Science Communication

Notes from the Undergrads 2016: Part I

This summer, undergraduate students from all over the United States have come to the University of Rhode Island Graduate School of Oceanography to conduct oceanography research as part of the Summer Undergraduate Research Fellowships in Oceanography (SURFO) program. Learn more about what they’ve been up to in this two-day series of short blog posts they’ve written for oceanbites!

The 2016 SURFO cohort: Standing from left to right: Christopher Vatral (Eastern Nazarene), Matthew Gentry (UMass Amherst), Jennifer Warmack (Humboldt State), Austin Grubb (Susquehanna), Nicole Flecchia (URI), Ariel Pezner (UCLA), Alexandra Norwood (Arizona State), Scott Goldberg (Northwestern). Seated from left to right: Jakob Gessay (Coastal Carolina), Annelise Hill (Reed), Elizabeth Wright-Fairbanks (Middlebbury), Adena Schonfeld (Miami), and Whitney Schultz (Colorado School of Mines)
The 2016 SURFO cohort: Standing from left to right: Christopher Vatral (Eastern Nazarene), Matthew Gentry (UMass Amherst), Jennifer Warmack (Humboldt State), Austin Grubb (Susquehanna), Nicole Flecchia (URI), Ariel Pezner (UCLA), Alexandra Norwood (Arizona State), Scott Goldberg (Northwestern). Seated from left to right: Jakob Gessay (Coastal Carolina), Annelise Hill (Reed), Elizabeth Wright-Fairbanks (Middlebury), Adena Schonfeld (Miami), and Whitney Schultz (Colorado School of Mines)

“You Eat What You Wear” by Jennie Warmack

“No Little Blobs to See Here” by Austin Grubb

“A Salty Subject: Does Wind Affect Salt Marshes?” by Annelise Hill

In Silico Microbes from the Deep Sea” by Matthew Gentry

“The Importance of A World Unseen” by Jakob Gessay

“Nutrients, Climate, and Currents in the Past” by Alexandra Norwood

“The Ocean’s Smallest Predators” by Liza Wright-Fairbanks


You Eat What You Wear

Jennie Warmack — Humboldt State University 

We have grown up hearing that “you are what you eat” and “you are what you wear”, but did you know that you might be eating what you wear? Recent studies have revealed that small fibers from our clothing are released in the washing machine just like lint in the dryer. Unlike dryers, however, washing machines don’t have a filter to trap these fibers, so the fibers are flushed away with the rest of the water at the end of the wash and rinse cycles. Where do they go from there? Nobody can say it better than Gill from Finding Nemo: “all drains lead to the ocean”.

Recovery of sediment trap array onboard the R/V Endeavor. Image Credit: Jennie Warmack, June 2016
Recovery of sediment trap array onboard the R/V Endeavor. Image Credit: Jennie Warmack, June 2016

Fibers that come from synthetic fabrics like polyester, nylon, and spandex do not easily break down in the oceans because they are plastic. There’s still a lot we don’t know about these plastic fibers, but it’s hard to believe they are doing any good. The potential for harm warrants study of where these plastics are going and what they are doing. We do know that animals like filter feeders, larval fish and even the smallest animals, zooplankton, will eat the fibers mistaking them for their favorite foods. By the laws of nature, those animals will be eaten by other animals until those animals are eaten by other animals who end up on our plate, where we might be eating last season’s fashion statements. Nothing like polyester to spice up a mussel stew. Yum!

Plastic fibers have blanketed the ocean floor around the world, but nobody has looked into how they get there. We know that the fibers leave the washing machine and pass through treatment facilities because they are so small, but their journey between your laundry room and the depths of the ocean is unknown. For my SURFO project at URI GSO, I looked at how many of these fibers are sinking in the ocean and how fast they are doing so on the shelf break south of Rhode Island. This process started by going to sea for a week on the R/V Endeavor and collecting sinking fibers with sediment traps for three and a half days.

Trap tube with polyacrylamide gel cup base intact fresh from recovery after the 3.5-day deployment. Image Credit: Jennie Warmack, June 2016
Trap tube with polyacrylamide gel cup base intact fresh from recovery after the 3.5-day deployment. Image Credit: Jennie Warmack, June 2016

Sediment traps act as floating rain gauges for the sinking plastic fibers. A thick, taut wire between a buoy and a heavy weight has tubes attached at different depths with a polyacrylamide gel cup at the bottom of each tube to catch the fibers. Four tubes were used in this study and ranged between 60 and 200 meters below the surface. Back on land, the fibers were counted, characterized by color, measured, and identified by type of plastic.

