Has it really been that long? Well, I’ve been busy.
The preparations of the last few months have now been tested in the field. I am returning from the first two weeks of a five week field study in Bahia de los Angeles in Baja California. As I think I posted earlier (apologies if I did not), the plan for the summer was to work with Ocean Discovery Institute on fleshing out some of the details of the life history and behavior of Elysia diomedea in Bahia de los Angeles. Specifically, we want to know more about where they are found in the bay, what they eat, and how they respond to light. This information will help us to understand more about the role of kleptoplasty, along with the significance of the dramatic population fluctuations of the slugs documented previously by Hans Bertsch.
Even before we left, there were several challenges. For example, for the project to get off the ground we needed permission from CONANP, the agency that oversees the marine reserve, to collect Elysia from the bay. Months before the project began, we submitted an application for a permit to allow us to collect and study Elysia. Unfortunately, that permit was rejected because we had not been clear about the relationship between the Elysia project and ongoing research in the bay islands. Naturally, this caused us significant anxiety. After a lot of work behind the scenes by folks at Ocean Discovery and by my very good friend Drew Talley at USD, our intentions were made clear, and we were given permission to go ahead with the project.
Among the items that were absolutely necessary were aquaria for holding, observing and testing the slugs’ response to light. In April, I had started working with a local company that builds custom aquaria to build two holding/observation tanks and two “I-mazes” for testing light preference. By early June, the tanks had not materialized, and I was beginning to get nervous that missed deadlines and excuses would continue until time ran out. I decided to go with a more experienced vendor, Glass Cages, and they got the tanks into production and had them air freighted to San Diego in plenty of time. The whole process of working with them was pleasant and reassuring.
The other critical pieces for extracting and amplifying DNA are a microcentrifuge and a PCR thermal cycler. Again, thanks to the persistence of Drew Talley, we borrowed an Eppendorf centrifuge from USD, and received the loan of a demonstration model thermal cycler from Thermo Fisher Scientific.
So, after months of planning, spending a semester making sure that the methods work, arranging for care of the system in Maryland while I was gone, and enjoying a roller coaster ride obtaining permissions and equipment, it was time to get into the field.
The trip down was slightly adventurous. We traveled with the Ocean Discovery students, starting out at Hoover High School in City Heights. This year, we took the eastern route, through Mexicali and San Felipe. It was a little longer, but somewhat more scenic, and had a whole lot less traffic. The road was not great in spots, and one of the vans developed a flat tire along the way. After a little delay, we were back on our way, and arrived in the early evening.
As always, I was very happy to be there. Its hard to think of a place that I would rather be. The sea is beautiful and full of life, and the surrounding desert is spectacular in its own right. Over the course of the two weeks at the station, I tried my best to savor the views, sounds and smells.
Naturally, I was eager to get started. It was all I could do to sit still during review of procedures around the field station, because I was eager to collect slugs in order to be ready for the students’ upcoming projects. Finally, I got into the water, and began to hunt for Elysia. It was wonderful to be in the bay again, and there was lots to see. The familiar zones of Padina, Codium, Ulva, and the many other algae on the rocks outside the station reminded me of where I thought I should look. After about 1 ½ hours of unsuccessful searching, I headed back to the station to get ready for the rest of my day.
I got to meet my crew in person for the first time. The five young women were full of energy, and ready to get going with the project. The goals of the “Photobiology” group (I needed a somewhat official sounding name, sue me) will be to flesh out some basic biology of E. diomedea here in the bay. As we did for E. clarki in Maryland, we want to extract DNA from E. diomedea, and compare the sequence of rbcL in kleptoplasts with those from potential food plants. Also, we will be looking at light preferences, using “I-mazes,” which give the slugs a chance to select their favorite light intensity. We are also hoping to have a chance to explore the bay, surveying for appropriate habitat and the presence of slugs. Lots to do to get set up and get the students trained.
