Category: Biology

The Biodiversity Collections Crisis

On By Dan KillamIn Biology1 Comment

You might be familiar with the concept of the present “biodiversity crisis“. There is an increasing consensus in the ecological research community that the current loss of species this planet is experiencing is not sustainable, in the sense that the loss of some species may precipitate the loss of more, in an accelerating spiral. The paleontological community has found that the pattern of species loss is unusual even at the scale of geological time, potentially placing us among the great extinctions in geologic history, or at least a notably bad extinction event. A less diverse biosphere means the loss of ecosystem services associated with all of the species we lose, and potentially a less resilient biosphere, stacking the deck against us as the climate continues to change and life is forced to adapt. Because our global civilization depends on the wealth of the biosphere for our own well-being, this is definitely very bad news for humanity (I usually tend to avoid rationalizing conservation based on ecosystems’ value to us, believing that we have a moral imperative to preserve the biosphere, and organisms have an inherent right to exist outside of their economic value, but that’s a topic for another blog).

We are only aware of the loss of species due to centuries of careful collecting, cataloging, categorization and curation undertaken by conservationists around the world, including indigenous communities, museum professionals, taxonomists, seed banks, herbaria, and other very highly specialized and educated people. I won’t refer to these biodiversity experts as “countless”, because they’re actually a pretty small group of folks entrusted with an almost incomprehensible responsibility: to quantify the biological wealth of our world. They figure out when baselines are shifting, and their work keeps us accountable as we seek to stop the current bleeding of biodiversity.

I am writing this post because biological collections are having a moment of attention, and it’s been a topic I have been thinking of for some time as an outsider. Duke University recently announced that they will be throwing out their herbarium, an archive of plant samples which is one of the leading such collections in the US. The herbarium supports a vibrant ecosystem of research on the classification of plants, and is an important archive of plant diversity. Duke University, which has an endowment of $11 billion, claiming to not have the resources to support this archive is an unacceptable dereliction of their duty to preserve and nurture knowledge. And sadly, this closure of such an important collection is not a one-off event. Worldwide, taxonomist and curator jobs are declining. These are the people who spend decades learning how to tell one species of snail from another based on their genitalia. They discover cryptic species in collections. They prevent collections from degrading due to improper preservation, and charge in to save samples from fires. They process loans and when someone like me is belated in returning samples, they write a polite email reminding me to send samples back. When these people leave science, their skills can’t be easily replaced. If collections are lost, they literally can’t be replaced.

I am a biogeochemist, and not a museum worker by any means, but so much of my work has relied on biological archives. But by my count, 3/4 of my ongoing projects have used biological collections in some way. I wanted to list out some of the ways that biological collections have enabled my research, because I don’t think I’m unusual. Biodiversity curators are the keystone species in a vast ecosystem of interconnected research that wouldn’t happen without the hard work of maintaining collections. Please do what you can to protect biodiversity collections, whether by pressuring your representatives, your alma maters, and through donations.

Projects that relied on curators:

  • Some of my most influential educational experiences relied on teaching collections, including at Cabrillo Marine Aquarium, USC, LA Museum of Natural History, UC Santa Cruz and elsewhere. Without collections to get my hands on in lab exercises and other educational opportunities, my skills in ecology, organism ID and more would be greatly diminished.
  • My second PhD chapter relied on samples of well-preserved Jurassic lithiotid bivalves which came from outcrops which mostly no longer exist, having been quarried out or already sampled. These were loaned by curators at the University of Padova and University of Verona Natural History Museums
  • My third and fourth PhD chapters, and one of my postdoctoral papers used shells of giant clams that were stored at the Hebrew University of Jerusalem Natural History Museum. These shells had been confiscated from poachers at the Egypt-Israel border and were loaned to me by curator Henk Mienis. I would rather these clams be still alive in the Red Sea, but at least we were able to use these for a series of papers about their ecology and physiology.
  • Before my PhD fieldwork in Israel, I visited the California Academy of Science collection to view shells of Red Sea giant clams and practice species ID using a taxonomic key. I would also note that one of the species I have studied, Tridacna squamosina, is named because of the work of museum curators at University of Vienna.
  • Another postdoctoral paper (in progress) on violet bittersweet clams from the Eastern Mediterranean made use of preserved samples collected during research cruises off the coast of Israel in the 1960s-1980s. These specimens, loaned by the Steinhardt Museum in Tel Aviv, represent some of the last observed live violet bittersweets seen off of Israel. They since have (likely) gone extinct in the region, probably due to sediment changes in the late 1980s following the construction of the Aswan Dam.
  • Yet another postdoctoral paper in progress resulted from study of the growth and chemistry of shells of wavy turban shells loaned from the Santa Barbara Museum of Natural History, which we were comparing to individuals that grew in the hot waters of the Biosphere 2 tropical reef ocean tank. I met the curator Vanessa Delnavaz at the Southern California Union of Malacologists 2021 meeting, which was hosted by the museum. Museums are important centers of scientific organization and networking in addition to the value of their collections!

So I hope all of these anecdotes help make clear that biological collections are absolutely vital to enable an entire universe of research, and that we often can’t possibly predict what collections are going to be useful for which scientific purposes until long after the samples were preserved. So any budgetary bean-counters (not talking about bean taxonomists) should think twice before closing any collections! This is a core responsibility of academic institutions and we cannot allow any of these collections to be lost. Fund your local biological curators! Without their hard work, we’d be flying blind in the current biodiversity crisis. They’re the heroes we need, and that our earth deserves.

Research Explainer: How giant clams record their diet in their shells

On By Dan KillamIn Biology, Chemistry, clams, scicomm1 Comment
Two giant clams near Eilat in the Northern Red Sea. To the left is the small giant clam, Tridacna maxima, and to the right is a mature individual of the rare endemic giant clam Tridacna squamosina, only found in the Northern Red Sea.

You are what you eat, and clams are too. We’re made of atoms, which come in “flavors” called isotopes, relating back to the mass of the atoms themselves (how many protons and neutrons they have). Nitrogen, for example, comes in two stable (non-radioactive) forms called nitrogen-14 and nitrogen-15. Much like scientists can track the composition of a person’s diet from the isotopes of their hair, researchers have used the isotopes of clams to figure out their diet.

Nitrogen isotopes provide us with a useful and detailed record of food webs. Plants and algae tend to have more of the light isotope of nitrogen in their tissues than the animals that eat them (primary consumers), and the animals that eat those animals have even higher nitrogen isotope values. We can measure the amount of “heavy” atoms of nitrogen with a unit called δ¹⁵N (“delta 15 N”). A carnivore at the top of the food chain will have a very high δ¹⁵N, while plants will be the lowest. Clams, typically being filter feeders, will usually have an intermediate value, since they’re eating a lot of phytoplankton (tiny microscopic floating algae) and zooplankton (animal plankton that eat other plankton).

But I study a special kind of clam, the giant clams, which have a cheat code enabling them to become giant: they have algae *inside* of their bodies. The algae make food using photosynthesis and share it with their hosts! In exchange, the clams provide the algae with a stable environment free of predators, plenty of fertilizer in the form of their own waste, and even channel extra light to help the symbionts grow faster. This partnership is called photosymbiosis, and is pretty rare in clams, though it is common in other animals like the corals that build the reefs where giant clams are found! Previous researchers have shown that giant clams have very low nitrogen isotopic values in their tissue, like a plant, because they get most of their nutrition from the algae, rather than filter feeding.

I am a sclerochronologist. That means I study the hard parts of animals, in this case the shells of bivalves. Like the rings of tree, bivalves make growth lines in their shells which can serve as a diary of their lives. Some of my past work has looked at using chemistry of the growth lines of giant clams to measure the temperatures they grow at, compare the growth of ancient and modern clams, and even look at how much the clams grow in a day! Today though, I’m talking about my most recent paper, which looks at how we can use the shells of giant clams as a food diary.

