Amanda Dice: Bongos in the Water, August 24, 2017

NOAA Teacher at Sea

Amanda Dice

Aboard NOAA Ship Oscar Dyson

August 21 – September 2, 2017

 

Mission: Juvenile Pollock Fishery Survey

Geographic area of cruise: Western Gulf of Alaska

Date: August 24, 2017

Weather Data: 11.5 C, Foggy

Latitude 56 35.5 N, Longitude 153 21.9 W

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This map on the bridge helps everyone keep track of where we are and where we are headed next.

Science and Technology Log

At each sampling site, we take two types of samples. First, we dip what are called bongo nets into the water off of the side of the boat. These nets are designed to collect plankton. Plankton are tiny organisms that float in the water. Then, we release long nets off of the back of the boat to take a fish sample. There is a variety of fish that get collected. However, the study targets five species, one of which is juvenile walleye pollock, Gadus chalcogrammus. These fish are one of the most commercially fished species in this area. I will go into more detail about how the fish samples are collected in a future post. For now, I am going to focus on how plankton samples are collected and why they are important to this survey.

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Juvenile walleye pollock are fish that are only a few inches long. These fish can grow to much larger sizes as they mature.

As you can see in the photos below, the bongo nets get their name because the rings that hold the nets in place resemble a set of bongo drums. The width of the nets tapers from the ring opening to the other end. This shape helps funnel plankton down the nets and into the collection pieces found at the end of the nets. These collection devices are called cod ends.

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Bongo nets being lowered into the water off of the side of the ship.

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This is the collection end, or cod end, of the bongo nets.

This study uses two different size bongo nets. The larger ones are attached to rings that are 60 centimeters in diameter. These nets have a larger mesh size at 500 micrometers. The smaller ones are attached to rings that are 20 centimeters in diameter and have a smaller mesh size at 150 micrometers. The different size nets help us take samples of plankton of different sizes. While the bongo nets will capture some phytoplankton (plant-like plankton) they are designed to mainly capture zooplankton (animal-like plankton). Juvenile pollock eat zooplankton. In order to get a better understanding of juvenile pollock populations, it is important to also study their food sources.

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Here I am, helping to bring the bongo nets back on to the ship.

Once the bongo nets have been brought back on board, there are two different techniques used to assess which species of zooplankton are present. The plankton in nets #1 of both the small and large bongo are placed in labeled jars with preservatives. These samples will be shipped to a lab in Poland once the boat is docked. Here, a team will work to identify all the zooplankton in each jar. We will probably make it to at least sixty sampling sites on the first leg of this survey. That’s a lot of zooplankton!

 

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A jar of preserved zooplankton is ready to be identified.

The other method takes place right on the ship and is called rapid zooplankton assessment (RZA). In this method, a scientist will take a small sample of what was collected in nets #2 of both the small and large bongos. The samples are viewed under a microscope and the scientist keeps a tally of which species are present. This number gives the scientific team some immediate feedback and helps them get a general idea about which species of zooplankton are present. Many of the zooplankton collected are krill, or euphausiids, and copepods. One of the most interesting zooplankton we have sampled are naked pteropods, or sea angels. This creature has structures that look very much like a bird’s wings! We also saw bioluminescent zooplankton flash a bright blue as we process the samples. Even though phytoplankton is not a part of this study, we also noticed the many different geometric shapes of phytoplankton called diatoms.

 

sea angel

A naked pteropod, or sea angel, as seen through the microscope.

Personal Log

Both the scientific crew and the ship crew work one of two shifts. Everyone works either midnight to noon or noon to midnight. I have been lucky enough to work from 6am – 6pm. This means I get the chance to work with everyone on board at different times of the day. It has been really interesting to learn more about the different ship crew roles necessary for a survey like this to run smoothly. One of the more fascinating roles is that of the survey crew. Survey crew members act as the main point of communication between the science team and the ship crew. They keep everyone informed about important information throughout the day as well as helping out the science team when we are working on a sample. They are responsible for radioing my favorite catchphrase to the bridge and crew, “bongos in the water.”

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A sign of another great day on the Gulf of Alaska.

Did You know?

You brush your teeth with diatoms! The next time you brush your teeth, take a look at the ingredients on your tube of toothpaste. You will see “diatomaceous earth” listed. Diatomaceous earth is a substance that contains the silica from ancient diatoms. Silica gives diatoms their rigid outer casings, allowing them to have such interesting geometric shapes. This same silica also helps you scrub plaque off of your teeth!

diatoms

Diatoms as seen through a microscope.

 

Christine Webb: August 19, 2017

NOAA Teacher at Sea

Christine Webb

Aboard NOAA Ship Bell M. Shimada

August 11 – 26, 2017

Mission: Summer Hake Survey Leg IV

Geographic Area of Cruise: Pacific Ocean from Newport, OR to Port Angeles, WA

Date: 8/19/2017

Latitude: 48.59 N

Longitude: 126.59 W

Wind Speed: 15 knots

Barometric Pressure: 1024.05 mBars

Air Temperature: 59 F

Weather Observations: Sunny

Science and Technology Log:

You wouldn’t expect us to find tropical sea creatures up here in Canadian waters, but we are! We have a couple scientists on board who are super interested in a strange phenomenon that’s been observed lately. Pyrosomes (usually found in tropical waters) are showing up in mass quantities in the areas we are studying. No one is positive why pyrosomes are up here or how their presence might eventually affect the marine ecosystems, so scientists are researching them to figure it out. One of the scientists, Olivia Blondheim, explains a bit about this: “Pyrosomes eat phytoplankton, and we’re not sure yet how such a large bloom may impact the ecosystem overall. We’ve already seen that it’s affecting fishing communities because their catches have consisted more of pyrosomes than their target species, such as in the shrimp industry.”

