Updates from Day 14 on the R/V Alucia: What is SPE?

Hey everyone,

In my last post, I explained the underwater surveys and briefly mentioned collecting a reef-depth water sample. In this post, I am going to talk about the method that I am using to extract the very small molecules from the reef seawater, a method called solid phase extraction (or SPE for short). All living things produce and release molecules into the environment. Microbes- like bacteria and archaea- produce, uptake, transform, and even communicate with these molecules. I am interested in how microbial communities influence the chemical composition of reef water and if we can use the chemical diversity and composition on reefs to understand the roles of these microbial communities on reefs.

I collect reef-depth water with a Niskin bottle at the end of my dive and I bring this water back to the Alucia so I can “process the water sample”.

Diving with the Niskin bottle, PC: Amy Apprill

When I use this phrase,  I am referring to two major separation steps. First, I separate the microbial cells (bacteria, archaea, and single-celled eukaryotes; “the biomass”) from the seawater by pumping the seawater through a filter with a very small pore size (0.22 micrometers) and I collect this seawater (I call this filtered seawater “filtrate”).

Second, I separate the small molecules that are present in this filtrate by passing it through a special material, called a SPE cartridge. The material in this cartridge has special chemical properties that allow it to bind to chemicals present in the seawater. This binding process removes chemicals from the seawater and retains them on the cartridge. You can also think of this cartridge as a chemical trap. I use vacuum filtration to pull the seawater filtrate through these cartridges. The seawater that has passed through this cartridge should be stripped of most of the chemicals in the seawater and I collect this seawater in a vacuum carboy.

Getting ready for SPE! In this picture, there is a vacuum pump, a glass SPE manifold, SPE cartridges, and tubing that leads into the cartridges (to move water from the bottle to the cartridges).

After I have passed all of the seawater through each cartridge (1 seawater sample per cartridge), I freeze each cartridge to prevent the molecules from degrading. I will finish processing these samples when I get back to Woods Hole Oceanographic Institution; I need a some special equipment to complete the final steps of this method!

Special thanks to the people of the Kujawinski Molecular Environmental Science Laboratory at Woods Hole Oceanographic Institution (Dr. Liz Kujawinski, Dr.  Krista Longnecker, Dr. Melissa Soule, and Gretchen Swarr) and Dr. Cara Fiore for teaching me how to use this technique to understand the chemical composition of reef seawater

Thanks for reading and let me know if you have questions!



Updates from Day 13 on the R/V Alucia: All about our diving!

Hey everyone,

Greetings from the R/V Alucia! We just celebrated another birthday on board the R/V Alucia. Carlos, one of the ship engineers, just turned 75 years old today! This morning, the crew mess was decorated with balloons and birthday messages! After dinner, we sang Happy Birthday to him and enjoyed some delicious cake.ou

As you probably know, diving has been a major component of our work during this cruise. So far, I have gone on 16 separate dives to help complete surveys, collect samples, and assist my colleagues with instrument deployment.

By now, we have gotten into a general diving routine (although this can daily depending on other needs, boat availability etc . . .) so I thought I would share a play-by-play about my roles and tasks underwater.

We typically leave the Alucia around 7:30-8 am with our prepared dive gear, sampling equipment (many coolers filled with different bottles for water sampling, mesh catch bags for holding samples that we collect underwater, and a Niskin bottle), additional cylinders for a second dive, divers, and a few crew members.

We arrive at the reef site and Amy or Maickel will jump into the water to inspect the reef location. If they deem it suitable, the boat is either attached to a mooring or anchored and all the divers get ready to dive! This involves fastening clip-boards, dive slates, transect tapes, cameras, and mesh bags to our BCs (the vest-like things that we wear that we can inflate or deflate underwater to change our buoyancy), making sure our air is “on”, de-fogging our masks (to keep them from fogging up underwater), finding our fins,  and making sure we have our weight belts/integrated weights on. We jump into the water in buddy groups (Amy is usually my buddy) and descend close the mooring/anchor so we can orient ourselves to wear the boat is in relation to the reef that we are diving on (this is important to do, especially on days when the water is more turbid and when it is harder to see).

Amy and I each decide on a general location to begin laying out our transects so we can begin collecting benthic coverage data. I hook one end of the transect tape around a piece of rubble (dead reef) and then I swim the transect tape 10 m across the top of the reef. When I get to the end of the tape, I hover over the line and estimate the coverage (using cm) of each substrate type (either living or non-living; coral, sponge, sand, rock, algae) that intersects with the transect tape. I do this for each meter along the line and when I finish, I reel in the line, swim over to another reef area, and complete the survey again. It usually takes me 30 minutes to complete 5 transects. Amy completes 5 transects as well.

