Nathan Pierantoni, Log, Friday, 4.8.11

Posted on April 8, 2011 by Teacher at Sea

NOAA Teacher at Sea: Nathan Pierantoni

University of Miami Ship R/V Walton Smith

South Florida Bimonthly Hydrographic Survey

Florida Keys, south of Key Largo

Friday, April 8 2011

Weather Data from the Bridge

1440 hrs Local Time

Barometric pressure = 1018 Millibars

79 F

74% Humidity

Visibility = good

Wind E 12 knots

Science and Technology Log

In this log I want to talk about the two marine biology graduate students whom I have been working with this week, Chelsea Bennice and Lorin West. They are both 2nd year students at the University of South Florida, and they have been conducting biological sampling all week long. They have been a lot of fun to get to know, and in discussing their research I have really been struck by the similarities between graduate level scientific research and the science projects that many of my students have worked so hard on for this year’s science fair.

***This is cool– as I sit on the deck of the boat writing this, a pod of bottlenose dolphins has joined us! We are cruising at about 7 knots and they are leaping out of the water at the edge of our wake.

Both Chelsea and Lorin are working with a genus of macro algae known as Sargassum. There are two pelagic (floating) species of Sargassum: Sargassum fluitans and Sargassum natans. These species form clumps/patches on the surface of the ocean and serve as habitat for small organisms like crustaceans (and other invertebrates) and juvenile fishes. Throughout the Florida Keys and the Florida Bay, we have seen Sargassum nearly everywhere.

At different stations along the cruise, Chelsea and Lorin have conducted net tows, in which a 2 m^2 fine mesh, windsock-shaped net is pulled along side of the boat for 30 minutes. At the end of this tube is a selectively permeable collection bucket (cod end) that traps Sargassum and the organisms that it hosts, but it allows the water to pass through. These net tows have been pretty cool, because every time we bring one in, there are always interesting creatures waiting to be discovered. Crabs, shrimp, nudibranchs, eels, fishes (including puffers, filefish, frogfish, jacks, flying fish, juvenile billfish, pipefish), copepods, amphipods, cnidarians (“by the wind sailor”), and a sea horse are just a few of the organisms that live in the uppermost meter of the ocean and make the Sargassum their home. And here I thought we had been floating past little chunks of lifeless seaweed! In fact, each patch of Sargassum is its own little ecosystem. Here is where Chelsea and Lorin’s work begins.

Chelsea is conducting a study in which she intends to describe the habitat architecure of pelagic Sargassum species. I had her describe her work: She intends to answer the question of how habitat selection among fishes and shrimp in the pelagic Sargassum community are influenced by the habitat architecture (interstitial spaces and depth) of a Sargassum patch. She will be manipulating the patches by changing their interstitial spaces (spacing the pieces of Sargassum differently among the surface of the patch). Sargassum pieces that are spaced tightly together are thought to create “microhabitats or niches” in the Sargassum for the fishes or shrimp to hide in. She will also be varying depth of the patches of Sargassum. Patches of Sargassum can range from 2cm to 12 cm (sometimes deeper!) in the water column. Having a deep depth patch may make it easier for a fish or shrimp to find its “home” in the open blue water.

Lorin is also working with Sargassum, but her work focuses on the mechanisms (visual and chemical cues) by which organisms are attracted to Sargassum in the open ocean. Her master’s thesis is titled “The role of chemical and visual cues used by the the sargassum crab Portunus sayi in selecting and locating habitats.” Sargassum is highly variable and broken up by waves and even washes up on shore. So, she has created controlled experiments in her lab where she can test whether the sargassum crab can detect chemicals from sargassum when they are dripped into the aquarium. She will also test to see if the crabs can visually detect sargassum without chemical cues and if they can distinguish between the two species of sargassum

As I spoke with Chelsea and Lorin, I couldn’t help but hope that some of my students go to college and graduate school in order to study ocean science. These women love their work and it shows. They describe their studies with enthusiasm and excitement. Chelsea and Lorin both teach introductory biology labs (they were grading punnett squares after hours during the cruise!), attend classes, and take research field trips to the ocean. They are each about to finish a thesis, graduate, and head into a promising career in marine biology!

