All posts by David Coil

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

Urchin/Crab Panama Expedition 2018: Day 6

Jarrod preparing to tie up to the mooring buoy
Turns out that Amazon sent Laetitita two left gloves
A sea urchin well hidden and protected from scientists
Corals and fish in the area

Busy day today.  Up early and a breakfast of borrowed PB&J since we hadn’t had time to shop yesterday.   Then out on the boat… the three of us along with a driver, Heather.  Pretty rough conditions… overcast skies and bouncing along big waves.  We made it out to Hospital Point on Isla Solarte and managed to tie onto a mooring buoy.  It was really not ideal conditions for collecting… big waves, low visibility and then it started to rain which made the visibility even worse and made it surprisingly cold.  I quit long before the other two because I was starting to shiver in the water.  It turned out to be relatively easy to find the two species of Echinometra (lucunter and viridis).  There were also a fair number of Diadema antillarum which are really a pain to collect since they are huge and sharp.  Jarrod got a nice one into our collection vessel (colander) with salad tongs.   But we couldn’t find any Eucidaris.  So we searched, and searched,  and searched.   We saw a lot of pretty fish, interesting corals (including fire coral… best to avoid that one!) but not Eucidaris.  We finally gave up and headed back.

Apparently the wind can make me look cool. Or something like that.
Free food!

Laetitita and I walked down the beach to a restaurant for lunch and hit the jackpot.  Turns out the restaurant had only very recently opened and so after we ordered our (cheap and delicious) food the owner came over and explained that she was teaching the kitchen staff how to make all the new dishes and would we like to sample them for free?  So she brought out little trays of all kinds of amazing and delicious things… like fish/yucca/cassava balls in passionfruit sauce and spiced plantain patties.   Then we loaded up at the grocery store and headed back to the station.

This was clean and empty before we arrived.

A lot of labwork this afternoon including dissecting/plating samples from the urchins, replating some samples from the Pacific, and preparing tubes for crab sampling.  I also tried (but failed) to set the lab on fire.   Alexandra Hiller arrived at the station today, so she and Laetitita will start looking for crabs tomorrow morning.

After the lab work was done, Alexandra and I headed downtown for dinner at a delicious Indian restaurant.  Jarrod was supposed to join us for dinner but got “stuck” in a bar for a few hours first.  We had some fascinating conversation about evolution, adaption, microbes, host phylogenies etc.  I think the the people next to us thought it was a bit odd.


Urchin/Crab Panama Expedition 2018: Day 5

Here’s what all the fuss was about

The suitcases arrived!  Just had to get that bit of information out of the way first.  So today started with housecleaning in Gamboa, prepping the plates for transport, and getting to the local airport (not the Panama City one).  While at the airport we got a call from Marcos Ramos who was the STRI contact working with the mysterious “broker”… who had obtained our luggage!  I have no idea if “taxes” were paid or what but Marcos was going to rush the luggage to our location.  Then a super helpful woman at Air Panama basically held our plane until the luggage came so we could check it to Bocas.  We were irrationally happy to see our stuff again.  And as a bonus, there were no problems getting it, or the stacks of cultured bacteria (buried under my dirty laundry) to Bocas.

Laetitia hard at work
Isla Colon

Landing in Bocas feels like “The Caribbean”. It’s a funky town with a chill vibe.  The buildings appear to be falling down and the roads are pretty bad but it just feels awesome.  We got settled in at the station and got our lab space and dorm rooms.  We got to work making up media and while it was in the autoclave we took a taxi down the road for a fabulous dinner at a beachside restaurant with Jarrod and his wife, Jamie.   Then back to the lab to pour plates and label tubes… tomorrow morning we’re off early on a boat trip for urchins and crabs.

A lab gecko on the wall
The dock at the Bocas STRI facility

Urchin/Crab Panama Expedition 2018: Day 4

Panama City from Naos Island

10:00am “Maybe tomorrow”

1:30pm “Probably by next Tuesday”

3:15pm “Good chance by Friday, but we need yet another official letter”

Those were the three main pieces of information we got today regarding the luggage, from three different people.  The last however is from the person talking directly to the “broker” who may send their daughter to the airport with the latest batch of paperwork.  So we’ll see.

From Echinometra coelomic fluid

Today was “let’s assume we never see our stuff again, what can we salvage scientifically?” day.  First of all we do have stuff happily growing on our “marine LB” concoction (20g LB powder, 15g agar, 10g NaCL, .5g KCl, and 2g CaCl if you’re wondering).  Anaerobic culturing is obviously out and DNA extractions are still a problem.

A gold mine! (Educational supply store)
The head shop where we bought sterilization equipment

So the three of us drove down to Panama City, to check out an educational supply store rumored to have Petri dishes.  They did!  As well as gloves, dissection tools, and a couple of other odds and ends.  Then Jarrod and Laetitita discovered that a head shop nearby had butane torches that would be awesome for sterilizing things.  MacGyver science!