After we complete these transects, Amy and I scope out coral colonies to sample. Amy uses a hammer and a chisel to separate off little pieces of different colonies and I hover beside her, record the samples that she is collecting, and hand her collection bags. We usually spend 15-20 minutes collecting these samples and by that time, it is time for us to complete the dive.

Our second dive of the day is almost identical, but with one sample collection addition – I collect reef-depth water with a Niskin bottle and I use this sample to understand the chemical composition of reef-depth water.

Thanks for reading!

Scuba gear
Amy (my advisor) and I on our way out to a dive site!


Updates from Day 12 on the R/V Alucia: Hasta luego y te veo de nuevo pronto!

Hey everyone,

Greetings from the R/V Alucia! We had another active day of diving, sample collection, and sample processing!

Early this morning, we also parted ways with two MIT-WHOI Joint PhD program students (Kalina and Tyler) and four of our Cuban science colleagues (Victor, Fredy, Mayelin, and Lake). Over the past week, I have had the privilege to work alongside with, learn with, dive with, eat with, dance with, and live with these excellent people.

Field work is the ultimate bonding experience: on the first day of this cruise, we were all strangers, but by day 12, we are all scientific colleagues and, more importantly, friends. Needless to say, I already miss having them on board the R/V Alucia and I wish them safe travels back home!

I compiled a list to remember all of the fun memories that we now share (this is not a comprehensive list by the way):

  1. Kalina and Tyler streaming their course lectures in the submarine mission control room on deck. They were so determined to keep up with their classes while they were on this cruise. Amy, Ashlee, and I were quite impressed! They even had to take an exam during the first couple days!
  2. Kalina and her excitement for the Disco/ sitting on the floor/ lugging the beast around the back deck and the labs.
  3. The fact that Tyler has made me laugh in every single conversation I’ve ever had with him. Seriously.
  4. Mayelin (donned in a lab coat) and Lake spontaneously salsa dancing in our tiny dry lab.
  5. Dancing under the stars on the top deck (twice!).
  6. Kalina’s birthday celebrations.
  7. Group workout/ photo-shoot session on the top deck at sunset.
  8. Soy de Cienfuegos!!!
  9. Where’s your passport, Tyler?
  10. Fredy’s dancing lessons.
  11. Celebrating Halloween (and mostly marveling at Ashlee’s amazing costume).

Colleen and Andrew, Kalina and Tyler’s advisors, just joined us to finish up the cruise and I am excited to work with and learn from them! I am sure we will make some new amazing memories together!

Thanks for reading!

Fredy, Ashlee, Victor, and Tyler
Tyler, Ashlee, and Kalina right before Ashlee and Kalina departed the Alucia to do a night dive with the DISCO



Updates from Day 11 on the R/V Alucia: What’s on the menu?

Hey everyone,

I am writing to you this morning about Day 11 on the R/V Alucia! We had a full day of “science-ing”. Yes, the catch phrase “let’s do some science today” has become a regular saying on our trips out to the reef! There were two dives in the morning and two in the afternoon. However, we changed it up a little by sampling two different reefs between the morning and afternoon. Tyler and I didn’t go on the afternoon trip because he had to breakdown his incubation experiment and I had to finish processing the samples that we had collected on the earlier morning dives. We still had fun though! Tyler managed to help me with filtering and finish his experiment!

We had a fun “picnic” on the aft deck to celebrate and give thanks for the excellent and amazing people who joined us for the first leg of the cruise and who will be leaving later today (on Day 12, more on these amazing people in a later blog post). Salsa dancing lessons, a few games of “Tiki Toss”- I keep getting better by the way; out to break to record, and dancing under the stars on the top deck ended a wonderful night.

I know I have mentioned the delicious food served to us on the Alucia so I figured that I would share pictures of some of the ridiculously amazing meals that we have enjoyed so far! I can honestly say that every dish we have been served has been exquisite! I tried to remember to take more photos, but I have a tendency to arrive late to meals/ forget my camera!



Dinner: Sesame soy salmon, veggie fritters, pink rice, veggie noodles
Breakfast- egg on a bagel, fruit, cranberry walnut muffin
Amazing fruit platter we have been served every day!
Another breakfast: Shashuka with basil and veggies!



Updates from Day 10 on the R/V Alucia!

Hey everyone,

We had another busy day today! Today had a similar structure to the past three days: there were two dives in the morning (coral diversity and health, benthic cover, water sampling, meiofauna (small animals that live in the reef sediments) sampling) and two dives in the afternoon (fish surveys, DISCO testing, hydrophone drifting). Amy and I spent the afternoon processing the samples that we had collected this morning.

To change up my blog content a bit, I thought I would spend some time sharing a few of my favorite macro coral pictures from the past week! This is just a small selection of coral species that I have observed on the reefs so far.

