The Breathing Bay

Latest update August 6, 2019 Started on June 23, 2005

We study how our coastal ocean breaths, and with each breath it takes we can learn how these ecosystems filter nutrients, sequester carbon, and improve water quality.

In The Field

Today, as I write this, I sit by the water’s edge. I came down to the sea to listen to the waves gently ease themselves on and off the shore. I came to gather my mind for the day ahead. I came to quiet the noise that crowds my thoughts when there is too much in the world to understand and the battles seem to loom too large. I wish for everyone that they may find peace upon some salty shore today. That they may realize we are earthlings first, and that this fact is the glue that binds us all.

We are not on Narragansett Bay this week. Instead my team is working in different coastal waters. Some are collecting sediment cores from the inland Delaware Bays, others are sampling seagrass beds in the shallows of Cape Cod, and still others are diligently working in the laboratory – testing new techniques and analyzing data. Next week however, we’ll be back out here testing the new corer I wrote about last time. And what will become of those cores we so carefully collect? Well, let me tell you.

We will carefully transport these sediment cores back to our lab at Boston University where they will be placed in a water bath in an environmental chamber for a “sediment incubation”. There they will rest overnight, with a gentle stream of air bubbling the water that lies atop them. In the morning, generally very early as this part takes the longest, we carefully siphon out this water overlying the cores. We then replace this water with filtered site water, letting it fill the cores again ever so slowly so we do not disturb the vertical structure of the sediment or the delicate flocculant layer. Next, we collect water samples for dissolved inorganic nutrients (i.e., nitrogen, phosphorus, and silica) – these you are most likely familiar with in terms of fertilizer you might add to your garden or your lawn (but really, we shouldn’t use too much in these circumstances, and we shouldn’t be fertilizing our lawns, but that’s an essay for another day). We also measure the dissolved oxygen concentration, temperature, and salinity of each core. We will take similar measurements at the end of the incubation and we can compare these initial measurements to the final ones to calculate how the nutrient and oxygen concentrations changed over the course of the incubation.

After these samples are collected, we seal the cores with a gas tight lid. This is the part that summons all your patience – because in order to collect the most accurate data – we cannot have any air bubbles in the cores. The details of why these bubbles matter I can explain another day. For now, just know that we spend a good deal of time, ever so carefully placing these core lids on, ensuring that no bubbles will cloud our samples- not even a teeny tiny one. Once sealed the only way in and out of these cores is through the inflow and outflow ports on the lid. And it is from these ports we collect gas samples over the course of incubation. We collect gas samples for oxygen, di-nitrogen gas, nitrous oxide, and methane. We collect these samples into gas tight vials, at five time points, spread over time – in the summer – generally over 6 to 24 hours. The timing depends on how active the sediment community is – how much oxygen they are breathing. If we keep the incubation going too long, most or all of the oxygen in the overlying water will be consumed, making the cores hypoxic (i.e., low oxygen) or anoxic (i.e., no oxygen). This would change the condition of the sediments, shifting how they breathe and how nutrients are processed. Because we are aiming to capture how the sediments behave in the field, under normal oxygen conditions, we stop the incubation before the oxygen concentrations drop too low.

These gas samples are the breath of the bay, and they reveal to us how the ecosystem is functioning, and when compared to similar historic samples, they help tell us how Narragansett Bay is changing overtime. We’ll tackle some of these concepts next time.

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Behold the sediment core! Within these clear tubes, we find a whole universe of life that transforms nutrients like nitrogen into various forms from particulate, to dissolved, to gaseous. If we want to understand how the sediments (and that universe they contain) breathe in Narragansett Bay or any ocean environment we first must capture these sediments.

There are many ways one can collect sediments (see photos below). For example, there are Van Veen Grabs (1) – composed of jaws that grasp the sediments into one big mouthful. Or box corers - ~1000 lbs of metal that travel swiftly through the water column, and upon touching the seafloor a weighted arm swings underneath, catching the sediment. While a boxcore is useful for offshore work – in the relatively shallow Narragansett Bay we prefer to use a pull (sometimes called pole) corer or even divers. We favor these methods because they are gentler than Van Veen Grabs or box corers – that is, they better maintain the vertical structure of the sediments, and even the delicate flocculent layer resting on top. The pull corer is best for shallow environments, so we use it to collect sediments from the Providence River Estuary. The corer is attached directly to a pole that we deploy off the side of the boat, pushing the corer into the sediment, and then we pull a line, closing a valve that allows just enough suction to keep the sediment in place until it’s on the boat. Similarly, the divers directly push the cores into the sediment, and place bottoms and tops on them while on seafloor bottom.

Need a better visual of how these coring techniques work? Imagine you are making biscuits or cookies – you take your favorite cookie cutter, and gently press it into the dough, moments later you have a piece of well-defined dough ready to place on the baking sheet. The same idea applies with the pull corer or divers – except instead of a thin piece of dough; we are cutting a chunk of sediment. In our work, we hope to retrieve ~ 6 inches depth, and instead of the oven, these cores are destined for our environmental chamber. In the chamber we place them in a water bath, at the water temperature we measure in the field. Our goal, is to try to mimic the field environment as closely as possible so that the measurements we make are realistic and useful for answering real world questions.

