The Fitzgerald Lab: Salt Marshes and Sediments

Hey y’all! I’m Carina Terry and this summer I’m working in Duncan Fitzgerald’s lab. I’m a rising sophomore in the College of Arts and Sciences. I started off as a physics major, but after a semester in the BURECS program, I decided to switch to earth and environmental sciences.

The Fitzgerald lab is a perfect internship for my major. We’re studying salt marshes; their composition, dynamics, and most importantly, how we can save them from impending sea level rise. The marsh we’re looking at now is the Great Marsh right here in New England. This marsh has a high occurrence of slump blocks – large pieces on the edge of the marsh that are slowly separated from the rest of the marsh until they reach a tipping point and cave into the tidal creek. The loss of these blocks isn’t great for the marsh, as it means the marsh is eroding even more quickly.

Tidal creek with slump blocks at high tide 

Many theories in the world of marsh studies state that erosion increases when wave power increases. This is applicable to many other cases of marsh erosion, but Professor Fitzgerald doesn’t believe high wave power is the cause of our marsh’s slump blocks. The blocks that we observe are found fairly far upstream in the tidal creek – far enough that the waves can’t get that powerful because the channel is fairly narrow. Since high wave power doesn’t seem to be the cause of the slump blocks, we have to figure out what is.

To solve this question, we test the marsh in several ways. After driving about an hour north of Boston, we park our truck and then hike out into the marsh. This hike usually takes about 10 – 20 minutes, depending on which part of the marsh we’re examining. Occasionally we have to crash our way through forest and brush, which can be a bit challenging, but it’s worth it – when we make it to our marsh site, the view is beautiful.

When we reach the tidal creek, someone has to climb down into the creek. (We have to make sure we go to the marsh at low tide, so the water is shallow enough that we can do this – we don’t want anyone to take an unpleasant swim!) After they’ve climbed down, they use a special syringe to take samples down the side of the creek bed. We do this for about 3 or 4 sites a day, then head back to the lab.

Once we’ve got the samples back in the lab, we first have to dry them for several days. When they’re dry we weigh them, which will allow us to calculate their bulk density. Then we split the samples in half and begin the rest of our analysis.

Dried marsh samples

The first half are assessed for organic content. We crush the samples up into a fine powder using a mortar and pestle, then place the crushed samples into crucibles. After weighing the crucibles to find the initial mass, we place them into the furnace. Then, at around 5 or 6 pm, one of us has to come back to turn the furnace on. The samples are burned at 550 degrees Celsius (1022 degrees Fahrenheit!) for 16 hours; we come back in the morning to turn the furnace off and let them cool, then weigh them once again. Since all the organic material was burned away in the furnace, this tells us what percentage of the sample was composed of inorganic sediments and what percentage was organic.

Mortar and pestle

Crucibles

The other half of the samples are analyzed for biomass. First, we use a sieve to separate the sediments from the vegetation in the sample. The vegetation is dried and then weighed by itself, to find what percent of the sample was composed of vegetation. The sediments are split in half; one portion is dried and weighed, while the other is stored in a vial for future use. Eventually, these samples will be sent to a lab in Louisiana, where the size of the sediment grains will be analyzed and recorded.

Sieves and brush

Clearly, a lot of the analysis we do is related to the mass and composition of the marsh: what percentage is inorganic, how much vegetation is present, and how big the sediment grains are. We analyze these factors because we suspect they could have a correlation to how stable the marsh is. Once we have collected all our data, we will look for trends and try to find which of these factors have the largest effect on marsh stability. Then, when we know the important factors, we can work on restoring the marsh and fortifying it against rising sea levels.

The salt marsh is an important ecosystem; it serves many functions, including sheltering young fish and insects and removing carbon from the atmosphere. It’s very important that we work to keep it from being destroyed due to climate change. And, of course, we wouldn’t want to lose this beautiful view.

Dietze Lab Internship

I’m Katie Ragosta, and this summer I’m interning with Professor Dietze and working on PEcAn, the Predictive Ecosystem Analyzer. While ecologists have collected a large amount of data, and are capable of collecting more with relative ease, that data is only useful for the kinds of large scale predictions that affect policy if we have a way to synthesize multiple data sets effectively, since no one data set will give anything close to a complete picture. Essentially, the Dietze lab aims to develop a model capable of integrating multiple data sources for more accurate predictions of the carbon cycle and biodiversity.

I’m majoring in Physics and Mathematics here at BU. While it sounds like those majors might not fit perfectly with an environmentally focused project, they provide a lot of experience with systems modeling and programming, both of which are important in the Dietze lab. I took Computational Physics last semester, which gave me experience with Fortran and C. I also have a job in the physics department during the school year which uses a lot of C++, and I learned some Python in high school. The experience has definitely helped a lot with my work here, but if you don’t have much formal training and still want to work in the Dietze lab, there are lots of free resources online. The Dietze lab actually mostly uses R, which I learned some of in the first few days of the job, but what I do specifically doesn’t require much R.

