Category Archives: Uncategorized

Learning to Love Benthic Algae

I am the type of person that attributes songs to the work that I do. And after my first day sampling for benthic algae last summer, I already had the chorus of the Beatles’ Twist and Shout running through my head.


My field partners Haley and Megan helping me take benthic algal cores in the mudflat and tall Spartina alterniflora zones.

That may seem an odd choice of song, but I assure you that there is no better musical masterpiece to describe the complete process of benthic algae sampling and running. In the field, with our four-centimeter diameter corers, we cut back the cordgrass Spartina patens in the high marsh to reveal the sediment beneath. The dense Spartina patens roots woven through the soil, however, force us to twist the corer to break up those roots, eventually releasing our sediment core sample. There we have the lyrics “Twist and shout,” shouting in joy (or frustration) optional.

The next week, I travel with my samples back to the lab at the Woods Hole Research Center, where I extract the cores in acetone before running them on a UV Spectrophotometer, to measure chlorophyll a absorbance at different wavelengths of UV light (which, in turn, tells us benthic algae abundance). With running the samples, though, comes a lot of tube shaking, after adding acetone and again before being spun down in the centrifuge to run on the Spectrophotometer. Hence, “Shake it up, baby, now.” Shake those samples!


Running benthic algae samples using the UV Spectrophotometer with my mentor Hillary.

If you couldn’t already tell, I’m quite passionate about benthic algae, the topic of my independent research. However, it took a little while for this interest to grow on me.

The first time I heard the words benthic and algae together was last summer, when it was proposed by the Lead Principal Investigator Linda Deegan that I be in charge of field sampling, organizing the past fifteen years of data, and eventually finding the story behind the microalgae response to nitrogen fertilization. I did my best to act knowledgeable about the topic, but in my two years of undergraduate study, I had only come across macroalgae, and never algae described as benthic. Cue the background research!


Demonstrating the “twist and shout!” portion of the sampling process–trying to separate sediment cores from plant roots!

What we refer to as benthic algae is microalgae, such as cyanobacteria and diatoms, found in the first few centimeters of marsh sediment. Benthic algae is important for the uptake of nitrogen and carbon, and serves as a source of energy for grazers, among a myriad other things. This algae is also resilient to many environmental factors like extended darkness and hypoxic or anoxic environments, which means that it could play a role in salt marsh recovery from nitrogen loading; but should benthic algae be negatively affected by that nitrogen addition, there could be potential consequences for the salt marsh ecosystem.

Through research, I began to see benthic algae as a link between marsh invertebrate ecology, a topic I was familiar with and loved, and biogeochemistry, an area new to me when I began with TIDE. Armed with my corers in the field, a UV Spectrophotometer in the lab, and fifteen years of historic data in the office, I hope to unlock the full, fifteen-year story of how benthic microalgae responds to nutrient loading and marsh recovery this upcoming year.


Written by Kate Armstrong

Strangers in a Strange Land: Bioinvasions in the Gulf of Maine

2101Imagine for a moment that you are a crab larva. Floating in the middle of an urban estuary (say, the Port of Rotterdam in the Netherlands), you just hatched, and are one of millions of little baby crabs hoping to survive long enough to make it to adulthood. Then suddenly, inexplicably, you are sucked up into a strong current that you don’t understand. The sun disappears, and you are surrounded by thousands of your brothers and sisters, but also many other larvae that you don’t recognize. Time seems to stand still, and you do what you can to make the best of a bad situation. Then suddenly, the same current again pulls you, but now in the opposite direction, back the way you came. Hooray, you are free! But wait, this new water feels different; this is not at all what you remembered of your home. By this time, you are a little older, a little larger, and a little bit more aware of your surroundings. You recognize you must be in a different place entirely, but you again make the best of a bad situation, and settle along the marshy shores of your new locale (not knowing you just entered Boston Harbor). You grow into an adult, and you discover to your relief that your home is not so bad after all. Predators don’t recognize you as prey, and parasites don’t infect you. So you yourself then reproduce, your offspring survive in massive numbers, and your species excels in this new home; a truly crabby paradise.

