathan, introducing the concept of microbiomes and the goals for the meeting of coming up with a set of guidelines for marine microbiome studies.

The rest of the morning was dedicated to breakout groups… we split into 4 groups, two groups working on “what is the core microbiome?” and the other two working on “how do we define the core microbiome?”.  These are very hard questions!  Our group (“define core microbiome”) spent some time wondering whether this was an important question, or at least needed for most systems.

Spaghetti worms

Having decided it was, we circled around a lot of the problems with defining the core microbiome.   Microbiome varies with age, location, context, dysbiosis, etc.  It matters whether you look at taxonomy or function and it might be that what you see changes based on taxonomic level queried.   That’s without even getting into all the questions of experimental design, standards, extraction/PCR/preservation bias, etc.

After some great discussions on these topics, we headed for the boats to go check out some of the reefs in the area.  We snorkeled in two different areas, one had a great transition from corals to seagrass to

Eating lunch on the boat


mangroves (but we forgot the underwater camera!).  Once we returned to the station we had a great discussion about the things we had seen and how they related to the broader topics of marine microbiomes and symbioses.    After dinner we had a long and productive session on sampling strategies, data bias, protocols, and other technical considerations.

Jonathan leading the field debrief

Here’s all the tweets from today:

Panama meeting day #2

Ambitious tree

Had the morning off, everyone got to do their own thing and then the last bunch of attendees arrived and we all had lunch.   I walked down the road this morning and tried a bit of fishing.

A “schoolmaster”

The meeting began after lunch (Twitter hashtag #istmobiome) with Matt Leray who gave an introduction to the project and to microbial symbiosis.  The next talk was Rachel Collins, who is an invertebrate taxonomist and the director of the Bocas station… she gave an overview of the station and the work that happens here.  Jarrod Scott was then tasked with giving an overview of the Panamanian isthmus (“istmo” in Spanish, hence the URL and hashtag).  Jarrod also talked about STRI and the various research facilities they have around Panama.   After a break, Ross Robertson talked about the differences between the two sides of Panama (temp, salinity, nutrients, etc.).   The Pacific is much more productive, but also more variable and stressful.   Ross also touched on some fish gut microbiome work… a teaser of more microbes to come.   Then Haris Lessios gave a talk provocatively titled “So, what is the Isthmus of Panama good for?”.  He gave a number of great reasons, but in particular he talked about the ability to calibrate molecular clocks to the rise of the isthmus.  Allen Herre then gave a talk on Terrestrial Symbioses… a lot more is known about microbial symbioses out of the water.  He asked some great high-level questions about things like community assembly… how general are the patterns we observe?  Or is every system a special case?  Emmett Duffy talked about the MarineGEO program of which he is the director.  He described it as a “healthcare system for marine ecosystems”… a distributed, global, effort to collect “vital signs” data in a standardized way.  The last talk of the day was our own Laetitia Wilkins, talking about the IstmoBiome project to which this site is dedicated.  We started with urchins and porcelain crabs and have now added snapping shrimp and lucinid crabs.

Here’s a collection of pictures from yesterday and today:

Laetitia and Ben looking for clams.
Fish under the STRI dock
More fish under the dock
ROV in action!
Pillar under a weather monitoring station

And here’s the Wakelet of Tweets from the meeting so far:

Panama meeting day #1

Playing with the underwater camera.

Long travel day today… started with our 1am departure from San Francisco, followed by the 7 hour flight to Panama city.  Bought a SIM card for the phone, then off by taxi to to domestic airport (Albrook).  Wandered around a bit waiting for our flight and then on the turbo-prop airplane out to Bocas del Toro.   Really interesting to be back so soon… I hadn’t planned to come back so it’s fun to have the sense of the familiar at the station and the town here.

First item on the agenda was testing out the ROV (underwater robot) that Jonathan brought with him.   I jumped in the water to check out the fish and get some underwater pictures of the ROV.  Jonathan played around with the toy important scientific device… got some good HD video

Sunset from the station

of fish under the dock.   Watched a nice sunset from the station and then headed into town for dinner and drinks with various folks affiliated with either the station the workshop or both.  All in all a great but very long day!   I don’t have the underwater pictures but here’s a few from my cell phone to whet the appetite.   The meeting partially starts tomorrow and begins in earnest on Tuesday.  Looking forward to it!

Jonathan in the water

Back to Panama!

Laetitia showing California crabs to Amy and Jolie

First an update on all the samples Laetitia and I collected in February… we’re still working on identifying all of the isolates from the crabs and urchins.   We’ll post some sort of summary when it’s all done.

Tomorrow it’s back to Panama (well Laetitia is already down there).   Jonathan and I fly out tomorrow, along with Raquel Peixoto, a visiting professor from Brazil.   There we will meet with a couple dozen other marine microbiome researchers… both from STRI and from other institutions.   The title of the meeting/workshop is “From model organisms to ecosystems: scaling-up our understanding of host-microbe symbiosis in the sea“.  Laetitia, Jarrod, and Matt have been working tirelessly for months on organizing this workshop and I’m excited to hear all the cool talks and discussions!

There will also be a bit field work and touring around Bocas del Toro.   I’ll probably post daily reports of the meeting and the sights.  Stay tuned…

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!