Personal Log

It is Friday now, and we have north back toward Miami. We had a few CTD stops along the way and couple of other samples to collect, but overall there is a general feeling on board the R/V Walton Smith that we are headed home! Everyone seems ready to head home to be with their family, including me. This ship will begin a 49 day cruise to ground zero of the Deepwater Horizon oil spill next week, and therefore everyone is anxious to get as much shore time as possible. This week went by very quickly, and I enjoyed all of the experiences I had on board, I wish I could stay longer, but I’m excited to get back to work at Heights!

Here are Chelsea, Lorin, Josh (a University of Miami student of Marine Policy), and Matt (the ship’s chef) hanging out on deck after a long day.

Chelsea, Lorin, Josh (a University of Miami student of Marine Policy), and Matt (the ship's chef)

Nelson, Dennis, Lorin, and Chelsea watching a net tow in progress.

Nelson, Dennis, Lorin, and Chelsea

Here is the net in action! Lorin keeps her hands on the cable so that it doesn’t come too far out of the water.

Net in action

In this shot, Chelsea is gathering the sargasum she collected in a bucket.

Chelsea gathering sargassum

Once all of the organisms had been rinsed off the seaweed, this is what she got! A ‘soup’ of fish and small organisms. These blue ones were unsuspected!

In the wet lab, everything gets rinsed again with sea water and filtered through a mesh.

Wet Lab

Here are the fish they collected in a net tow. Sometimes fish use sargasum like a nursery to raise their juveniles. In this case, a small school of fish were found all at once.

Fish in an aquarium

Like all field science, they have plenty of work to do in the lab once their collection is done! Here they are writing their results. Nelson is also at his computer working on graphs from his experiments.

Lab work

Here is a group shot we took at sunset off of Key West on Thursday night. From left to right, Josh, Lorin, Erik, Cheryl, Nate, Chelsea and Nelson.

The crew near Key West

A nice sunset cruise passes by off of Key West (in the background). As we worked a CTD offshore, about 10 of these ships came out of the harbor and did circles around us. It was a really nice sunset, too!

Sunset cruise

Nathan Pierantoni, Thursday 4.7.11

Posted on April 7, 2011 by Teacher at Sea

NOAA Teacher at Sea: Nathan Pierantoni

University of Miami Ship R/V Walton Smith

South Florida Bimonthly Hydrographic Survey

Florida Bay, in transit from Dry Tortugas to Key West.

Thursday, April 7 2011

Weather Data from the Bridge

1400 hrs Local Time

Barometric pressure = 1017 Millibars

79 F

78% Humidity

Visibility = good

Wind SE 16 knots

Science and Technology Log

Dr. Neslon was very gracious and gave me free reign to learn as much as I could while aboard the R/V Walton Smith. Water sampling requires the most manpower and it is most common thing we are doing for this cruise, and therefore I have been involved in many vertical casts of the CTD. CTD stands for Conductivity, Temperature, and Depth, and when I refer to “the CTD” I am referring to the hefty apparatus that is pictured below, sitting on the fantail (the open deck at the stern of the ship). The procedure is as follows: as we get to our stations along our survey route, the boat stops and the we don our hardhats and life jackets and go out to the fantail,. We then lower the safety lines and prepare for a cast. Next, the captain goes to the stern of the upper deck where there is a winch cabin, from where he can pilot the ship and control the cast. The CTD is attached to a cable and is raised and lowered via an A-frame. The scientists give signals to the captain, and together, the device is lowered into the water where it does its work.

The CTD is actually a dual-purpose piece of equipment. It has sensors that measure conductivity (salinity), temperature, depth, chlorophyll, and dissolved oxygen. These sensors are built into a unit at the base of the apparatus and are protected by a metal cage.Above the sensor array is a rosette of tubes, which are able to collect water samples. Each tube holds 10 L of water, and our CDT has 12 tubes, called Nisken Bottles. The whole thing is electronically linked to the science deck through its cable, and in addition to the 2 scientists on deck who deploy the device, there is a CTD operator inside who monitors water parameter changes as the CTD goes from the surface to the bottom. This scientist is in communication with the captain in the winch cabin, and as the device returns to the surface the scientist is able to fire the Niskin bottles so that they fill with water. For example, we just finished a 340m CDT sample, and Nelson fired the CTD at three depths, 338 m, 70m, and 2 m. On the way down he was able to determine ‘where’ in the water column he wanted to collect his samples, because he was able to ‘watch’ the water parameters change on his computer monitor as the data from the CTD’s sensors streamed in. Interestingly, they fire two bottles at each depth in case one of them fails. It’s just another way to prevent against errors that would be too time consuming and thus too costly to fix. Once at the surface, the scientists and the winch operator guide the CTD back aboard the ship, and secure it to the deck.

