Thomas M. Arnold, Departments of Biology and Environmental Studies, Dickinson College

Ecological Biochemistry, Plant Polyphenolics in Nature and Human Health, Polyphenol / Protein Interactions

Introduction to our laboratory

arnoldtI’m a member of the Biology department and the program in Biochemistry & Molecular Biology at Dickinson College, where I’m also serving as the chair of the Environmental Studies Department .  I’ve held a variety of positions at other institutions, including at the University of Queensland, the Smithsonian Institution, and the College of Charleston as well as the Maryland Department of Natural Resources and the U.S. Fish and Wildlife Service.  I am a broadly-trained plant biochemist who studies the natural products of plants and marine organisms.  Many of these serve as anti-microbials, herbivore deterrents, or chemical cues.  Some are potential new medicines or dietary supplements as well.  My research focuses on understanding how plants respond to stress by re-configuring primary and secondary metabolic pathways in a way that alters the production of these substances.  Then, understanding the role of these substances in nature and as potential drugs.  I am particularly interested in plant polyphenols that may inhibit protein misfolding in Alzheimer’s Disease, and related disorders

Ocean acidification weakens seagrass defenses

Photograph © David Liittschwager / National Geographic Stock.

Chesapeake Bay, USA / Island of Vulcano, Italy.  The world’s oceans absorb carbon dioxide (CO2) and slow the pace of climate change.  At the same time the absorbed CO2 lowers the pH of ocean waters, changing seawater chemistry in the process called ocean acidification.  This can have devastating impacts on corals and shellfish, disrupting the process of calcification essential for the construction of coral reefs and the cultivation of oysters and clams in aquaculture.  However, the added CO2 could boost the photosynthesis and growth of coastal seagrasses, according to recent studies suggesting that seagrasses will be “winners” in future acidified seas (1).  This is a critical question for those hoping to manage or restore coastal waterways because seagrass meadows reduce coastal erosion and serve as nursery grounds for fish and shellfish, but have been in steep decline world-wide.

The results of a recent study published in the journal PLoS ONE challenge the assumption that seagrasses would necessarily be “winners” in a future high CO2/ low pH world (2).   The team, led by Dr. Tom Arnold from Dickinson College, examined the effects of ocean acidification on seagrasses, particularly their ability to produce a range of protective chemicals called phenolics.

“Like most plants,” explained Arnold, “seagrasses produce phenolic substances that can act as structural and chemical defenses,inhibiting the growth of disease organisms and deterring fish and other grazers from consuming the leaves.”  Indeed ecologists have long understood that plant phenolics can have numerous roles in plants.  Slight changes to their chemical structure give them useful properties as antimicrobials, antioxidants, sunscreens for harmful UV radiation, bitter-tasting deterrents, digestion reducers, and flower pigments, as well as making them the building blocks for forming wood.  “On land, more CO2 often means more phenolic substances in plants,” Arnold explained “and this too could be beneficial if it helps protect them from insects or disease”.

To test this a team of researchers, including Dr. Whitman Miller from the Smithsonian Environmental Research Center and three undergraduate students from Dickinson College1, simulated ocean acidification using an instrument called a F.O.C.E., which stands for Free Ocean Carbon Enrichment.  The instrument generates high CO2 / low pH seawater and releases it into experimental areas of seagrass meadows.  By dialing in the correct settings on the F.O.C.E. they mimicked conditions predicted to occur within the next 100 years in several meadows of aquatic plants, including widgeon grass Ruppia maritima and redhead grass Potamogeton perfoliatus, in the Chesapeake Bay.  In each of their experiments they found that high CO2 conditions led to a dramatic loss of the phenolic protective substances in these plants.  “We were quite surprised.” said Arnold “This was different than what has been observed on land.”