2103Congratulations! You just experienced what it was like to be an invasive (i.e. non-native, non-indigenous, etc.) species transported from the Europe to the Eastern United States by ballast water from a commercial vessel. In order to maintain buoyancy and pitch while at sea, ships take on various kinds of ballast including rocks and water. Rock ballast was more commonly used in early shipping in New England in the 17th, 18th, and 19th centuries. In fact, the first arrival of the European green crab Carcinus maenas to New England was through British and American merchants unloading rocks (which also contained crabs) at ports along the Gulf of Maine. A second wave of green crabs was introduced to the eastern seaboard more recently in the 1980s through water ballast (much like your own crab experience). Although seemingly beneficial for the crab, bioinvasions rapidly became a problem by the mid to late 1980s not only for native organisms, but also for people. In 1988, the zebra mussel was introduced accidentally to the Great Lakes in North America from Bulgaria in Europe. A fouling species of mussel that grows on practically any surface it touches, intake pipes from Lake Michigan to Chicago were clogged for weeks until utility companies were able to replace the critical infrastructure. The result: zebra mussels cost taxpayers millions to remediate the problem. Therefore, it is incredibly important to continue to understand global effects of bioinvasions on a variety of ecosystems including the Plum Island Estuary, and how to prevent their spread; no matter how much those crabs need a change of scenery!

Written by Michael Roy

Ode to Flux Week

By Sophie Drew

Adapted from Lewis Carroll’s “Jabberwocky”


Sophie (that’s me!) and Bridget in the zone mid-flux

‘Twas brilliant, when the golden sun
Did show its face upon the marsh
All set were we to work as one
The heat arising, greenheads harsh

Behold the power of plants, my friend!
CO2 in, oxygen out!
I’ll tell you before poem’s end
What my research is about

We have a chamber, logger, tubing,
Across the marsh these things we heave
We set it up, we get it grooving
And watch, in real time, marsh grass breathe

Full sun, then shade, then darkness too
That’s three light levels for ya
To see how our dear friend responds,
Spartina alterniflora


My project partner Bridget modeling proper gear-carrying technique and flux week style

And why do this? What can we learn?
Seems an odd summer vacation
It’s to find out if these plants just might
Recover from eutrophication

When nitrate’s added in excess
To a system so fine tuned
The carbon cycle becomes a mess
If we’re not careful, it’s all doomed

‘Twas brilliant, when the golden sun
Did set across the shining creeks
Carbon fluxes, July, done!
Until again, in four short weeks



A high marsh flux in action


New England’s salt marshes were some of the first ecosystems I was immersed in (literally) as I began my jaunt into marine science. For many people, the draw is their tranquility, as looking out onto a cordgrass meadow gently rippling in the breeze can be quite relaxing. Something that fascinated me then, and still does now, is how these peaceful feelings can be evoked by such a harsh environment. Large, strong tides, cold, salty water, and hot, unrelenting sun all represent real hazards for animals residing in these coastal margins. Yet salt marsh critters don’t run from these dangers: in fact, food webs in these areas are designed to meet stressors head on, taking life-threatening risks in order to reap the energetic rewards that pushing these boundaries can provide.


I am here studying Plum Island’s food webs. One of the major cogs in the always-churning ecosystem machine is the mummichog, a small minnow that easily dominates the other marsh critters in terms of sheer numbers of individuals residing in the creeks. You can catch these baitfish by the hundreds in all sorts of traps and nets, and though they can eat a plant-based diet, in order for them to truly grow big and strong, they need some protein! Big fish can eat the shrimp and invertebrates found in the creeks, but how can a mummichog get to that size in the first place? The answer is by risking life and fin and riding the tide up to the dangerous high marsh, to snack on unsuspecting insects and spiders. Seems crazy, but the risk of getting stranded up there, or eaten by a bird or other predator, is definitely worth it for the potential energetic boost they can get. In this way, mummichog function as an incredibly important link between these two (high marsh and creek) distinct habitats, gathering energy in the form of food produced in the high marsh (insects and spiders) and making it available to the consumers we all love, like striped bass and flounder in the creek. Not bad for such a little guy!