While data from the sensors is logged and converted electronically to graphs, the chemical oceanographer begins her work. Cheryl Brown, aka ‘CB’ is an ocean scientist who I have had the pleasure of working with on the day shift. Cheryl works for the Cooperative Institute for Marine and Atmospheric Studies, a University of Miami institute that receives funding through NOAA. She participates in a variety of water quality projects, and spends about 25% of her time at sea. The other 75% of her work is in the lab, where she has multiple responsibilities that include filtration, data processing, and plotting of the samples from her fieldwork. This is common to most areas of field science, where for every hour of fieldwork yields at least double the time in the lab. CB has a degree in marine science, and specialized in marine invertebrates before finding her way to Miami.

The responsibilities on the chemistry deck are numerous. For each CDT deployment, there are a variety of samples that must be prepared from the water collected by the CTD. Each of this same series of samples is required for each depth of water that has been tested. On average, three depths are sampled per CTD deployment, but on this cruise some casts have collected water from four depths, and some have only collected water from the surface. The water from each depth is transferred to a bottle, which has been rinsed three times to avoid contamination, and brought into the wet lab. From there, a nutrient samples, chlorophyll samples, and dissolved CO2 samples are taken.

A nutrient sample is a general measure of ocean health, and includes many of the same samples that might be taken in a home aquarium, like ammonia, nitrates, and nitrites. To prepare the sample, we manually filter 50 ml of seawater into a sterile container, and preserve it with chloroform. It is then placed into the lab cooler. Finally, the time, location, depth, sample number, and collection number are logged.

The next step is to prepare a chlorophyll sample, and this is done with another process. In order to increase accuracy, two-200 ml samples are filtered through a small pad that is connected to a vacuum system. The water passes through the filter and is discarded, but the dissolved chlorophyll stays behind. Both small filters are placed into one vial, and the vial is stored in a liquid nitrogen container on deck. Then the samples are logged.

At some of our stations we have collected dissolved CO2 samples. This measure is also an important measure of ocean health, because CO2 is important to the photosynthetic processes that many reef organisms require. To collect a CO2 sample, a sterile flask is filled to the top with seawater, and 2 microliters of Mercury Chloride (HgCl2) are added. These samples are also logged.

This entire process gets repeated for each depth of water that was brought up in the tubes on the CTD. In the end, a whole lot of lab methods are practiced in a very short amount of time. You can imagine that as the week has gone on, these tasks have become easier and easier. At first, we were running stations about every half an hour, and the seas were quite rough. The amount of work to do in short intervals was a little bit overwhelming, but Cheryl let us all know that is would get easier as the week went on, and we she was right! As I finish up this log and we steam from the Tortugas back to the Keys I am looking forward to perfecting my CTD technique before we finish off the week!

Personal Log

It’s been really inspiring to get to know more about the people I am working with. Everyone here is very passionate about the work they are doing, and it is clear that if it weren’t for the love of the job they wouldn’t be out here bobbing around in the ocean! It is also interesting to hear about the different routes that people have taken to get here. This morning during breakfast I had the chance to talk at length with Cheryl about her recent Peace Corps experience. She was sent to the South Pacific island nation of Vanuatu for 27 months to do environmental work and to help facilitate a bank that was going to make micro-loans to women in business. When she got there, plans changed, and she ended up living on a small island called Paama. The island was 2 miles x 7 miles and has 21 villages spread around the coast. What had been an environmental mission turned into an educational one, and she ultimately spent her time on Paama rebuilding a primary school that had been destroyed by a cyclone. She had a canoe specially built for her so she could move about roadless island, and while on Paama she had to adapt to the lifestyle that sounds a lot like backcountry camping to me! Ultimately she had to jump islands on small planes, bargain with shipping captains and work with the entire community to get the school completed.

