This Week In The Lab

Leavin’ on a jet plane

I’m terribly sad to be leaving this beautiful city and a new assemblage of friends and colleagues who I will forever cherish. My time at UNSW has been eye opening in so many ways, from the culture of collaboration in my host lab and department, to the suite of new critters I encountered (link), to the daily evidence of ecology and evolution that abound when one first becomes acquainted with life in the opposite hemisphere (link). My EAPSI host, Emma Johnston, has provided inspiration and ideas that will keep me motivated for much time to come. With luck, that motivation will be matched with interesting findings from the stable isotope and genetics data we’ve collected.

Top: Sydney Opera House as seen while underway to Gore Cove, one of our field sites. Bottom: Side of our SIMS-based research vessel, heading west past the opera house and towards Balmain, another inner-harbor site.

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This Week In The Lab

So. Many. Tiny. Cups.

Henna Wilckens preparing stable isotope samples

So. Many. Tiny. Cups. That’s the conclusion today after my first foray into stable isotope analysis with Henna. Though I must admit, chemistry was my least favorite subject in my early years, with a few years more wisdom, its benefits have become evident. Stable isotope analysis is a tool that allows us to measure the relative weight of carbon and nitrogen in freeze dried tissue samples. The weight of carbon helps us discern the original source of primary productivity in the tissue sample of interest. For instance, organisms that feed on suspended phytoplankton, such as diatoms, should have a different carbon isotope signal than organisms that feed on seaweed, this signal is proliferated up through each subsequent level in the food web. The weight of nitrogen in an organism’s tissue is correlated with its trophic level, or its position in the food web. Organisms that are higher order consumers such as sharks will have a heavier isotopic nitrogen signal than lower order consumers such as sea urchins.

Next, it’s off to the mass spectrometer for these little samples. Within a few weeks, we hope to have data back which give us a first look into how food web structure compares between natural and man-made shorelines in Sydney Harbor.

The tiny cups and tweezers used to prepare stable isotope samples

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Background, This Week In The Lab

Niche Theory In Everyday Life

SYDNEY, AUS: In the day to day here, as I commute to work, take the bus around town, and observe, I’m frequently overwhelmed by daily demonstrations of niche theory and convergent evolution in the world around me. The terrestrial flora in Sydney is of an entirely different lineage, primarily of the Myrtoideaen tribe Eucalypteae, than what I know from the Pacific Northwest. Though Eucalypts have long been present on Earth, their radiation in Australia is apparently relatively recent. Eucalypts now make up ¾ of the vegetation on this island continent, and fill nearly every ecological function that I, as a North American, attribute to other trees. For instance, coastal swamplands similar to the cypress swamps of Louisiana and Texas are here inhabited by swamp gum trees, other Eucalyptus spp., and their Myrtoideaen cousins, the paperbark trees. Savanna and temperate grassland habitats that in the US would have scattered oaks, cottonwoods, or willows, are here are inhabited by bimble box and coolibah eucalyptus trees. The Sydney red gum is one of several Eucalypts that plays the role of North American fruit trees, providing food for fruigivores. On my commute home at night, I often get to watch enormous ‘flying foxes’, or Ku-ring-gai bats (Pteropus poliocephalus), indulging in the tree’s nectar.

This, of course, is entirely tangential from my work on man-made alterations to urban shorelines in Sydney Harbour. While I know I should be entirely focused on the project that brought me here, the natural history nerd within has a hard time ignoring what Darwin and many others since found astonishing upon first traveling to the opposite hemisphere: That a similar set of ecological professions (niches) exist everywhere, and who fills them (which species) is heavily influenced by chance.

Post about ancient Eucalyptus from Eliza’s Instagram

Eliza’s instagram

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This Week In The Lab

Next Generation Sequencing – Life Forms of Sydney Harbor

Leonard Nimoy as Spock from Star Trek: The Original Series.

In the original Star Trek, Lieutenant Spock, upon beaming down to a new planet from the Starship Enterprise, would immediately pull out a Tricorder and begin scanning the environment for life forms. Results were instantaneous, providing a comprehensive view of the surrounding ecosystem within seconds.