The goal of PEcAn is to synthesize multiple data sources, so one of the ongoing projects in the Dietze lab is incorporating new models into ours. There’s a to-do list of pre-existing models that are being gradually added. My job is to add one called CABLE, or the Community Atmosphere Biosphere Exchange Model.

The files for CABLE are written mostly in Fortran, which is why I was assigned this particular job. The CABLE website in that screenshot has some documentation on how you should go about building and running the model, so my first step was to read through that. Then, I got to work on trying to build it. There are two versions of CABLE, an offline version that uses its own input data and an online version that can use any input data. I’ve been focusing on the online so far. Getting the model to build involved a fairly large amount of debugging, and I actually just finished building the online version today.

Now I need to run the model as a test to make sure I built it correctly and see how it’s supposed to work. This is important because my next step will be converting CABLE to the format that PEcAn’s models are supposed to use, and we don’t want anything to get lost or changed in translation. I’ve been told that transitioning into PEcAn generally goes more smoothly than the initial stages of building the model, so I’m looking forward to that. When (or if) I get CABLE fully integrated into PEcAn, I’ll take another model from the model to-do list and repeat. Working in the Dietze lab has been a great experience, and I’m really glad to have this opportunity through BURECS.

A visit from the Boston Leadership Institute

Throughout the 2016-2017 academic year, our lab group hosted several groups on campus in an effort to promote STEM disciplines (and specifically climate science) to high school students. Twice in the spring we were joined by TeenSHARP chapters from Delaware and New Jersey, in addition to a visit from Boston Collegiate Charter School's entire 9th-grade class.  On Friday we welcomed another group of students, this time from the Boston Leadership Institute (BLI), to the BURECS lab for a day-long introduction to Antarctic Earth science research. The students, all of whom have expressed interest in studying STEM in college, had the opportunity to hear Dr. Marchant speak about his research before multimedia presentations in the Digital Image Analysis Lab (DIAL) and a hands-on exploration of the main lab. We thought we would share a few photos from their visit with you here on the blog.

Dr. Marchant discusses the various rock formations present in the McMurdo Dry Valleys (MDV) before the students take a virtual reality tour of the central Dry Valleys. (LAB TIP: you can do this at home by going to buriedice.com. The system works with virtual reality headsets and on desktop computers.)

Here Drew Christ, one of the BUARG graduate students, guides the BLI students through the use of the scanning electron microscope (SEM). They were able to view ancient, preserved diatoms from the MDV at over 6000x magnification!

Olivia explains the various types of grains present in an ash sample. Under the optical microscope, it's sometimes difficult to distinguish anorthoclase crystals (the important bits) from glass fragments due to their similar translucence. These students had the opportunity to try crystal picking for themselves; some found it frustrating, but a few had the sharp eyes and steady hand necessary to be quite good at it.

Donovan discusses the methods for segregating fossilized moss fragments from the encompassing mud. The mosses are some of the last known remains of vegetation from Antarctica, and have been dated to between 14.07 and 13.85 million years old. Though delicate, several students carefully separated the mosses without breaking them--we were impressed!

Noah Conley, another BURECS summer intern in the Marchant lab, gave an overview of Martian topography for the students. Using several of the labs high-resolution screens, he helped students identify the topographical features on Mars, and shared what these features indicate with respect to ice buried beneath the surface.

All in all, a great visit from BLI--we were excited to meet so many students excited about Earth science! We look forward to seeing them again next summer.

Are you and/or your students interested in visiting the BURECS lab? Send us an e-mail at burecscience at gmail dot com or ddennis at bu dot edu.

Fitzgerald Lab - The Great Marsh

Hi! I’m Miyu Niwa, a Biochemistry & Molecular Biology major born and raised in Tokyo.

I’ve had the great opportunity of being able to work under Dr. Duncan Fitzgerald the past month, helping investigate marsh erosion in New England and the effects of sea level rise.

The marsh, simply put, is a beautiful place. From afar, you can see the fluffy green colliding with the clear blue sky as the water shimmers at the edge. It almost looks like one of those scenery default desktop pictures you can choose from on the computer. Having lived in Boston and Tokyo, I am accustomed to the bright city lights and energetic atmosphere, so the drastic difference in this new environment highlights the peacefulness of the marsh.

But the salt marsh’s beauty does not stop there – it has multiple benefits that make it extremely valuable. Marshes filter water, provide habitat and breeding grounds for various species, and are highly productive ecosystems. More importantly, marshes act as shoreline protection, shielding the coastal areas from storms and stabilizing the shoreline with their wave dampening effect.