As I listened to Cheryl tell her story, enthralled by the adventure and romance of her experience, I was reminded of how lucky we are in America to have the education system that we have. It is my hope for my students and colleagues that you all really take advantage of the resources, facilities, and especially the technology what we probably take for granted at times. As I learn more about the future of oceanography I have been especially interested in the direction it is moving, toward space. As more and more remote sensing capabilities are developed, the need for ground proofing will also increase. What is clear to me is that oceanography, like all fields of science, will require dedicated researchers who are passionate about their work and skilled in technology, math, and engineering. There is only one place to get these skills, and its at school, and it requires practice, time, and patience. Thanks to Cheryl’s work, students in that small village on the coast of Paama are able to work toward their education. I challenge everyone at Heights Middle School, myself included, to do their personal best to taking advantage of all of the resources we have in order that our students will become the problem solvers of tomorrow!

I’ll keep posting pictures when I can, and I’m excited to come back to school on Monday!

Here is a shot from the CTD monitor inside the ship. The operator can see what is going on on deck, and follow the ater parameters at the same time.

CTD Monitor inside the ship

In this shot Cheryl and I are preparing to Launch the CTD. I am signaling the winch operator.

Launching the CTD

Another shot of the fantail, and you can see the CTD controlled by a cable via the A-frame.

Fantail

Here is the CTD collecting a surface sample.

Collecting a Surface Sample

Here I am in the process of collecting water out of a Niskin bottle, so that I can take it inside for preparation. Notice the instrumentation on the bottom of the CTD.

Collecting Water out of a Niskin bottle

Here is a shot of Cheryl getting started in the lab on the sample preparation.

Sample Preparation

I like this shot, it shows a clean filter pad and a ‘dirty’ one. The pad attached to the vacuum has just finished filtering 200 ml of seawater. The materials on the pad will be analyzed back in Cheryl’s lab on land.

Filter Pads

Here is a shot of Nelson Melo. He has been operating the CTD during the day, and he is holding a graph that charted Chlorophyll, temperature, O2, and salinity. This CTD was launched to a depth of 340 m.

Nelson Melo

Nelson’s work (which I described in my Tuesday log) and the data Cheryl pulls out of the samples we’ve collected will help to refine scientist’s capabilities for remote sensing in oceanography. I think its pretty significant that the latest issue of the scientific journal

Oceanography Journal

Oceanography has a satellite on it. This is the direction that ocean science has headed!

Nice Sunset! Almost as good as our New Mexico sunsets!

Sunset

Nathan Pierantoni, Tuesday 4.5.11

Posted on April 5, 2011 by Teacher at Sea

NOAA Teacher at Sea: Nathan Pierantoni

University of Miami Ship R/V Walton Smith

South Florida Bimonthly Hydrographic Survey

Florida Bay

Tuesday, April 5 2011

Weather Data from the Bridge

1400 hrs Local Time

Barometric pressure = 1014 Millibars

80 F

94% Humidity

Visibility = good

Wind S 14 knots

Science and Technology Log

Its Tuesday evening and I am finally taking the opportunity to organize my thoughts. The ship has been a whirlwind of activity since Sunday evening when scientists and crew began arriving and preparing for this 5-day research cruise to the Florida Keys and the Florida Bay. I have done my best to learn as much as I can in my time aboard the Walton Smith. The science that is being conducted on this cruise falls into three different areas of oceanography: physical oceanography, ocean chemistry, and marine biology. At all times there are scientists doing the fieldwork necessary to answer questions in these areas of science. In this log I will discuss the physical oceanography that is being conducted by Nelson Melo, a physical oceanographer, and our mission’s chief scientist.

Nelson is the leader when it comes to the organization and coordination of all of the work aboard the ship. Nelson is thoughtful and helpful, and has provided me with all of the information I need to make sense of the myriad of activities going on aboard our ship. Nelson Works for NOAA, and has multiple degrees in areas of physics ranging from nuclear physics to solid state transistors. He holds a PhD in Oceanography and is passionate about protecting and preserving the ocean. Originally from Cuba, he came to the United States 8 years ago.

