sample sorting – Page 2 – NOAA Teacher at Sea Blog

July 7, 2014August 21, 2021

Crystal Davis, When Science Goes Wrong, July 6 2014

NOAA Teacher at Sea

Crystal Davis

Aboard NOAA Ship Oregon II

June 23 – July 7, 2014

Mission: SEAMAP Groundfish Survey

Geographical area of cruise: Gulf of Mexico

Date: Sunday July 6, 2014

Weather: Clear and Sunny

Waves: 1-2 feet

Science and Technology Log:

The title of this post should actually be, “when science doesn’t go exactly as planned,” but that doesn’t sound quite as dramatic.

If you have ever written a lab report, you know that there is a section for procedures (what you did). The procedures need to be explicit so that they can be replicated by another individual who will obtain the same results. If your experiment cannot be replicated, your experiment is not valid and is useless. While it is okay for your hypothesis to be different than your expected outcomes, you always have to follow your procedure.

But . . . what if you’re in the middle of the ocean potentially hundreds of miles away from shore and on a deadline? You can’t go back to shore. There are at least thirty people on your boat and a lot of money invested in this data collection. Yet you still have to come up with a way to complete your survey. The events that follow are incidents that occurred on the Oregon II from July 26-July 6 and how the scientists coped with these situations.

Sharks

Juvenile Hammerhead Shark — Hammerhead Shark, Courtesy of Robin Gropp

In August, NOAA conducts a Longline Survey surveying sharks. Sharks are captured, identified and many are tagged with tracking devices to monitor the location and population density of sharks. Other sharks are sampled to determine age, analyze growth, sexual maturity and study stomach contents.

When sharks are captured in the trawl net on the Groundfish Survey, Robin (the intern) has been releasing them back into the Gulf after collecting data. However, not all of the sharks survive being pulled up in the net. The picture to the left is of a juvenile Hammerhead that did not survive. While this saddens me, he has been frozen and will be used to educate students in the outreach programs that NOAA participates in.

Nature vs Science

Waves crashing on the bow of the Oregon II. This picture was not taken on my survey, but this is what the weather felt like to me.

Sometimes mother nature interferes with the survey and things don’t go exactly as planned. For the first week of my trip we ran into some bad weather. There was a series of storms that came off the coast bringing rain, thunder, lightning and waves that were five to seven feet high. The weather conditions were so bad that the day shift couldn’t immediately collect data at a number of stations. They spent a lot of time waiting for the squalls to pass until it was safe to collect data. In fact, the weather in the Fall Groundfish Survey is so bad that there are a few extra days built in to run from hurricanes.

This morning we were trawling off the mouth of the Mississippi River and brought up a net full of sargassum (seaweed). The entire net, all 42 feet of it, was completely full of sargassum and very little marine life. No one on the boat had seen this much sargassum in the net before. This catch had to be thrown back overboard because the data is not usable. Basically, with that much sargassum in the net, the scientists are not sure if the trawl was fished properly. There is the possibility that because the net was so heavy, it was bogged down, uneven or not scraping the bottom of the ocean floor evenly.

The beginning of a squall courtesy of Andre DeBose

Squall moving the doors on the trawl net courtesy of Andre DeBose

Trawl Net filled with Sargassum

Warren and Mike checking to see if we are keeping the trawl

Mike and Eloy checking out the Sargassum

Formalin

On the Oregon II, plankton samples are preserved in Formalin (40% Formaldehyde). Formalin is a clear substance that stops cells from breaking down. A few days ago we noticed that the Formalin was no longer clear, it was in fact opaque. You can see this in the picture on the left. My night shift crew was worried that it was no longer useful and that we could not bring planktons samples back to the lab in Pascagoula. However, our chief scientist assured us that we could still use the Formalin and that it would be effective. The color change indicated that the base in the mixture was breaking down but since we only have a couple more days of plankton sampling, that it will be fine.