The hunt for Elysia continued during the morning of our first full research day. In the past, the morning hours have been the most productive in terms of slug hunting, so I had planned several mornings during the first week for collection. The crew was becoming very proficient in the water, and we hunted for about 90 minutes in the shallows in front of the station. Sadly, despite our efforts, no Elysia were to be found. After a quick cleanup, we headed for the classroom for a briefing on algal diversity, lab equipment and safety before lunch. The students had other activities in the afternoon, which gave me the opportunity to continue setting up tanks and equipment.
Our “molecular lab” is located in the garage, along with equipment for other Directed Research groups. We share the space with a group studying ways of reducing bycatch of unwanted fish species and turtles, and another group that documents the flow of energy between the rich waters of the sea and the relatively barren land of the bay islands. The space is a hive of activity at 7 am, when the other groups are rushing to get on boats. After that the space is essentially ours until lunchtime.
The other part of our “lab” consists of the observation tanks. These are in another part of the station containing the kitchen and computer lab. The 16” cube tanks sit on a sturdy table, with circulation provided by air pumps, and lighting provided by morning sunlight supplemented by desk lamps with full-spectrum LED bulbs. Once the slugs are in, the tanks hold slugs for DNA extraction and behavioral assays, with one being used solely for observation of the daily rhythms of undisturbed slugs.
Although we had not found any Elysia, at least a dozen small Aplysia rode into the tank with the plants. This will actually be handy for comparison with the responses of Elysia to light. Aplysia do not store chloroplasts, and might be expected to be repelled or indifferent to light.
Day 2 was reserved for a field trip for the students. It is supposed to be a non-work day, used to introduce the students to some aspect of the bay. It started off great, with a visit to a sea lion colony, and up close encounters with very large fin whales.
We did squeeze in a little work, because part of the trip involved time for snorkeling at Coronadito island, at the far north end of the bay, and we were not explicitly banned from looking for Elysia. Although we did not find any, it was useful to note and photograph the nature of the bottom, and the dominant algae species that were present. Lots of Sargassum, some turfy coralline algae, but not a lot of large green algae.
The days continued, with more briefings about identification of algae and molecular biology methods. The big question was whether we would actually find any Elysia. Fieldwork always requires some improvisation, but it’s a real challenge to improvise your way around the absence of your research subject. Stay tuned.
The project seems to be where it needs to be. Since the last post, I ordered new “degenerate” primers, which consist of a mix of almost all possible sequences that would match the rbcL gene of the algae of interest. The folks at Midland Certified Reagent Co. were very helpful, and the primers arrived quickly.
As can be seen below, we get a much more robust signal from the presumed Avrainvillea with the new primers. There was, however, no signal for Bryopsis species 1. Because that batch of DNA consistently amplified in the past, I am going to attribute the failure to technical issues for the moment.
As was true for the previous run, the lane for Elysia clarki still had no signal. The repeated failure to get a PCR product from this extract suggests that it is not a simple technical glitch. The obvious culprit is mucus. Even though we used a small amount of tissue, it produced copious mucus, some of which may have remained in the sample after purification. The polysaccharides in mucus are expected to interfere with the PCR reaction, so that could be our problem.
Because his lab group has successfully extracted and sequenced DNA from Elysia species, I contacted Gregor Christa from Heinrich-Heine Universität Düsseldorf. He suggested a very simple fix: dilute the DNA template. It seemed too easy, but I performed another run yesterday, and, lo and behold, it worked! The undiluted DNA (& mucus) gave no signal, but the diluted DNA amplified nicely. I guess the dilution reduced the concentration of mucus enough to allow the reaction to proceed, while the sensitivity of the PCR reaction allowed amplification of the diluted DNA.
Everything seems to be on track. The next step is to send some of our PCR products out for sequencing, hopefully within the next few days.
The subject of this year’s Journal Club (Has it really been over a year? Oh dear.) is a paper by Gregor Christa and colleagues from back in 2013.
In this paper, the authors try to develop a scientifically rigorous explanation for long-term retention (LTR) of chloroplasts in Plakobranchus and Elysia.