One of the most interesting effects of increased nutrient load on these coastal systems is IMG_3934the sloughing and disintegration of the low marsh area of the creeks, which normally act as a ramp for these mighty minnows to make their daring climb. How does the loss of that ramp affect the mummichog’s ability to bridge the two ecosystems, and what does a change in the strength of that link mean for the creek’s other residents? How does the ecosystem respond to this decoupling of the creek and high marsh? These are the questions I’m hoping to answer this summer. As we head out to West Creek with our trusty seine net to collect fish, shrimp, and other marine critters for our analyses, we come across a dead American eel on the path, stranded as the tide receded and desiccated by the strong summer sun. Clearly, the high marsh bounty is worth risking everything for, and I hope to understand how that link, and its loss, drives the function and long-term stability of these “peaceful” ecosystems.



Fiddlers on the Marsh

The day begins early, tide dependent of course. My team assembles. We are a small group consisting of PhD candidate Michael Roy, Jarrett Byrnes’ undergraduate lab assistant IMG_2978Richard Wong, and I, Byrnes lab undergraduate field tech. We gather our gear; our scientific instruments, our boots and buckets. We set out for a glorious day of experimental set up in the salt marsh. I am so excited to be here as this is my first time working in the field. This is the reason I went to college for Biology, to have a career in which I am spending copious amounts of time in nature.

So far I have gotten to be very close to nature, sometimes waist deep in it when catching the fiddler crabs for our particular experiment. I feel beyond honored to have been selected to be a field tech this summer. Michael reminds me that I earned my place helping him at the field station with my hard work and enthusiasm in my marine ecology this past school year. Michaels’ experiment is on comparing the affects the marsh fiddler crab at various densities have on the marsh sediment in there native region South of Cape Cod verses the Gulf of Maine were they have recently expanded their range to include because of the changing climate. It just so happens to be a question I find myself very interested in as well.

We are headed to the marsh today to catch the crabs that will be occupying the cages we built for them in the marsh. We have taken our initial measurements of the sediment strength, buried a log of peat in mesh to examine root growth, and buried small mesh bags of grass to assess how decomposition may increase as the crabs burrow into the sediment.

I can’t help but think that our cages look beautiful when they are up and running, with their steel flashing affixed around the tops which ensures no crabs crawl out or in. I am really enjoying my job as I am standing in the cool creek on a beautiful sunny summer day, poking crabs out of their holes in the mud. We will leave them over the rest of the summer and measure how they have changed the marsh in their cage after some time has passed. I truly can’t wait to evaluate the results and find out!



Written by Linnea Sturdy 

How saltmarsh plants respond to nutrient pollution

Flowering salt marsh plant, Spartina alterniflora. © DS Johnson/VIMS.

Flowering Spartina alterniflora. (c)David Samuel Johnson

A study recently published in Ecological Applications from the TIDE Project reveals that plants don’t respond to eutrophication the way you might expect. Below is a press release originally posted by the Virginia Institute of Marine Scientists.  


Add fertilizer to your garden and your plants will probably grow bigger and taller. Add fertilizer to a salt marsh and the plants may not get any bigger. That’s according to a new study led by Dr. David Samuel Johnson of William & Mary’s Virginia Institute of Marine Science.

Salt marshes are intertidal grasslands that grow at the interface between land and sea. These ecosystems can receive excess concentrations of nutrients such as nitrogen from wastewater and runoff of agricultural fertilizer. This “eutrophication” affects coastal waters and estuaries worldwide and can lead to fish kills, harmful algal blooms, and areas of low oxygen. Johnson and his team wanted to know how eutrophication impacted salt marshes.