Personal Log:

I arrived back home last night and let me tell you it is strange to be back on land. I was never seasick on the Oregon II, but I am 100% landsick now. I find myself swaying from side to side anytime I’m standing still (Dock Rock is the official term). And when I woke up last night to get a glass of water, I fell over because I was swaying so much. It’s actually pretty funny but I will be glad once this goes away.

I’m still taking in my experience from the last two weeks but I am so grateful for the people I met and was able to work with. Everyone on the Oregon II was helpful, accommodating, friendly and made me feel at home. They took time out of their day to answer my questions, give me tours, tell me stories about their history and adventures on board, go over their research and they were genuinely interested in what I do in my classroom. XO (Executive Officer) LCDR Eric Johnson spent a good chunk of his time telling me about the NOAA Corps and made me want to sign up. Although I’m not too old to apply, (I have too many attachments at home to do so) if I could do the last ten years over I would apply to their program. I will definitely make sure my students know that the NOAA Corps is an option for them and am hoping to make a trip down to San Diego to take them on one of the boats next year.

I’m particularly grateful to the Chief Scientist Andre DeBose and Watch Leader Taniya Wallace who made sure I knew I was not going to die at sea. As the boat was leaving Galveston I could not stop crying because I was 100% certain I was never coming back ( I may have watched The Perfect Storm too many times). Andre and Taniya were so reassuring and comforting and I can never thank them enough for that.

I’m looking forward to using the knowledge, pictures and data from this trip in my classroom next year. I’m also excited because I heard that I can apply to be a volunteer on a NOAA cruise and am looking forward to this in the future.

July 3, 2014August 21, 2021

Crystal Davis, Female, Male? How do you tell? July 2, 2014

This Common Octopus was found in a 7-Up can.

NOAA Teacher at Sea

Crystal Davis

Aboard NOAA ship Oregon II

June 23-July 7, 2014

Mission: SEAMAP Groundfish Survey

Geographical area of cruise: Gulf of Mexico

Date: Wednesday July 2, 2014

Weather: Clear and sunny with isolated showers and thunderstorms

Winds: 5-10 knots

Waves: 2-3 feet

Science and Technology Log:

Shortly after boarding the Oregon II, the science crew had orientation with the Operations Officer LTJG Thomas reviewing basic procedures for emergencies on board. But what stuck out for me the most, was when Operations Officer LTJG Thomas said we were on a S.A.D. boat. It turns out that S.A.D. means no sex, alcohol or drugs are allowed on the Oregon II. This ensures that the boat is safe and reduces the number of accidents on board. This is the opposite of SAD and makes me feel much safer on board. But luckily for KISS fans, rock and roll is still allowed and is on consistently. Sometimes there’s so much rocking and rolling that I fall on the floor, but that’s happening less frequently as I’ve found my sea legs.

In the Groundfish Survey, after the organisms are separated by species, they are sexed. Overall, this gives the scientists an idea of what future generations will look like. Although all the organisms vary in the way you differentiate their gender, the following are some of the most common organisms found in the groundfish survey.

Sexing Shrimp

Brown Shrimp Female (top) Male (bottom) — Paneaus Aztecas Shrimp Female (top) Male (bottom)

As shown in the pictures on the left, male shrimp have a set of claspers (they look like an extra set of legs) called the petasma that is the equivalent of a penis. Females do not have a petasma.

In young (juvenile) shrimp, it can be difficult to identify the males from females as the petasma is very small and not easily visible. At this age they can easily be confused for females. When this is suspected, they are input into the computer as unknown so as not to generate inaccurate data.

Sexing Crabs

When you pick up a crab you have to be very careful to stay away their claws (cheliped). I have found that they like to grab onto you as soon as you pick them up. My roommate had a large blue crab grab her finger that would not let go and she still has bruises from it.

Mature female crabs are called a “Sook” and have a dome or bell shaped abdomen. This is shown in the top row and looks like the U.S. Capitol Building.