Some species of marine slugs in the Plakobranchoidea, which includes the genera Elysia and Plakobranchus, can store chloroplasts for many months. These are stored in branches of the digestive system that ramify throughout the slugs’ bodies. Perhaps foreshadowing their conclusions, Christa et al. refer to this phenomenon as delayed digestion, rather than maintenance of the chloroplasts.
So what do the food-derived chloroplasts (“kleptoplasts”) do for these months? In 1975*, Trench found that Elysia viridis could incorporate 14C from labeled CO2 into its tissues, and concluded that kleptoplasts retained the ability to generate sugars from light, water and CO2. Based on this observation, he coined the term “leaves that crawl” to indicate that he believed the kleptoplasts generated energy for the slugs and made them partially or totally independent of the need for ingested food. This idea took hold, both in the scientific literature and in the popular imagination.
There were a few complications in this story, however.
First, how are functional kleptoplasts maintained for such a long period outside of a plant cell? A functioning organelle needs a constant supply of new proteins to replace those that are degraded with time and use. Although chloroplasts retain a small number of genes (including rbcL, which is important for the kleptoplast identification project), the vast majority of genes required for their continued function are located in the nucleus of plant itself. That is a problem, because the plakobranchids rapidly digest the nuclei of the algae on which they feed.
The problem appeared to be solved, and in an interesting way, when reports appeared that suggested the slugs had incorporated algal genes into their own genomes, a phenomenon called “lateral gene transfer,” or “horizontal transfer of genes.” Newly-synthesized algal RNAs and proteins were identified in slugs (reviewed in Pierce et al., 2007). However, the absence of algal gene products in eggs or newly settled slugs (Bhattacharya et al., 2013), and the relative scarcity of chloroplast RNAs and proteins in slugs, indicates that lateral transfer is unlikely to have occurred. It seems unlikely that kleptoplasts could be self-sustaining in the long term.
Another issue is that animals are capable of incorporating small amounts of CO2 into organic molecules, through carboxylation reactions. This being the case, how do we interpret Trench’s results of 14C incorporation into E. viridis?
Furthermore, starved plakobranchids (the shorthand term Christa et al. use for Elysia and Plakobranchus) do not stay fat and happy if they are provided with light. They shrink, and change color from green to yellow, which indicates that they are breaking down their tissues and the kleptoplasts, in order to survive.
Back to the original question: what is the purpose of storing kleptoplasts? Christa et al., asked two very basic questions about the role of kleptoplasts, using E. timida and Plakobranchus ocellatus.
The answer to Question 1, was an emphatic “yes, 14CO2 incorporation is much higher in the light.” As shown in Figure 2, below, both E. timida and P. ocellatus showed significant incorporation in the light at 60 and 120 minutes, but essentially none in the dark. Incorporation was also significantly reduced by monolinuron, which blocks photosynthesis.
So, it appears that the kleptoplasts fix carbon, which should provide energy to the slugs. Does this keep the slugs from starving?
This brings us to question 2. The authors examined two aspects of starvation to determine how the different conditions affected the ability to photosynthesize and maintenance of body weight.
First, they looked at what happens to chlorophyll function during starvation using Pulse Amplitude Modulated (PAM) Fluorimetry. The authors suggest that those kept under more intense light declined more rapidly, but the sample sizes were small and the variation was large, so the strongest conclusion one can safely make is that quantum yield (their measure of photosynthetic function) decreased significantly with starvation.
Perhaps the most interesting result was that exposure to light made no difference in terms of weight loss. Figure 4b, below, shows that all slugs, regardless of whether they were in light, darkness or treated with monolinuron, lost about the same amount of weight over 50 days.
Again, the sample sizes were tiny (two slugs each), so sweeping conclusions are not in order. However, the shapes of the curves are intriguing. The slugs in the light seemed to decline more rapidly than those in the dark, and the monolinuron treated slugs both showed a rapid decline followed by more gradual weight loss. It would be interesting to know if there was interesting biology underlying these results (slugs burn through reserves faster in the light?), or whether they are quirks of a small sample.