According to the authors, the surprising observation may be caused by something else that plagues many coastal waterways – nutrient pollution.  On land, plants often struggle to acquire nutrients such as nitrogen and phosphorous for growth and, thus, excess CO2 is diverted to the production of phenolics.  This might protect plants from grazers at a time when they would find it most difficult to regrow lost tissues (3).  However, coastal plants may respond differently because they are often bathed in nutrient-rich waters, the result of nutrient pollution (called “eutrophication”).  In this scenario excess CO2 can be combined with nutrients to fuel rapid plant growth instead of phenolic synthesis (4).

To confirm the discovery, Arnold traveled to the Island of Vulcano in the Mediterranean Sea, where CO2 is emitted not only from volcanic craters on land but also from underwater volcanic seeps, creating a natural laboratory for the study of ocean acidification.  Here a short swim towards the underwater seep provides a glimpse of the future.  As CO2 levels increase closer to the seeps the ecosystem changes visibly – seagrasses and some seaweeds thrive, while creatures such as sea urchins and molluscs disappear (5).  On Vulcano Arnold joined forces with Dr. Jason Hall-Spencer from the University of Plymouth and Dr. Marco Milazzo from the Dipartimento di Scienze della Terra e del Mare at the University of Palermo.  Together they compared populations of the seagrass Cymodocea nodosa growing near the seeps.  They analyzed populations growing at control sites, where the average pH was 8.1 and concentrations of CO2 were 422 ppm – well within the “normal” range for ocean waters.  Closer to the seeps, however, the average pH was as low as 7.3 and CO2 levels were nearly ten times higher.  They once again found the surprising decrease in concentrations of the phenolic protective substances near the vents, confirming the work done thousands of miles away in the Chesapeake Bay.

“What this means for seagrasses and the creatures that depend upon them isn’t clear yet”, says Arnold.  “It is something we are working to understand.”

Recently, he traveled to the world’s second largest sand island, North Stradebroke Island in Australia, to study unusual underground springs flow through mangrove forests to acidify coastal areas.  There the team is working to determine if high CO2 causes seagrasses growing there to become more vulnerable to grazing by local rabbitfishes2.  Other groups are studying CO2 impacts on seagrass pathogens, such as the slime-mold like microbe that triggers outbreaks of the infamous wasting disease, which is believed to have contributed to a world-wide die-off of eelgrass in the 1930s.  “We wonder, will seagrasses really be ‘winners’ in future acidified seas?  If ocean acidification stimulates the growth of seagrasses but at the same time reduces their natural defense mechanisms, what does this mean for grazers such as fishes, turtles and dugongs and microbes that cause disease?” he explains.  “We just don’t know.  We really need this information before we can predict how seagrasses, and therefore coastal communities, will respond.”

Coastal acidification is like beer….

b1_Page_14One of our goals is to communicate the difference between “ocean acidification”, a relatively steady drop in ocean pH caused by carbon dioxide absorption form the atmosphere, and “coastal acidification” which is the result of powerful biological processes in nearshore habitats and is extremely variable.  One way we think about this is to highlight the difference between making a carbonated beverage by direct injection of carbon dioxide (ocean acidification) and brewing a beer, creating carbonation via yeast fermentation of sugars (coastal acidification).  Both are important and troubling consequences of human activities. Both are increasing.  Both can be harmful to marine and estuarine organisms.  But they arise mostly from different processes, and we must manage them accordingly.  Hence, this slide from a recent presentation on climate change in the Chesapeake Bay.

Congratulations! Senior B&MB major awarded program honors.

b1_Page_66Congratulations to Andrew McGowan ’16 who earned B&MB honors for his work on climate change impacts on antimicrobial metabolites in seagrasses.  Andrew’s work showed how natural changes in pH and carbon dioxide levels within seagrass meadows can alter plant biochemistry, suggesting how these plants will respond to increasing coastal acidification.  Andrew also won several senior prizes along the way!  Many thanks to his committee members and advisors.

Tracking acidification in the coastal zone


One of our goals is to understand an important aspect of climate change called “coastal acidification” and to demonstrate that this process is a bit different than “ocean acidification” occurring in the open oceans.

