Lab work

Get your optimism from the past

When we think about a “pristine” untouched ecosystem we often have a single, preconceived image in mind. It could be a grassland with thousands of bison, a thick tropical forest, or a coral reef teeming with fish and sharks. These places certainly existed, and in many cases are now lost or replaced by alternatives, but there has always been variation and not everywhere would fit into these limited boxes. There must always have been marginal ecosystems and vast amounts of variation.

It is this variation that we propose can help conservation. If we can describe that variation we can do a better job at placing modern ecosystems into context. In this paper, published in Conservation Biology, BaselineCaribbean members discuss our ideas of how the fossil record can be used to redefine what should be considered “pristine” and the positive benefits of doing so for conservation.

Open Access available

O’Dea, A., M. Dillon, E., H. Altieri, A. and L. Lepore, M. (2017), Look to the past for an optimistic future. Conservation Biology. doi:10.1111/cobi.12997

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DCIM105GOPRO

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Denticle side view

Some of the denticles that we find in the sediments are exceptionally well-preserved. Here is an example of a denticle that still possesses the basal plate that once held it to the underlying skin. In many cases, though, we only find the crown (the top part). This side view taken via scanning electron microscopy (SEM) can give you an idea of the three-dimensionality of a fully intact denticle. It almost looks like some strange sort of hat (which perhaps I will 3D-print, patent, and sell online if our funding runs out prematurely or is frozen by the government… just kidding).

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Some things you may notice about this denticle:

  • It has a very thick crown proportional to the crown length. While many fast swimming shark species have denticles that are thin and light, this denticle means business. Its thickness lends durability, forming a protective ‘armor’ around the shark. This type of denticle is generally found on sharks that live in close-association with the benthos.
  • The crown is positioned at a slight angle relative to the base. This angle can alter the way in which water flows over the denticle, thereby changing the hydrodynamics of the shark on a micro level. Some of the fastest swimming species are thought to be able to vary this angle through adjustments to the basal plate and skin tension (Raschi & Tabit 1992).

 

Literature cited

Raschi W, Tabit C (1992) Functional aspects of placoid scales: a review and update. Aust J Mar Freshw Res 43:123–147

Evidence of a nighttime visitor

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Scanning electron microscope image of a denticle extracted from the fossil reef in Bocas del Toro, Panama. 283x magnification.

Here is a denticle that I was not expecting to find. It belongs to a shark that I only on second thought included in my denticle reference collection, one that ought not belong on a coral reef. This appears to be the denticle of a crocodile shark (Pseudocarcharias kamoharai). While denticles can normally only be identified at the family level, this one fails to resemble any other denticle in my reference collection… except one. It looks almost identical to those that I isolated from the skin of a verified crocodile shark at the Smithsonian National Museum of Natural History (image below), except that it is a little smaller and much more weathered.

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Scanning electron microscope image of a denticle isolated from the body of a crocodile shark for inclusion in our reference collection. 185x magnification.

Not only are crocodile sharks unassociated with coral reefs – in fact they generally only ascend from the depths at night to feed – but this shark has not been documented in the region in which this denticle was found. What’s more amazing is that this denticle is not even modern. It was extracted from our  6,600-year-old fossil reef!

While you may have never heard of a crocodile shark, they are listed as ‘Near Threatened’ on the the International Union for Conservation of Nature (IUCN) Red List. We obviously need to learn more about this species of shark in order to better protect it.

Our finding suggests that crocodile sharks did occasionally venture onto the lagoonal reefs of Bocas del Toro, Panama in the past (and perhaps even in the present day as well). More importantly, to me, this denticle epitomizes the beauty of the technique. Extracting and analyzing dermal denticle assemblages can reveal the rare, cryptic, or ephemeral elasmobranch visitors on reefs, an otherwise very challenging task to accomplish.

Crocodile shark. Source: PIRO-NOAA Observer Program. Wikimedia commons.

 

The next installment of shark denticle photos is here!

Over the next several weeks, I’ll be showcasing scanning electron microscope (SEM) images of some of the denticles that we extracted from the modern and ~7,000-year-old fossil coral reefs in Bocas del Toro, Panama. While the SEM images that I released previously were from known species of sharks in my reference collection, the denticles that I’m about to show you came from sediment samples we collected and processed. Our job now is to become sleuths and figure out what types of shark shed them.

Like a portrait, these denticles can paint a picture of the sharks they came from. They are the bards of the sharks of lore, lost in the sands of time… Ok, that’s one massive cliché (and I might be a bit too obsessed with denticles), but you get the point. Denticle morphology can provide us with useful insight into the historical ecology of sharks. For example, a denticle’s thickness can reveal whether its owner lived in the crevices of a reef or up in the water column. Its ridges can tell us whether or not it was a fast swimmer, speed which it may have used to catch nimble prey or swim long distances.