Christa et al. conclude that the slugs are not photoautotrophic, i.e., they do not survive on light. Instead they propose that the kleptoplasts are a food reserve. This is certainly a plausible model, but others have not yet been ruled out.
For example, the authors suggest that the kleptoplasts could be required for the biosynthesis of compounds required for development or egg production. One potentially interesting, and relatively straighforward, experiment would be to compare rates of egg laying between Elysia that are fed, but kept under high- and low-light conditions. Given the metabolic demands of producing and provisioning egg masses, it would be interesting to see if kleptoplasty contributes to the process.
Another possibility is that the kleptoplasts help to “fatten up” the slugs before starvation. In this scenario, slugs use both food and photosynthesis to fill storage tissues when times are good. When food is scarce, or experimenters starve them, they use the kleptoplasts and stored tissue to produce energy and necessary metabolites. This may be especially important for species that live on scattered or sparse food sources. I don’t think anyone has done the math to determine how the energy estimated to be produced by photosynthesis (e.g., the amount of carbon fixed per unit time by the slugs in the light) compares with the metabolic demands of the slug. It may be too small to keep a starving slug alive, but might help fatten up a feeding slug.
One final random thought regards the maintenance of kleptoplasts. It is pretty clear that the slug does not have the genetic equipment to produce the proteins required for the upkeep of the chloroplasts. However, plakobranchids (at least the E. clarki watching me here in my office) eat prodigious amounts of algae daily. Would it be possible for ingested algal RNAs and proteins to find their way to the kleptoplasts? It seems like a non-trivial problem to get the materials across a few membranes and into the plastids, but it would help to explain how chloroplasts can survive for months in cells that are lacking important equipment.
*note that all the references can be found in the full list of papers.
We made our first try at extrtacting and amplifying DNA from kleptoplasts. It was relatively straightforward to get the tissue from the slug. First, she was “relaxed” with isotonic MgCl2, which blocked synaptic transmission and paralyzed and anesthetized her.
Then, a small piece of parapodium was removed (see her left side, at bottom). DNA was extracted using the same method as for the plants.
In case you were worried, she was fine the next day.
We also tried a new species of algae, which I am calling Avrainvillea. It may be Rhiphilia, I’m not completely certain.
Unfortunately, the amplification was not a success this time around. The positive control samples, DNA extracted from Bryopsis during previous sessions, worked well. “Avrainvillea” showed a much weaker signal, and there was no signal from the slug extract.
A number of things may have gone wrong. The slug sample was extremely slimy with mucus, and those polysaccharides could have interfered with extraction or amplification. Also, the Bryopsis-specific primers may not have annealed adequately with the DNA from Avrainvillea and whatever is in the slug.
Now that things are calming down after the semester, I am going to try again, making a few changes. Most importantly, I have ordered “degenerate” primers, which contain a mix of sequences that will complement just about any algal sequence. Still waiting on tips regarding the slime.
It has definitely been a good week for the Solar Slug Project. Yesterday, all of the pieces for the barcoding project started to fall into place. As I described a few weeks ago, the idea is to use a sensitive method called polymerase chain reaction (PCR) to amplify DNA from chloroplasts within the slugs in order to figure out what they have been eating. Our first step was to extract and amplify DNA from potential food plants, just to be certain everything was working. Below, you can see Maryam and Haseeb, the two USG students who have been working on this project, diligently extracting DNA from Halimeda and Bryopsis samples.
After a few false starts, we got conditions to the point that everything appears to be working. One key change was switching to GE Healthcare’s “Ready-To-Go” beads as the source of polymerase, buffers, nucleotides, etc. The beads can be stored at room temperature (as opposed to being frozen, like other “master mixes”), which will make life a lot easier at the field station.
The PCR products are the right size (about 600 base pairs), and there aren’t any extra bands. We used primers specific to Halimeda discoidea (“H primers”) for the products in the first four lanes, and primers for Bryopsis plumosa (“B primers”) for the last four. The species names, “Halimeda 1″ etc, indicate the following species:
Halimeda 1 (Presumed H. discoidea).