The process of “ocean acidification” occurs when excess carbon dioxide from the atmosphere enters the oceans to lower the pH and dramatically alter the carbonate chemistry.  This has been termed the “other CO2 problem” and, together with a recent two degree increase in ocean temperatures, is threatening ocean life.  For example, acidification prevents some shellfish from constructing calcium carbonate shells, and is devastating the west coast shellfish industry.  Calcification is also disrupted in many species of coral.  We’ve shown that it alters the metabolism of marine plants and fish grazing rates.  Acidification even hinders the ability of fish to smell and hear, and therefore to find prey, hide from predators, and communicate.  This is the natural consequence of having too much CO2 in the atmosphere.  Carbon dioxide levels are now over 400 ppm, up from 260 ppm at the dawn of the industrial revolution.  The oceans have taken up ~ 1/3 of this excess carbon, slowing climate change, but at a price.  The price is the acidification of the open oceans.

Here’s a description from one of our recent works: “Since the industrial revolution atmospheric carbon dioxide levels have increased from 280 to 400 ppm (parts per million), the highest levels occurring on our planet in 800,000 years (Doney et al. 2009; Sabine et al. 2004). Approximately one-third of the CO2 emitted from human activities has been absorbed by the oceans, slowing the rate of global climate change. However, this generates carbonic acid (H2CO3), resulting in an increase in the total H+ concentration (i.e., increasing seawater acidity and lower pH) and conversion of carbonate ions (CO32-) to bicarbonate ions (HCO3) in seawater. The establishment of high CO2/low pH conditions in blue waters is termed ‘ocean acidification’ (OA).  In the open oceans this process is relatively well understood. In the past 150 years, the oceans have become net CO2 sinks and the average ocean pH has dropped from 8.21 to 8.10 (Royal Society 2005). By the end of the century it is expected to fall another 0.3 to 0.4 units (Doney et al. 2009; Orr et al. 2005). This shift in ocean chemistry represents a 150% increase in hydrogen ions and a 50% decrease in levels of carbonate ions (CO32-) (Doney et al. 2009; Orr et al. 2005). OA lowers the availability of CO32-, and therefore the seawater saturation states with respect to several carbonate minerals (Ω), so that the formation and deposition of new CaCO3 minerals is reduced, and the dissolution of existing minerals is enhanced. This disrupts the growth of many calcifying organisms, including important species of shellfish, plankton, and corals, which struggle to form CaCO3 shells, skeletons, and tests.”

Here’s a good description of the problem, from the Pacific Marine Ecology Lab:

And from National Geographic:

Acidification is also occurring along our coastlines, but the process is somewhat different.  We call it “coastal acidification”.  Here the excess carbon comes mostly from the land as run-off, via rivers, bays, and marshes.  Much of this results from land use practices related to agriculture, nutrient over-enrichment, development, deforestation, etc.  The amount of carbon input is much higher, and much more variable.  For example, the daily fluctuations in carbonate chemistry near coastal marshes can be a thousand times greater than the fluctuations recorded in the open ocean over a period of many years!

Here’s how we described in recently: “Within the Chesapeake Bay, and other estuaries, the process is more complex. The sources of carbon are different: for example, estuarine waters do not generally absorb CO2 from the atmosphere but rather as dissolved organic carbon (DOC) from the land. Powerful biological processes, e.g. respiration and decomposition (i.e., heterotrophy), convert DOC to inorganic carbon.  High levels of CO2 can also be generated from DOC by microbial respiration in anoxic bottom waters as a consequence of eutrophication (Wallace et al 2014; Melzner et al 2013). Other processes can be influential as well. For instance, in some areas acid sulfate soils or nitrogen deposition may contribute to acidification. In other areas, ocean mixing or coastal upwelling may deliver high CO2/low pH waters from the open ocean.  The Chesapeake, like most estuaries, is surrounded by terrestrial and intertidal environments which export massive amounts of organic carbon to the oceans via the “land–ocean continuum” (Cia, 2010). Historically, this terrestrial organic carbon flowed to the oceans where heterotrophy converted it CO2, which was in turn emitted to the atmosphere. However, due to human activities, this has changed in several ways: (1) the mass flow of organic carbon along this land–ocean continuum has increased dramatically and (2) the oceans act as carbon sinks, absorbing excess anthropogenic carbon from the atmosphere. In short, today’s estuaries import terrestrial organic carbon, convert it to inorganic carbon, release a fraction to the atmosphere as CO2, store some, and export the rest as organic carbon to the oceans.”

