harmful algal bloom – NOAA Teacher at Sea Blog

July 6, 2018

Angela Hung: “The Solution to Pollution is Dilution”, July 3, 2018

NOAA Teacher at Sea

Angela Hung

Aboard NOAA Ship Oregon II

June 27-July 5, 2018

Mission: SEAMAP Summer Groundfish Survey

Geographic Area of Cruise: Gulf of Mexico

Date: July 3, 2018

Weather Data from the Bridge

Conditions at 1610

Latitude: 29° 30’ N

Longitude: 92° 51’ W

Relative Humidity: 83%

Temperature: 26° C

Wind Speed: 13 knots

Cloudy with rain

Science and Technology Log

“The solution to pollution is dilution” was a common refrain during the midcentury as large scale factories became more common. This mindset applied to both air and water as both seemed limitless. Looking out over the Gulf of Mexico, a relatively small body of water, it’s easy to see how this logic prevailed. Even the Great Lakes, the largest body of fresh surface water in the world, accepted incalculable amounts of pollution and sewage from coastal factories, steel and wood mills, and of course major cities.

Sky and water as far as the eye can see. (It's hard to take a steady shot on a rocking boat!) — Sky and water in the Gulf of Mexico as far as the eye can see from the deck of NOAA Ship Oregon II. (It’s hard to take a steady shot on a rocking boat!)

The rise of the modern technological age that took humans to the moon gave us the first glimpse of the fallacy of the “solution”. “Earthrise” is the first photo of the entire Earth taken from space, showing us how thin our protective atmosphere really is and how delicately the Blue Planet floats in the vastness of space. This is the beginning of the modern environmental movement.

"Earthrise" Photo courtesy of nasa.gov — “Earthrise” Photo courtesy of nasa.gov

To truly guide the development of national policies including those that protect air and water quality, federal agencies such as NOAA are responsible for collecting data about our atmosphere and oceans, now knowing that these ecological compartments cannot endlessly dilute the pollution we generate. What seemed to be an obvious solution has today ballooned into a number of serious problems, from acid rain and blinding smog in cities to burning rivers, mass fish die offs that wash up on Lake Michigan beaches and dying coral reefs in the oceans.

The Cuyahoga River that runs through Cleveland, OH caught fire over a dozen times. This fire in 1969 finally motivated action towards creating the Clean Water Act. Photo from: https://www.alleghenyfront.org/how-a-burning-river-helped-create-the-clean-water-act/

A major pollutant in the Gulf is sourced from industrial agriculture practices from as far away as Illinois and the rest of the Midwest farm belt. Fertilizer and pesticides enter local rivers that find their way to the Mississippi River which carries contaminants into the Gulf of Mexico.

We have reached the Gulf’s “Dead Zone”, yielding a few tiny catches. Station W1601 may have given the smallest catch ever—a clump of seaweed and a whole shrimp.

The case of the shrinking trawls. On left, a catch from the night of July 2. Center and right, samples from two stations in hypoxic waters. The fish in the right photo may have been stuck in the net from the previous trawl. — The case of the shrinking trawls. On left, a catch from the night of July 2. Center and right, July 3 samples from two stations in hypoxic waters. The fish in the right photo may have been stuck in the net from the previous trawl.

Hypoxia literally means “low oxygen”. When fertilizers used to grow corn and soy enter bodies of water, they likewise feed the growth of algae, which are not technically plants but they are the aquatic equivalent. But plants make oxygen, how can this lead to low oxygen? Algae and land plants only produce oxygen during the day. At night, they consume oxygen gas through respiration. They do this during the day as well, but overall produce more oxygen in the light through photosynthesis. For hundreds of millions of years, that’s been fine, but the recent addition of fertilizers and the warm Gulf waters cause an explosion of the kind of microscopic algae that are suspended in the water column and turn water bright green, or red in the case of “red tides”. These explosions are called algal blooms.