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Sorting through a bin of pyrosomes

Pyrosomes are a type of tunicate, which means they’re made up of a bunch of individual organisms. The individual organisms are called zooids. These animals feed on phytoplankton, and it’s very difficult to keep them alive once they’re out of the water. We have one alive in the wet lab right now, though, so these scientists are great at their jobs.

We’ve found lots of pyrosomes in our hake trawls, and two of our scientists have been collecting a lot of data on them. The pyrosomes are pinkish in color and feel bumpy. Honestly, they feel like the consistency of my favorite candy (Sour Patch Kids). Now I won’t be able to eat Sour Patch Kids without thinking about them. Under the right conditions, a pyrosome will bioluminesce. That would be really cool to see, but the conditions have to be perfect. Hilarie (one of the scientists studying them) is trying to get that to work somehow before the trip is over, but so far we haven’t been able to see it. I’ll be sure to include it in the blog if she gets it to work!

One of the things that’s been interesting is that in some trawls we don’t find a single pyrosome, and in other trawls we see hundreds. It really all depends on where we are and what we’re picking up. A lot of research still needs to be done on these organisms and their migration patterns, and it’s exciting to be a small part of that.

Personal Log:

The science crew continues to work well together and have a lot of fun! Last night we had an ice cream sundae party after dinner, and I was very excited about the peanut butter cookie dough ice cream. My friends said I acted more excited about that than I did about seeing whales (which is probably not true. But peanut butter cookie dough ice cream?! That’s genius!). After our ice cream sundaes, we went and watched the sunset up on the flying bridge. It was gorgeous, and we even saw some porpoises jumping in the distance.

It was the end to another exciting day. My favorite part of the day was probably the marine mammal watch where we saw all sorts of things, but I felt bad because I know that our chief scientist was hoping to fish on that spot. Still, it was so exciting to see whales all around our ship, and some sea lions even came and swam right up next to us. It was even more exciting than peanut butter cookie dough ice cream, I promise. Sometimes I use this wheel to help me identify the whales:

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Whale identification wheel

Now we’re gearing up for zooplankton day. We’re working in conjunction with the Nordic Pearl, a Canadian vessel, and they’ll be fishing on the transects for the next couple days. That means we’ll be dropping vertical nets and doing some zooplankton studies. I’m not exactly sure what that will entail, but I’m excited to learn about it! So far the only zooplankton I’ve seen is when I was observing my friend Tracie. She was looking at phytoplankton on some slides and warned me that sometimes zooplankton dart across the phytoplankton. Even though she warned me, it totally startled me to see this giant blob suddenly “run” by all the phytoplankton! Eeeeep! Hopefully I’ll get to learn a lot more about these creatures in the days coming up.

Kimberly Scantlebury: It’s All About the Little Things, May 8, 2017

NOAA Teacher at Sea

Kimberly Scantlebury

Aboard NOAA Ship Pisces

May 1-May 12, 2017

Mission: SEAMAP Reef Fish Survey

Geographic Area of Cruise: Gulf of Mexico

Date: May 8, 2017

Weather Data from the Bridge

Time: 18:00

Latitude: 2755.757 N, Longitude: 9200.0239 W

Wind Speed: 14.21  knots, Barometric Pressure: 1015.3 hPa

Air Temperature: 24.56  C, Water Temperature: 24.4  C

Salinity: 36.37  PSU, Conditions: 50% cloud cover, light wind, seas 2-4 feet

Science and Technology Log

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The CTD

The CTD (conductivity, temperature, depth) array is another important tool. It goes down at each station, which means data is captured ten-twelve times a day. It drops 50 m/min so it only takes minutes to reach the bottom where other winch/device systems can take an hour to do the same. This array scans eight times per second for the following environmental factors:

  • Depth (m)
  • Conductivity (converts to salinity in ppt)
  • Temperature (C)
  • Dissolved oxygen (mg/mL)
  • Transmissivity (%)
  • Fluorescence (mg/m^3)
  • Descent rate (m/sec)
  • Sound velocity (m/sec)
  • Density (kg/m^3)

There are two sensors for most readings and the difference between them is shown in real time and recorded. For example, the dissolved oxygen sensor is most apt to have calibration issues. If the two sensors are off each other by 0.1 mg/L then something needs to be done.

Software programs filter the data to cut out superfluous numbers such as when the CTD is acclimating in the water for three minutes prior to diving. Another program aligns the readings when the water is working through the sensors. Since a portion of water will reach one sensor first, then another, then another, and so on, the data from each exact portion of water is aligned with each environmental factor. There are many other sophisticated software programs that clean up the data for use besides these two.

These readings are uploaded to the Navy every twelve hours, which provides almost real-time data of the Gulf. The military uses this environmental data to determine how sound will travel through sound channels by locating thermoclines as well as identifying submarines. NOAA describes a thermocline as, “the transition layer between warmer mixed water at the ocean’s surface and cooler deep water below.” Sound channels are how whales are able to communicate over long distances.

NOAA Ocean Explorer: Sound in the Sea 2001

This “channeling” of sound occurs because of the properties of sound and the temperature and pressure differences at different depths in the ocean. (NOAA)

The transmissometer measures the optical properties of the water, which allows scientists to track particulates in the water. Many of these are clay particles suspended in the water column. Atmospheric scientists are interested in particulates in the air and measure 400 m. In the water, 0.5 m is recorded since too many particulate affects visibility very quickly. This affects the cameras since light reflecting off the clay can further reduce visibility.   