Both processes are driven by excess carbon.  But to study them, we must employ different strategies.  To work on open ocean systems one must be very precise and patient, to work in coastal systems one must become comfortable with constant variation in large data sets, and design experiments appropriately.

It can be a challenge to obtain the measurements needed to accurately characterize a coastal community – a tidal marsh or seagrass meadow, for example.  Modern technologies are helping us to monitor these systems at multiple locations at rates as high as one observation per second.

In the past we’ve been using an in situ real-time pCO2 monitor, developed by Dr. Whitman Miller (from the Smithsonian Environmental Research Center), to measure carbon dioxide concentrations in estuarine waters.

IMG_0439We have recently expanded our capabilities to monitor atmospheric carbon concentrations in the coastal zone using airborne sensor packages.  This means that, together with our collaborators, we can now monitor carbon above and below the waterline simultaneously, in real-time in coastal waterways, marshes creeks, and in the air above them – all without getting wet!

To see how it works check out this video: IMG_0415

By coordinating many sensor packages, and taking frequent water samples for later analyses, we can track carbon into and out of coastal ecosystems.  By analyzing plant tissues and conducting tracer experiments with stable (non-radioactive) isotopes we can follow the flow of carbon through plants and into metabolic pools of carbohydrates, proteins, and phenolic substances – above and below ground.  We can even track the carbon among trophic levels as plants are consumed by herbivores, and so forth.

Questions we hope to answer:

How to salt marshes process carbon?  How do they take it in and release it?  What are the local conditions that estuarine organisms experience near marshes?

Can seagrass meadows take up and safely store large amounts of excess carbon – acting as a helpful “carbon sponge” to help slow climate change?

Does the carbonate system change in predictable ways within seagrass beds?  And what are the consequences for organisms, such as bay scallops, that live there?

We thank Dickinson College’s Research and Development Committee for funding, and the folks at Valarm for technical assistance.

New publication on seagrass responses to high CO2 / low pH conditions



Fish collecting is always better at night (but beware sharks!)

Fish collecting is always better at night (but beware sharks!)

We recently published an article in the journal PLoS ONE entitled “Impacts of Groundwater Discharge at Myora Springs (North Stradbroke Island, Australia) on the Phenolic Metabolism of Eelgrass, Zostera muelleri, and Grazing by the Juvenile Rabbitfish, Siganus fuscescens”.  This article describes the impact of natural “acid springs” on eelgrass meadows near North Stradbroke Island, Queensland, Australia.  The data support the findings we published from the Chesapeake Bay (USA) and Sicilian CO2 vent sites (Italy): high CO2/low pH conditions dramatically reduce soluble phenolic levels in seagrasses, often with an increase in the levels of insoluble lignin.  Dickinson students, including co-authors Grace Freundlich,Taylor Weilnau, and Arielle Verdi participated in this research.  Marine scientist and director of global education programs, Ian Tibbets, was our University of Queensland collaborator.  Support was provided by grants from the Smithsonian Institution and NASA.  Seventeen other Dickinson students, enrolled in the College’s Global Scholars pilot program, contributed in other ways.  We’re grateful for Dickinson’s continued support of innovative undergraduate research programs.

Science Research at Dickinson College

It’s great to work with talented and hard-working colleagues and students in the Biology and Environmental Studies Departments!


Check out recent research projects in the news including:

Snake research in Guam, Professor Boback

Boa constriction research just published in the Journal of Experimental Biology, Professors Zwemer and Boback

Climate research in local lakes, Professor Strock

Cancer Research and Bioinformatics, Professor Roberts




Congratulations to our graduating students!

Under the Australian Sun!

