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.

About David Coil

David Coil is a Project Scientist in the lab of Jonathan Eisen at UC Davis. David works at the intersection between research, education, and outreach in the areas of the microbiology of the built environment, microbial ecology, and bacterial genomics. Twitter

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