Fluorescence allows scientists to measure chlorophyll A in the water. The chlorophyll molecule is what absorbs energy in photosynthetic plants, algae, and bacteria. Therefore, it is an indicator of the concentration of organisms that make up the base of food chains. In an ecosystem, it’s all about the little things! Oxygen, salinity, clay particles, photosynthetic organisms, and more (most we can not actually see), create a foundation that affects the fish we catch more than those fish affect the little things.  

The relationship between abiotic (nonliving) and biotic (living) factors is fascinating. Oxygen is a great example. When nitrates and phosphates wash down the Mississippi River from the breadbasket of America, it flows into the Gulf of Mexico. These nutrients can make algae go crazy and lead to algae blooms. The algae then use up the oxygen, creating dead zones. Fish can move higher up the water column or away from the area, but organisms fixed to the substrate (of which there are many in a reef system) can not. Over time, too many algae blooms can affect the productivity of an area.

Salt domes were created millions of years ago when an ancient sea dried up prior to reflooding into what we have today. Some salt domes melted and pressurized into super saline water, which sinks and pools. These areas create unique microclimates suitable to species like some mussels. A microclimate is a small or restricted area with a climate unique to what surrounds it.

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The ship’s sonar revealing a granite spire a camera array was deployed on.

Another great example is how geology affects biology. Some of these salt domes collapsed leaving granite spires 30-35 meters tall and 10 meters across. These solid substrates create a magical biological trickle down effect. The algae and coral attach to the hard rock, and soon bigger and bigger organisms populate this microclimate. Similar microclimates are created in the Gulf of Mexico from oil rigs and other hard surfaces humans add to the water.

Jillian’s net also takes a ride with the CTD. She is a PhD student at Texas A&M University studying the abundance and distribution of zooplankton in the northern Gulf of Mexico because it is the primary food source of some commercially important larval fish species. Her net is sized to capture the hundreds of different zooplankton species that may be populating the area. The term zooplankton comes from the Greek zoo (animal) and planktos (wanderer/drifter). Many are microscopic, but Jillian’s samples reveal some translucent critters you can see with the naked eye. Her work and the work of others like her ensures we will have a deeper understanding of the ocean.   

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Personal Log

Prior to this I had never been to the Gulf of Mexico other than on a cruise ship (not exactly the place to learn a lot of science). It has been unexpected to see differences and parallels between the Gulf of Mexico and Gulf of Maine, which I am more familiar. NOAA scientist, John, described the Gulf to me as, “a big bathtub.” In both, the geology of the area, which was formed millions of years ago, affects that way these ecosystems run.   

Quote of the Day:
Jillian: “Joey, are we fishing at this station?”
Joey: “I dunno. I haven’t had my coffee yet.”
Jillian: “It’s 3:30 in the afternoon!”

Did You Know?

Zooplankton in the Gulf of Mexico are smaller than zooplankton in the Gulf of Maine. Larger species are found in colder water.  

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Zooplankton under microscope (NOAA)

Michael Wing: Introduction to El Niño, July 22, 2015

NOAA Teacher at Sea
Michael Wing
Aboard R/V Fulmar
July 17 – 25, 2015

Mission: 2015 July ACCESS Cruise
Geographical Area of Cruise: Pacific Ocean west of Bodega Bay, California
Date: July 22, 2015

Weather Data from the Bridge: Northwest wind 15-25 knots, wind waves 3’-5’, northwest swell 4’ – 6’ at eight seconds, overcast.

Science and Technology Log

UC Davis graduate student and Point Blue Conservation Science intern Kate Davis took some plankton we collected to the Bodega Marine lab in Bodega Bay. She said she is seeing “tropical” species of plankton. A fellow graduate student who is from Brazil peeked into the microscope and said the plankton looked like what she sees at home in Brazil. The flying fish we saw is also anomalous, as is the number of molas (ocean sunfish) we are seeing. Plankton can’t swim, so some of our water must have come from a warm place south or west of us.

Farallones

The Farallon Islands are warmer this year

The surface water is several degrees warmer than it normally is this time of year. NOAA maintains a weather buoy near Bodega Bay, California that shows this really dramatically. Click on this link – it shows the average temperature in blue, one standard deviation in gray (that represents a “normal” variation in temperatures) and the actual daily temperature in red.

NOAA buoy data

Surface seawater temperatures from a NOAA buoy near Bodega Bay, California

http://bml.ucdavis.edu/boon/climatology.html

As you can see, the daily temperatures were warm last winter and basically normal in the spring. Then in late June they shot up several degrees, in a few days and have stayed there throughout this month. El Niño? Climate change? The scientists I am with say it’s complicated, but at least part of what is going on is due to El Niño.

Ryan at flying bridge

San Francisco State University student and Point Blue intern Ryan Hartnett watches El Nino

So what exactly is El Niño?

My students from last year know that the trade winds normally push the surface waters of the world’s tropical oceans downwind. In the Pacific, that means towards Asia. Water wells up from the depths to take its place on the west coasts of the continents, which means that places like Peru have cold water, lots of fog, and good fishing. The fishing is good because that deep water has lots of nutrients for phytoplankton growth like nitrate and phosphate (fertilizer, basically) and when it hits the sunlight lots of plankton grow. Zooplankton eat the phytoplankton; fish eat the zooplankton, big fish eat little fish and so on.

During an El Niño event, the trade winds off the coast of Peru start to weaken and that surface water bounces back towards South America. This is called a Kelvin wave. Instead of flowing towards Asia, the surface water in the ocean sits there in the sunlight and it gets warmer. There must be some sort of feedback mechanism that keeps the trade winds weak, but the truth is that nobody really understands how El Niño gets started. We just know the signs, which are (1) trade winds in the South Pacific get weak (2) surface water temperatures in the eastern tropical pacific rise, (3) the eastern Pacific Ocean and its associated lands get wet and rainy, (4) the western Pacific and places like Australia, Indonesia, and the Indian Ocean get sunny and dry.