This year, we have been experimenting with a new type of corer – called a HYPOX Corer(2) – designed by Dr. Wayne Gardner from the University of Texas Marine Science Institute. This corer works similar to the pull core described above, but in deeper water. Instead of pole alone, the corer is attached to a PVC frame. We are planning to use this new corer at the mid-Bay site, where we typically use divers. While we love working with our divers, we need this corer so that we can sample more frequently and in different conditions when diving is less safe (e.g., more wind, higher currents, colder weather, etc.). Alas, our first deployment was unsuccessful. But the course of field work rarely runs smooth, so we are back in the lab modifying the design to work for us.

(1) Link to Van Veen Grab Photo:

(2) Gardner, W. S., McCarthy, M. J., Carini, S. A., Souza, A. C., Lijun, H., McNeal, K. S., ... & Pennington, J. (2009). Collection of intact sediment cores with overlying water to study nitrogen and oxygen dynamics in regions with seasonal hypoxia. Continental Shelf Research, 29(18), 2207-2213.

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When people learn I’m an oceanographer, the usual first question has to deal with whales or dolphins – or some other charismatic megafauna that dominates our worldview of the oceans. I understand these questions, whales and dolphins, sea otters and puffins – they are beautiful, fascinating creatures. But they are not the reason I wake early to get to work, or toss and turn in bed at 3 am with a pressing question I am working through. No, my actions are driven instead by a different passion. I love studying the things we cannot see with the unaided eye: microbes, nutrients, even gases dissolved in water.

For 15 years now, we have been sampling two sites in Narragansett Bay. Some years, depending on funding, we have the ability to study more sites. But these two – shall we call them *sentinel sites – provide a benchmark for a changing bay (see map below). The first site is located in upper Narragansett Bay in the Providence River Estuary. This site is close to the city of Providence and represents the most human impacted site. The sediments we collect here are dark and muddy, imagine a rich dark chocolate pudding. Sometimes these sediments are rich in hard clams, slipper shells, or dense Ampelisca sp. (a tube-building amphipod) mats that look like shag carpeting.

Our second sentinel site is located in mid-Narragansett Bay – between the islands of Prudence and Jamestown. The sediments here are a mixture of sand and mud. Generally, they also have a delicate flocculent layer that shimmies across the surface of the sediment cores. The animals seem come and go here. When I first started sampling this site, the sediments were a moonscape. These days, there are usually small snails and Polychaete worms – we can track by the small trails they leave on the surface of the sediments. Sometimes these sediments harbor larger infauna (i.e., animals that live in the sediment) like mud anemones.

Of course, at both sites, the sediments are chock full of organisms we cannot easily see. These include cyanobacteria and diatoms, ciliates and flagellates, bacteria and fungi. All together, the big and the small – help drive the ecology of Narragansett Bay. One way we quantify how they do this is by measuring the production and removal of certain gases (e.g., oxygen, nitrous oxide, di-nitrogen) and nutrients (e.g., ammonium, nitrate, phosphorus).

Next post – I’ll describe these methods. Stay tuned.

*please note, this idea of sentinel sites is in my head, because my colleague and friend Dr. Autumn Oczkowski refers to Narragansett Bay as a sentinel estuary.


I think all good expeditions start with and periodically include reflection. This past weekend I rose early to watch Narragansett Bay, to see the wind run up the coast, a southerly breeze that started earlier than normal. By mid-morning the whole of the mid- and lower bay were churning, almost steady white caps foaming on each crest. I started thinking about all those water particles, all that orbital motion, churning and spinning. I thought of the elements in that water too – and how they were interacting with the bay floor. How long would the wind need to blow like this to churn the water column to the bottom? To start to mix the delicate flocculant layer off the muds? Or to begin to permeate sands? I thought about the animals too – those that graze on particles in the water column with their delicate tentacles grasping for food and the industrious amphipods churning through the sediment. They too would be impacted by a well-mixed water column brought on by this wind today. Maybe they’d feed more, burrowing deeper into the sediments bringing oxygen, nutrients, and organic matter – food for microbes. All of this, the mixing water column, the activity of the sediment animals, all will increase the breathing of the bay sediments.

It amazes me that we’ve been capturing these processes for over a decade. And yet, we have so much more to learn. Some of what we still need to learn is fundamental – like how do wind-mixed water columns alter sediment nutrient and gas fluxes?. Some of what we need to learn is based on the major changes humans are causing to coastal systems like what’s the role of increasing temperature and changing nutrient loading on sediment nutrient and gas fluxes?

So off to work we go. Capturing the pulse of this bay, so we can learn more about the coastal ocean – one breath at a time.

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Expedition Background

We study nutrients - elements such as nitrogen, phosphorus, and silicon. These elements are essential for phytoplankton growth, the microscopic photosynthetic cells that provide around 1/2 of the oxygen we breathe, and are the basis of key marine food webs.

We focus on how these elements are transformed by microbes in the coastal ocean. You can think of what we do as following the microbial coastal ocean breath. We use traditional techniques to follow this breath in water and sediments. We also help design, build, and test cutting edge sensors to measure this breath in the environment.

Here we will examine the long-term trends as well as the current state of this breath in Narragansett Bay, RI. The summer of 2019 marks the 15th (!!) year of these measurements. And it will be the first year we deploy an underwater mass spectrometer to measure this breath in the environment.

Our goal is to share with you the important and exciting stories that you cannot see with the unaided eye.


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