But when they’re babies, the symbiosis in giant clams is not yet fully developed. During this early period of their lives, giant clams actually get more of their nutrition from filter-feeding like a “normal” non-photosymbiotic clam, until they’ve had a chance to grow in surface area and become a living solar panel. Like all bivalves, the shells of giant clams are made of calcium carbonate, bound together by a protein scaffold we call the shell organic matrix. Proteins are made of amino acids, which contain nitrogen! If we can get the nitrogen out of the shell from the early part of the clam’s life, and compare it to the nitrogen at the end of the clam’s life, it might record the clam’s transition from filter feeding to its mature plant-like lifestyle! If our hypothesis holds, we should record a decrease through its life in the shell δ¹⁵N values.

A model I made of the clams’ nitrogen intake, with the left plot how they switch from filter feeding to getting most of their nitrogen from dissolved sources around 5-6 years of age. Because the nitrogen isotopes of those two sources are different, that manifests in the expected values from the clam’s body (the right plot)!
A map made by my talented partner, Dana Shultz!

So I gathered a team of talented collaborators and set out to test that hypothesis, using giant clam shells that I was able to get on loan from the Hebrew University of Jerusalem Museum. These shells had been confiscated from poachers at the Egypt-Israel border. While I would have rather known these clams were still alive in the waters of the Northern Red Sea, being able to use them for research to understand the biology of their species was the next best thing! I had originally planned on pursuing a postdoc undertaking this project with Rowan Martindale, a professor at UT Austin who has studied the nitrogen isotopes of photosymbiotic corals, but when I started up at Biosphere 2, we ended up continuing with the project anyway as a collaboration! We measured the nitrogen isotopes of the shell material in the lab of Christopher Junium, a professor at Syracuse University, who has developed an exquisitely sensitive method to measure the nitrogen from shell material by essentially burning the shell powder and then scrubbing out unwanted material to isolate the nitrogen, to measure the isotopes in a machine called a mass spectrometer. Katelyn Gray is a specialist in isotopes of biominerals and assisted with drilling out powder from the shells with a Dremel. Shibajyoti Das, now at NOAA, is a specialist in measuring the shell nitrogen isotopes of other bivalves and he was master at doing much of the mass spectrometer work, and assisting in interpretation. Adina Paytan is a professor at UC Santa Cruz. She first provided the funding and support for me to go to the Gulf of Aqaba and collect these shells as part of an NSF-funded student research expedition! She also provided environmental data which helped us to interpret what the clams were actually eating!

A figure showing the four shells we sampled from, with the sampling areas in each hinge area showing colored and matching with the corresponding isotope plot to the right (colored points). 3 of the 4 shells show declines in isotope values with age. Shaded ribbon behind the data shows the model output.

So what did our crack team of scientists find out? We found that three of the four tested giant clams did indeed measure a decline in nitrogen isotopes over the course of their lives. Their earliest growth lines in the hinge areas of their shells record elevated δ¹⁵N values similar to other filter-feeders from the region. But as they aged, their later growth lines show much lower δ¹⁵N values, more like photosymbiotic corals and plants from the region. So clams indeed recorded the transition in nutrition as they became solar-powered! This degree and directionality of change in nitrogen isotopes was much greater than has been observed in any other clams measured in this way, which made sense considering their unique physiology. The clams have another area of the shell, the outer shell layer, which is closer to the symbionts than the hinge area. In this outer shell area, we did not observe much of a consistent trend in nitrogen isotopes. It’s likely that the outer layer is highly influenced by the photosymbionts even at the earliest stages of life.

Growth lines in the hinge area of two of the shells lit from behind, with the drilled areas for this study visible as well. The outer shell layer is the opaque and was also sampled for this study.

There was one clam that differed from the others in showing low δ¹⁵N values through life in its hinge shell layer. To help explain these differences, I created an independent model of the clams’ internal chemistry based on their growth rate, which slows as they age, and also is faster in the summer. When the clams are young filter feeders, they get most of their nitrogen from plankton, debris and other material floating in the water column making up floating material we call Particulate Organic Matter (POM). Meanwhile, when they are in their photosynthetic life stage, they get most of their nitrogen from nitrate, which is essentially Miracle Gro for the symbionts. The model showed that the clams should record a flip from filter feeding to photosynthesis around 4-5 years of age, which was confirmed by three of the shells! But what about the one that didn’t show this trend? My colleague Adina had fortunately measured the isotopes of POM and nitrate in different seasons in the Gulf of Aqaba. We found that in summer, as expected, POM δ¹⁵N is lower than nitrate. In the winter, meanwhile, that relationship is flipped! So if a clam grew more in winter, it would not record the same transition as was seen by the other clams. We think the clam that was the exception to the rule might have been more of a winter grower.

The chaotic nutrient environment of the Northern Red Sea, showing how in different seasons, dissolved nitrate has higher or lower δ¹⁵N values than the Particulate Organic Matter that the clams filter-feed on.

But long story short, we were able to demonstrate for the first time that giant clams show nitrogen isotopic values in their shells in line with expectations from their diet. Other clams have been measured this way, but the fact that we were able to conduct these analyses at all is a testament to the sensitivity of the elemental analyzer in Chris’s lab. Giant clams have *very* low concentrations of organic matter in their shells, so the forward march of technology was a major factor enabling this study to be possible.

Why does it matter that we can measure the transition of the clams from filter-feeding to photosymbiotic in their shell records? Well, giant clams are not the only bivalves which have photosymbionts. There are other clams in the fossil record which have been proposed to have had symbioses with algae, but until now we’ve never had a definitive geochemical way to measure this in fossils. We hope that this approach can be applied to the organic material in fossil shells, which is often well preserved, to see if huge clams in the Cretaceous and Jurassic had a similar way of life to the modern giant clams! If we can demonstrate that was the case, we can see how such species responded to past intervals of climate change, which will help us understand how giant clams will fare in the warming, acidifying ocean of the present.

These results also help explain the lives of giant clams themselves. We hope this kind of data can be used to measure the symbiotic development of giant clams in different places, with different types of food and nitrogen available, where we’d have the potential to measure pollution. Interestingly, the time that the model shows the clams transitioning to photosynthetic maturity is right around the time that they reach reproductive maturity (5-10 years of age). We’d like to investigate whether the time of clam maturity is controlled by the development of their symbiosis, which itself might relate to nutrients in the clams’ environment. If clams can grow faster, then they can mature faster, and potentially reproduce sooner in life. Will giant clams be able to thrive in the presence of increased nitrate, which is a common pollutant in coral reef environments? Like all worthwhile research projects, we have dozens of new questions to pursue as a result of this work, so stay tuned for the next installment in this journey of clam knowledge!

A coral, a worm and some clams walk into a bar…

On By Dan KillamIn Biology, clams1 Comment

The tree of life is often portrayed as a neatly branching structure, with each division point cleanly delineated and separated from its neighbors. The truth is that the various twigs of the tree of life often overlap and become tangled in a process we call symbiosis. I’ve talked about symbiosis before on this blog, which falls along a spectrum of wholesomeness. At one end we have mutualism, a partnership where both organisms benefit and achieve more than the sum of their parts. The other extreme is parasitism, when one organism benefits at the expense of the other. Between the two, there is a broad gray area including commensalism, when one organism’s presence doesn’t necessarily cost or benefit the other in any way. The tree of life is crowded and unpruned, and so sometimes the twigs might wrap around each other quietly and without much fuss. We live on a small planet, and have had to get used to living in uncomfortable intimacy with all sorts of creatures, such as the mites that are living on your eyelashes right now.

But things start to get really weird and tangled when the tree of life loops over on itself twice, or three times, or more. “Three-way” symbioses are surprisingly common, and the more you look for them, the more you realize that the tree of life is more of a knot than anything else.

A view of the Heteropsammia coral from the side

A recent paper from researchers in Bremen (Germany) and Saudi Arabia looked at such a three-way symbiosis between a coral, a worm and bivalves found off of Tanzania in East Africa. The relationship between solitary corals (Heteropsammia cochlea and Heterocyathus aequicostatus), a sipunculan worm (Aspidosiphon muelleri muelleri) and the clam Jousseaumiella, is a complex triangle of dependencies that had previously been noticed by other researchers, but never investigated at great depth. The worm lives with multiple tiny clams attached, all inside of a small solitary coral the size of a dime (1 cm long). Is the coral a willing host for this crowded boarding house, or has it been parasitized? Does the worm gain anything from the clams? The researchers sought to find out.