Male crabs are called a “Jimmy” and have a T-shaped abdomen that looks like the shape of the Washington Monument.

To mate, the male crab will carry the female until her shell softens and she is able to mate. During mating, the female stores the males sperm to fertilize her eggs later. Once her shell hardens, the male releases her and she will fertilize her eggs later.

After fertilization, the eggs are stored outside the female’s abdominal area and look like a sponge. They’re very squishy when you touch them. Although this shows orange eggs, they can also be a gray or black color. I have been told that the darker the egg color, the closer to hatching the offspring are. I am not sure that this is scientifically valid and am still trying to verify this.

Sexing Flatfish

Flatfish include fish such as flounder, halibut and turbot. These fish begin their life swimming vertically in the water. However, as they get older they sink to the bottom and their eyes move to one side of their body. They then spend the rest of their life on the bottom of the ocean floor. Luckily their top half matches the ocean floor and they are easily camouflaged from predators. The bottom half of the flounder on the ocean floor is clear or white.

The easiest way to sex a flatfish is to hold them up to a bright light. When doing this you will see that the female has a long curved gonad while the male does not.

A Confused Flounder (right) Normal Flounder (bottom left)

This Flounder is very confused. He should be a clear or light white on the bottom but as you can see his bottom half matches his top half. This could be due to a mutation but no one on the boat is exactly sure why he looks this way. This is one of the most interesting things I have seen so far. In fact, no one on the boat had seen this before.

Sea Jellies

Sea Jellies differ from most of the other marine organisms discussed so far. Sea jellies reproduce both sexually and asexually depending on what stage of life they are in. In an early stage of life sea jellies are called a polyp and they attach to a rock. The polyps reproduce asexually by cloning themselves and breaking off (budding). Imagine 300 people that came from you and look exactly like you. It’s actually pretty creepy. But back to the sea jellies. Eventually the sea jelly will develop into an adult (medusa) that reproduces sexually with sperm and egg.

Personal Log:

I have a three day backpacking trip to Mt. Silliman scheduled almost immediately after my NOAA trip is over. Under normal circumstances I wouldn’t worry, but after spending two weeks not hiking or training, I’m a little concerned. Luckily there are weights and a rowing and elliptical machine on board, so I have been able to do a bit of training. Being on a ship that’s moving has made working out even more intense. I have to stabilize every time the boat moves, so I don’t fall over. But even if I did, or have, how could I complain with this view.

Rowing on the bow

Pelican watching me workout

Frigate

Boat Personnel of the Day

Holland waiting for a trawl to come in — Holland on the stern

Holland McCandless-Lamier

Holland is my roommate on the Oregon II and is a member of the scientific party. She was contracted by Riverside in response to the Deep Water Horizon (BP) blowout in 2010. She attended the University of Mississippi and majored in marine biology. During college, Holland had an internship in Florida where she led students (from 4th grade to college) in marine science activities. This included snorkeling, visiting coral reefs and other hands on activities.

After college, Holland met an individual from the NOAA Corps at a job fair. They put her in touch with NOAA FIsheries MSLabs Groundfish Unit, where she began volunteering as a participant on surveys. This hands on experience led to her current job. Holland currently spends most of her time in the NOAA South East Fishery Science Center (SEFSC) Pascagoula lab where she works with plankton. Her current project is updating decapod (crustacean) taxonomy.

Did You Know?

A female sunfish can lay 300 million eggs each year. Each egg is smaller than the period at the end of this sentence.