To do so, the team conducted an unprecedented experiment and flooded football-fields worth of salt marsh in northeastern Massachusetts with fertilizer-rich water for almost a decade. Scott Warren, a professor at Connecticut College and study co-author who has studied salt marshes for four decades, says “When we were able to mimic a eutrophied estuary at an ecosystem scale—quite a challenge I must add—we found that salt marshes did not respond as you might have predicted from fertilization experiments done over the past half a century or so.”

Despite the abundant supply of nitrogen, a key plant nutrient, plants in the fertilized marshes didn’t grow much bigger than those in unfertilized marshes. “We were surprised at the mild responses, even after almost a decade of fertilization,” says Johnson. Earlier salt marsh studies reported plants growing larger in response to adding fertilizer. Previous studies also found that fertilizer changed species composition, causing some species to outcompete others. “The species composition didn’t budge during the entire experiment,” Johnson says.

One reason the team’s results differed from previous studies may be their choice of fertilizer. “We used nitrate fertilizer, which is the most common form of nitrogen in eutrophied estuaries,” says Johnson. “Much of the previous work used ammonium fertilizer. Those studies had different questions than ours; they weren’t specifically looking to understand eutrophication.” Wetland plants prefer ammonium to nitrate because it takes less energy to process, so bigger plants with application of ammonium would not be unexpected.

Another reason the plants may not have responded strongly was the way the fertilizer was delivered—with flooding tidal water, which meant that less fertilizer reached the plants compared to previous studies that had added fertilizer directly to the marsh surface.

The mild response of plants doesn’t mean that salt marshes are safe from eutrophication, however. Johnson notes that when it comes to understanding eutrophication’s impact on salt marshes, the answer may lie beneath the surface. In an earlier paper from the same field study, published in Nature, the research team found that fertilizer treatments caused the marsh edges to collapse and erode away. Again, this is opposite of what they had predicted. “We hypothesized that the grass would grow taller, which would trap more sediment and help the marsh grow,” says Johnson. Instead they found that plants in fertilized marshes had fewer roots and rhizomes than those in non-fertilized ones, which may have contributed to the collapse.

The team’s research results have important implications for the management and care of salt marshes. These critically important coastal resources are thought to be “nutrient sponges” that soak up excess nitrogen to help prevent dead zones and fish kills. One way they can do so is by putting the nitrogen into bigger plants. Since the plants in the current study didn’t grow bigger, it limited the marsh’s ability to absorb excess nitrogen.

Johnson adds, “Our work underscores that we can’t simply rely on salt marshes to clean up nutrient pollution. We need to do a better job at keeping nutrients out of the water in the first place.”


REUs Gone Wild: A Weekend in Woods Hole

Friday afternoon, and five marsh-logged REUs eagerly stuffed clothes into bags, piled into cars and headed south. After a long week, we were more than ready for time off. Three hours later, after driving like salmon through Boston traffic, we arrived at the Cape and hit the town for some shopping and seafood. Our rag-tag group was prepping for what promised to be a wild weekend. But by wild, I mean there were a lot of people. And by people I mean scientists. And by scientists, I mean the speakers and attendees for the Celebrating Discovery conference at the Marine Biological Laboratory of Woods Hole.

“A Summer Camp for Scientists”

Woods Hole, MA has an international reputation as the hub for marine science research. Along a half-kilometer long road, the Marine Biological Laboratory (MBL), Woods Hole Oceanographic Institute (WHOI), and the National Oceanic and Atmospheric Administration (NOAA) all have prestigious research facilities. A mere five minute walk and I could have caught flies – my jaw dropped, and never have I felt like such a kid in a candy shop. Within the greater Woods Hole area, the United States Geological Survey, the National Academy of Sciences, and Semester at Sea also have facilities.

The coastline is peppered with hulking research vessels, docked for the summertime. Quaint coffee shops and restaurants attract tourists and scientists alike, where it is not uncommon to overhear sincere discussions about the future of bioinformatics. I was thrilled to be in an area associated with such prestige and history (MBL has produced over 50 Nobel laureates), and even more awe-struck that I somehow fit into the giant cog of this machine.