Part of the reason I enjoyed reading this study so much was that it had to take a narrative structure to describe the evolutionary ménage à trois of its focus. So much of modern science has moved away from anecdote to hard data, and while there is plenty of that to find in the study, it turns out that a lot of the study of symbiosis is storytelling. We need to know the setting and the characters.

In this case, the main characters are small solitary corals living in the tropical reefs of the Indo-Pacific. We denote them as solitary to distinguish them from their giant colony-forming compatriots that construct the coral reefs currently threatened by climate change and pollution. But like those giant reef-builders, these solitary corals get much of their food from sunlight through a mutualistic partnership with algae called Symbiodinium. The algae provide the host with sugars and other photosynthetic products, and the hosts give them nutrients and a safe cozy home in their tissue.

You might be thinking, “Wait! Dan just said this was a three-way partnership between a coral, a worm and some clams. So this is actually a four-way partnership between corals, worms, clams and algae?” You’d be exactly right. And I’m happy to say that the plot of this sordid story is about to thicken even further.

The side of the coral. See the little pores?

The Aspidosiphon worm is found in a spiral-shaped burrow inside of the skeleton of the coral. It is a pretty cozy home, with walls made of calcium carbonate by the coral, with breathing holes in the sides to allow the worm to breathe and release waste. The researchers wanted to know more about the structure of the burrow. Was it dug out by the worm using acid or an abrasive motion, like some clams use to dig into coral? So the researchers essentially gave the coral a CT scan to see its 3D internal structure. Inside they found growth features suggesting the coral grew around the worm, as if intentionally providing it a home.

Cross-sectional CT scans of the coral skeleton. In figure D, you can see the silhouette of the chambers of the snail shell where the worm made its first home!

Even more crazily, they found evidence that the worm had first settled inside an empty snail shell, like a hermit crab! The coral probably settled on a snail shell as a larva, and grew to engulf the whole snail shell, leaving growing space for the worm inside, with windows and all! So to review, this is now a five-way symbiosis between a dead snail, a worm that moved into its empty shell, the coral (powered by algae) that grew around it and encased the snail shell within its skeleton, and we haven’t even gotten to the clams. How many creatures are hiding stacked in this trench coat? Please bear with me as I explain!

An SEM image of Jousseaumiella. These are less than 1 mm long! Pinhead sized!

What are the clams doing in this picture? Jousseaumiella is part of a family of clams called Galeommatidae, which we previously mentioned on this blog in the context of some bivalves found growing in the gills of unfortunate sand crabs. Many members of the Galeommatidae family are parasitic or commensal with other marine organisms. In this case, Jousseaumiella are tiny flat-bodied clams less than 1 mm long, found attached to the body of the worm, squeezed inside the burrow in the coral’s skeleton. It feeds on the worm’s waste and potentially food particles coming through the pores in the sides of the burrow. Not the most dignified existence, but a more mobile home means more opportunities to eat a varied diet similar to that that the worm and coral are seeking out, and the clam also gets protection from predation tucked inside the coral. It is unclear if it benefits the worm directly to have clams attached to it.

A time lapse of the coral+worm moving from the paper’s supplement! It would be handy to navigate to greener pastures, if it became too muddy in a certain place!

It is, however, clear how living inside a coral would be a pretty good deal for the worm, which gets a stable, protective suit of carbonate armor to protect it from predators, and grows to fit it as it gets larger. They are normally found inside of rocks, shells and other hard inanimate objects, but having a living home is a cool upgrade. What is the coral getting out of the deal? The researchers note that the corals are often found in the crevices between other large reef-building corals, in areas of the reef that receive high supplies of nutrients and turbidity (dirt that blocks out light). These sorts of environments aren’t necessarily friendly places for a coral to be, since they reduce the light and therefore the food that the coral can receive from photosynthesis. These crevices also have a lot of variability in other conditions like temperature and water flow. But because the coral has hitched a ride on the back of a worm, it can actually move in the sediment to react to changing conditions and avoid being buried by piles of sediment floating by! The worm can also act as a sort of anchor preventing the worm from sinking in the sediment underneath, which would be a big hazard for the small, stubby coral on its own. The coral seems to go to great pains to make its partner comfortable, not growing its skeleton to cover the pore windows to the outside. The researchers note that as coral reefs worldwide are subject to increasing human-made pollution and climate change, it would be interesting to research whether this complex three-(five?) way symbiosis provides the various participants with an advantage compared to other corals.

So like any good story, this symbiosis features complex, growing characters, a dynamic setting, and still plenty of mystery demanding a sequel! To that end, there are lots of other great three-way symbioses to investigate. Snails which farm fungus that parasitizes plants. Bryozoans living on snail shells that have a hermit crab inside. Gobies serving as lookouts at the entrances of burrows built by shrimp, with a crab freeloader along for good measure. Algae and bacteria teaming up to attack mussels. The list keeps going! I could see this becoming quite a franchise!

New job! Where I’m going and how I got here

On By Dan KillamIn academia, BiologyLeave a comment
Richmond, California’s Finances Remain Shaky
Richmond, CA from the air, showing the turbid waters of the SF Bay

Well folks, it finally happened. I found a permanent scientific job. On January 31st, I’ll be starting as an Environmental Scientist at the San Francisco Estuary Institute (SFEI), working on the Nutrient Management Strategy (NMS) program. NMS is a group trying to understand how nutrient supply in the San Francisco Bay works.

The SF Bay is an extremely nutrient-enriched environment (eutrophic) due to human pollution and natural factors, to the extent that if all other factors were equal, scientists would expect it to be a nasty green sludgy mess. Yet up to today, due to factors that are still debated, the SF Bay is in much better shape than it should be. It is not a dead zone, choked off by algal blooms and oxygen-starved in the way that other high-productivity regions such as parts of the Gulf of Mexico have become. Those factors may include the cloudiness (turbidity) of the Bay’s water limiting algae growth, naturally rapid tidal mixing with ocean water, and the influence of clams and other grazing animals keeping the populations of potentially harmful plankton suppressed.

However, there is also evidence that this resilience may be fading as water temperatures in the Bay increase and the ecology of the system changes with climate change. Oxygen levels are dropping and levels of harmful algae are rising, which endangers the health and livelihoods of millions of people in the SF Bay area who depend on a clean, ecologically functioning SF Bay. In my role at NMS, I will be assisting in processing and interpreting huge quantities of environmental data on temperature, dissolved oxygen, water flow, light levels, algae concentrations, and harmful algae toxins, to help figure out how the SF Bay works and how we can protect it. I will be assisting another scientist joining the team in deploying more sensors to monitor the Bay on a minute by minute basis, and also packaging the data to help create models which allow us to figure out the various moving parts that make it work.

In a way, this is oddly similar to the work I’ve done during my postdoc at Biosphere 2, where I’ve been growing giant clams in their 700,000 gallon ocean tank since May 2020. The clams are biological sensors have been recording the environment of the Biosphere 2 ocean through their shells and valve opening/closing activity, and I have had to decode their diaries through comparison with the environmental data we collect on light, pH, dissolved oxygen, chlorophyll and other measurements. The SF Bay is a site of enormously influential research which has been important to understand estuaries around the world, but it is still a mysterious body of water in many ways. NMS is trying to understand how all its complex pieces fit together, much like I’ve been doing at Biosphere 2, which is why I jumped at the opportunity to apply for the job.

I also am excited to get involved in this work because it’s immensely important for everyday people’s lives. The SF Bay provides millions of people with food, employment, recreation and overall well-being, and the science that NMS produces has real-world value for making policy and a concrete plan to keep the Bay healthy. It represents exactly the kind of science that I wanted to do since I first jumped into environmental biology as a 19-year-old at USC. At that time, I was interning at JPL studying historical trends in California rainfall data, so this new job represents a homecoming of sorts to California water science!