Congratulations to our three graduating lab members on completing their programs of study and submitting their undergraduate research, Impacts of groundwater discharge at Myora Springs (North Stradbroke Island, Australia) on the phenolic metabolism of eelgrass, Zostera capricorni, and grazing by the juvenile rabbitfish, Siganus fuscescens, for publication this spring!

This work built on the work of the 2012 Global Scholars team.  Check out their site on under “Pages”.


Ocean Acidification Report: West Coast Seagrass Studies


This summarizes some interesting, ongoing work on seagrasses and coastal carbon that is similar to what our group is doing in the Mid-Atlantic.

Eric Swenson, Editor
Brad Warren, Publisher

Research exploring how seagrasses in Washington, Oregon, and California bays and estuaries affect carbonate chemistry are due to start this spring and summer. The principal investigators are George Waldbusser of Oregon State University, who will focus on Netarts Bay; Jennifer Ruesink of the University of Washington, working in collaboration with the Washington Department of Natural Resources at several sites; and Tessa Hill, University of California, Davis, studying Bodega and Tomales Bays. Sea Grant is funding the California and Oregon research.

The three will be using different instrumentation, techniques, and measuring systems in a variety of venues, looking to identify habitats and conditions with the greatest potential for local reduction of carbon dioxide dissolved in water. Collectively, they will shed light on how fast seagrasses can draw down carbon dioxide through their photosynthesis, whether this carbon is sequestered longer term, and therefore the potential for primary producers to improve water conditions for sensitive shell-forming organisms.

Ruesink notes that some seagrass habitats may be net emitters of CO2 by trapping organic material that decomposes, releasing the gas. Similarly Waldbusser will be comparing native eel grass and Japanese eel grass habitats as he tries to understand the “carbon budget” of Netarts Bay. The scientists will make their findings known to policymakers, stakeholders, and the public in late 2015 to enable comparisons at broad geographic scales from a variety of estuaries.

Read more here.

A beach bum’s guide to ocean acidification

Baltimore native Jim Meyer is a stand up comedian and freelance writer who wrote this piece about ocean acidification.  While it’s probably not going to get him invited to testify before congress he is reaching people that we usually don’t, which is critically important.  And he does mention Jimmy Buffett.  So, thanks Jim and thanks to Lee Karrh for sending this my way.  This is our post of the day:……Over the last 200 years, human pollution has caused the oceans’ pH to drop 100 times faster than it did in the previous 650,000 years. To give you an idea what the oceans are going through, try to imagine taking in the entire six seasons of The Wire in 32.4 seconds. You’d have 11 strokes. And that’s just the tip of the iceberg (a cliché that will baffle your grandkids).  Read more:


The Real “Hot Tub Time Machine”

castleBlog readers will already know about the hydrothermal vents along the Italian coastline, some of which vent pure carbon dioxide into the sea at normal temperatures.  In conjunction with our coworkers we’ve examined these vents as potential ‘living laboratories’ which give us a glimpse of marine life in future high carbon dioxide / low pH oceans.  This photgraph, by Jimmy Harris (see link below), shows the Castello Aragonese near Naples, Italy.  Yes, the Italian translates to the ‘Aragonate Castle’.  It’s carved into the calcium carbonate rock of the island.  Want to see more?  Well our colleague, Jason Hall Spencer, has some great YouTube videos of the site, above and below the waterline.  Well, we thought the title of a recent blog post article, “Hot Tub Time Machine” by Elizabeth Kolbert, was clever.  Here’s the link: Off the coast of Italy, CO2-spewing vents are giving scientists a glimpse at the acidic oceans of our future. The results are Elizabeth Kolbert  @ElizKolbert • February 11, 2014  This article is adapted from the author’s new book, The Sixth Extinction: An Unnatural History, on sale today.  We haven’t read the book yet.  Have you?  If so, what did you think?

Virtual poster presentation for OAPI meeting (2013)

C nodosa low pHGreetings to those attending the Ocean Acidification Principle Investigators Meeting in Washington D.C. This is our virtual ‘poster’ presentation, posted here instead of in print in an effort to be more sustainable.