WHOI's Knorr. Fun fact--it's the ship that found the wreck of the Titanic

WHOI’s Knorr. Fun fact–it’s the ship that found the wreck of the Titanic

The Celebrating Discovery conference took the form of “plenary sessions”, meaning a series of speakers would give talks within the same general topic. Speakers from UC Berkeley, WHOI, Harvard, Duke University, Brown, Dartmouth, the Amazon Environmental Research Institute, Argonne Laboratories, the Smithsonian, Howard Hughes Medical Institute and more, presented on everything from eco-evolutionary biology to computational modelling and medical breakthroughs in tissue regeneration. MBL is officially affiliated with Brown University and the University of Chicago, and collaborates with other universities and laboratories across the world. By simply walking into the auditorium for a lecture, you felt smarter. Some of the most brilliant minds in the marine sciences were in the room. While the weekend may not have been “wild” by Cape Cod’s standards, it was an intellectually stimulating and highly social event.

Scientists are often portrayed as socially awkward, brooding, and plain weird; in the digital age of professional-networking platforms (e.g LinkedIn and ResearchGate) and email-related frenzy, it would be more than easy for scientists to entirely block out physical connection with the outside world. Publications are the primary way that the scientific community connects with one another. Yet, it is during conferences that we make the most interdisciplinary connections. Conferences provide dedicated venues and forums for scientists of all specialties to meet and learn from one another. The standing joke is that MBL is a summer camp for scientists, as we much prefer sitting on beaches in deep conversation than locked away in a cold dark basement lab. (Beach time was existent but unfortunately minimal). By the end of the weekend, each of us had further honed our interests and met someone who was driving scientific inquiry in their field. It opened our eyes to the deeply collaborative nature of the MBL, and showed that despite the name, MBL does not restrict its limitless ideas to the seas.

Selfie in between plenary sessions.

Selfie in between plenary sessions. “It’s for the blog”

MBL’s remarkable collaboration with numerous institutions is further highlighted in its equal success in communicating its research. While conferences are wonderful places for scientists to share new ideas, it is meaningless unless conveyed to policy-makers, medical experts, and the general public. As one example, MBL sponsors Friday evening lectures throughout the summer that draw crowds to fill two auditoriums, with internationally known speakers. The lecture is followed by a beautiful reception, where people of all backgrounds can mingle. Local outreach is equally as important; non-scientific residents can appreciate the importance of those hulking research vessels that block their view of the ocean. Our own blog gives the TIDE project a digital presence to communicate to public the imperative nature of our own work, and even attract future researchers. (It also provides excellent writing practice for the interns – that’s me!)

When communication of new ideas and questions is effective, it can change the people’s perception of environmental problems. Communication comes in a plethora of forms, from books that start a green revolution, to 140 character tweets. We cannot keep our ideas to ourselves; science is worth nothing if no one else knows. MBL’s weekend of discovery was about asking relevant scientific questions to reach novel intellectual destinations and foster a diverse intellectual community. The depth and breadth of researchers that are attracted to Woods Hole is already staggering, but the MBL is pushing the frontier of discovery.

If ideas are truly the currency of the 21st century, then these giddy summer-campers struck gold.

We made it to the beach! (From left to right: Frankie Leech, Bryn Mawr; Nathalie Moore, College of William and Mary; Kassandra Baron, Washington and Jefferson; Caitlin Bauer, Bryn Mawr)

We made it to the beach! (From left to right: Frankie Leech, Bryn Mawr; Nathalie Moore, College of William and Mary; Kassandra Baron, Washington and Jefferson; Caitlin Bauer, Bryn Mawr)

Nathalie Moore is a rising junior at the College of William and Mary. She is a double major in Biology and Environmental Science, and her summer research for the MBL focuses on salt marsh creek bank degradation and foraging success of a top predator, F. heteroclitus. She will be presenting her work on Austral invasion and fire ecology at the 100th Meeting of the Ecological Society of America in Baltimore, MD on August 13th.