This job will be a bit of a change of pace from my present work as at first, because I’ll be part of a scientific team with a shared mission, unlike most of my prior research, where I came up with ideas, pitched them to my advisors and funders and then coordinated the projects to collect and analyze data. There will be more teamwork, and while academic publications will still be one of our products, we also will be writing reports for policymakers and stakeholders who are deciding on how to regulate nutrient levels in the Bay.

I also won’t be working with clams on an everyday basis! But as I mentioned before, clams do play a major role in the Bay in terms of filtering the water, and so it is likely we will need to understand the activities of the clams and other grazers to explain the trends in nutrients that we see. I didn’t start as a Clam Man, but my curiosity about clams meant that my attention kept being drawn to these enigmatic but influential creatures, and I expect that dynamic will continue. I am, and always will be, Dan the Clam Man.

I will continue to get my present clam projects out the door as publications, so there will be lots of clamsplaining in the future months as those get out the door. Regarding the Biosphere 2 clams, we still have four individuals of Tridacna derasa (the smooth giant clam) growing in the 700,000 gallon ocean tank, and intend to leave them as long-term research subjects and an exhibit for visitors to enjoy and learn about. We also have proposals in the work for new projects to expand on this work. I hope I can continue to visit in the coming decades and see our clams grow to be true giants, two feet in length! I also hope to acquire pet giant clams of my own, with names rather than specimen numbers, to be my friends rather than my research subjects.

I’ll be starting the new job remotely at the end of this month, to give myself time to tie off loose ends in Tucson, intending to move to the Bay Area by March. I will really miss Biosphere 2 and Tucson, but this isn’t the last they’ll see of me, because my collaborations with people here will continue into the future. I knew from the start as a postdoctoral researcher that my position would not be permanent, but it is still bittersweet to leave. I will miss hiking in the Sonoran desert, swimming in the Biosphere 2 ocean tank and also my advisor Diane Thompson and her lab here, full of people who have been a joy to work with.

But I am excited for this new chapter, because the postdoc life has been lately losing its luster for me. I’ve enjoyed being a postdoc for the freedom it entails, both in my research topics and the way I structure that work. But postdoc work is emotionally exhausting, as I have been a journeying academic contractor on “soft money”. My employment for the following year has always been contingent on the next grant coming through. Moving between different institutions on different continents has been a big weight on my family and my partner, who I miss greatly.

As a postdoc, while I’ve had fun and wouldn’t change anything about it, I have felt like a plane trying to take off in unfavorable weather. I could see the end of the runway approaching as my current funding ends in May, which was a scary feeling. I’m willing to hustle and fight for research funding, but not my basic income. Looking back, I have applied to around 45-50 academic positions (including postdocs) since finishing my PhD and got interviewed for less than ten percent of those, and received offers for two postdocs. When I got the offer from SFEI, which was itself a rigorous, multi-stage process over months, I cannot describe what a relief it was to clear out my “job applications” folder in my to-do list. This SFEI job will allow me to pursue marine science that helps the environment and people, in a more emotionally sustainable way.

I’m excited to start my next chapter and share with you all the discoveries our team makes about the SF Bay, while also continuing to clamsplain here on my own time. Keep an eye out for my Biosphere 2 studies, which will be rolling out over the next months as the data arrives!

Biosphere 2 Update!

On By Dan KillamIn Biology, clams3 Comments
A view from my parking spot at work

I am now several months into my postdoctoral fellowship at Biosphere 2 in Oracle, Arizona! I am working with Professor Diane Thompson on a project measuring the shell and body chemistry of giant clams in Biosphere 2’s huge reef tank. Our goal is to find better proxies (indirect ways of measuring) the symbiosis of these clams with the algae they farm within their bodies. The controlled, closely monitored conditions of the Biosphere 2 ocean tank represent the perfect balance between the real ocean and the more controlled environment of a lab. Using trace metals and isotopes in their shells and tissue, we can trace back the ways that clams record their own internal biology. Wild giant clams make chemical records via the growth lines in their shells, similar to tree rings. These have been the subject of many cool past studies, but there are aspects of the “language” they use to write their shell “diaries” that are poorly understood. Much like researchers used the Rosetta Stone to decode heiroglyphics, we are observing clams as they grow in order to better translate the shell diaries of their prehistoric ancestors. Doing so, we can better understand how their ancestors reacted during past periods of climate change, and identify similar bivalves in the fossil record which may have harbored symbionts.

A view of the ocean tank at Biosphere 2

I started my postdoc remotely in May. The following months were spent sheltering at home in Southern California with my mom, supervising the installation of a cohort of giant clams into the 700,000 gallon ocean tank over Zoom. It felt like a science fiction movie, watching technicians Katie Morgan and Franklin Lane from hundreds of miles away on my computer screen as they nurtured and installed the little clams in their new home. I felt like Mission Control back on earth, watching a group of space colonists work with strange alien creatures.

Some of the T. derasas in the Biosphere tank

But in August I was able to finally move to Tucson to meet these clams in person! We had three species in the first batch: Tridacna derasa, T. squamosa and T. maxima. Of the three, T. derasa (the smooth giant clam) has proven to be the most successful in the Biosphere 2 ocean tank. All of the derasa clams from May have survived and thrived, attaching themselves to the bottom with byssal threads and growing their shells, both very positive signs of clam health!

Some of our newer batch of T. derasa in the quarantine tank

So we have doubled down on T. derasa and installed 11 more individuals last week, sourced from Palauan clam farms via a reef supply company in Florida called ORA. They are currently in a shallow quarantine tank where we will monitor them for disease and unwanted hitchhikers before introducing them to the broader Biosphere tank.

The workers at Biosphere 2 are very creative problem solvers. Giant clams need intense amounts of light to sustain their symbiotic algae and create food for themselves, a quantity of light higher than is available in the current Biosphere tank. To provide a light supplement, the engineering team at Biosphere 2 constructed a floating lighting rig with hanging LED lighting, right over the lagoon where we have the clams!

The lighting rig glows with a blue light as the sun goes down outside the Biosphere

To make sure the clams have enough light, we installed a Li-Cor light sensor to measure the exact amount of photons (light particles) hitting the clams over the course of a day. The light is measured in units of micromoles of photons per meters squared per second. A mole is 6.02 * 1023 particles, and other clam experts like James Fatheree have suggested that the clams need light levels of at least 200 micromoles/m2s to make enough food for themselves. That’s 120,400,000,000,000,000,000,000 light particles we need to hit every square meter of their habitat every second. The clam channels as many of those photons as it can to its algae residing within tubes in its tissue. The symbionts use it in photosynthesis to make sugars, which they share with their host. A well lit giant clam is a happy, well-fed giant clam! But because the glass dome of Biosphere eats up some of the light, and plankton and floating particles in the seawater eat up another portion, we use the lights to make sure the clams have the boost they need to maintain their symbiosis like they would in the clear, shallow waters of a tropical coral reef.

The Li-Cor sensor floats above the clams, telling us how much light they’re getting

Much like a new dad might read parenting books to get ideas for baby care, I am always poring through the literature trying to figure out how to maximize the growth of these clams. Dr. Fatheree is kind of like Dr. Lipschitz from Rugrats, except unlike the suspect childcare advice in the show, this real-life giant clam advice is very valuable. Like human babies, these clams can be a challenge! The clams sometimes decide to move around and get themselves into trouble, requiring us to rescue them if they get trapped behind a rock or under a pile of sand. So I have had to do a fair amount of clam-herding during my time here.

We are growing the clams for science, and there will be data to collect. We will be monitoring data like the trace metal chemistry of the clams’ tissue and shells, the color of their mantles, and the pH, temperature and oxygen levels of their environment, all to relate together to make the best clam record of their environment possible. So far, I have been snorkeling in the tank every couple days maintaining their setup. Next week, I will dive in the Biosphere tank for the first time to collect data on their shell chemistry! I have other projects in the works to measure their valves opening and closing using magnetic sensors, and to measure their color changes through time through computational photography.