June 28, 2014August 21, 2021

Crystal Davis, Bottom Trawl for Shrimp, June 27, 2014

NOAA Teacher at Sea

Crystal Davis

Aboard NOAA Ship Oregon II

June 23 – July 7, 2014

Mission: SEAMAP Groundfish Survey

Geographical area of cruise: Gulf of Mexico

Date: Friday June 27, 2014

Weather: Partly cloudy

Winds: 15-20 knots

Waves: 5-6 feet

Science and Technology Log: Bottom Trawling

The Oregon II is a participant and contributor to SEAMAP (The Southeast Area Monitoring and Assessment Program) which monitors the biodiversity of marine life in the Gulf of Mexico. The primary way the Oregon II assists SEAMAP is by conducting bottom trawls with a 42 foot semi-balloon shrimp trawl net.The net is slowly lowered into the ocean until it reaches the bottom and is then dragged along the ocean floor for thirty minutes. The net has a tickler chain between the doors which scrapes the bottom of the ocean floor and flicks objects into the net. The net is then brought to the surface and all of the organisms inside are put into baskets (see video above). The total weight of the catch is massed on scales on the deck. If the catch is large (over 20 kilos), it is dumped onto a conveyor belt and a random sub-sample (smaller) is kept, along with any unique species while the rest of the catch is dumped overboard.

Once the sample has been selected, the marine organisms are sorted by species and put into baskets. Each species is then massed and counted while the data is recorded into a system called FSCS (Fisheries Scientific Computer System). To obtain a random sampling, every fifth individual of the species (up to twenty) is measured, massed and sexed (more on this later). Once the data has been verified by the watch manager, the marine organisms are put back into the ocean. The following are pictures of a sample on the conveyor belt and the organisms divided into a few species.

Scallops and fish on the conveyor belt waiting to be sorted

The sorting process for shrimp (white, brown and pink) differs slightly from that of the other marine organisms. Every shrimp (up to 200 of each species), is massed, measured and sexed.This data is then used by various government agencies such as the Fish and Wildlife Service, Gulf of Mexico and South Atlantic Fishery Management Councils, etc… to determine the length of the shrimping season and to set quotas on the amount that can be caught by each issued license. States will not open the shrimping season until SEAMAP reports back with their findings from NOAA’s shrimp survey.

The shrimp trawl net used on the Oregon II differs from a shrimp net used on a commercial boat in two main ways. Commercial shrimping boats have BRD’s (Bycatch Reduction Devices) and TED’s (Turtle Excluder Devices). BRD’s and TED’s are federally required in the U.S. to reduce the amount of bycatch (unintentionally caught organisms) and sea turtles. Shrimping boats typically trawl for hours and turtles cannot survive that long without air. TED’s provide turtles and other large marine organisms an escape hatch so that they do not drown (see the video below). Unfortunately, larger turtles such as Loggerheads are too big to fit through the bars in a TED. Additionally, TED’s may become ineffective if they are clogged with sea debris, kelp or are purposefully altered.

Boat Personnel of the Week:

Warren Brown:

Warren is a gear specialist who is working as a member of the scientific party. He is contracted by Riverside for NOAA. While aboard the Oregon II, Warren designs, builds and repairs gear that is needed on the boat. Unfortunately, on this leg of the trip either sharks or dolphins have been chewing holes in the nets to eat the fish inside. This means Warren has spent a large chunk of his time repairing nets.

Warren is not a crew member of the Oregon II and actually works at the Netshed in Pascagoula where he spends his time working with TED’s. He has law enforcement training and will go out with government agencies (such as the Coast Guard or Fish and Wildlife Service) to monitor TED’s on shrimping boats. He also participates in outreach programs educating fishermen in measuring their nets for TED’s, installing them. Warren will bring TED’s and nets to make sure that every everyone at the training has a hands on experience installing them. While he regularly does outreach in Alabama, Mississippi, Florida, Georgia, North Carolina and Texas, his work has also taken him as far as Brazil.

Robin Gropp:

Robin will be a junior at Lewis & Clark College in the Fall. He is currently an intern aboard the Oregon II. Robin received a diversity internship through the Northern Gulf Institute and is one of eight interns for NOAA. For the first two weeks Robin worked at the NOAA lab participating in outreach at elementary school science fairs. He brought sea turtle shells and a shrimp net with a TED installed. The students were very excited to pretend to be sea turtle and run through the TED. They proclaimed, “we love sea turtles.” After leaving the Oregon II, Robin will return to the NOAA lab to study the DNA of sharks.