The specimen of Halimeda 2 (H. incrassata) was a bit bleached, but yielded some nice DNA
Bryopsis “species 1” has a much finer structure.
Bryopsis 2 is stouter and longer. It is unlikely to be a different growth form of the same species, because they were cultured right next to each other. It’s a good opportunity to let the gene sequences unravel who’s who.
The astute observer will notice that we got products from (almost) all species using both sets of primers. Overall, that’s a good thing, in that we can use these primers to amplify DNA from many species of algae, then submit the DNA for sequencing. On the other hand, we could use more stringent conditions (like a higher annealing temperature, for those who care about such details) to use primers to amplify DNA only from a particular species. For example, we could use Bryopsis primers on DNA extracted from slugs to ask specifically whether the animals contain Bryopsis DNA.
The quick summary is that we have worked out the details of methods needed to extract, amplify, and ultimately sequence DNA from chloroplasts. Haseeb and Maryam will be able to put together some nice reports about their work, and in Bahia de los Angeles this summer, we should be able to determine the species of algae that E. diomedea eats.
In the “one reefer’s pestilence is a slug’s tasty snack” department, Marcos from Exotic Reef Creations sent over a batch of rock and zoanthids and live rock that were covered with lush Bryopsis growth. Although the dedicated algae tanks have helped keep the supply up, I was very excited to receive the new infusion. The gals are over the moon about it. The photos below show the whole gang hunkered down in feeding posture. They have been face down in it for almost 24 hours now.
The goal is to have them clear the algae so the corals can go back home. It will be interesting to see how long that takes.
Meantime, the molecular experiments are moving along. More soon.
Decisions have been made, orders have been placed, and materials have arrived. It turns out that we are treading a relatively well-worn path of DNA bar-coding. The goal for the semester is to extract, amplify and sequence the rbcL gene for the candidate food plants and the chloroplasts maintained by the slugs. Because rbcL encodes a component of the photosynthetic complex of the chloroplast, and the gene is found in the genome of the chloroplast (rather than the nucleus of the plant), the origin of the chloroplasts that the slugs are carrying can be identified on the basis of the sequence of the gene. Fortunately for us, the sequence of the rbcL gene has been studied by a lot of people. The chloroplasts of all plants have it, but it varies a little from one species to another. That variation can be used to examine how closely related different species are, or to determine if two populations that resemble one another are actually different species. Each species has a unique sequence or “bar code,” that can be used to identify it, and to distinguish it from other species.
Therefore, much of the work has been done for us. Kits, such as the one in the above photo, are readily available, procedures are largely worked out for amplifying the amount of DNA using polymerase chain reaction (although the primers for these algae may be a little tricky), and there are companies such as GeneWiz that provide a relatively inexpensive and simple resource for sequencing the resulting DNA. Makes a nice change after a career spent soldering and tweaking in order to perform experiments using arcane methods.
On your next visit, you may find a photo of DNA bands on an agarose gel. Or maybe something else.
The trip to Bonaire ended too soon. Six days of dives, with a bonus of kayaking and snorkeling in the mangroves on our no-dive day. The best slug-watching happened in the first few days.
The site with the highest slug count this year was Jeff Davis Memorial (named for the physician, not the Confederate leader). It is usually a favorite of ours, but this year seemed to have more dead coral than usual. On the positive side, we easily found at least a dozen E. crispata among the rubble.
The blue of this one was so intense, it jumped out from many feet away. The camera did not really capture the intensity.
The slug below was more acrobatic than most. The average E. crispata just sits there, or moves along gracefully, but this gal seemed to have somewhere to go. Eventually she fell off, and found herself in a new spot.
We also got a chance to explore the mangroves on the east side of the island. Although no actual Elysia were found this year, the conditions look good. For example, the clump of Halimeda and Caulerpa below would be a great place to find E. tuca, among other species. Maybe next year?
The sponges, tunicates and hydroids, like those below, would also be excellent places to hunt for nudibranchs.
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