That brings me to what I’ve found to be the coolest part about Biosphere 2: the people. Something about this place attracts creative, brilliant, can-do people who solve problems on the fly and are always jumping into the next project. It has been a privilege to learn and pick up technical skills from them in the brief time I’ve been here. This place is really like a space colony out of The Expanse or Silent Running. There are endless valves, pipes, tanks, exchangers and other hardware needed to keep Biosphere 2 running. Getting to witness the technical competence behind the whimsical solutions the staff comes up with, like the floating light rig, has been the most exciting part of this job for me. Everyone has a deeply ingrained curiosity and passion for science that is inspiring to see; they are as interested in my clams as I am in their corals, tropical plants, and geochemical experiments. I would argue that the human team behind Biosphere 2 is a bigger treasure than the unique metal-and-glass structure they work under, and I look forward to seeing the results all of the collaborations we have in the works!

The Mystery of the Giant Clams of the Red Sea and Indian Ocean

On By Dan KillamIn Biology, clamsLeave a comment

I have always been fascinated by scientific discoveries that are hanging right in front of our noses. Cryptic species are one such surprise. Sometimes, researchers using genetic sequencing are surprised to discover that a group of animals that all look the same from the outside are actually reproductively isolated from each other; separate twigs on the tree of life. This surprise has happened over and over in the history of natural science.

It turns out such puzzles are frequent among the giant clams. These unusual bivalves are specialists in coral reef environments, growing to large size with the help of symbiotic algae that create sugars through photosynthesis. Within the genus Tridacna there are ~10 accepted species which vary in size, shape, color and mode of life.

Tridacna squamosina (right) sitting next to the small giant clam T. maxima (left) on the Israeli Red Sea coast

I specialize in the three species known (so far) from the Red Sea, including the small giant clam Tridacna maxima and the fluted giant clam T. squamosa, which are both found worldwide, all the way from the Red Sea to down past the equator along the Great Barrier Reef. The third local species, T. squamosina is more unusual, so far being only known from the Red Sea (an endemic species). T. squamosina is an example of a cryptic species, having previously been assumed to be a local variant of T. squamosa. It looks pretty similar, with long scutes (flap-like appendages) protruding from its shell, thought to help stabilize it on the flat bottom of loose coral rubble. But unlike T. squamosa, T. squamosina lives exclusively at the top of the reef in the shallowest waters closest to the sun. It has a very angular, zig-zag pattern in its plications (the wavy shapes at the edge of the shell) and a characteristic pair of green stripes where the soft tissue meets the edges of the shell. The soft tissue is covered with warty protuberances.

Pictures of details of T. squamosina from Richter et al. 2008

It was only first described in detail in the early 2000s, when an international team of researchers figured out using genetic sequencing that it was a distinct species and named it T. costata. They noted that in their surveys all around the shores of the Red Sea, they only found 13 live specimens, making it an extremely rare and possibly endangered species. Fossil specimens on local reefs appeared to be much more common, suggesting it had a much larger population in the past. Then in 2011, another team at the Natural History Museum in Vienna discovered a shell of one had been forgotten in its collection for over 100 years. Rudolf Sturany, the researcher on the 1895 research cruise who had originally collected the clam, had called it T. squamosina.

The T. squamosina shell in the collection of the Museum of Natural History in Vienna (from Huber and Eschner, 2011)

In taxonomy (the science of naming and classifying organisms), the first team to name the species wins, so the name T. costata was synonymized (retired) in favor of the earlier name T. squamosina, which became the name of record. It must be annoying to spend so much time working to name a species and then discover you had been scooped over a century before! But such is science.

A mystery clam thought to be T. squamosina, later identified as T. elongatissima found off of Mozambique by iNaturalist user bewambay

The strange part was that there were some murmurs over the last few years that T. squamosina was not only found in the Red Sea, but also had been seen along the coast of Africa as far south as Kenya, Mozambique and Madagascar. Divers and snorkelers had taken pictures of a giant clam that did indeed look strangely like T. squamosina, with a zigzag shell opening and green stripes at the edge of its tissue. But some aspects of these individuals seemed off. In the Red Sea, T. squamosina lives freely, not embedded in the coral as these pictures showed, and the geometry of the angles of the shell seemed a bit different. It also would be difficult for T. squamosina to be connected in population from the Red Sea all the way South to Mozambique, as there are natural barriers which would prevent its planktonic larvae from riding currents to intermix between the two regions. When populations are separated by a barrier, the flow of genes between them is cut off and evolution begins to separate the populations from each other until they are separate species, a process called allopatric speciation.

A large specimen of T. elongatissima observed by iNaturalist user dawngoebbels off of Kenya

I figured that someday, researchers would collect tissue samples from these mystery clams to settle whether they were actually T. squamosina or something else. And this year, a team did just that, traveling along the coast of Mozambique, Madagascar, Kenya and other places, collecting samples of tissue to compare how all the different clams they saw were related in a family tree. They genetically sequenced these “clamples” and in the process, found that the mystery clams were a new cryptic species, which they called T. elongatissima!

Shells of T. elongatissima from the Fauvelot et al. 2020 paper
For comparison, a shell of T. squamosina collected off of Sinai, Egypt. You can see why they’re easy to mix up!

T. elongatissima closely resembles T. squamosina, and they are sister species on the bivalve family tree. It’s hard to tell them apart without training. Even a professional would probably mix some of them up if they were all placed sitting next to each other. The major differences appear to relate to shell shape, with T. elongatissima having a less symmetrical shell than T. squamosina, and a bigger opening at the rear hinge for a foot to poke through. The symmetrical shell and closing of the foot opening may represent changes that T. squamosina took on to adapt to be able to sit freely on the bottom, rather than embedding in the coral like T. elongatissima seems to prefer. If you’ve read this far, you may be thinking “Who cares? A clam’s a clam and these look practically the same. Aren’t you just splitting clams at this point?” At the end of the day, a species is a man-made concept; an organizing tool for use by us humans. Species are the characters in our reconstruction of the history of the world. What can we learn about the world by having identified this species T. elongatissima?

A giant clam family tree! Notice T. squamosina and T. elongatissima right next to each other.

The researchers behind the new paper discuss that based on statistical analyses of the genetic differences between the species, the most recent common ancestor for T. elongatissima and T. squamosina probably lived more than 1.4 million years ago! Some researchers have previously suggested that T. squamosina probably began its development as a separate species due to geographic isolation by low sea level, caused by repeated glaciations. With so much water trapped as ice on land during this period, the narrow Strait of Bab al Mandab, currently the gateway to the Red Sea, became a land barrier as sea level fell (kind of like opposite of the Bering Sea land bridge that formed allowing humans to migrate to the Americas). Ancestral clams trapped on the Northern end of this barrier were proposed to have evolved to become the rare T. squamosina.

This has occurred with a variety of species that became Red Sea endemics (meaning they are unique species that evolved in the Red Sea and are found nowhere else), including a unique crown of thorns starfish. The issue is that during this time of low sea level, the Red Sea went through periods where it was a rather unfriendly place for clams to live. All sorts of creatures went extinct in the period when the sea was repeatedly cut off, because the water became extremely salty, along with other unfriendly changes. So it’s unlikely T. squamosina would be present for us to see today if it only lived in the Red Sea throughout the entire length of time.

A map from Fauvelot et al. 2020 showing the distributions of different giant clams the researchers identified along the coasts of Africa and the Red Sea. Notice the bright red dots representing T. squamosina, only found in the Red Sea, while green dots represent T. elongatissima. Notice how the currents (arrows) seem to meet and then go offshore from Kenya. More on that in the next paragraph.

The researchers of this new paper propose that T. squamosina was more likely to have initially branched off due to the barrier of the Horn of Africa. The seas off of Kenya and Somalia harbor a meeting of southward and northward currents which then group and head offshore, away from the reefs that giant clam larvae are trying to get to. So any tiny floating planktonic clam larvae would experience a strong “headwind” preventing them from crossing that point. It would also mean that during times that the Red Sea was not a happy place to be a clam, T. squamosina may have found refuge on the coasts of places like Eritrea, Oman and possibly even as far as Pakistan. During times when sea levels rose and Red Sea conditions became friendlier, it recolonized the area.