This study was one of the first to look at the movement of plastic fibers through the water column. Hopefully more research will take place in the near future and the understanding of related environmental and biological effects will continue to grow. Once we know more about how plastics are populating the ocean, we can raise awareness and prevent more fibers from ending up on your plate.

No Little Blobs to See Here

Austin Grubb — Susquehanna University

When someone mentions microbes or microorganisms, what do you picture? If you’re like most people, you probably picture tiny dots or amorphous blobs that don’t take on a defined shape. However, there are many microorganisms that have evolved complex forms like the image you see below.

Marine microorganism called a dinoflagellate (top), two marine dinoflagellates (bottom right), and a marine microorganism known as a copepod (bottom left). Note photo are not to scale. Photo credits Austin Grubb.
Marine microorganism called a dinoflagellate (top), two marine dinoflagellates (bottom right), and a marine microorganism known as a copepod (bottom left). Note photo are not to scale. Photo credits Austin Grubb.

So wait, why is this little creature shaped like this and that little critter shaped like that? Imagine all the different plants and animals that you are accustomed to seeing. Their bodies and forms have evolved in a manner that increase the organism’s ability to do something. This obviously varies across every species, but the important thing is that we can apply the same idea to these microorganisms- in other words, their forms and their bodies have evolved to increase the microbe’s ability to do something. But what?

Single-celled diatom (left) and chain-forming diatom colony (right). Note, photos are not to scale- the colony is actually much larger than the single cell. Photo credits Austin Grubb.
Single-celled diatom (left) and chain-forming diatom colony (right). Note, photos are not to scale- the colony is actually much larger than the single cell. Photo credits Austin Grubb.

Phytoplankton are an abundant and widespread group of microorganisms that live in the ocean and use photosynthesis to create their own food from light, much like the plants we’re all familiar with. Phytoplankton are responsible for about half of the oxygen in the atmosphere, meaning that you have phytoplankton to thank for every other breath you take. We are interested in one group within the phytoplankton called diatoms.

Diatoms make their cells walls from silica, meaning that they are essentially made of glass. Most diatoms are single-celled organisms however, there are some that form chain-like colonies. Since diatoms are photosynthetic organisms, we believe that light can have a profound impact on them. Light plays a role in altering their growth rate, but no one knows if it affects their shape and size.

We believe that chain-forming diatoms have evolved their bodies to increase and maximize their ability to absorb light. Longer colonies increase the area that can be used to absorb light for the colony. This would be especially advantageous when there is not a lot of light available, such as when diatoms are deeper in the water column or there are other particles, organic and/or inorganic, above them.

Our hypothesis is that these chain-forming diatoms are adapted to grow longer colonies in low-light conditions in order to maximize the area for light absorption. In order to test this hypothesis, I am growing diatoms under specific light conditions, high-light and low-light, and will use light microscopes to determine how this affects their size and shape. In addition, I am collecting data that will allow me to generate growth rate curves to see how the different light conditions affect diatoms’ growth rate.


A Salty Subject: Does Wind Affect Salt Marshes?

Annelise Hill — Reed College

A salt marsh on Assateague Island Source: National Park Service
A salt marsh on Assateague Island
Source: National Park Service.

Local folklore has it that when a Spanish Galleon sunk in 1750 the horses on board swam until they found land. Today, the descendants of those horses can be seen on the beaches, swimming in the bay, and stealing visitor’s food at Assateague Island National Seashore. This National Park is located on a 37-mile long barrier island that separates Chincoteague Bay from the Atlantic Ocean.

While the wild ponies are the stars of this island, the salt marshes that are their stage need our protection. Climate change is causing sea level rise and an increase in storm intensity that is making survival for salt marshes more difficult. The National Park Service is trying to understand the natural forces affecting this ecosystem so that they can better manage it.

My research this summer will answer two questions about one natural force: wind. Firstly, does wind have an effect on the amount of flooding experienced by the Assateague salt marshes? And secondly, does wind affect dissolved oxygen levels in Chincoteague Bay?