Though we have yet to fully see such a novel invention on Earth, I’m overwhelmed today by how close we actually are to inventing the Tricoder in real life. I spent the day in lab at the Sydney Institute of Marine Science, extracting DNA from marine sediments and their invertebrate inhabitants. Thanks to support from the IGERT Program on Ocean Change at UW and from the Applied Marine and Estuarine Ecology Lab at UNSW, the genetic material I extracted will be sequenced and matched to a database of known organism sequences, in a process called DNA barcoding.

Eliza looking very serious in her white lab coat

Like DNA extractions of the old school variety, the endeavor required donning a white lab coat, goggles, and gloves, and making sure not to sneeze or shed excessively. Unlike genetic adventures past, the materials needed for the extractions were available in a self-contained kit shipped par avion from Texas — no gels or interpretation of specific sequences was needed, and the entire process for many 10s of samples took only a single work day (20 years ago, comparable work might have been the focus of an entire PhD).

Vials and pipetting tools for the final stage of DNA extractions

I hope results from the day’s genetic escapades will yield helpful information about both the microbial and invertebrate community on manmade and natural shorelines in urban settings, such as Sydney. And I’m thrilled to report there is a chance that by the end of my lifetime, I could be scanning Earth’s ecosystems, Tricoder in hand, with my best interpretation of a female embodiment of Lieutenant Spock.

Tricorder from Star Trek: The Next Generation.

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This Week In The Lab

Hello again from down under

Hello again from down under! Henna Wilckens (intern) and I are deep into processing the sediment samples we collected last month from the bottom of Sydney Harbour. From our temporary work post at the University of New South Wales, we aim to sort through each of the millions of tiny sediment grains in our frozen samples to extract anything that once wriggled, crawled, filtered, or respired. The identity and number of creepy crawly critters in our samples will help us discern whether marine communities adjacent to man-made seawalls and pilings differ from those adjacent to natural rocky shorelines. All of this is part of a project I’m doing as an NSF EAPSI fellow with my Australian host, Dr. Emma Johnston, and post-doctoral researchers in her lab (link to earlier post).

Surprising as it may be, we’ve thus far encountered a number of striking and beautiful organisms within the urban muck.

A carnivorous polychaete worm from Syndey Harbor

Snail from Sydney Harbor

A snail cacophony from Syndey Harbor

Ostracods (tiny shelled crustaceans) from Sydney Harbor

Foraminifera from Sydney Harbor

Single foraminifera

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This Week In The Lab

Gettin’ Dirty in Sydney Harbor

It’s been a week of gettin’ dirty in what must be the world’s most beautiful urban waterway: Sydney Harbor. After several early mornings, a bit of sea time, and some good ole manual labor, I’m happy to say our field work is complete! We’ve collected sediment samples and epilithic (animals that live on rocks) specimens from four sites and are now ready to hit the lab.

Top: Sydney Opera House as seen while underway to Gore Cove, one of our field sites. Bottom: Side of our SIMS-based research vessel, heading west past the opera house and towards Balmain, another inner-harbor site.

We launched out of the Sydney Institute of Marine Science (SIMS), a marine lab in the heart of Sydney Harbour that was established just over a decade ago in a collaboration between four major universities: University of Technology Sydney (UTS), the University of Sydney, Macquarie University, and UNSW. SIMS has provided easy boat access, lab facilities, and much more established means for collecting samples than I’m used to in Seattle. Sample collection didn’t even require trespassing or intertidal bouldering with heavy equipment! It was lovely.

The only downside was learning that Bull Sharks are not just a curse inflicted on the good people of Florida; these aquatic hunters also patrol the waters of Sydney Harbor and also happen to be to source of all my deepest darkest fears (“great whites? tigers? no problem… wait did you say bull sharks?”). So, my usual approach of diving in to collect samples by hand was not going to work. Luckily we were able to deploy tools from the surface to collect samples at the murkiest of our sites. I’m happy to say all samples are now safely stashed in cold storage awaiting analysis, and I still have all my appendages and a beating heart.