As far as we know, the Red Sea is the only place T. squamosina is now found, but it may well be present elsewhere like Yemen or Oman. If T. squamosina was found in other regions, it would be tremendously important for its conservation. Right now, the species is thought to be extremely rare, with a very small native range. If it inhabited a broader area, that would mean more reservoirs of genetic diversity. This would reduce the odds that it will go extinct as reefs are put under stress from climate change, pollution and overharvesting. To survive as a species, it helps to not put all your eggs in one basket. If you’re only found in one small place, it increases the chances that a disaster (like climate change) will wipe you out.

The only way we will know for sure is to visit reefs in understudied places like Yemen, Oman, Pakistan, Eritrea and Somalia, to understand the richness of the giant clams present. These areas are understudied for various reasons: lack of research funding for non-Western researchers, lack of interest from the scientific community too focused on familiar places, and geopolitical situations that make it difficult to conduct research. But I hope someday to collaborate with people in these countries to better understand the giant clams present in such understudied regions of the globe. It is virtually certain that there are more species of giant clams, both alive and as fossils, waiting to be discovered.

Apps that Darwin would have loved

On By Dan KillamIn Biology, UncategorizedLeave a comment

Was Charles Darwin first? Kind of depends – Harvard Gazette

Most people know that Charles Darwin was a cerebral, deep thinking type. He traveled the world, collecting data about those finches and other stuff on field expeditions, synthesizing big ideas over decades to form his magnum opus, On the Origin of Species, where he set out his theories on natural selection and its role in evolution. However, you might not know that on a day-to-day level, Darwin was an all-around nerd’s nerd who just wanted to learn everything he could about the world, motivated by an unending sense of curiosity.

Darwin was a man who pulled plankton nets, filtering seawater just to see what cool stuff would show up when he put the resulting sample of goo under the microscope. He fiddled for earthworms and wrote a book about them over 40 years (including an experiment where he watched their progress burying a bunch of rocks over a 30 year period). He kept a heated greenhouse where he studied orchids and carnivorous plants. I consider Darwin a role model, because it’s hard to find a topic in natural history that he didn’t write about. The dude was just an unfillable sponge of knowledge.

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A view of Darwin’s greenhouse. Source: The Darwin Correspondence Project

I think Darwin would have marveled the online information that we have easy access to today. If Darwin were a researcher today, I could imagine him hosting a forum or listserv where he’d moderate, muse over the natural world and keep correspondence with the other leading scientific minds, much as he was a prolific letter writer with other researchers of his time. He might not be huge on Twitter: a bit too fast paced for his liking I bet; but I think he’d love two apps that I have also fallen in love with over the last few years.

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The Explore page on iNaturalist, where you can see what species other people have recently observed in your area!

The first is iNaturalist (Android, iOS), a website and social network where you can upload pictures of any lifeform, attach information about its location, time of day and other info, and the machine learning powering the site will try to identify it for you, with amazingly accurate results. If the AI can’t figure it out, experts are waiting in the wings to provide an identification or confirm yours. Think of it like a Pokedex or Pokemon Go, but for “collecting” real life creatures. And like Pokemon Go, it can be insanely addictive to find out about all the species that are all around us at all times. iNaturalist also has an app called Seek that makes the process even more gamified!

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a view of my observations

I am definitely an iNaturalist addict, and have accumulated a healthy collection of observations over the past couple years. My first was a red-shouldered hawk that I saw on campus during my PhD, but then I moved onward to fungi and plants I saw walking from my car to the office, and went back through my past pictures to identify bats I saw in Belize, fish I saw diving, and of course, my beloved banana slugs. I find it’s particularly satisfying to find out how life around you changes through the year, with the seasons. When I felt like pulling my hair out during my PhD, it kept me grounded to be able to know that the first spring flowers were opening, or the fledglings of birds were leaving the nest, or the winter rains were bringing all sorts of new fungus and banana slugs to life among the undergrowth.

I think being in touch with our natural world can help us now. While we’re sheltering in place, we don’t have to be trapped within ourselves. Even in the densest cities, there are so many bugs, flowers, birds and squirrels all around us going about their lives while we are effectively on pause. It brings me relief to know that life continues, and satisfaction to be able to understand them. Knowledge really is power, and if you know the relations between all the types of life both in evolution and ecology, it makes the world make sense in a way that provides a weird zen-like peace.

To that effect, there is a #citynaturechallenge happening starting yesterday, from 4/24-4/27/20. Take pictures of living things around you and upload them to iNaturalist, Twitter and elsewhere with that hashtag! My uploads there have been of interest to researchers studying rare snails of the Negev desert, writing books about tropical bats, and researching invasive beetles. I have been following uploads of giant clams on iNaturalist for quite some time, including the newest described species, Tridacna elongatissima, which users had been observing on the Eastern coast of Africa before it was formally described in a recent paper! I bet Darwin would have been a major, influential user on iNat.

Darwin was also a big nerd regarding rocks and fossils. Evolution is the story of life, and we can only understand that story by turning to the fossil record for information. Environmental changes provide a major motivating factor pushing life to constantly change. Geology in Darwin’s day was a developing field, with the first geological maps appearing only due to the work of William Smith and others, mere decades before Darwin’s work came to be. But his work would not have happened without the growing understanding of the massive passages of time needed to deposit the rocks all around us today. Evolution typically needs time, and fossils provide proof of how life has changed during those almost incomprehensibly long intervals.

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One of William Smith’s geologic maps

To find a fossil of an age we are interested in, we must know the rocks present in the area. And the second app I’ll mention today is RockD (Android, iOS), which we can use to figure out the type of rocks right under our feet, how they were made, how old they are and even what kind of fossils have previously been found within. The data in RockD is pulled from two sources that scientists have lovingly curated. Macrostrat is a database of stratigraphic (rock layer) data that scientists have aggregated into one of the most detailed and comprehensive geologic maps ever made. And the Paleobiology Database collects observations that scientists have made over the decades of almost every fossil that has ever been found and recorded.

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Of local geology when you first open RockD (my detailed coordinates obscured ;))

Rather than relying on only printed maps for his work, Darwin would have loved the ability to pull out his phone in the field and instantly know the combined work of dozens of previous researchers to understand the rock he was looking at. You can even “check in” and upload your own pictures of rocks to help researchers improve their databases, and go back in time to look at where the continent you live on was during the time of the dinosaurs!

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Geologic map of my area. Darwin would have seriously nerded out checking out the locations of faults, formations and other features

These are only two of many apps and websites that I think would have blown Darwin’s mind. We are living in a golden age of digital science, with so many new discoveries being precipitated by the availability of easily accessible, free information in the palms of our hands. But more than that, it is fun to go outside and be able to decode the mysteries of the world around you without even being an expert in natural history. In the process, you might find yourself becoming an expert!

What good is a clam?

On By Dan KillamIn Biology, clamsLeave a comment

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When I mention to people that I study bivalves, I can sometimes sense from their facial expressions that they are secretly asking “why?” While clams are perfectly content to keep doing what they’re doing without being thanked, I think it’s important to enumerate all of the ways they make our world more livable and functional.

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Various roles that freshwater mussels can play in their local food webs (Source: Vaughn and Hoellein, 2018)

Bivalves are ecosystem engineers. While they may seem rather stationary and not up to much at any particular time, they are actually always working to actively maintain their habitat. The majority of clams are filter-feeders, meaning that they use their gills to gather particles from the water column for food. Some of these particles are ingested as food and later pooped out. Some inedible particles are discarded immediately by the clam as “pseudofeces”. Both mechanisms serve as a bridge between the water column and the benthos (the sediment at the bottom). In this way, clams are engines that take carbon fixed by algae floating in the water and transfer that material to be stored in the sediment. Their bodies also act as nutrition to feed all sorts of animals higher on the food chain like sea stars, lobsters, seabirds, sea otters and humans that depend on bivalves as food. They are literally sucking up the primary productivity (algae) to be used by the rest of the food chain.