This happens every two to seven years, but most of the time the effect is weak. The last time we had a really strong El Niño was 1997-1998, which is when our current cohort of high school seniors was born. That year it rained 100 inches in my yard, and averaged over an inch a day in February! So, even though California is not in the tropics we feel its effects too.

Sausalito sunset

Sunset from the waterfront in Sausalito, California

We are in an El Niño event now and NOAA is currently forecasting an excellent chance of a very strong El Niño this winter.

NOAA map

Sea surface temperature anomalies Summer 2015. Expect more red this winter.

What about climate change and global warming? How is that related to El Niño? There is no consensus on that; we’ve always had El Niño events and we’ll continue to have them in a warmer world but it is possible they might be stronger or more frequent.

Personal Log

So, is El Niño a good thing? That’s not a useful question. It’s a part of our climate. It does make life hard for the seabirds and whales because that layer of warm water at the surface separates the nutrients like nitrate and phosphate, which are down deep, from the sunlight. Fewer phytoplankton grow, fewer zooplankton eat them, there’s less krill and fish for the birds and whales to eat. However, it might help us out on land. California’s drought, which has lasted for several years now, may end this winter if the 2015 El Niño is as strong as expected.

Golden Gate Bridge

Rain will come again to California

Did You Know? El Niño means “the boy” in Spanish. It refers to the Christ child; the first signs of El Niño usually become evident in Peru around Christmas, which is summer in the southern hemisphere. The Spanish in colonial times were very fond of naming things after religious holidays. You can see that in our local place names. For instance, Marin County’s Point Reyes is named after the Feast of the Three Kings, an ecclesiastical holy day that coincided with its discovery by the Spanish. There are many other examples, from Año Nuevo on the San Mateo County coast to Easter Island in Chile.

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Michael Wing takes a selfie in his reflection in the boat’s window

Michael Wing: How to Sample the Sea, July 20, 2015

NOAA Teacher at Sea
Michael Wing
Aboard R/V Fulmar
July 17 – 25, 2015

Mission: 2015 July ACCESS Cruise
Geographical Area of Cruise: Pacific Ocean west of Marin County, California
Date: July 20, 2015

Weather Data from the Bridge: 15 knot winds gusting to 20 knots, wind waves 3-5’ and a northwest swell 3-4’ four seconds apart.

Science and Technology Log

On the even-numbered “lines” we don’t just survey birds and mammals. We do a lot of sampling of the water and plankton.

Wing on Fulmar

Wing at rail of the R/V Fulmar

We use a CTD (Conductivity – Temperature – Depth profiler) at every place we stop. We hook it to a cable, turn it on, and lower to down until it comes within 5-10 meters of the bottom. When we pull it back up, it has a continuous and digital record of water conductivity (a proxy for salinity, since salty water conducts electricity better), temperature, dissolved oxygen, fluorescence (a proxy for chlorophyll, basically phytoplankton), all as a function of depth.

CTD

Kate and Danielle deploy the CTD

We also have a Niskin bottle attached to the CTD cable. This is a sturdy plastic tube with stoppers at both ends. The tube is lowered into the water with both ends cocked open. When it is at the depth you want, you clip a “messenger” to the cable. The messenger is basically a heavy metal bead. You let go, it slides down the cable, and when it strikes a trigger on the Niskin bottle the stoppers on both ends snap shut. You can feel a slight twitch on the ship’s cable when this happens. You pull it back up and decant the seawater that was trapped at that depth into sample bottles to measure nitrate, phosphate, alkalinity, and other chemical parameters back in the lab.

Niskin bottle

Niskin bottle

When we want surface water, we just use a bucket on a rope of course.

We use a hoop net to collect krill and other zooplankton. We tow it behind the boat at a depth of about 50 meters, haul it back in, and wash the contents into a sieve, then put them in sample bottles with a little preservative for later study. We also have a couple of smaller plankton nets for special projects, like the University of California at Davis graduate student Kate Davis’s project on ocean acidification, and the plankton samples we send to the California Department of Health. They are checking for red tides.

Hoop net

Hoop net

We use a Tucker Trawl once a day on even numbered lines. This is a heavy and complicated rig that has three plankton nets, each towed at a different depth. It takes about an hour to deploy and retrieve this one; that’s why we don’t use it each time we stop. The Tucker trawl is to catch krill; which are like very small shrimp.  During the day they are down deep; they come up at night.

Tucker trawl

Part of the Tucker trawl

 

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A mass of krill we collected. The black dots are their eyes.

What happens to these samples? The plankton from the hoop net gets sent to a lab where a subsample is taken and each species in the subsample is counted very precisely. The CTD casts are shared by all the groups here – NOAA, Point Blue Conservation Science, the University of California at Davis, San Francisco State University. The state health department gets its sample. San Francisco State student Ryan Hartnett has some water samples he will analyze for nitrate, phosphate and silicate. All the data, including the bird and mammal sightings, goes into a big database that’s been kept since 2004. That’s how we know what’s going on in the California Current. When things change, we’ll recognize the changes.

Personal Log

They told me “wear waterproof pants and rubber boots on the back deck, you’ll get wet.” I thought, how wet could it be? Now I understand. It’s not that some water drips on you when you lift a net up over the stern of the boat – although it does. It’s not that waves splash you, although that happens too. It’s that you use a salt water hose to help wash all of the plankton from the net into a sieve, and then into a container, and to fill wash bottles and to wash off the net, sieve, basins, funnel, etc. before you arrive at the next station and do it all again. It takes time, because you have to wash ALL of the plankton from the end of the net into the bottle, not just some of it. You spend a lot of time hosing things down. It’s like working at a car wash except with salty water and the deck is pitching like a continuous earthquake.