The species in a salt marsh must be in an area where they will get the right amount of flooding. Mean High Water (MHW) is the mean of the heights of high tides while Mean Low Water (MLW) is the mean of the heights of low tides, where these are determines where the plants are. Source: USGS
The species in a salt marsh must be in an area where they will get the right amount of flooding. Mean High Water (MHW) is the mean of the heights of high tides while Mean Low Water (MLW) is the mean of the heights of low tides, where these are determines where the plants are. Source: USGS

A salt marsh is a complicated ecosystem: they are regularly flooded with salt water and then drained by the tides. Different plants do better with different amounts of flooding which leads to species being in areas that experience the specific amounts of flooding that they are adapted to. Tides are the primary factor causing salt marshes to flood but winds can also have an effect. The direction from which wind is coming from can lead to water being pushed away from the shore, leaving marshes more exposed. Alternatively, wind can push more water onto the marsh, making tidal flooding more extreme.

The NPS manages salt marshes as important habitat for fish as well as for ponies. Fish need oxygen just like people. Theirs is just dissolved in the water. Phytoplankton and submerged plants produce this oxygen during the day through photosynthesis. Oxygen can also get into the water at the surface, where it diffuses into the water from the air.

Wind can affect dissolved oxygen levels in two ways. First, wind creates more waves at the surface, which allows more oxygen to enter the water. Wind can also affect the circulation within a water column. As organisms in deep water consume oxygen, the oxygen needs to be replaced with new oxygen so that these organisms can keep breathing. Different wind directions can lead to more or less oxygen in deeper waters by changing the amount of oxygen moved to these waters.

To determine how wind affects salt marsh flooding and dissolved oxygen concentration, I am looking at water level, dissolved oxygen, elevation, and wind data from Assateague Island National Seashore. I will use the wind and water level data to determine how much wind affects water level. I can then use elevation data to determine how this change in water level can change the amount of flooding the salt marshes experience. I will also use the wind data and dissolved oxygen data to see if wind affects the concentration of dissolved oxygen. Understanding the impacts wind has on a salt marsh ecosystem will help improve the management of these vital ecosystems.


in Silico Microbes from the Deep Sea

Matthew Gentry — University of Massachusetts Amherst 

Metabolic Models

An in silico metabolic model is a computer representation of how an organism grows. At the center of a metabolic model is a list of interacting biochemical reactions that describe the conversions that produce the basic building blocks of life (e.g. proteins, lipids, and nucleic acids). The reactions are connected to one another like a network of pipes with different diameters and flow rates. The reaction flows determine the cycling of various carbon-, nitrogen-, and sulfur-containing nutrients in a cell.

Gentry_1Metabolic models are useful tools for visualizing the mechanisms underlying cell growth. They can integrate large datasets from modern genomic studies, and by providing a map of the metabolic connections within a cell, metabolic models can help engineer new bacterial strains for producing useful compounds (e.g. acetate). A model could be used to predict which genetic alterations might produce desired effects in microbes without the need for extensive experimental trial and error. This saves money and time.

The diagram on the right is an example of what a very simple metabolic model might look like. Reactions are denoted as blue arrows, and compounds are denoted as red circles.

Adding Dynamic Gene Expression

Metabolic models are often constructed based on the genes in an organism’s DNA because these are its instructions for making enzymes that are essential for its metabolism. Although this approach guarantees a full representation of the organism’s potential, it may not capture the organism’s activity under specific conditions.

As a summer research fellow in Dr. Ying Zhang’s lab, my project is to implement new methods in an existing software, the Portable System for the Analysis of Metabolic Models (PSAMM, pronounced like Frodo and PSAMM) for including gene expression in the model. This will allow it to simulate differing environmental conditions. We are doing this in two ways: first, by approximating the on and off state of reactions according to the increasing or decreasing of gene expression levels. Second, by using expression levels directly as numeric constraints to tune the allowed flow through each reaction. This is like adding knobs to the network of pipes to control its fluxes. I am going to try each of these methods and compare the results.

Gentry_2The Software

Dr. Zhang’s group has developed PSAMM, which is used similarly to how a writer might use Microsoft Word. The metabolic model is like the novel. PSAMM is like Microsoft Word – the tool used to write, edit, and use the project. In addition to model editing, PSAMM provides tools for quantitatively analyzing the model. Simulations provide an estimation of experimentally observable features, such as the growth yield, which can be compared with experimental data to validate models.