Some denticles are better storytellers than others, however, so we need to figure out who is who. This is one of the more unusual denticles that I’ve found so far. What type of shark do you think it may have come from? Stay tuned for my interpretation.

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The third iteration of sediment processing

The sediment processing workshop will now resume in a new location: UC Santa Barbara. First things first, I had to transform the lab. Since the size of each sample was smaller, I could also downsize the set-up a bit and move everything indoors. This meant no more massive outdoor ‘drying bubbles’ or tent-covered mazes of 5-gal buckets for digesting sediments… at least for now. We did, however, order 100 gallons of acetic acid. What a lot of vinegar!

The funnest challenge was building the new drying oven from an old storage cabinet, several power strips, and a box full of incandescent light bulbs. Drilling through the metal cabinet to feed the cords through was by far the hardest part. Standard drill bits didn’t cut it, so I had to upgrade to a step drill bit. That worked like a charm, but it still took several hours of drilling. Once everything was installed, I turned on the power strips and basked in the glow for a moment. It was toasty – exactly as intended! When I did a test run the next morning, I was pleased to find that the sediment dried in under a day.

Now, we are just about ready to rock and roll…

Nicte-Ha’s farewell!

Earlier this year, the coral project was set. The research question was clear, the samples – the key to the question – were at hand, and I was making good progress. But the coral team had only one member: me. This was not great because I love working in teams and to learn new stuff. How best to learn if not by teaching?

Potential interns had shown interest in working in the lab. Not always, however, this works well for the intern or researchers. It is hard to find a good match. Then, a young woman emailed Aaron. Shortly after, she was standing in front of us. “Gosh! Nicte-Ha is very determined”, I initially thought. And she was.

On day one, Nicte-Ha said that she aimed to find a research job in Bocas del Toro. We were sitting hundreds of kilometers from Bocas, but for Nicte-Ha, we were pretty close. A few hours after she analyzed the last sample in our lab, she headed off to Bocas del Toro.

What do you think happened between day one and the last sample she analyzed? Success! That is what determined people consistently get. Just to name a few of her achievements, Nicte-Ha learned fast and taught others, analyzed hundreds of kilograms of coral samples, developed and presented a poster at a conference, and was actively engaged in the daily life and discussions of our scientific community. More than anything, she got a special place in everyone’s heart.

Thank you, Nicte-Ha. Today we see you leave, moving in the direction you chose. We are happy and proud.

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Nicte-Ha Muñoz presents a poster in APANAC.

Great news from the coral team!

The coral team has great news to share: one reef from Bocas del Toro may be a bright spot! This blog explains what a bright spot is, why it is important and where we may have found one.

Coral reefs are declining worldwide but not all of them are in bad shape. Bright spots are, among coral reefs, those reefs that are in better condition than expected given the environmental and socio-economic conditions they are exposed to (Cinner et al. 2016). If we can learn why bright spots are different, we may be able to improve degraded reefs. But first we need to identify bright spots! And we may have found one in Bocas del Toro, Panama.

To do this, we became time-travelers! We compared (fossil) reef corals that lived in Bocas del Toro around 7 000 years ago (figure 1a) with (subrecent) reefs corals that have lived here over the past few decades (figure 1b). We measured the amount and type of reef corals both in fossil and subrecent reefs. From this data we are learning how reefs changed since substantial human impact began.

Our preliminary results show that one reef from Bocas del Toro, Punta Caracol, is a potential bright spot. Compared to other subrecent reefs, Punta Caracol is exposed to similar environmental conditions and human pressures but it seems substantially healthier. In fact, it is almost identical to the pristine reefs that lived in the region 7 000 years ago.

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Figure 1. When fossil (a) and modern (b) reefs from Bocas del Toro are compared, Punta Caracol is outstanding, likely a bright spot. It is healthier than other subrecent reefs and similar to pristine reefs that lived in Bocas 7 000 years ago.

Our next step is to refine this exciting finding. We plan to precisely describe how Punta Caracol is special. For example,

  • What type of corals drive the difference between Punta Caracol and other subrecent reefs?
  • What are the key similarities between Punta Caracol and the pristine reefs that lived in Bocas del Toro 7 000 years ago?

We will let you know what we find out!

It’s Melisa’s farewell

Today we say farewell to Melisa! Because she has done great and has big plans ahead, we want to celebrate.

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Melisa never gets stuck (except this one time)!