The weather has gone back to “normal”, which today means 15 knot winds gusting to 20 knots, wind waves 3-5’ and a northwest swell 3-4’ only four seconds apart. Do the math, and you’ll see that occasionally a wind wave adds to a swell and you get slapped by something eight feet high. We were going to go to Bodega Bay today; we had to return to Sausalito instead because it’s downwind.

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The sea state today. Some waves were pretty big.

We saw a lot of humpback whales breaching again and again, and slapping the water with their tails. No, we don’t know why they do it although it just looks like fun. No, I didn’t get pictures. They do it too fast.

Did You Know? No biologist or birder uses the word “seagull.” They are “gulls”, and there are a lot of different species such as Western gulls, California gulls, Sabine’s gulls and others. Yes, it is possible to tell them apart.

DJ Kast, Interview with Megan Switzer and the Basics of the CTD/ Rosette, May 28, 2015

NOAA Teacher at Sea
Dieuwertje “DJ” Kast
Aboard NOAA Ship Henry B. Bigelow
May 19 – June 3, 2015

Mission: Ecosystem Monitoring Survey
Geographical area of cruise:
Gulf of Maine
Date: May 28, 2015, Day 11 of Voyage

Interview with Student Megan Switzer

Megan Switzer and her sampling collecting. Photo by: DJ Kast

Megan Switzer and her sampling collecting. Photo by: DJ Kast

Chief Scientists Jerry Prezioso and graduate oceanography student Megan Switzer

Chief Scientist Jerry Prezioso and graduate oceanography student Megan Switzer

Megan Switzer is a Masters student at the University of Maine in Orono. She works in Dave Townsend’s lab in the oceanography department. Her research focuses on interannual nutrient dynamics in the Gulf of Maine. On this research cruise, she is collecting water samples from Gulf of Maine, as well as from Georges Bank, Southern New England (SNE), and the Mid Atlantic Bight (MAB). She is examining the relationship between dissolved nutrients (like nitrate and silicate) and phytoplankton blooms. This is Megan’s first research cruise!

In the generic ocean food chain, phytoplankton are the primary producers because they photosynthesize. They equate to plants on land. Zooplankton are the primary consumers because they eat the phytoplankton. There are so many of both kinds in the ocean. Megan is focusing on a particular phytoplankton called a diatom; it is the most common type of phytoplankton found in our oceans and is estimated to contribute up to 45% of the total oceanic primary production (Yool & Tyrrel 2003). Diatoms are unicellular for the most part, and a unique feature of diatom cells is that they are enclosed within a cell wall made of silica called a frustule.

Diatom Frustules. Photo by:  3-diatom-assortment-sems-steve-gschmeissner

Diatom Frustules. Photo by: Steve Schmeissner

Diatoms! PHOTO BY:

Diatoms! Photo by: Micrographia

The frustules are almost bilaterally symmetrical which is why they are called di (2)-atoms. Diatoms are microscopic and they are approximately 2 microns to about 500 microns (0.5 mm) in length, or about the width of a human hair. The most common species of diatoms are: Pseudonitzchia, Chaetocerous, Rhizosolenia, Thalassiosira, Coschinodiscus and Navicula.

Pseudonitzchia. Photo by National Ocean Service

Pseudonitzchia. Photo by National Ocean Service

Thalassiosira. Photo by: Department of Energy Joint Genome Institute

Thalassiosira. Photo by: Department of Energy Joint Genome Institute

Photo of Coscinodiscus by:

Photo of Coscinodiscus

Diatoms also have ranges and tolerances for environmental variables, including nutrient concentration, suspended sediment, and flow regime.  As a result, diatoms are used extensively in environmental assessment and monitoring. Furthermore, because the silica cell walls are inorganic substances that take a long time to dissolve, diatoms in marine and lake sediments can be used to interpret conditions in the past.

In the Gulf of Maine, the seafloor sediment is constantly being re-suspended by tidal currents, bottom trawling, and storm events, and throughout most of the region there is a layer of re-suspended sediment at the bottom called the Bottom Nepheloid Layer. This layer is approximately 5-30 meters thick, and this can be identified with light attenuation and turbidity data. Megan uses a transmissometer, which is an instrument that tells her how clear the water is by measuring how much light can pass through it. Light attenuation, or the degree to which a beam of light is absorbed by stuff in the water, sharply increases within the bottom nepheloid layer since there are a lot more particles there to block the path of the light. She also takes a water sample from the Benthic Nepheloid Layer to take back to the lab.

Marine Silica Cycle by Sarmiento and Gruber 2006

Marine Silica Cycle by Sarmiento and Gruber 2006

Megan also uses a fluorometer to measure the turbidity at various depths. Turbidity is a measure of how cloudy the water is. The water gets cloudy when sediment gets stirred up into it. A fluorometer measures the degree to which light is reflected and scattered by suspended particles in the water. Taken together, the data from the fluorometer and the transmissometer will help Megan determine the amount of suspended particulate material at each station. She also takes a water sample from the Benthic Nepheloid layer to take back to the lab. There, she can analyze the suspended particles and determine how many of them are made out of the silica based frustules of sinking diatoms.

 This instrument is a Fluorometer and is used to measure the turbidity at various depths. Photo by: DJ Kast

This instrument is a Fluorometer and is used to measure the turbidity at various depths. Photo by: DJ Kast

She collects water at depth on each of the CTD/ Rosette casts.