Professor Fitzgerald’s lab investigates the current eroding of the Great Marsh, and how the marshes are responding to climate change and the accelerating rate of sea-level rise. Specifically, he focuses on Plum Island Sound, MA and takes samples from the different rivers there (Ipswich, Rowley, Parker, Essex). For us interns, work happens both in the lab and in the field. Whatever samples collected in the field are processed in the lab, which is usually why it’s right after fieldwork days that we are busiest with work. Some of the things we analyze are the organic and inorganic/biomass content in the marsh samples.

There are different kinds of work out in the field, but this particular week, we went out to four sites to set up sediment pads along 100 meters from the water. Every 5 meters there will be sediment pads set on the ground next to the flags. Every other flag will have holes dug out for cups to be placed right underneath the surface to collect the water that runs through. When we collect them after the spring tide comes, we will run the water through a filtration process to determine the amount of organics left, as well as the total sediment content. Eventually, we will have enough data to plot a graph and map out which areas tend to have more or less sediment in the water.

  

The great part about working with this project is how I can experience first-hand the full process of research: collecting samples in the field, analyzing them in the lab, and then creating models to visually show the data. I get to take part in every step of the research process and see how each part affects the overall results. I never thought I would have this experience of going out into the field and collecting samples, and it has now brought in a whole new dimension to my understanding of the different kinds of research. I am excited for the rest of my internship as I learn more about the work Professor Fitzgerald does in trying to protect the Great Marsh.

This summer, I’ve been working as an evaluation intern at Harvard’s Museum of Natural History. My main project so far has been remedial exhibit evaluation in the Next of Kin exhibit. Exhibit evaluation is how museums figure out what people are learning from exhibits, and the evaluation is remedial because it's taking place while the exhibit is completed in its final form and open to the public. The exhibit I've been evaluating, Next of Kin, is an exhibit on the anthropogenic extinction crisis. An artist from outside the museum designed the exhibit, and it primarily focuses on presenting endangered and extinct animals very directly to museum-goers in ways that force them to face, sometimes literally, the creatures humans have harmed. The exhibit includes artifacts such as a skeleton of the extinct Moa, a preserved ear from an endangered species of whale, and large, striking heads of different kinds of deer whose habitats are threatened. The exhibit has a lot in it, and there is a strong intended narrative about the role humans have played in mass extinction. To see which of the items are eliciting responses from visitors and whether the message comes through clearly, I track and interview visitors.

the deer heads positioned so that you look at them face to face

I track every third adult who comes into the exhibit to make sure my sampling is random. When the person I’m going to track walks in, I refer to a simplified map of the exhibit that has every point of interest marked as a location. When the person stops at one of those points, I start a timer to see how long the person stays there, then when that person moves on to the next point, I record that as well. By the end of even a quick trip through the exhibit, I usually have a sheet full of crisscrossing lines connecting X’s and numbers to mark what felt to the person like an intuitive way to move through the exhibit.

the view from the entrance to the exhibit

the map I use to mark down peoples' paths

After marking down someone’s movement pattern, I ask them directly what they thought about the exhibit. I have several interview questions that get qualitative data to match up to the quantitative tracking data. People are usually very open to being interviewed, and have interesting insights about the design, content, and layout of the exhibit even if they only walked through fairly briefly. Using this data, my next step is to analyze what people did and did not learn so that the artist who made the exhibit can use the information to shape future designs with the audience in mind.

Fulweiler Lab: Something New Every Day

I’m Victoria Momyer, and I’m currently interning in Wally Fulweiler’s biogeochemistry lab. I’m a Biochemistry and Molecular Biology (BMB) major, but I’ve always loved science of all kinds. The posters that decorate my room center around Einstein and the periodic table, my favorite place in the world is the Museum of Natural History in New York, and my favorite book is Carl Sagan’s Cosmos. So you could say I have a borderline-disturbing obsession with science.

This, however, means I feel right at home in a lab like the Fulweiler lab. As an intern, I get a little taste of pretty much all the research that’s being done in the lab. I never feel like I’m doing busy work, but rather really contributing and helping the graduate and PhD students who are working on independent projects.

One of the projects I’m helping with is investigating whether methane leaks around Boston allow for the growth of an insect community in the city’s groundwater wells, which, in recent years, has shown to house bugs rarely ever found in water. Our field work consists of collecting bug samples by sending a camera and a net ten feet down to the water level, and drying them to analyze the contents of the biomass. We also collect water and gas samples, treating different samples with different chemicals in order to detect levels of several different types of components. It’s very interesting to be working in wells right at BU, as it feels like I’m helping solve a problem that’s so close to home.