Data collection in Sydney Harbour. Left: Deploying the “Van Veen grab” to collect sediment. Right: Transferring a small amount of sediment into tiny vials for DNA extraction, while intern Henna Wilckens deploys the Van Veen grab over the side for another sediment sample.

Stay tuned for more on the wild and beautiful creatures in our samples, and on my adventures in lab as I explore food web relationships in Sydney’s urban marine ecosystems.

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Sites and Critters, This Week In The Lab, Uncategorized

What’s out there?

What lives out there in Seattle’s underwater landscape? That’s been the question of undergraduate interns in the Sebens Lab over the last 2 months, as they’ve analyzed photos from our recent benthic surveys.

This work was no small undertaking. It required learning hundreds of new species and species codes, and spending many many hours zooming in and out of digital photos to identify invertebrates and algae, and quantify their relative abundance on photographed surface. The curious critters they’ve encountered at times seem stranger than fiction and offer a window into Seattle’s vibrant, underwater world. Here is a compilation of their favorite finds of the quarter:

Balanus nubilis

Balanus nubilis, (c) Minette Layne

Balanus nubilis, (c) Minette Layne

Most people wouldn’t call barnacles interesting, and truth be told, I can understand why. Barnacles aren’t exactly the most thrilling things in the ocean; they aren’t as dangerous as sharks, they aren’t as beautiful as angelfish, but just because they aren’t as flashy as their mobile compatriots doesn’t mean they are any less interesting. In particular, the Giant Acorn Barnacle, Balanus nubilis, is an intriguing creature. Growing up to approximately six inches in diameter and twelve inches in height, the B. nubilis is a filter feeder related to shrimp, and has the largest known muscle fibers in the animal kingdom. Also, the “glue” that these, and other, barnacles produce cannot be dissolved by either acidic or alkaline solutions. This has piqued the interest of some researches in the medical field, particularly dentists, in hopes of developing new medical adhesives. Giant Acorn Barnacles also provide important habitat even after they die. The shells of dead acorn barnacles sometimes form reef like structures and can act as nurseries for small fish. So although barnacles aren’t the supermodels of the ocean, they are important parts of the ecosystem and are worthy of study.

– Christopher Scott Mowers (Class of 2018)

Chris Mowers

Chris Mowers

 

Cryptochiton stelleri

Cryptochiton stelleri, (c) Jerry Kirkhart

Cryptochiton stelleri, (c) Jerry Kirkhart

Cryptochiton stelleri, also known as the Gumboot Chiton or the “Wandering Meatloaf,” is the largest species of chiton. It lives 20-40 years, weighs up to 4.4 pounds, and grows up to 14 inches long, and is found throughout the coast of the northern Pacific Ocean. The Gumboot Chiton has armored plates along its back, which help it bend and attach to curved surfaces. It is red because approximately 20 species of red algae live on it and because red algae makes up much of the gumboot chiton’s diet. Its tongue-like radula, used for scraping algae off rocks, has teeth tipped with magnetite, a magnetic mineral! One defense mechanism used by the gumboot chiton, as well as other chiton species, is to curl up so that its soft underside is protected from predators. Because of this, chitons are sometimes called “sea cradles”. An interesting fact is that about 25% of Gumboot Chitons have small segmented worms living on them, near their gills. These worms help clean the gills by eating material found there.

– Maia Tian Sebek (Class of 2015)

Maia Tian Sebek

Maia Tian Sebek

 

Metridium farcimen

Metridium farcimen, (c) James Watanabe

Metridium farcimen, (c) James Watanabe

Metridium farcimen is a species of sea anemone that is more commonly known as the Giant Plumose Anemone. It is native to the west coast of the United States and Canada. Metridium has enormous plumes and striking white, red or reddish-brown coloration that makes it impossible to miss. Large Metridium farcimen are also known to drive away other organisms and capture prey with its large tentacles. Additionally this particular species is able to reproduce sexually and asexually, through pedal laceration, leading to dense populations of the anemones. These organisms can survive for centuries. One specimen in particular lived for more than one hundred years in captivity before human error lead to its death. This species is an enormous, highly adapted filter feeder that dominates the substrate when present.