Rosette with the 12 Niskin Bottles and the CTD. Photo by DJ Kast

Rosette with the 12 Niskin Bottles and the CTD. Photo by DJ Kast

Rosette with the 12 Niskin Bottles and the CTD. Photo by DJ Kast

Rosette with the 12 Niskin Bottles and the CTD. Photo by DJ Kast

Up close shot of the water sampling. Photo by DJ Kast

Up close shot of the water sampling. Photo by DJ Kast

CTD, Rosette, and Niskin Bottle basics.

The CTD or (conductivity, temperature, and depth) is an instrument that contains a cluster of sensors, which measure conductivity, temperature, and pressure/ depth.

Here is a video of a CTD being retrieved.

Depth measurements are derived from measurement of hydrostatic pressure, and salinity is measured from electrical conductivity. Sensors are arranged inside a metal housing, the metal used for the housing determining the depth to which the CTD can be lowered. Other sensors may be added to the cluster, including some that measure chemical or biological parameters, such as dissolved oxygen and chlorophyll fluorescence. Chlorophyll fluorescence measures how many microscopic photosynthetic organisms (phytoplankton) are in the water. The most commonly used water sampler is known as a rosette. It is a framework with 12 to 36 sampling Niskin bottles (typically ranging from 1.7- to 30-liter capacity) clustered around a central cylinder, where a CTD or other sensor package can be attached. The Niskin bottle is actually a tube, which is usually plastic to minimize contamination of the sample, and open to the water at both ends. It has a vent knob that can be opened to drain the water sample from a spigot on the bottom of the tube to remove the water sample. The scientists all rinse their bottles three times and wear nitrile or nitrogen free gloves to prevent contamination to the samples.

On NOAA ship Henry B. Bigelow the rosette is deployed  from the starboard deck, from a section called the side sampling station of this research vessel.

The instrument is lowered into the water with a winch operated by either Adrian (Chief Boatswain- in charge of deck department) or John (Lead Fishermen- second in command of deck department). When the CTD/Rosette is lowered into the water it is called the downcast and it will travel to a determined depth or to a few meters above the ocean floor. There is a conducting wire cable is attached to the CTD frame connecting the CTD to an on board computer in the dry lab, and it allows instantaneous uploading and real time visualization of the collected data on the computer screen.

 

CTD data on the computer screen. Photo by: DJ Kast

CTD data on the computer screen. Photo by: DJ Kast

The water column profile of the downcast is used to determine the depths at which the rosette will be stopped on its way back to the surface (the upcast) to collect the water samples using the attached bottles.

Niskin Bottles:

Messenger- The manual way to trigger the bottle is with a weight called a messenger. This is sent down a wire to a bottle at depth and hits a trigger button. The trigger is connected to two lanyards attached to caps on both ends of the bottle.  When the messenger hits the trigger, elastic tubing inside the bottle closes it at the specified depth.

Todd with the manually operated Niskin Bottle. Photo by: DJ Kast

Todd holding a messenger to trigger the manually operated Niskin Bottle. Photo by: DJ Kast

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Todd with the manually operated Niskin Bottle. Photo by: DJ Kast

Todd with the manually operated Niskin Bottle. Photo by: DJ Kast

Manual CTD fully cocked and ready to deploy. Photo by DJ Kast

Manual CTD fully cocked and ready to deploy. Photo by DJ Kast

Here is a video of how the manual niskin bottle closes: https://www.youtube.com/watch?v=qrqXWtbUc74

The other way to trigger Niskin bottles is electronically. The same mechanism is in place but an electronic signal is sent down the wire through insulated and conductive sea cables (to prevent salt from interfering with conductivity) to trigger the mechanism.

Here is a video of how it closes electronically: https://www.youtube.com/watch?v=YJF1QVe6AK8

Conductive Wire to CTD. Photo by DJ Kast

Conductive Wire to CTD. Photo by DJ Kast

Photo of the top of the CTD. Photo by DJ Kast

Photo of the top of the CTD showing the trigger mechanism in the center. Photo by DJ Kast

Top of the Niskin Bottles to show how the white wires are connected to the top.

Top of the Niskin Bottles shows how the lanyards are connected to the top. Photo by DJ Kast

The pin on the bottom is activated when an electronic signal is sent through the conductive sea cables. Photo by DJ Kast

The pin on the bottom is activated when an electronic signal is sent through the conductive sea cables. Photo by DJ Kast

Using the Niskin bottles, Megan collects water samples at various depths. She then filters water samples for her small bottles with a syringe and a filter and the filter takes out the phytoplankton, zooplankton and any particulate matter. She does this so that there is nothing living in the water sample, because if there is there will be respiration and it will change the nutrient content of the water sample.

Filtering out only the water using a syringe filter. Photo by DJ Kast

Filtering out only the water using a syringe filter. Photo by DJ Kast

Photo by: DJ Kast

Syringe with a filter on it. Photo by: DJ Kast

This is part of the reason why we freeze the sample in the -80 C fridge right after they have been processed so that bacteria decomposing can’t change the nutrient content either.

Diatoms dominate the spring phytoplankton bloom in the Gulf of Maine. They take up nitrate and silicate in roughly equal proportions, but both nutrients vary in concentrations from year to year. Silicate is almost always the limiting nutrient for diatom production in this region (Townsend et. al., 2010). Diatoms cannot grow without silicate, so when this nutrient is used up, diatom production comes to a halt. The deep offshore waters that supply the greatest source of dissolved nutrients to the Gulf of Maine are richer in nitrate than silicate, which means that silicate will be used up first by the diatoms with some nitrate left over. The amount of nitrate left over each year will affect the species composition of the other kinds of phytoplankton in the area (Townsend et. al., 2010).