During her three-month internship, Melisa was outstandingly productive. For example, she (a) identified over a hundred kilograms of tiny coral fragments, (b) planned a fieldtrip, (c) reviewed literature, (d) developed a guide and a reference collection to identify coral skeletons, (e) wrote an abstract and produced a conference poster, (f) presented interesting topics at multiple lab meetings, (g) attended to multiple scientific seminars and (h) organized the research collection of the coral team. And most importantly, Melisa connected personally with everyone she met. She is easy going, kind, and respectful.

But the semester starts soon so she has to go back to college. For her farewell, we gave Melisa a little present and took her out to lunch. The restaurant we chose was Napoli’s Restaurant and Pizzeria, a place that has hosted the special occasions of the O’Dea lab and its scientific family, including the legendary Tony Coats and Jeremy Jackson, over decades.

The coral team, the O’Dea lab and many others at the Smithsonian Tropical Research Institute will remember and miss her a lot. Because she is smart, positive and hard working, Melisa will never hit a roof. So I am confident this is only the beginning of something even bigger and better.

Melisa, we wish you the best because you deserve it!

Yamilla Samara reflects

The first big experience I had as a marine biology student was being an intern as part of a scientific investigation at the Smithsonian Tropical Research Institute in Panama. I had the opportunity to help Erin Dillon with her project by processing sediment samples for dermal denticles. During the past three months, I learned a lot about shark dermal denticles’ morphology and physiology. I also practiced the methods to process marine sediment (washing, drying, digestion, peroxide, and picking) in order to collect the denticles from each sample. The skills I developed through this internship helped me comprehend what lab work is like, how long the procedure can be, and how patient a scientist has to be in order to collect data and get results. In the end, I gained priceless knowledge, and helping Erin was another experience that confirmed my passion for marine life.

-Yamilla Samara

What’s next for Yamilla?: Yamilla is now headed to Florida International University as a transfer student to continue pursuing her studies in marine biology. She’s very excited to take upper division classes, explore the multitude of topics within the field of marine science, and further refine her interests.

How to find a denticle

How do we move from the residue remaining after a round of acid digestions to an isolated denticle ready for measurement and identification? It’s not as easy as it sounds.

As I peered down through the ocular of my microscope at the diverse array of particles illuminated by the bright light above, I spotted countless sponge spicules (minuscule glassy spears that compose their porous skeletons), fish teeth, bone fragments, otoliths (fish ear bones), and the occasional strand of organic material or remnant chunk of calcium carbonate. These stood out against the black gridded background of my metal picking dish, recounting the history of the menagerie of creatures that left their mark on this particular patch of sediment before it was collected from the reef. Paintbrush in hand, I was ready to begin. However, I would be painting no masterpieces today.

I spread a small scoop – maybe equivalent to the size of a pinch of salt – of my sediment sample out over the area of the picking dish, trying to evenly distribute it and produce a single layer of particles. Now came the fun yet tedious part. I began to manually brush through the particles, visually scanning them with care in hopes that a denticle would catch my eye. Each time I found one, a little flurry of excitement would well up within me and I would suddenly feel like I had the endurance to pick for five more hours (as well as the inspiration to write a blog post). It’s a seemingly endless treasure hunt, but my tiny yet precious haul of denticles validates every minute of the search.

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Creating an acid digestion ‘factory’

While sieving the bulk bags of sediment allows us to constrain the particle sizes that we eventually pick for denticles, we are still left with around 260kg of sediment to work with. This is an enormous task, perhaps impossible. However, with acetic acid, we can make it feasible. Our samples are largely composed of coral and shell (calcium carbonate). These react with acetic acid to produce water, CO2, and calcium acetate, therefore eliminating the carbonate. This reaction can remove up to 99% of the sample weight, leaving behind just pieces of rock and resistant microfossils such as bone, teeth, denticles, and sponge spicules that we are interested in studying.

Our samples are so large that we’ve built a processing ‘factory’ outside the lab, where the sediment can react with acid and bubble off CO2 without ventilation issues or space limitations. Each size fraction is placed in a five gallon bucket, and acid rinses (10% acetic acid) are added daily over the course of about a week and a half. A little over 300L of 100% acetic acid is required to complete the digestion of the 65 bulk bags we collected in the Dominican Republic. That’s a lot of acid! We can also process 39 size fractions, or 13 bulk bags, simultaneously, which is 11 bulk bags more than what I was able to digest in the past using just the fume hood in the lab. This has cut the total digestion time down by months.

While this step requires a large quantity of acid to complete, it is crucial, as it turns the task of finding a needle in a haystack into the task of finding a needle in a small sprinkling of hay. Denticles are sparse in the sediment samples, but digesting away the calcium carbonate makes it possible for us to find them and reveal their secrets.