Taking insect samples from a groundwater well on Comm Ave.

Another project I’m assisting with looks into the nutrient cycling brought about by oysters, and how this has been impacted as oyster populations have declined. I recently went out into the field to Bissel Cove, RI and Allen Harbor, RI in order to sample and test the water. We went out on a beautiful day, and I never imagined taking chlorophyll samples and testing water parameters for hours could be so relaxing and so rewarding. After filtering out the chlorophyll, we freeze the filters in a dark setting (so as not to excite and thus lose chlorophyll) to be extracted and analyzed later. Chlorophyll extraction and analysis has become a core skill for me at the lab.

Chlorophyll extraction and analysis must be done in a dark room so none of the molecules are excited and lost by light. Only green light can be used to see one's work, as chlorophyll does not absorb green light. The machine pictured is a fluorometer, used to measure the amount of fluorescence in a chlorophyll sample to help ascertain the amount of chlorophyll and thus the amount of plankton.

Finally, I’ve been working on taking nutrient, silica, and phytoplankton samples from the Charles River, as well as testing various parameters—pH, temperature, salinity, conductivity, dissolved oxygen—one to two times per week. Eventually, we will compile the data to help figure out why there have been sudden drops in silica and large cyanobacteria blooms in the river for the past two summers. We will also work on analyzing the plankton under a microscope, photographing them, and keying them out to create our own library of Charles River microorganisms.

Bissel Cove, Rhode Island.

With all the projects going on in the lab, it never gets boring—there’s always something to work on, so nothing ever gets monotonous. Each week brings a new activity or two—next week, for example, we will learn how to analyze gas samples with the gas chromatograph, and will be traveling to Pigeon Cove in Rockport, MA to collect algae samples to compare to samples we have from 1890! I can’t wait to see what new skills and discoveries I’ll find with the lab in the weeks to come.

Signing off,

Victoria

Ecological Forecasting: Reevaluating Ecology in the Face of Climate Change

The Science of Ecological Forecasting
The field of ecology is approaching new horizons through the work and innovation done at the Dietze research group here at Boston University. The development of computational and statistical models, built with analyzing vast amounts of ecological data in mind, has recast the ecological sciences as a predictive, informative endeavor, particularly in the face of climate change and its dynamic effects on ecosystems and biological systems.

The Internship
This summer internship dives right into the process of developing and implementing ecological models through computer programming languages. I joined this internship on the basis of my experience in mathematics, computing, and the biological sciences. I enrolled in BI 303: Evolutionary Ecology as well as MA 226: Differential Equations this past Spring semester, and the interdisciplinary connections between the two classes were obvious and manifold. Dynamical mathematical models are abundantly used in ecological and biological contexts to make predictions and establish theories about ecological systems. Last Fall semester I enrolled in CS 111: Introduction to Computer Science I, where I was introduced to the Python coding language. All of these experiences have inadvertently helped prepare me for the work in the internship. In the development of computational ecological models, the Dietze lab uses the statistical computing language of R, in addition to many others. Seeking to broaden my knowledge of coding languages, and given my classroom experience, this opportunity seemed a natural fit.

As you would expect, a typical day in the lab is dedicated to coding, using the software version control platform of GitHub. Many other software components are used in developing the various ecological analyzers. One such project has been PEcAn.

Picture 1. Associate Professor Mike Dietze of the Earth and Environment Department delivers a seminar on the "emerging imperative" of ecological forecasting, which seeks to synthesize vast amounts of existing ecological data into coherent, analytical, statistical forms that can then be used to make predictions (21 June 2017).

The PEcAn Project

A large project of the Dietze lab has been PEcAn, which stands for the "Predictive Ecosystem Analyzer". http://pecanproject.github.io

It's goals, as established by the lab, includes:

"Climate change science has witnessed an explosion in the amount and types of data that can be brought to bear on the potential responses of the terrestrial carbon cycle and biodiversity to global change. Many of the most pressing questions about global change are not necessarily limited by the need to collect new data as much as by our ability to synthesize existing data. This project specifically seeks to improve this ability. Because no one measurement provides a complete picture, multiple data sources must be integrated in a sensible manner. Process-based models represent an ideal framework for integrating these data streams because they represent multiple processes at different spatial and temporal scales in ways that capture our current understanding of the causal connections across scales and among data types. Three components are required to bridge this gap between the available data and the required level of understanding: 1) a state-of-the-art ecosystem model, 2) a workflow management system to handle the numerous streams of data, and 3) a data assimilation statistical framework in order to synthesize the data with the model."

Screenshot 1. A workflow log of various model runs on the PEcAn web interface.

Screenshot 2. A typical R Studio working environment within the PEcAn development process.

By: Elias Kastritis

Mathematics and Philosophy double major