I have really enjoyed observing the beauty and diversity of corals on these Cuban reefs and I am so thankful that I get to experience this beautiful ecosystem first hand. There really is nothing like it!

Montastraea cavernosa
Orbicella faveolata
Diploria labyrinthiformis
Dendrogyra cylindrus

Thanks for reading!

Updates from Day 9 on the R/V Alucia: High fives all around!

Hey everyone,

Today we surveyed and sampled another reef site (located to the east of the other reefs that we have been sampling)! The morning diving and sampling went smoothly and we even had time for some underwater high fives and a group picture!

A high five with Tyler!
Look at all the divers in the water! From Left to right: Viktor, Laura, Fredy, Maickel, Tyler, Amy, Mitchell

I spent the afternoon processing sample and washing bottles while listening to some of Michael Jackson’s best hits! A few crew members even joined in on some of the songs ;).

Ashlee and Kalina went on a night dive around 6 pm. Kalina wants to test her instrument under different light conditions and we are excited to see what happens! Their dive went well and they had fun observing the corals at night!

That’s it for today- more tomorrow!





Updates from Day 8 on the R/V Alucia – A Day in the Life on the Alucia

Hey everyone,

For those of you who are curious about what a day looks like for me on the Alucia, here is a breakdown!

6:00 am – Wake up, get dive equipment ready and prepare for diving, and prepare for water sampling at two sites (17 bottles of various sizes and a Niskin bottle).

7:15 am – breakfast time! Pancakes, savory cornbread, fruit (delicious)!

7:45 am – load the smaller boat with our dive equipment, sampling gear, and divers

Scuba gear!

8:20 am – Jump into the water at the first site, conduct benthic cover surveys, and collect coral tissue samples. Everyone really enjoyed this site – beautiful reef topography, large coral colonies and sponges, and high fish abundance compared to the other sites.

9:40 am – Amy and I sample water at our first dive site and then we take the boat over to our second site and sample water there. We also wait a little bit longer to complete our surface interval before diving at the second site.

10:30 am – Jump into the water at the second site, conduct benthic cover surveys, and collect more coral tissue samples. I also collected a sample of reef-depth water with the Niskin bottle so I can study the chemistry of the seawater. Tyler named the Niskin bottle “NisKing” and said I was the “NisQueen”. We enjoyed diving on this site too!

11:30 am – Ascend to the surface, collect surface water samples, and drive the dive boat back to the Alucia.

12:00 pm – Get back to the Alucia, remove our dive gear and equipment from the dive boat, place large coolers containing samples in the lab, take a quick shower, and eat lunch (DIY gourmet sandwiches).

1:00 pm – Filter and process samples and clean bottles. Amy and I listen to music to entertain ourselves. Today we listened to some “Greatest hits from the 80’s” and a Karaoke album (with some great songs)!

5:00 pm – Enjoy some time on the Helipad with Amy, Tyler, Ashlee, and Kalina

5:45 pm – Watch Kalina cut her hair without a mirror. She did a great job!

Haircut by Kalina

6:15 pm – Eat delicious pizza on the back of the boat and watch the sunset

Early evening on the back of the ship!

7:30 pm – Label cryovial tubes for tomorrow

8:30 pm – Write this blog post!

Thanks for reading!





Updates and highlights from Day 7 on the R/V Alucia

Hey everyone,

Happy Monday! I am writing to you after another full day of diving and collecting and processing samples! Today was almost exactly like yesterday for me – Amy and I conducted coral benthic surveys and then collected water samples in the morning. We spent the rest of the day processing samples and cleaning to prepare for sampling tomorrow!

The rest of the team did different things! Ashlee departed the Alucia on a zodiac early this morning to pick up two arrays of of her hydrophones. I call Ashlee the ‘reef whisperer’ – she records the sounds that creatures living on the reef make (like the tiny Rice Krispie popping sound that snapping shrimp make) with her hydrophones and she is also interested in how sound influences coral larval settlement.

Fredy and Viktor conducted coral health and benthic cover surveys at both of our morning sites! It takes a tremendous amount of buoyancy control and patience to do these surveys and we are glad to have Fredy and Viktor on our team! Leo and Lake completed fish surveys at this reef site too!

Tyler successfully set up and began an on-board incubation experiment that is designed to understand how corals use different forms of nitrogen (a limiting nutrient in coral reef seawater). He also set up this incubation on the helipad on the ship – the incubations look impressive and I can’t wait to see what he finds!

Kalina dove with the DISCO (a novel instrument that is designed to measure the concentration of superoxide radicals in real-time) and tried it out on a bunch of different corals.

Maickel collected more invertebrates from the reef so he can determine the invertebrate biodiversity on different reefs!

Mayelin managed to culture some bacteria from reef seawater!