The silica in the frustules of the diatom are hard to breakdown and consequently these structures are likely to sink out of the euphotic zone and down to the seafloor before dissolving. If they get buried on the seafloor, then the silicate is taken out of the system. If they dissolve, then the dissolved silicate here might be a source of silicate to new production if it fluxes back to the top of the water column where the phytoplankton grow.

Below are five images called depth slices. These indicate the silicate concentration (rainbow gradient) over a geographical area (Gulf of Maine) with depth (in meters) latitude and longitude on the x and y axis.

Depth slices of nitrate and silicate. Photo by:  This is the type of data Megan is hoping to process from this cruise.

Depth slices of nitrate and silicate. Photo by:  GOMTOX at the University of Maine
This is the type of data Megan is hoping to process from this cruise.

DJ Kast, Interview with Jessica Lueders-Dumont, May 22, 2015

NOAA Teacher at Sea
Dieuwertje “DJ” Kast
Aboard NOAA Ship Henry B. Bigelow
May 19 – June 3, 2015

Mission: Ecosystem Monitoring Survey
Geographical area of cruise: East Coast

Date: May 22, 2015, Day 4 of Voyage

 

Interview with Jessica Lueders-Dumont

Who are you as a scientist?

Jessica Lueders-Dumont is a graduate student at Princeton University and has two primary components of her PhD — nitrogen biogeochemistry and historical ecology of the Gulf of Maine.

Jessica Lueders- Dumont, graduate student at Princeton cleaning a mini bongo plankton net for her sample.

Jessica Lueders- Dumont, graduate student at Princeton cleaning a mini bongo plankton net for her sample. Photo by: DJ Kast

 What research are you doing?

Her two projects are, respectively,

A) Nitrogen cycling in the North Atlantic (specifically focused on the Gulf of Maine and on Georges Bank but interested in gradients along the entire eastern seaboard)

B) Changes in trophic level of Atlantic cod in the Gulf of Maine and on Georges Bank over the history of fishing in the region. The surprising way in which these two seemingly disparate projects are related is that part A effectively sets the baseline for understanding part B!

She is co-advised by Danny Sigman and Bess Ward. Danny’s research group focuses on investigating climate change through deep time, primarily by assessing changes in the global nitrogen cycle which are inextricably tied to the strength of the biological pump (i.e. biological-mediated carbon export and storage in the ocean). Bess’s lab focuses on the functional diversity of marine phytoplankton and bacteria and the contributions of these groups to various nitrogen cycling processes in the modern ocean, specifically as pertains to oxygen minimum zones (OMZs). She is also advised by a Olaf Jensen, a fisheries scientist at Rutgers University.

In both of these biogeochemistry labs,  nitrogen isotopes (referred to as d15N, the ratio of the heavy 15N nuclide to the lighter 14N nuclide in a sample compared to that of a known standard) are used to track nitrogen cycling processes. The d15N of a water mass is a result of the relative proportions of different nitrogen cycling processes — nitrogen fixation, nitrogen assimilation, the rate of supply, the extent of nutrient utilization, etc. These can either be constrained directly via 15N tracer studies or can be inferred from “natural abundance” nitrogen isotopic composition, the latter of which will be used as a tool for this project.

Nitrogen Cycle in the Ocean. Photo credit to: https://wordsinmocean.files.wordpress.com/2012/02/n-cycle.png

Nitrogen Cycle in the Ocean. Photo credit to: https://wordsinmocean.files.wordpress.com/2012/02/n-cycle.png

On this cruise she has 3 sample types — phytoplankton, zooplankton, and seawater nitrate — and two overarching questions that these samples will address: How variable is “baseline d15N” along the entire eastern seaboard, and does this isotopic signal propagate to higher trophic levels? Each sample type gives us a different “timescale” of N cycling on the U.S. continental shelf. She will be filtering phytoplankton from various depths onto filters, she will be collecting seawater for subsequent analysis in the lab, and she will be collecting zooplankton samples — all of which will be analyzed for nitrogen isotopic composition (d15N).

Biogeochemistry background: 

Biogeochemists look at everything on an integrated scale. We like to look at the box model, which looks at the surface ocean and the deep ocean and the things that exchange between the two.

The surface layer of the ocean: euphotic zone (approximately 0-150 m-but this range depends on depth and location and is essentially the sunlit layer); nutrients are scarce here.

When the top zone animals die they sink below the euphotic zone and into the aphotic zone (150 m-4000m), and the bacteria break down the organic matter into inorganic matter (nitrate (NO3), phosphate (PO4) and silicate (Si(OH)3.). In terms of climate, an important nutrient that gets cycled is carbon dioxide.We look at the nitrate, phosphate, and silicate as limiting factors for biological activity for carbon dioxide, we are essentially calculating these three nutrients to see how much carbon dioxide is being removed from the atmosphere and “pumped” into the deep sea.  This is called the biological pump. Additionally, the particulate matter that falls to the deep sea is called Marine Snow, which is tiny organic matter from the euphotic zone that fuels the deep sea environments; it is orders of magnitude less at the bottom compared to the top.

Cycling

Visual Representation of the aphotic and euphotic zones and the nutrients that cycle through them. Photo by: Patricia Sharpley

 

Did you know that the “Deep sea is really acidic, holds a lot of CO2 and is the biggest reservoir of C02 in the world?” – From Jessica Lueders- Demont, graduate student at Princeton.

One of the most important limiting factors for phytoplankton is nitrogen, which is not readily available in many parts of the global ocean. “A limiting nutrient is a chemical necessary for plant growth, but available in quantities smaller than needed for algae and other primary producers to increase their abundance. Organisms can grow and reproduce only when they have sufficient nutrients. For algae, the carbon source is CO2and this, at least in the surface water, has a constant value and is not limiting their growth. The limiting nutrients are minerals (such as Fe+2), nitrogen, and phosphorus compounds” (Patricia Sharpley 2010).