Red tide. Photo credit: https://ocean.si.edu/ocean-life/plants-algae/red-tide

Algal blooms can cloud up water, making life hard for other photosynthetic organisms such as coral symbionts and larger seaweeds. At night, animals can suffocate without oxygen. During red tides, some algae release toxins that harm other life. When these organisms die and sink, bacteria go to work and decompose their bodies. The population of bacteria explodes, consuming the remaining oxygen at the sea floor. Animals that wander into the hypoxic zone also suffocate and die, feeding more decomposer bacteria that can survive with little to no oxygen. Thus, hypoxic areas are also called “dead zones”. The hypoxic zone is just above the sea floor, as little as a half a meter above, and oxygen levels can drop precipitously within a meter of the bottom.

A lone denizen of the Dead zone, a shark eye snail, Neverita duplicata.

A Synodus foetans skull that will not be measured from this trawl. — A Synodus foetens skull that will not be measured from this trawl.

NOAA scientists including those conducting the SEAMAP Summer Groundfish survey on Oregon II track the location, size and movement of the Gulf hypoxic zone using the conductivity-temperature-dissolved oxygen probe, or CTD. The CTD is sent into the water before every trawl to take a variety of measurements. Besides conductivity (a measure of ions), temperature and oxygen, the CTD also checks the salinity, clarity and amount of photosynthetic pigments in the water, which gives an idea of plankton populations. Ours uses two different sensors for conductivity, salinity, temperature and oxygen, double-checking each other. A pump pulls water through the various sensors and the measurements are sent directly to a computer in the dry lab to record these data.

The CTD is lowered to just under the surface of the water to make sure the pump is working and to flush the system. Then it is lowered to within a meter of the bottom. The CTD also has an altimeter to measure the distance from the bottom, while the ship also uses sonar to determine the water depth at each station. Water is measured continuously as the CTD is lowered and raised, creating a graph that profiles the water column. Crewmen are on deck controlling the winches according to the directions from a scientist over the radio who is monitoring the water depth and measurements in the dry lab.

Conductivity, temperature, dissolved oxygen sensor (CTD). The gray cylinders are bottles that can store water samples.

Casting the CTD is a coordinated effort.

The CTD also has bottles that can store water samples so oxygen can be tested a third time in the lab onboard. When we only get a few fish where the CTD recorded normal oxygen, the CTD is launched again to verify oxygen levels using all three methods. In the CTD output, oxygen is coded in green as a line on the graph and in the data tables. Most stations read in the 5-6 range, the cutoff for hypoxia is 2. We are reading less than 1 in the Dead Zone.

CTD output. Depth is on the vertical axis and each measurement is scaled on the horizontal axis, showing how each variable changes as the CTD moves to the bottom and back to the surface.

Quadruple check on dissolved oxygen in Gulf waters the "old fashioned" way using a Winkler titration. — Triple check on dissolved oxygen in Gulf waters the “old fashioned” way using a Winkler titration.

With storms in the path and not-so-plenty of fish in the sea, today is a slow day.

Personal Log

Looking out over the water, I can’t help but think how intrepid, even audacious, early mariners must have been. I know we are within a couple miles of the coast but there’s no sign of land anywhere in any direction. Even with the reassurance that satellites, radar, radios, AND trained NOAA Corps officers steering in the bridge are all keeping track of us, I still swallow a moment of panic. What kind of person decides to sail out in search of new continents when it only takes a couple hours to lose track of where you came from? And yet, the Polynesians set out thousands years ago in canoes from mainland Asia, the Aborigine ancestors managed to find Australia, and of course, Europeans sailed across the Atlantic to the Americas, whether they knew it or not. It was all possible through careful observations of the winds, waves, ocean currents, stars and other indications of direction, but I still have to think that that’s a pretty bold move when you don’t know if land lies ahead.

At least we’re not alone out here. These are some other animals that we’ll leave for the mammal survey and birders to count.

Dolphins appear around large catches for some pickings from the net.

Frigate birds, male in the upper left appear black, female below with a white breast.

Frigate bird inhabit tropical waters and are relatively uncommon in the U.S.

Brown pelican, Pelecanus occidentalis

Gulls never left the side of NOAA Ship Oregon II.

Did You Know?