Personal Log:

Overall I have had a hard time processing and accepting the groundfish survey portion of the trip. I am a vegetarian that does not eat meat, including fish, for ethical and environmental reasons. Yet here I find myself on a boat in the Gulf of Mexico surveying groundfish so that others can eat shrimp. A large part of me feels that I should be protesting the survey rather than assisting. Because of this I spent a lot of time talking to the other scientists on my watch and Chief Scientist Andre Debose. After many discussions (some still ongoing) I do realize how important the groundfish survey is. Without it, there would be no limits placed on the fishing industry and it is likely that many populations of marine organisms would be hunted to extinction more rapidly than they are now. This survey actually gives the shrimp species a chance at survival.

Did You Know?

Countries that do not use TED’s are banned from selling their shrimp to the U.S.

July 16, 2009April 5, 2021

Megan Woodward, July 16, 2009

NOAA Teacher at Sea
Megan Woodward
Onboard NOAA Ship Oscar Dyson
July 1 – 18, 2009

Mission: Bering Sea Acoustic Trawl Survey
Geographical Area: Bering Sea/Dutch Harbor
Date: Tuesday, July 16, 2009

All bony fish have otoliths (ear bones) that can be used for calculating the age of the fish.

Weather and Location
Position: N 58 13.617; W 171 25.832
Air Temp: 7.2 (deg C)
Water Temp: 6.54 (deg C)
Wind Speed: 15 knots
Weather: Overcast

Science and Technology Log

One of the most interesting things I’ve learned while participating in the pollock survey is the importance of otoliths. Otoliths are small bony structures situated in the head of all bony fish, and are often referred to as “ear stones.” For each haul we brought on board, 50 otoliths were taken from large fish (3+ years) and/or 5 from small fish (younger than 3 years old). The otolith holds the key to accurately calculating the age of a fish (scales and vertebrates can also be used, but are not as reliable). The average age of fish from the samples collected in the survey helps scientists estimate the strength of a year-class and size of the stock in the future.

Back in the lab, otolith samples are carefully catalogued.

The first step in taking an otolith is pictured above. An incision is made on the back of the pollock’s head, and an otolith is removed using tweezers. Once the otolith is removed, it is rinsed with water and placed in a glass vial containing a small amount of 50% ethanol solution for preservation purposes.

The otoliths are taken back to NOAA’s aging lab where ages are determined by reading rings similar to those on a tree trunk. A crosscut is made through each otolith revealing a pattern of rings. Scientists then count the rings to determine the age of the fish. Lightly burning or staining the otoliths makes the rings more visible.

New material is deposited on the surface of the otolith creating the rings as the fish grows. The translucent/light zones indicate the main growth that takes place in the summer months. The opaque/darker rings appear during the winter months when growth is slower. Because of the slower growth rate, new material is deposited on top of the old layers resulting in the dark ring. Each pair of light and dark zones marks one year. In fish younger than one year of age, rings can be identified for each day of life!

Personal Log

I was surprised to discover otoliths have been used for aging fish since the early 1900’s. While working in the fish lab I observed the scientist removing otoliths, however I did not remove any myself. The cracking sound heard when cutting the head open was like fingernails on a chalkboard to me. I spent most of my time in sorting and measuring fish, as well as assisting with the stomach collection project.

For the next two days we will be heading back to Dutch Harbor, and the likelihood of trawling for more fish is minimal. Our remaining work assignment is to give the fish lab a thorough cleaning. Everything in the lab is waterproof, so we’ll put on our Grunden’s (orange rubber coveralls) and boots and spray down the entire space. Working and living at sea for nearly 3 weeks has been an eye opening experience. My time aboard the Oscar Dyson has flown by. I have learned so much about fisheries research and life at sea. Dry land, however, will be warmly welcomed when we get back to Dutch Harbor. Would I do it again? Absolutely.