– Jack Berrigan (Class of 2019)

Jack Berrigan, UW Class of 2019

Jack Berrigan, UW Class of 2019

Parastichopus californicus

Parastichopus californicus, (c) James Watanabe

Parastichopus californicus, (c) James Watanabe

Parastichopus californicus is a large sea cucumber that can be up to 50 cm in length and about 5 cm wide, with large cone-shaped pseudo spines, and tube feet on the underside for movement. Their body is soft and cylindrically shaped, with reddish-brown to yellowish, leathery skin and an endoskeleton just below the skin. They feed upon organic detritus and other small organisms by eating bottom sediments, and pooping out sand. Occasionally, they will position themselves in a current where they can use their tentacles to catch food (such as plankton) the floats by. Typically found in the low intertidal zone down to about 90 m depth (although occasionally as far down as 250 m), they are generally loners that are active at night. A few interesting things about P. californicus is that they have the ability to regenerate all parts of their body, similar to their relatives, the starfish. When threatened, they can expel all the contents of their stomach (instantaneous poop!) or a sticky white substance that confuses predators. They are a commercially fished species that is popular in Asian markets in the United States and overseas, which has led some areas to be overfished.

– Dejah L. Sanchez (Class of 2015)

Dejah Sanchez

Dejah Sanchez

 

Pugettia producta

Pugettia producta, (c) James Watanabe

Pugettia producta, (c) James Watanabe

Pugettia producta, the Northern Kelp Crab, is a ubiquitous feature anywhere kelp grows. It does not decorate it’s carapace to the same extent that other majid crabs do. There is speculation that when it does attach items to it’s carapace, it is doing so to eat them later. It is omnivorous, but mainly feasts on algae–only when this food source is scarce will it resort to a eating barnacles, mussels, hydroids, or bryzoans. P. producta is at times parasitized by the barnacle, Heterosaccus californicus, which modifies their behavior and physiology. The crab becomes sluggish, and during their next molt, the barnacle pushes it’s reproductive sack through the crab’s abdomen. The crab’s gonads are damaged severely if not destroyed. In some cases, male kelp crabs exhibit female morphology after being parasitized, including carapace and claw modifications, and even production of eggs in addition to sperm.

– Ian McQuillen (Class of 2015)

Ian McQuillen

Ian McQuillen

 

 Serpulid worms

Serpulid worm, (c) Jim Lyle

Serpulid worm, (c) Jim Lyle

The rocky subtidal substrate lining the bottoms of our waters is teeming with life. My personal favorite creatures are the serpulid worms. These suspension feeders bind to solid substrate and extend their beautifully patterned feathers in order to sift nutrients floating through the water around them. If startled, they quickly retreat into their shell like home. If enough of the worms live together, they can form a cool, reef-like structure. As urban structures are being developed closer and closer to the shoreline, we disrupt their fragile habitats.  They are definitely small and easy to miss but fascinating nonetheless.

– Rianne Peterson (Class of 2018)

Tritonia festiva

Tritonia festiva, (c) Kevin Lee

Tritonia festiva, (c) Kevin Lee

Tritonia festiva (also known as the Diamondback Tritonia), is a nudibranch of the family Tritoniidae. They are distributed all the way from North-Central Alaska to Baja California, and are 2-3cm in length. Tritonia festiva use their sensitive frontal veil to hunt their prey, carefully positioning their mouth over expanded polyps of octocorals before swiftly attacking. If you ever get the chance to look at an octocoral colony after a Tritonia attack, you will see holes where the missing polyps have been torn out by the nudibranch. I would say Tritonia festiva is definitely one of the prettier sea slugs, though there are over 3,000 sea slug species. Like other sea slugs, they are hermaphrodites, and so can mate with any individual passing by them.