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The filtration rate of oysters. Graphic from The Nature Conservancy

Different clam species vary in their precise filtration rate (how fast they can inhale and exhale water, filtering the particles within), but it is prodigious. Some freshwater mussels, for example, can pick-through 1-2 liters of water per hour for every gram of their own flesh. Since these individual bivalves can weigh over 100 g, they are capable of picking the food out of an immense quantity of water. In doing so, bivalves help improve the clarity of the water column, allowing more sunlight to reach deeper into the water body (the photic zone), providing more energy for additional photosynthesis to occur. While there are examples where invasive bivalves such as zebra or quagga mussels take this phenomenon too far, in well-functioning ecosystems, the filtration activity of clams helps improve the productivity of the community.

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An oyster reef. Source: The Nature Conservancy

Bivalves help make sediment through their filtration of material from the water column, and they also engineer and manipulate the sediment directly. Some bivalves, like oysters, are able to make huge mounds of dirt that serve as habitat for all sorts of life, increasing the diversity of the community. They do so both by excreting sediment, and also by passively trapping it between the shells of neighboring oysters (“baffling”). By doing so, they reduce rates of coastal erosion and increase the biodiversity of wetlands. For this reason, New York and other communities plan to seed oyster reefs to help fight sea level rise and reduce the threat of storm surges like the one that occurred during Superstorm Sandy.

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Comparison of sediments without bioturbation by digging animals, and with. Notice how the non-bioturbated sediment is layered and darkened due to activity by anaerobic bacteria, while the well-oxygenated, mixed sediment is light all the way through. From Norkko and Shumway, 2011

Other “infaunal” bivalves (burrowers) help to aerate the sediment through their tunneling, bringing oxygen deep under the surface of the dirt. This mixing of the sediment (also called bioturbation) ensures that nutrition from deep under the sediment surface is again made available for other organisms. Some bivalves can bore into coral reefs or solid rock, creating burrows which serve as habitat for other animals and can free up minerals for use by the surrounding ecosystem. Helpful shipworms assist in eating wood, assisting in returning nutrients stored in that tissue to the ecosystem as well.

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Enormous grouping of giant clams in a lagoon in French Polynesia. From Gilbert et al., 2005

Bivalves of course are also famous for their shells, and this activity also provides habitat to sponges, snails, barnacles and many other encrusting organisms specially adapted to live on bivalve shells and found nowhere else. Giant clams are the most legendary “hypercalcifiers,” and in some regions like New Caledonia can rival reef-building corals in terms of biomass. In areas where soft-bottoms dominate, bivalves like hammer oysters, adapted to “rafting” on the quicksand-like surface of the soft sediment, can assist by providing a platform for other animals to take refuge. In the deep sea, bathymodiolid mussels and other chemosymbiotic bivalves can feed directly on the methane and sulfur emitted from hot vents or cold seeps with the help of symbiotic bacteria, creating dense reefs which provide food and habitat for all sorts of life. Even once the clams die, their shells can continue to serve as homes for other creatures.

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Crabs feeding on Bathymodiolus in the deep sea (NOAA)

The shells of clams provide great scientific value in understanding our world. Much like tree rings serve as a record of environment thousands of years into the past, growth rings in clam shells serve as a diary of the animal’s life. These rings can be yearly, lunar, tidal or even daily in rhythm, with each ring serving as a page in the diary. The chemistry of those “pages” can be analyzed to figure out the temperature the clam experienced, what it ate, whether it suffered from pollution, and even the frequency of storms! The study of rings in the hard parts of animals is called sclerochronology, and it’s what first drew me to study bivalves. I was so fascinated by the idea that our beaches are covered with high-resolution records of the ocean environment, waiting to be cut open and read.

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This giant clam shell recorded an interruption in the animal’s daily growth caused by a typhoon! From Komagoe et al., 2018

While they don’t owe us anything, clams provide a lot of value to humans as well, serving as a sustainable and productive source of food. Humans have been farming bivalves for thousands of years, as evidenced by “oyster gardens” and shell middens which can be found all over the world. Particularly in seasons when food is scarce on land, native peoples could survive by taking advantage of the wealth of the sea, and bivalves are one of the most plentiful and accessible marine food sources available. But they aren’t just the past of our food; they may be part of the future. Bivalves are one of the most sustainable sources of meat known, requiring very little additional food to farm and actively cleaning the environment in the process. Mussels grown out on a rope farm are an easy investment, growing quickly and with very little required energy expenditure. Someday, giant clams may provide the first carbon-neutral meat source, as they gain their food from symbiotic algae within their flesh. I have never eaten one, but I’ve heard they’re delicious.

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A shell midden in Argentina. Photo from Mikel Zubimendi, Wikipedia

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Mussels being farmed on ropes

Clams are heroes we didn’t know we needed and maybe don’t deserve. They ask for nothing from us, but provide vast services which we take for granted. So the next time you see an inconspicuous airhole in the sand, thank the clam that could be deep below for aerating the sediment. The shell of that long-dead mussel at your feet may have fed a sea star, and now is a home for barnacles and many other creatures. While that mussel was alive, it sucked in algae to improve water quality on our beaches. And the sand itself may contain countless fragments of even more ancient shells. Clams silently serve as an important cog in the vast machine that makes our oceans, rivers and lakes such amazing places to be. Thank you clams!

 

Thoughts of a clam

On By Dan KillamIn Biology, clams, Uncategorized14 Comments

To us active, dynamic mammals, the humble clam can appear positively…inanimate. Their nervous system is decentralized relative to ours, lacking any sort of brain, and to the untrained eye, it can appear that their only discernible reaction to the outside world is opening or closing. Open = happy, closed = not happy; end of story, right? Some vegans even argue that the clams are so nonsentient that it is okay to eat them and think of them as having no more agency than a vegetable!

You might already have predicted I intend to tell you about just how animate and sentient clams can be. But let’s start out by describing the nuts and bolts of their nervous system. As with many invertebrates, their nervous system is distributed throughout their body as a system of ganglia. Ganglia are clumps of nerve cells which may have local specialization, and transmit messages within neurons using electrical potentials. At the connection between cells (called a synapse), neurotransmitters are used to pass signals to the next cell. Researchers have found that bivalves use “histamine‐, octopamine‐, gamma‐aminobutyric acid‐ (GABA)…like immunoreactivity” in their central and peripheral nervous systems, much like us vertebrates do, and other studies have even found that the response to serotonin and dopamine is localized in nervous tissue linked to different organ systems.

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Nerve cells (bright green) highlighted in a larval oyster with fluorescent dye (from Yurchenko et al 2018)

These systems of chemical nerve transmission are truly ancient, likely dating back to the formation of complex animal body plans in the earliest Cambrian. Researchers have great interest in studying these nervous and hormonal signaling systems in mollusks because they can shed light on the relative flexibility and limitations of these systems throughout the animal tree of life. Characterizing these systems can also allow us to understand the mechanisms that bivalves and other animals use to react to environmental stimuli.

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Electron microscope view of gill cilia, zoomed in 1000x (from Dan Hornbach)

Like humans, bivalves spend a lot of time and effort eating. Most bivalves eat by filtering food from passing water with tiny cilia on their gills. These cilia work to capture food particles and also act as a miniature rowing team moving water along the gill surface. The bivalve needs a way to control this ciliar activity, and researchers found they could directly control the speed at which oysters move their cilia by dosing them with serotonin and dopamine, which respectively increased and decreased activity.

Bivalves also work very hard to make babies. Most bivalves reproduce by releasing sperm and eggs to fertilize externally in the water column. To maximize their chances to find a mate, they typically save up their reproductive cells in gonads for multiple months and release them in a coordinated mass spawning event. It appears that this process is controlled by hormonal releases of dopamine and serotonin. Researchers have determined that serotonin concentrations vary through the year, with mussels in New England using it to regulate a seasonal cycle of feeding in summer, followed storing of that energy for winter. During the winter when food is less available, they use that stored energy to bulk up their gonads in time for reproductive release in spring months, when their larvae have plentiful access to food and oxygen, ensuring them the best chance of survival. In recent decades, aquaculturists have learned to use serotonin injections to induce spawning in cultured clams, to ensure they will have a harvest ready at a certain time of year.