Animal Sightings

The whales have an incredible way of showing up when I don’t have my camera. Yesterday I spotted two orcas, but did not get a photograph. The seabirds continue to circle. I like the murres most. They look like small, flying penguins.

New Vocabulary

Otoliths- Small bony structures situated in the head of all bony fish. Often referred to as “ear stones.”

Stock- Refers to the number of fish available, supply.

*** Much of the information used for this log entry was found on the Centre for Environment, Fisheries & Aquaculture Science (Cefas) web site.

July 12, 2009April 5, 2021

Megan Woodward, July 12, 2009

NOAA Teacher at Sea
Megan Woodward
Onboard NOAA Ship Oscar Dyson
July 1 – 18, 2009

Mission: Bering Sea Acoustic Trawl Survey
Geographical Area: Bering Sea/Dutch Harbor
Date: Tuesday, July 12, 2009

Any bycatch in a haul has to be measured and weighed if there are more than 25 of the same species caught. — Any bycatch in a haul has to be measured and weighed if there are more than 25 of the same species.

Weather/Location
Position: N 60.35.172; W 174.08.187
Air Temp: 6.1 (deg C)
Water Temp: 5.24 (deg C)
Wind Speed: 25 knots
Weather: Overcast, rain

Science and Technology Log

How is all the data collected from a trawl and acoustic lab used? By collecting data about weight and length from a sample, scientists are able to connect the size of fish caught to the amount of return seen in the acoustic lab. The return is assigned a name (PK1, PK2, etc.) and all schools showing a similar acoustic pattern are given the same name. In the end, scientists can estimate the number of fish and their size for a given area based on the acoustic and fish lab data collected. This is repeated throughout the survey resulting in an estimate for the total number of fish in the survey area.

Both during and after the survey estimates of abundance in the same location over the past several years are compared. Scientists evaluate the data and determine if the pollock population in the survey area is increasing, declining or stable. Their conclusions are used to make a recommendation about pollock fishing limits for the upcoming year. In the past few years the pollock population has been lower than in previous years. Due to the decline, the fishing quota has been reduced. However, the 2006 year-class is proving to be strong. At 4 years of age pollock are considered mature and fishable. Therefore, the fishing quota is predicted to rise in the next year or two.

Personal Log

While discussing the acoustic survey project with the scientists on board, I was quite surprised to hear the pollock survey had been going since 1979. Acoustic technology has changed and improved, but in essence the project has remained the same. Modern computer technology has allowed collection and analysis of enormous data sets and greatly reduced the amount of paper work needed for the project’s success.

The concept of strong vs. weak year-class is also quite interesting. There doesn’t seem to be a direct connection between a year-class’ success and environmental factors. Environmental factors that are potentially influential are water temperature, available zooplankton, ice cover, storms and predators. The fish currently being caught by commercial fisherman are 5-7 years old. Can you figure out which year classes those fish are from?

We continue to spot plenty of seabirds and a few more minke whale pods. I was able to watch a group of Dall’s porpoises play in the wake of the bow for half an hour yesterday. There haven’t been any new animal sightings during the past few days.

Although we are out here working in the best interest of pollock, I have found it difficult to watch thousands of pollock come through the fish lab. I have to remind myself that sampling the fish is truly for the good of the order. In addition, after being measured the fish are sent back into the ocean where they become food for other organisms such as crab or birds. One of their natural predators is having a good meal, something that was likely to happen anyway.

Animal Sightings

Seabirds
Dall’s porpoises

New Vocabulary

Bycatch – Anytime something is caught during a trawl other than pollock it is labeled bycatch. Jellyfish has been the most common form of bycatch.

Year-class – All the fish born in a given year are members of that year-class. We have caught a lot fish from the 2008 year-class (1 year old fish).