Then on to the facility at Naos so that Jarrod could do some extractions, Laetitia could work on a review, and I could work hard on stuff go fishing.    A special bonus was that Alexandra Hiller was willing to drive our new acquisitions to Bocas so that we don’t have the same problem on the internal flight.  However, we will be carrying plates with the bacteria on them… guess we’ll see what happens!

Party time!

On the way back to Gamboa we got to experience the famous Panama City traffic jams… taking 2 hours to go 30 km.  Grabbed a quick dinner and then back to the lab for a late night culturing session to pick colonies in preparation for our move tomorrow.   We fly to Bocas del Toro so we can begin sampling from the Caribbean side of the Isthmus.


Urchin/Crab Panama Expedition 2018: Day 3

First of all… no equipment/luggage still.  Other than that, it was a relatively chill day.   We did some lab work in the morning (we appear to have some bacteria growing!) and caught up on e-mail.  After lunch, Laetitia and I went on a long walkabout.  First up over a ridge on a jungle trail… saw some monkeys and cool birds.  And tons of leafcutter ants… some awesome microbiology going on there! Then we ended up in the middle of a resort (which kicked us out).   Took another nature trail over to a big river which we followed the Panama Canal.  Pretty cool to see those giant ships go by!  Walked from there down the canal a couple of miles to a dock where I fished for a bit before being informed it was a protected area and being kicked out of there as well.

Finally cooked up the fish we caught in Taboguilla yesterday… amazing stuff!  If you ever have the chance to eat a finescale triggerfish that you catch, don’t pass it up.

Still trying to figure out how to do the rest of our work with no stuff.  We can wing some more culturing stuff but the DNA extractions would be tricky.  Wondering if the old “grain alcohol, meat tenderizer, and detergent” trick would be good enough for 16S analysis later?  Jarrod, Laetitia, and I had a 3 hour meeting tonight to discuss how to do the rest of the work assuming that we never see any of our stuff again.  I’m wondering if the UCD travel insurance covers things commandeered by a foreign government?

Urchin/Crab Panama Expedition 2018: Day 2

What a day.  Up at 5:00am, granola bars for breakfast and getting ready for the day.  Went down the visitors office only to find that our scientific visit hadn’t been approved and we couldn’t do any work.  Got that all sorted in a couple of hours and then raced off to the boat in Naos.  Headed out on an urchin/crab sampling trip with Harilaos Lessios, Alexandra Hiller, and a couple of divers.  Because customs had taken my snorkel mask I stayed on the boat… but that’s okay because I just fished for a couple of hours.  The sampling trip was a success… Haris collected several dozen urchins for his own work as well as representatives of the three Pacific species of interest for our project.  Those are Diadema mexicanum, Echinometra vanbrunti and Eucidaris tribuloides.  Alexandra and Laetitia were lucky enough to find a few porcelain crabs as well (Petrolisthes  agassizii).

Then the problems began.  Another STRI person went to the airport for our luggage and was rejected.  Now they want a “commercial invoice” from UC Davis and they won’t deal with any of us or STRI anymore, we have to work through a “customs broker” to “exonerate” our luggage.  What a mess.

We then went around the research facility in Naos and begged/borrowed some petri dishes and LB.  Then Laetitita stayed behind to dissect the crabs while Jarrod and I raced to the grocery store to stock up, then up to Gamboa.  He found an old tub of chemicals and we made a new invention “David’s marine LB” which we autoclaved (after weighing chemicals on ads torn out of a phone book).   Then off to our housing… which we couldn’t find!  We literally ended up going from dark house to dark house trying my key until we got in somewhere.  Grabbed some dinner and then headed back to the lab to pour plates, dissect the urchins, and plate out some (hopefully) bacteria.  Interesting process with no dissection tools, no alcohol, no flame (we eventually found a cigarette lighter).  Meanwhile Laetitita finished up in Naos and caught an Uber up to Gamboa.  We crashed after midnight… though were awoken in the middle of night by what Laetitita assumed was someone breaking into the house but was actually the living room light fixture falling and shattering.

Urchin/Crab Panama Expedition 2018: Day 1

An agouti outside our apartment in Ancon

So Laetitita and I arrived in Panama City ready to get settled in and prepared for our first day of sampling the following day.  However, it was not to be… we didn’t get out of the airport without problems.  As soon as the customs folks saw the petri dishes/tubes/extractions kits etc they freaked out.  Off we went into a little room filled with piles of contraband (the women ahead of us appeared to be arguing that there was a perfectly good reason for her suitcase to contain 13 empty new purses).  We argued and pleaded with several different people (almost all in Spanish… and ours isn’t very good).  Not only did they make us leave all the research gear, we weren’t allowed to use our cell phones to get assistance from the Smithsonian.   So away we went, checked into our STRI lodging, and went to get food.   From which we got picked up by Bill Wcislo, the deputy director of STRI, and back to the airport.  To get back to the contraband area we had to get employee access badges (in exchange for passports) and go through employee security.  However, they weren’t budging and his uniform and business card weren’t enough to relinquish our suitcases of microbiology stuff.


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!