The CTD also shows the layers of ocean water. Looking at the graph again for the red (salinity) and blue (temperature) lines, we can see where they cross at about 15 meters. This shows where colder, saltier water starts compared to the warm surface water that is diluted by fresh water and mixed by wind.

September 1, 2017

Chelsea O’Connell-Barlow: Full Steam Ahead, August 30, 2017

NOAA Teacher at Sea

Chelsea O’Connell-Barlow

Aboard NOAA Ship Bell M. Shimada

August 29 – September 12, 2017

Mission: Pacific Hake Survey

Geographic Area of Cruise: NW Pacific Ocean

Date: 8/30/2017

Weather Data from the Bridge:

Latitude: 48.472837N

Longitude: -124.676694W

Temperature 59 F

Wind 9.7 knots

Waves 3-5 feet

Science and Technology Log

We have not started fishing yet because we are heading to our first transect off the western coast of the Haida Gwaii archipelago. I thought this would be a perfect time to introduce another research project that is gathering data on the Shimada. One of my roommates, Lynne Scamman, is on-board researching Hazardous Algal Blooms (HABs).

Lynne in Chem lab — Lynne Scamman running wet chemistry tests and identifying phytoplankton.

What are Hazardous Algal Blooms?

They are large numbers of phytoplankton, either diatoms or dinoflagellates, who produce toxins. Phytoplankton are essential to the ecosystem because they produce half of the global oxygen. However under certain circumstances these organisms reproduce rapidly, skyrocketing the population, this is a bloom. Some of these phytoplankton produce toxins. When the populations are low the toxins aren’t a big deal. However, when a bloom of phytoplankton that produce toxins occurs there can be health concerns for organisms exposed to the toxins. We have to consider the marine food chain and something called bioaccumulation. Phytoplankton along with zooplankton create the base of the marine food web. Organisms who eat toxin producing phytoplankton retain the toxin in their body. Then any organism who eats them will also hold that toxin. You can see how the toxin would accumulate along the food chain and potentially hold serious side effects for organisms with high levels of toxin.

Why is research being done on HABs?

HABs are becoming a problem for humans along the coasts and in the Great Lakes. Basically all of the factors that contribute to the increase in HABs are a product of human impact. Global climate change, increased nutrient pollution and global sea trade are all factors contributing to the rise in Hazardous Algal Blooms. We want to monitor so that eventually we will be able to predict when, where and why the HABs will occur.

Why are YOU studying HABs?

One day I walked into my college biology lab and met a guest instructor who specializes in all things phytoplankton related. I was blown away by the complexity that some of these single celled organisms held. The professor shared a few species names and I started investigating. The species that grabbed my attention is called Nematadinium armatum. This organism has a rudimentary eye called a melanosome and nematocysts for hunting, again this is pretty impressive for an organism made of one cell. Once I learned about the variety in this microscopic world and how influential they were to the health of the entire ocean, I knew that I wanted to learn more.

Personal Log

I am still figuratively pinching myself every few hours at just how amazing this experience is to participate in first hand. Yesterday we left the dock of Port Angeles at 10am and the boat hasn’t slowed down since. We did drills to ensure that all aboard knew where to go in case of fire and if we needed to abandon ship. Part of the abandon ship drill is to make sure that everyone has and can get into their Immersion Suit aka “Gumby Suit.” This suit is amazing! This portion of the Pacific is quite cold and the Immersion suit would keep you warm and buoyant until a rescue can occur.

OCB Gumby — Trying on the Immersion suit.

After our drills several of the science crew went up to the Flying Bridge to look for marine mammals. We were cruising between Cape Flattery, Washington and Vancouver Island, British Columbia with high hopes of seeing activity. WOW, we lucked out. We spotted 17 Humpback whales, 2 Harbor porpoise and 2 Dall’s porpoise. We are also seeing several types of sea birds but I am still brushing up with the Sibley to id birds from this area.

Shimada Flags — The *Shimada* under two flags as it enters Canadian waters.

Did You Know?

The island cluster that we are heading to had a name change at the end of 2009. What was formerly called Queen Charlotte Islands is now called Haida Gwaii. This name change came as part of a historic reconciliation between British Columbia and Haida nation. Haida Gwaii translated means “island of the people.”