Conversely, phosphorus is the limiting factor on land. The most common nitrogen is molecular nitrogen or N2, which has a strong bond to break and biologically it is very expensive to fix from the atmosphere. 

Biological, chemical, and physical oceanography all work together in this biogeochemistry world and are needed to have a productive ocean. For example, we need the physical oceanography to upwell them to the surface so that the life in the euphotic zone can use them.

Activities on the ship that I am assisting Jessica with:

  • Zooplankton collected using mini bongos with a 165 micron mesh and then further filtered at meshes: 1000, 500, and ends with 250 microns, this takes out all of the big plankton that she is not studying and leaves only her own in her size range which is 165-200 microns.
  • She is collecting zooplankton water samples because it puts the phytoplankton that she is focusing on into perspective.
The last of the mesh buckets that's filtering for phytoplankton. Photo by: DJ Kast

The last of the mesh buckets that’s filtering for phytoplankton. Photo by: DJ Kast

    • Aspirator pump sucks out all of the water so that the zooplankton are left on a glass fiber filter (GFFs) on the filtration rack.

 

  • Aspirator pump that is on the side sucks out all of the air so that the plankton get stuck on the filters at the bottom of the cups seen here. Photo by: DJ Kast

    Aspirator pump that is on the side sucks out all of the air so that the plankton get stuck on the filters at the bottom of the cups seen here. Photo by: DJ Kast

  • Bottom of the cup after all the water has been sucked through. Photo by: DJ Kast

    Bottom of the cup after all the water has been sucked through. Photo by: DJ Kast

  • Jessica removing the filter with sterilized tweezers to place into a labeled petridish. Photo by: DJ Kast

    Jessica removing the filter with sterilized tweezers to place into a labeled petri dish. Photo by: DJ Kast

    Labeled petri dish with GFF of phytoplankton on it. Photo by: DJ Kast

    Labeled petri dish with GFF of phytoplankton on it. Photo by: DJ Kast

Video of this happening:

Phytoplankton filtering:

Jessica collecting her water sample from the Niskin bottle in the Rosette. Photo by DJ Kast

Jessica collecting her water sample from the Niskin bottle in the Rosette. Photo by DJ Kast

Up close shot of the spigot that releases water from Niskin bottle in the Rosette. Photo by DJ Kast

Up close shot of the spigot that releases water from Niskin bottle in the Rosette. Photo by DJ Kast

DJ Kast helping Jessica collect her 4 L of seawater from the Niskin bottle in the Rosette. Photo by Jerry P.

DJ Kast helping Jessica collect her 4 L of seawater from the Niskin bottle in the Rosette. Photo by Jerry P.

DJ and Jessica collect her 4 L of seawater from the Niskin bottle in the Rosette. Photo by Jerry P.

DJ and Jessica collect her 4 L of seawater from the Niskin bottle in the Rosette. Photo by Jerry P.

Chief Scientist Jerry Prezioso and Megan Switzer next to the CTD and Rosette

Chief Scientist Jerry Prezioso and Megan Switzer next to the CTD and Rosette Photo by: DJ Kast

 

May 21, 14:00 hours: Phytoplankton filtering with Jessica.

In addition to the small bottles Jessica needs, we filled 4 L bottles with water at the 6 different depths (100, 50, 30, 20, 10, 3 m) as well.

We then brought all the 4 L jugs into the chemistry lab to process them. The setup includes water draining through the tubing coming from the 4 L jugs into the filters with the GFFs in it. Each 4 L jug is filtered by 2 of these filter setups preferably at an equal rate. The deepest depth 100 m was finished the quickest because it had the least amount of phytoplankton that would block the GFF and then a second jug was collected to try and increase the concentration of phytoplankton on the GFF.

Phytoplankton filtration setup. Photo by DJ Kast

Phytoplankton filtration setup. Photo by DJ Kast

The filter and pump setup up close. Photo by DJ Kast

The filter and pump setup up close. Photo by DJ Kast

Up close shot of the GFF within the filtration unit.

Up close shot of the GFF within the filtration unit. Photo by DJ Kast

Jessica keeping an eye on her filtration system to make sure nothing is leaking and that there are no air bubbles restricting water flow

Jessica keeping an eye on her filtration system to make sure nothing is leaking and that there are no air bubbles restricting water flow. Photo by DJ Kast

Here I am helping Jessica setup the filtration unit.

Here I am helping Jessica setup the filtration unit.Photo by Jessica Lueders- Dumont

The GFF with the phytoplankton (green stuff) on it.

The GFF with the phytoplankton (green stuff) on it. Photo by: DJ Kast

There are 2 filters for each depth, and since she has 12 filtration bottles total, then she would be collecting data from 6 depths. She collects 2 filters so that she has replicates for each depth.

Here they are all laid out to show the differences in phytoplankton concentration.

The 6 depths worth of GFFs. See how the 30 m is the darkest. Thats evidence for the chlorophyll max. Photo by: DJ Kast

The 6 depths worth of GFFs. See how the 30 m is the darkest. Thats evidence for the chlorophyll max. Photo by: DJ Kast

She will fold the GFF in half in aluminum foil and store it at -80C until back in the lab at Princeton. There, the GFF’s are combusted in an elemental analyzer and the resulting gases run through a mass spectrometer looking for concentrations of N2 and CO2. The 30 m GFF was the most concentrated and that was because of a chlorophyll maximum at this depth.

Chlorophyll maximum layers are common features of vertically stratified water columns. There is a subsurface maximum or layer of chlorophyll concentration. These are found throughout oceans, lakes, and estuaries around the world at varying depths, thicknesses, intensities, composition, and time of year.