Today is also our last day with the current media team. We have enjoyed working with them and are sad to see them go. I also learned that it’s really hard to get interviewed on camera – lol!

That’s it for today! Thanks for following along!

Mayelin is making media so that she can culture microbes from the reef seawater.
Sunrise zodiac trip to collect hydrophones.
One of Tyler’s time-points ;).




Updates from Day 6 on the R/V Alucia!

Hey everyone,

Thanks for tuning in for another round of updates from somewhere south of Cuba ;).

We had quite a busy day of diving, sampling, and sample processing! At 8 am, our larger tender (one of the boats that we use to get to our dive sites) departed from the Alucia. It was packed full with divers, dive gear, diving cameras, boat tenders, boat drivers, and coolers.

We spent about an hour driving the boat to our dive site from the Alucia. Once we were anchored, all the divers descended. Amy and I assisted Viktor and Fredy by conducting benthic cover surveys of the reef. In these surveys,  we lay a 10m transect tape (otherwise called a measuring tape) across the reef. For every meter, we estimate and record the percent coverage of different benthic macro-organisms that help build the 3-D structure of the reef. We estimated the percent coverage for coral (hard and soft/octocorals) macroalgae, sand, rock/rubble, and sponges. Amy also collected some coral tissue samples and before we knew it, it was time to ascend for water sampling and a surface interval.

Amy and I jumped into another small boat (operated and owned by the Avalon diving company) to complete our water sampling at our dive site. Then we boated over to our other dive site (nearby) and completed water sampling there.

After water sampling, Amy and I jumped back onto our main boat, got geared up for diving, and descended. This site was closer to the fore-reef and had more coral cover! We completed some benthic coverage surveys, Amy collected some coral samples for Tyler’s incubation experiment, and I collected a sample that I will use to understand the chemistry of the reef seawater.

We arrived back to the boat around 1 pm and rushed inside the boat to eat a delicious lunch and refuel. Amy and I spent the next 6 hours processing our seawater samples and then an additional 2 hours cleaning all of our tubing! I managed to squeeze dinner and a sunset in there too! Oh, and some selfies with friends!

Thanks for reading! Another busy day tomorrow!

This is what solid phase extraction (SPE) looks like! I’m using vacuum filtration to pass filtered reef water through a special cartridge. This cartridge traps molecules and separates them from the seawater, allowing me to understand the chemical composition of the reef water!
Another sunset!
This is what a filter looks like when you pass 10 L of benthic reef water through it! We use filtering to separate the microbial cells from the seawater.
A WHOI group selfie (although we are missing our fearless leader, Amy!).We tried to get everyone’s face into the frame . . . I guess this will do!

Updates from Day 5 on the R/V Alucia- Science time!

Hey everyone,

After six days of travel, transit (I’m including flights to meet the boat), logistics, packing, and unpacking, we have finally started diving, collecting samples, and conducting science!

All of the science team and most of the crew were up bright and early this morning! Today also happens to be Kalina’s birthday! I woke up, walked downstairs, and saw balloons everywhere! The Alucia crew decorated the crew mess  with birthday decorations and even made a birthday crown for Kalina! They are so sweet and have truly helped make this day special for her!

The first group of divers (including myself) left the Alucia and boated over to our dive site at 8:00 am. Amy and I jumped into the water at 8: 33 am and dove to collect coral tissue samples and small volume seawater samples from two different species of coral. The current was very strong! To prevent ourselves from drifting far away from where our boat was anchored, we swam continuously into the current. We spent 43 minutes underwater and had a maximum depth of 34 feet (10.36 m).

We had to motor back to the Alucia to swap out tanks and we decided to scrap the second morning dive because of the choppy sea state and the strong current. Amy and I went back out to the dive site and collected seawater samples from the surface and from reef depth. Then we came back to the boat and I began processing our samples!

For the next two hours, I filtered seawater samples and preserved samples for flow cytometry, nutrient, and dissolved organic carbon analysis. I had a lighter sample load today (because of the second scrapped dive), so I was finished processing right in time for lunch! We had a delicious Mexican feast including: burritos, nachos, rice, beans, and a ridiculously delicious salad!

After lunch, the second group of divers departed the Alucia and I stayed back to finish cleaning up the lab and enter data into spreadsheets!

Before I knew it, it was time for dinner (which was – you guessed it – delicious!). The chefs even baked an epic homemade chocolate cake for Kalina and it was presented to her accompanied by a beautiful chorus of “Happy Birthday!” We ended the night with an incredibly fun salsa-dancing party and dancing tutorial session on the top deck of the boat.

We are preparing for another busy day of diving and sampling tomorrow! Wish us luck! I tried to upload pictures with this post, but it was taking way too long. See my other photos on Instagram and Twitter!

Thanks for reading!