Nelson’s work involves the synthesis of remote sensing data that is being shot from space via satellite with corollary data that he is working to collect from our ship as we pass through waters of the Florida Bay. For example, as the ship moves from one location to the next, the water might appear green or deep blue. These color changes are also visible from space and are being collected via satellite. The satellites used to collect this data are scanning the sea and creating multispectral images which, when processed and combined, appear like a color photograph of the ocean. These colors change as the conditions in the ocean change, and can be used to tell scientists about the health of the ocean. From the ship, we are moving throughout the Florida bay in order to sample many different parameters of water quality. One of them is chlorophyll. Nelson is most interested in the amount of chlorophyll in the water, because it serves as an indicator for the autotrophic life in the water column. Put simply, the presence or absence of chlorophyll in the water is valuable scientific information as it relates to many areas of study for ecologists, marine biologists and nearly every scientist who studies the ocean. As we collect water samples from different locations throughout the cruise, Nelson is using a sensor to measure the light as it appears at different depths of water. Today we were in about 7 m of water, and while the chemistry team sampled chlorophyll levels at different depths of water, Nelson put a photosensitive device over the side of the ship and slowly lowered it to the bottom. This device captured the intensity of light as it moved from the surface to the bottom, and all of the data was recorded on his computer. Then, he graphed his results. With the chlorophyll levels that the chemistry department has collected and the information from his submersible, as well as other parameters such as water current, salinity, and temperature he and many other scientists from the University of South Florida will work toward building an algorithm that will allow scientists in the future to use remote sensing from satellites to measure water parameters from space.

In fact, this work is already being done and oceanographers already have the tools to do this very accurately for offshore waters where there is less distortion from the reflection of the bottom or noise from particles in suspension due to shore currents or dissolved organic materials. Nelson is part of a team of scientists that is fine -tuning the algorithms used to measure water parameters from space that is more accurate for inshore waters.

Personal Log

Wow! Its been a busy couple of days!!! There is so much going on its kind of hard to know where to begin. The thing that I think I most appreciate right now is just how hard everyone is working. There hasn’t been much time to ‘mingle’, because everyone on the ship has a job to do, and it’s a full time operation. I think this is mostly due to the fact that this cruise it in relatively shallow waters, with many stops in close proximity to one another. And the ‘stops’ aren’t even really stops; they are simply the places where we slow down enough to do a CTD (which I’ll explain in a chemistry log tomorrow) or to do a net tow or to run the submersible photometer. Other than that, there is recording, chemistry, data analysis, and preparation for the next station to be done during transit times. The ship just keeps on following our prescribed cruise plan, from station to station, and if there is work to do during mealtime then everyone finishes their work before they get to eat. And the boat is divided into day shifts and night shifts for the science crew, and 6 hour on and off shifts for the ships crew. I appreciate that Nelson is packing in as much science as he can into this operation, because its obvious that great amounts of resources are going into these studies. I feel very lucky to get the opportunity to participate in this operation!

It is too bad that there are some other members of this cruise who I will not get to know as well, simply because they are asleep while I am awake. The ship is the most lively during the shift changes, when everyone is up for a meal of to catch each other up on the progress we had made during the day.

A special note to my classes:

Keep writing on the blog with questions, and I will keep catching opportunities to answer them, to upload pictures, and to go into more depth tomorrow about the chemistry and biology that are going on on the ship!

Here is the machine that Dr. Nelson uses to take his measurements, the PRR 2600.

PRR 2600

Here is a shot off of Dr. Melo’s computer, it is recently acquired satellite data measuring the light specra from the earth. Notice the curvature at the left hand side of the screen, that is how the satellite sees the earth.

Dr Melo's computer

Here is the PRR 2600 at the surface of the water.

PRR 2600 in the water

This is data from the ship. Notice duplicate measurements for parameters such as temp and salinity, and notice four sig figs. Those are real measurements, to a 10,000th of a degree!

Data from the Ship

Here is a shot of Dr Melo and with his submersible. He is slowly lowering the machine to the bottom while it takes accurate measurements of the light from the sun. At different depths the spectra of light change, and the amount that they change is related to the amounts of chlorophyll and other water parameters. This type of information from near-shore locations is what scientists will use to build accurate algorithms for interpreting future remote sensing data.

Dr. Melo lowering his Submersible

NOAA Teacher at Sea Blog

Monthly Archives: April 2011

Nathan Pierantoni, Log, Friday, 4.8.11

Nathan Pierantoni, Thursday 4.7.11

Nathan Pierantoni, Tuesday 4.5.11