– Ashley Pierson (Class of 2018)

Ashley Pierson

Ashley Pierson

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Sites and Critters, This Week In The Lab

Interns share their favorite critters

In the Sebens Lab in Seattle, we are very lucky to have a group of fantastic interns. This fall, we’ve been spending a lot of time sorting through sediment samples from an experiment we conducted in West Seattle last summer. After many, many hours in the lab, the Sebens Lab interns are true experts at finding and extracting worms, clams, and other critters in sediment samples. Inevitably when you’re doing this type of work, you come to favor certain organisms, be it for their beauty, their bizarre life history, their unusual appearance, or the ease with which you can find them within an expanse of similarly sized sand grains. For this post, two interns, Monisha Ray and Amy Green, have provided us with a look into their favorite soft sediment organisms and a description of what they like about them.

Monisha writes:

Photo of Monisha Ray

Monisha Ray, Sebens Lab Intern

One of the most interesting finds for me while processing our enrichment sediment samples was the presence of ostracods, tiny crustaceans that look like little reddish brown sesame seeds. Although they are related to shrimp, they have a clam-like resemblance due to the valves that enclose the rest of their body. These valves are made up of calcite or chitin. Usually the body of the ostracod ranges from 0.2 to 1mm, but the ostracods in our sediment analysis tended to be a bit larger (2-4mm) which was interesting to note. They were almost easy to overlook as some sort of marine seed, until upon closer examination the bivalved hinge becomes apparent as well as the sensory and swimming appendages protruding from within the carapace. Up to a third of the body of ostracods is dedicated to their reproductive organs, and the sperm of an ostracod can be up to 10 times the length of the body. Certain species of ostracods are also bioluminescent and produce a blue light that has been observed in Japan and Australia amongst other regions. Although the ones in our sample weren’t quite this spectacular, they were still an interesting find and a new encounter for me in my marine science experience. 

Photo of an ostracod

Ostracod, (c) Peter J. Bryant

Amy writes:

Photo of Amy Green

Amy Green, Sebens Lab Intern

My favorite infauna genus includes the Lacuna marine gastropod.  In the family Littorinidae, they are commonly known as chink shells.  They are found on eelgrass, rocks and seaweed low in the intertidal. They are herbivores and lay egg clusters that look like tiny donuts colored yellow or tan (kind of like spaghetti-Os). They have a thin shell with five to six whorls. The shell seems smooth to the naked eye, but has fine spiral ridges upon magnification. They usually have brown bands on whorls, but not always.  A study done by Chavanich and Harris (2001) in the Gulf of Maine found that L. vincta prefer Antithamnionella floccose, Ulva lactuca and Laminaria saccharina. These charismatic snails are my favorite because of their pretty banding, and cute squat shape.

Photo of Lacuna

Photo of Lacuna, (c) Amy Green

Check in soon for more postings on soft sediment organisms and our work in the lab. And thanks so much for reading!

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This Week In The Lab

Urchins on hunger strike

The results are in.  After several months of tethering urchins and measuring their feeding rates, it seems that we can now conclusively say that tethered urchins go on hunger strike. Given that the whole operation was rather comical (try putting urchins on leashes, building little urchin boxing rings, and feeling normal!), I am tempted to present this conclusion jokingly and without the context you probably need to understand why it matters.  The bottom line is that I am still without a means of quantifying the effect of urchins on urban marine ecosystems in the field. So that’s unfortunate.

Tethered urchin

Tethered urchin

A huge thanks to the folks at MaST aquarium for letting me set up kiddie pools in on their dock and use their flow through seawater system. Throughout August and September, I used these tanks to test whether tethering impacted the way that urchins feed. Urchins exhibit an extremely patchy distribution in urban marine ecosystems. When they are present, the algal community appears to be considerably different, with less foliose red algae and a different suite of sessile invertebrates. My overarching question is whether urchins alter the community structure on rocky habitats when they are present in urban marine ecosystems, or whether these differences are the result of some other process. In order to do this, I ideally would conduct a transplant experiment, moving urchins to sites where they currently are absent and measuring any changes in community structure that result.  But pilot studies demonstrated that transplanted urchins are not easy to keep track of – they move away from transplant sites quickly, often disappearing into deep crevices between the rocks.  If they don’t stay on experimental plots where they’re transplanted, I can’t effectively quantify their effect.  Tethering was the last of several attempts to contain the urchins within experimental plots and would only have been effective if they continued to feed once tethered. Since they did not continue to feed, we can rule it out as an approach for measuring the impact of urchin feeding in the field.