Deep-Sea Microbe WP3

We will use metabolic models to explore the metabolism of a deep-sea bacterium, Shewanella piezotolerans WP3, affectionately called WP3. WP3 is from the cold depths of the West Pacific Ocean and survives begrudgingly at cold temperatures (<20 °C or 68 °F) and extremely high pressures (up to 500 times higher than air pressure at the Earth’s surface). For comparison, typical living conditions for familiar species of bacteria are at one atmosphere and roughly body temperature (37 °C or 98.6 °F). Our goal is to use models and experimentally measured dynamics of gene expression to explore the metabolism of WP3 under variable conditions (i.e. temperature, pressure, oxygen concentrations). We expect to reveal the metabolic pathways that help WP3 adapt in extreme conditions.


The Importance of a World Unseen

Jakob Gessay — Coastal Carolina University 

For a lot people it is hard to recognize the complexity of environments too large or small to be seen through the scope of our human eyes. Everyone has heard of plankton, but it becomes an abstract idea if you haven’t spent hours looking at it through a microscope. There are two major groups of plankton: plant plankton called phytoplankton, and animal plankton called zooplankton. My research this summer focuses on phytoplankton, which are single-celled organisms.

Although phytoplankton cannot be seen with the naked eye, their influence is important to understand. Phytoplankton are plant cells, which take up carbon dioxide from the atmosphere. They generate a large portion of the oxygen we breathe via photosynthesis, so their contribution to the global cycle of gases is profound. The carbon dioxide that is taken up by phytoplankton gets transformed and stored in the cell tissues as organic carbon. Phytoplankton are the base of the food web in most marine environments and understanding how much carbon is available to be transferred to larger organisms, including organisms that we eat, such as fish, is important for our overall understanding of marine food webs.

For my summer research, I am focusing on diatoms, a specific type of phytoplankton. While there are many different types of diatoms, I am specifically looking at one group of species, or genus, whose name is Skeletonema. Like all other diatoms, Skeletonema is photosynthetic and has a shell-like structure called a frustule, which is made out of silica. We chose Skeletonema because of its abundance and importance in Narragansett Bay, and also because of the readily available preexisting data for the genus. We are using data sets that have been collected by other researchers for past projects and compiling them together to get a unified and inclusive representation of the patterns in the genus.

These data sets include many metrics such as cell volume, cell surface area, and the carbon, nitrogen and chlorophyll content of the cell. Using these metrics, my goal is to find a relationship that allows researchers to accurately estimate the biomass of the genus Skeletonema. While this has been attempted in the past for various types of phytoplankton, this is the first time it has been conducted for an individual genus of diatom.

Once a measure for biomass can be derived from the data, I plan on using it to see how the yearly timing of the Skeletonema bloom has changed over time. Typically, Skeletonema has a winter-spring bloom, however, given a multi-decadal change in time, we think that the timing of the bloom in the year has shifted, and we hope to find a pattern of this shift in our data. Understanding how a bloom shifts with time is important when considering seasonal community dynamics. This change in bloom time could negatively affect species that depend on the diatom for food during a given time of the year, and this could translate up the food chain. This could alter management practices for established fisheries and also have an impact on local and global carbon dioxide and oxygen cycles.


Nutrients, Climate, and Currents in the Past

Alexandra Norwood — Arizona State University

Climate change has become a buzz phrase over the last few decades. As we try to better understand how our actions influence the climate, we have to understand how climate through time has changed without us. We do this by looking into the past. As an archaeology student, I really care about creating tools that help us to better reconstruct the past, so this research is really exciting to me.

This map shows the path of the Agulhas current with blue arrows. The sites we are studying are marked with yellow stars.
This map shows the path of the Agulhas current with blue arrows. The sites we are studying are marked with yellow stars.

Through my summer research project, I hope to understand past climate change by looking at sediments (dirt) from the bottom of the ocean around the coast of southern Africa. This is an important region because of the Agulhas Current, which flows from the Indian Ocean down the east coast of Africa to its southern tip. At the southern tip it turns back and goes east again. As it returns eastward, the Agulhas Current sends spinning columns of water from the Indian Ocean out into the south Atlantic Ocean.

Water from the Indian Ocean is different from the water in the Atlantic Ocean in a few ways. It’s warmer, saltier, and has less nitrogen compared to other nutrients. Nitrogen is an important nutrient for controlling how much life the ocean can support, just like nitrogen-rich fertilizer can help things grow in your yard. The lack of nitrogen in the Indian Ocean comes from a process called denitrification.

Denitrification happens in areas below the surface of the ocean where there is no oxygen. It occurs because certain kinds of bacteria thrive without oxygen, instead consuming nitrate (NO3), the most abundant form of nitrogen available to life in the ocean. They release nitrogen gas, which leaves the ocean.