CLICK HERE TO DOWNLOAD OAPI as pdf for reading and teaching.

You are welcome to view our poster now for viewing on your mobile device or download it for viewing later, at your convenience.


Thomas Arnold (Dickinson College)
Whitman Miller (SERC)
Jason Hall-Spencer (U Plymouth)
Marco Milazzo (U Palermo)

Plant resource allocation: from Goethe and Darwin to today.

Our new 2013 review of plant defense responses and resource re-allocation published in Frontiers in Plant Science and online HERE.  Read about the uncommon wisdom of early poets and natural historians, who had a pretty good idea of how plants should allocation precious resources to maximize their fitness.  For example The budget of nature is fixed; but she is free to dispose of particular sums by an appropriation that may please her. In order to spend on one side, she is forced to economize on the other side”  (in Darwin 1872)

Seagrass work profiled in Chesapeake Quarterly

cover_largeWe study acidification in estuarine systems.  And at this time last year our work on the impacts of ocean acidification, with Whitman Miller from the Smithsonian, was  profiled in the Maryland SeaGrant magazine.  In case you missed it, read it here:

Seagrass responses to ocean acidification: Chris M earns departmental honors



Biology Honors Presentations.  Wednesday, May 1, 4:30 p.m.Stafford Auditorium.  Christopher Mealey presents “Climate Change Effects on Marine Ecosystems” 

Chris Mealey will present his honors thesis research, including work from the Chesapeake Bay (USA) and Moreton Bay (Australia) this week.  Chris arrived in our lab four years ago and also conducted research at the School for Field Studies – Turks and Caicos site on invasive lionfish and at the University of Queensland as a part of our Global Scholars Program.  Some of his work was published in the journal PLoS ONE in 2012 and he will be attending the graduate program in marine biology at the University of Charleston in the fall.  Come hear about his work on Wendesday!

NEW UPDATE: Chris was awarded departmental honors for his thesis “Impacts of Ocean Acidification on the Polyphenolics of Seagrasses” on May 14, 2013.  Congratulations Chris!


Atmospheric carbon dioxide (CO2) has increased by about 40% since the Industrial Revolution, with current levels residing around 395ppm. A portion of this excess CO2 is absorbed by the oceans resulting in the increase of H+ and carbonic acid concentrations, as well as a corresponding reduction in mean pH. This phenomenon is termed ‘ocean acidification’ (OA). Multiple studies demonstrate a decline in calcification of many marine organisms as a result of OA, but greater photosynthetic productivity in algae and seagrasses has also been reported. However, little is known regarding the effects of OA on the chemical defenses produced by these marine angiosperms. Three forms of CO2 enrichment were utilized in this study to observe the effects OA may have on secondary metabolite accumulation in four species of seagrass. These include a Free Ocean Carbon Enrichment (F.O.C.E.) system – Severn River, MD (USA), a natural volcanic vent – Vulcano (Italy), and the naturally acidified Myora Springs – North Stradbroke Island (AUS). Additionally, herbivory tests examined preferences of juvenile black rabbitfish on eelgrass grown in low and normal pH regions near the naturally acidified Myora Spring (AUS). Phenolic acids, the main chemical defenses of these species, were identified and measured via HPLC, whereas more complex tannin concentrations were measured by colorimetry. The results of this experiment observed a significant decrease, about 60% in some instances, in the production of these secondary metabolites corresponding to a decrease in average oceanic pH and an increase in pCO2 concentrations. The reduction in the accumulation of these chemical defenses within the observed seagrasses implies a greater susceptibility to herbivory and harmful pathogens, which reveals location dependent impacts of OA on marine plants.

PMEL Carbon Program: An Introduction to Ocean Acidification

pmel-oa-imageee_medOcean Acidification: The Other Carbon Dioxide Problem.  The PMEL’s website summarizes the work of the NOAA-sponsored Carbon Program and provides basic information and links to recent discoveries pertaining to ocean acidification.  For more information see:

« Older posts