What was striking about the results of the experiment was that the differences in feeding rates between tethered and non-tethered urchins were consistently so significant. I conducted the experiment with three different types of algae: Ulva sp. (fleshy green algae), Chondracanthus exaperatus (a red alga known as Turkish towel), and Laminaria saccharina (“sugar kelp”). Urchins that had not been tethered consistently ate 2-3 grams of algae per day, while tethered urchins ate less than a gram or nothing at all. Statistically, this led to highly significant differences in feeding rates.  Before-and-after weights of algae in stalls with tethered urchins did not, on the other hand, differ significantly from empty stalls where urchins were left out as an experimental control.

For now, I’m taking some time to regroup and reconsider how we can test the effect of urchins on algal communities. It is an issue that we’d love to understand better, particularly since urchins play such an important role in temperate marine ecosystems in less urbanized environments. The lesson of the day is that designing effective field experiments can be more challenging than one might expect. We’ll keep working at it though, and will let you know develops.

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Urchins in experimental "stalls"
This Week In The Lab

Urchins on leashes

Unfortunately, the urchin corrals (see previous post) proved unsuccessful.  After numerous adjustments to the design, escapees continued to find their way to freedom.  By the end, the only prototypes that were successful at containing urchins were also trapping algae and confining other species that will need to move freely in and out of experimental plots in the field.  So, I’ve moved on to plan B: urchins on leashes.

Tethered urchin

Tethered urchin

This is a rather sad alternative, as it requires piercing the side of the test (exoskeleton) of urchins and threading it with monofilament line. While it seems likely that this is uncomfortable for them, a close look at their anatomy gives me reassurance – the area that I’m puncturing is basically a hollow cavity without organs. Urchins are also very different from us in their make up, and a limited exposure of the interior part of their body to the surrounding environment does not have the same implications for them as it does for us.  Indeed, the individuals I have tethered are recovering well and appear to be going about life as usual.

The method I’m using is borrowed from previous work by Nick Shears, Russell Babcock, and Anne Salomon.  Shears and Babcock describe the method in a paper they published in Oecologia in 2002 (link). Anne Salomon was also gracious enough to offer some additional tips via email based on her experiences tethering purple urchins, Strongylocentrotus purpuratus.

While urchin tethering has been used successfully in several previous studies, it has primarily been used as a means for quantifying predation on urchins themselves.  This is a common technique in marine ecology; Remember the goat they put into the T-Rex enclosure in Jurassic Park? It’s kind of like that but with lots of replicates and on a much smaller scale. By tethering urchins and placing them in the field, previous studies have evaluated relative rates of predation on urchins across different sites. (It’s only relative because the process of tethering may itself alter predation rates).

In my case, however, the question is not about predation on urchins, but about the impact of urchin feeding on the rest of the biological community. In other words, I’m not interested in how many goats the T-Rex will eat – but in how the goats impact the grass and flowers and shrubs when they are present.  Goats have a big impact on the biological community (just type ‘rent a goat’ into your google browser if you want proof); How about urchins?

In order to use tethered urchins as an experimental “treatment” in the field, I need to first see whether being tethered affects their feeding behavior.  So this is what I’m doing now at MaST aquarium. I’ve got 24 “stalls” housing individual urchins.  Half of them are tethered and half are not.  They have each been given a pre-weighed quantity of food.  I am running multiple trials of this lab experiment, but in each trial, I re-weigh the remaining algae from each urchin stall to see how much they’ve eaten after a few days.  I should have a comparison of feeding rates between tethered and un-tethered urchins compiled and available within a few weeks. Assuming all goes well, it will then be off to field for these little guys, where they’ll have the opportunity to eat their way through macroalgae that has grown wild. Just like rent-a-goats.

Urchins in stalls with algae

Tethered and untethered urchins in their stalls with pre-weighed pieces of macroalgae.

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