So bivalves are very sensitive to the seasons. How about shorter term sources of excitement? You might have observed this yourself through the clam’s most iconic activity: opening and closing its shell. Clams close their shells with powerful adductor muscles which pull the two valves together. A springy ligament at the hinge pulls the shell open when the muscles relax. Just like us, the clam needs to use nerve cells to signal the muscle to do its thing. In addition, two different sets of ganglia act to control the foot that some bivalves can extend to dig into sand, with one ganglion acting to extend the foot and the other causing it to contract. While clams don’t have a centralized brain with specialized regions for different uses like we have, this represents a sort of specialization of neural systems with a similar result.

Clam licking salt - Imgur
This iconic gif is often shared along with the claim it shows a clam “licking” salt. It is actually using its foot to search for a place to dig. The salt was not needed.

When a certain neuron is used repeatedly, it can form a cellular memory allowing the organism to acclamate (ugh sorry) and moderate its response to a particular stimulus over time. Giant clams, for example, close their shells when their simple eyes detect a shadow overhead. This behavior can protect them from predation. When I conducted some of my PhD research, sampling body fluid of aquarium and wild giant clams with a syringe, I noticed that captive clams didn’t close up in response to my shadow overhead, while wild clams required me to sneak up and wedge their shells open with a wooden block to do my work. I suspected that after exposure to frequent feedings and water changes by aquarists, the clam had “learned” that there was no reason to expend energy closing its shell. Meanwhile, in the process of proving that our sampling technique was not harmful to the animal, I discovered that clams which detected my shadow would quickly reopen within seconds when I hid from them, while those that were stuck by a syringe would stay closed for minutes before opening and beginning to feed again. Makes sense!

Other researchers noticed this phenomenon as well. One group found that giant clams repeatedly exposed to shadows of different sizes, shell tapping and even directly touching its soft tissue began to habituate (become accustomed) to the stress, opening more quickly and staying open longer each time the stimulus occurred. Even more interestingly, they did not transfer that habituation between stress types; for example, the clams that saw a shadow again and again would still react strongly to a different stress like tapping its shell. This suggests the animal can distinguish between different threats along a spectrum of seriousness, with touching of tissue (similar to a fish pecking at its flesh) being the most serious threat with the most dramatic response.

Another study determined that larger giant clams stayed closed longer than smaller ones in response to the same threat. They proposed this was related to the greater risk large clams face as they have more tissue area vulnerable to attack. While the clams might not have made a “conscious” decision in the way we do as thinking creatures, they were able to place their individual risk in context and vary their response. This ability to tailor a response to different risk levels is a sign of surprisingly complex neurology at work.

Inside the Scallop
Close up of the eyes of a scallop. Each is a tiny crystalline parabolic mirror (photo by Matthew Krummins on Wikipedia)

Scallops show some of the most complex bivalve behaviors. This relates back to their unique adaptations, including simple eyes that can resolve shapes and the ability to swim away from danger. Scallops have been found to discern between predator types by sight alone, to the extent that they did not initially recognize an invasive new predatory seastar as a threat. When swimming, they are capable of using this vision to navigate to places where they can hide, such as seagrass beds. It would be very interesting to compare the behavior of scallops in marine protected areas to those that can be freely harvested. Do they vary their behavior in response?

I hope I’ve made clear that while clams are not exactly intellectual powerhouses, their behavior is much more complicated than simply sucking up water and opening or closing their shells. Like us, they inhabit a complex environment that requires a multitude of responses. Their nervous systems have evolved to allow them to survive and adopt nuanced behaviors which they can vary on the fly, and which us “higher” animals are only just beginning to comprehend.

Mystery of the “spurting” mussels

On By Dan KillamIn Biology, clams2 Comments

If you’ve read any of my posts, you should realize by now that clams are pretty weird. Some catch live prey. Some have algae in their bodies that they “farm” for food. Some can bore into hard rock. Some sail the seas on rafts of kelp. Clams live in a competitive world and have had hundreds of millions of years of time to evolve to try out all sorts of weird, unlikely ways of life.

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U. crassus in a Slovenian river (Alexander Mrkvicka)

The thick shelled river mussel (Unio crassus) is known from many rivers and streams of Central Europe. As this is a very well-studied region of the world, many generations of academics have noted an unusual, seemingly inexplicable behavior undertaken by these mussels at certain times of year.

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U. crassus propped up on its foot (UCforLife)

Using its muscular foot, U. crassus pulls itself to the edges of the streams and rivers it lives in until it is partially exposed to air. It orients itself at a right angle with the surface of the stream with its siphons (two little snorkels coming out of the shell) facing out towards the water. Like all bivalves, U. crassus can act as a bellows by opening and closing its shell to pull in and push out water through those siphons. It has one siphon above the water and one below, and it proceeds to suck in water and spray it into the center of the stream using the power of its suction. The water can travel over a meter away and they continue this spurting about once a minute, sometimes for hours.

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Squirting water into the stream! (Vicentini 2005)

Needless to say, this is a very strange and unlikely behavior to observe in a mussel. It is exposing itself to potential dessication or suffocation from exposure to air. It is vulnerable to predation from terrestrial mammals and birds. There has to be a very powerful benefit from this behavior to outweigh those risks. And why squirt water into the air?

Some researchers proposed that the mussels were traveling to shore to harvest from the more plentiful food particles deposited there. But why would they face their siphons away from the shore then? Other workers suggested that it was a way to reduce heat stress through evaporation, though that also seems unlikely, considering the water is warmest in the shallows. The question persisted for decades in the minds of curious malacologists.

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Top-down view of spurting behavior (Vicentini 2005)

In 2005, Heinrich Vicentini of the Swiss Bureau for Inland Fisheries and Freshwater Ecology decided to try settle the question of why these mussels spurt. He observed several dozen of the mussels crawl to the edge of the water and diligently begin squirting into the streams. In the name of science, he put himself in the path of these squirts, caught the water and used a hand lens to observe that the squirted water was full of mussel larvae (glochidia).

Lifecyle of U. crassus (Rita Larje via UCforLife)

U. crassus falls in the order Unionida, a group of freshwater mussels distinguished by a very unusual method of reproduction. They are parasites! Because they can’t swim well enough to colonize upstream against the current, they need to rely on fish to hitch a ride. Some have evolved elaborate lures to convince fish to take a bite, then allowing them to release their larvae, which attach to the fish’s gills like binder clips and ride all the way upstream. Once they have reached their destination, they detach and grow up into more conventional burrowing mussels. It’s a weird, creepy and wonderfully brilliant strategy that enabled the mussels to invade the inland rivers which would otherwise be inaccessible to them.

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Loach (type of freshwater fish) gills with unionid larvae attached (UCforLife)

The mussels appear to be spurting out not only water, but their babies. They gain a couple of advantages from this. For one, their larvae can distribute further than would be possible from the bottom of the creek. Instead, they are released at the center of the surface of the stream, where they can be carried for a much longer distance by the current before they settle at the bottom. In addition, the splash of water on the surface may mimic the behavior of insects and other fish food falling in the water. A curious minnow might venture to investigate the source of the splash, where it would promptly breathe in a cloud of larvae that get stuck on its gills. A pretty rude surprise, but a brilliant trick to give the baby mussels the best chance of surviving.

So again, clams prove themselves to be far more clever and interesting than they might initially seem. U. crassus and other members of the Unionida are an ancient and globally distributed lineage which have evolved all sorts of weird and wonderful ways to maintain their river lifestyle. Unfortunately, rivers are some of the most widely damaged environments in the world. A majority of freshwater mussel species worldwide including U. crassus are endangered by habitat loss, overharvesting and pollution. But more research into their unusual biology can help us understand ways we can enhance their conservation, with the hope of providing more habitat for them to recover populations in the future. New projects in Sweden and other countries aim to recover habitat for their larvae to settle along 300 km of rivers, and research the fish species which their larvae prefer to hitch a ride on. With more work, we can hopefully ensure that the streams of Europe will harbor little mini super-soakers for millennia to come.