Here I am in the lab, preparing samples.
Here I am in the lab, preparing samples.

As these bacteria use up nitrate they change the isotopic composition of the nitrate in the ocean. There are two nitrogen isotopes, or nitrogen atoms with different weights: 14N and 15N. Denitrifying bacteria prefer the lighter nitrogen (14N) and leave the heavier nitrogen (15N) behind. Plankton then consume the remaining nitrate, die, and drift to the sea floor. When they do, the ratio of heavy to light nitrogen gets transferred to the sediment, where we can test for it.

To see if the low-nitrogen waters from the Indian Ocean are being carried into the Atlantic by the Agulhas, we will look at the nitrogen isotope ratio in the sediment from 3 different spots along the current. This sediment comes from cores, which are tubes of sediment drilled from the bottom of the ocean. They represent the passage of time because the new sediment that has just fallen to the bottom of the ocean is on top. The deeper in the core you go, the farther back in time you’re looking. We are looking at samples from different depths (and therefore ages!) at each of these three sites. This way, we can look for changes in the relationship between the sites over time. We’ll then compare the timing of these changes with changes in climate that we already know about to see how climate may have impacted denitrification.

By studying how climate change has affected nitrogen use and distribution in the Agulhas Current over time, we will be able to better understand how the nitrogen cycle works. This will give us a tool to use to look at how nutrient availability changed when we look at the history of climate change on our planet.


The Ocean’s Smallest Predators

Liza Wright-Fairbanks — Middlebury College

Food chains in the ocean are made up of an incredible variety of creatures, from small reef fish to sea stars to top predators like sharks. All of these organisms interact in different ways, but one thing is always true: their food chains begin with microscopic organisms called plankton.

Isochrysis galbana, an autotroph (from NOAA)
Isochrysis galbana, an autotroph (from NOAA)

Plankton are living beings that are unable to move on their own in water; they depend on the ocean’s currents and waves to move them from place to place. Though some plankton are large, like jellyfish, most are invisible to the naked eye. Plankton are everywhere – a single drop of seawater holds many thousands of plankton cells! Plankton can be autotrophic, using the sun’s energy to create food, or heterotrophic, relying on the consumption of other organisms for energy. This summer I am studying how autotrophic and heterotrophic plankton interact in the ocean.

My lab has done a lot of great work studying interactions between the two basic food chain levels of plankton – autotrophs and their small heterotrophic predators. For my project, I am attempting to incorporate a third level, mesozooplankton, into this established food chain. Some of the small predators are able to “smell” chemicals that mesozooplankton emit into the water, and I will be measuring how those chemicals affect the predators’ ability to find and feed on phytoplankton.

Copepod: the top predator in this study (taken by Ariel Pezner in the Rynearson Lab at the University of Rhode Island. )
Copepod: the top predator in this study (taken by Ariel Pezner in the Rynearson Lab at the University of Rhode Island.)

For my experiment, I’m using three different model organisms to represent each of the three levels of the plankton food chain; Isochrysis galbana represent phytoplankton, Oxyrrhis marina represent microzooplankton, and copepods represent mesozooplankton.

Oxyrrhis marina, a single-celled heterotroph (taken in the Menden-Deuer Lab at the University of Rhode Island)
Oxyrrhis marina, a single-celled heterotroph (taken in the Menden-Deuer Lab at the University of Rhode Island)

In the lab, I’ll be researching how copepod excretions affect the ability of Oxyrrhis to feed on Isochrysis. I am using a chemical called ammonium to represent the excretions. Ammonium is the main component of copepod pee, so if Oxyrrhis can smell excretions, they will most likely respond to ammonium. After exposing the Oxyrrhis to ammonium, I will allow them to feed and grow over a three-day period, taking daily measurements of the predator and prey populations to see how ammonium affects the growth and grazing abilities of Oxyrrhis. I will also compare their growth to a control group which had no ammonium added to it.

This experiment will show us how Oxyrrhis react to the presence of their predators. This information will help us develop our knowledge of predator-prey relationships of plankton, which is important because plankton make up the base of every food chain in the ocean. We need to understand how they interact in order to better understand the transfer of energy throughout the ocean, which will help us predict what will happen to fish populations if the ecosystem changes in any way. If we want to keep the ocean and all of its inhabitants happy and healthy, we need to make sure plankton are too!

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