August 25, 2017August 25, 2017

Christine Webb: August 23, 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: 8/23/2017

Latitude: 48.19 N

Longitude: 125.29 W

Wind Speed: 7.9 knots

Barometric Pressure: 1021.70 mBars

Air Temperature: 62.1 F

Weather Observations: Partially cloudy

Science and Technology Log

For today’s science and technology log, I interviewed my roommate Tracie. You only have to talk to Tracie for five seconds to learn that she’s passionate about marine chemistry and marine biology and marine physics…all things marine. She’s the HAB (harmful algal bloom) specialist on board, and she’s been squirreled away in the chemistry lab every day collecting lots of great samples as we travel up the coast. Before we left Newport, she taught me a bit about algae by taking me to the beach to see some bioluminescent dinoflagellates. When we stomped in the water, the dinoflagellates would glow! It looked like puddles full of blue lightning bugs, and it was amazing. One of her quotes from that night was, “I imagine this is what unicorn footprints would look like if they were traipsing over rainbows.” Everyone should have the chance to see that at some point in their life. It gave me a taste of why it makes sense to be so passionate about algae. So, without further ado, here’s your chance to learn a bit more about HABs from my friend Tracie!

What is a HAB, and why should we care about them?

HABs are phytoplankton that have negative consequences either for us or the ecosystem. Some can release neurotoxins that can be damaging to mammals (including humans), amongst other things. A harmful algal bloom (HAB) can also create a dead zone by a process called eutrophication. Bacteria eat the phytoplankton once they begin to die, which removes oxygen from the water.

What makes it a bloom?

A “bloom” is when there is so much algae that the ecosystem can’t support it and they start to die off. There aren’t enough nutrients available in the water. Some people call this a “Red Tide.” There are certain species, such as Alexandrium spp., where even one cell per liter would be enough to create a harmful effect.

What made you decide to study HABs?

During a lab in college, we were allowed to go to the beach and sample phytoplankton. When we got back to the lab with our samples, we found a huge amount of Pseudo-nitzschia spp. It releases a neurotoxin that gives mammals amnesiac shellfish poisoning. That year, we couldn’t eat shellfish and crab from our area because of this bloom. There’s no antidote to this toxin, and it affects the brain function of mammals who eat it. Whales died that year because they forgot how to breathe. This made me super interested in studying more about these types of species.

What are you specifically hoping to find in your research aboard this cruise?

We’re trying to find where blooms start, how blooms begin, and follow them within the California Current system. It’s part of an ongoing study of the California Current system and how species are transported. California fisheries have been dramatically affected by HABs.

Have you been finding what you need so far?

It’s been really interesting…we’ve seen quite a few Dinophysis species (which I find to be the cutest), and some really interesting Pseudo-nitzschia spp., but no blooms. Close to the coast, within 15 nm of shore, I see a lot more diversity in my samples. This is mostly due to upwelling.

Has anything in your research so far surprised you?

There are very few species that I haven’t recognized, which is interesting because we’re so far north. We have fjord-like environments up here by Vancouver Island, so I expected there to be a higher abundance of phytoplankton up here than I saw.

What is a common misconception about HABs?

The term “HAB” itself – they’re called harmful because they’re harmful to us as humans and to various industries, however – they provide a huge amount of support to other animals as primary producers and as oxygen producers.

They’re basically plants that can swim, and they’re all food for something. They’re not harmful for most things, so the name is kind of a misnomer. In defense of the HABs, they’re just trying to survive. Phytoplankton are responsible for around 50% of the world’s oxygen, and they’re the primary producer for marine and freshwater ecosystems.

Anything else you want people to know?

There’s still a lot that we need to learn, and I would like everyone at some point in their life to see how beautiful these fragile organisms are and appreciate how much they contribute to our world.

If you weren’t a marine chemist, what would you be?

I would write nonfiction about the beauty of the world around us. Or maybe I’d be an adventure guide.

What are some fun facts about you that not a lot of people know?

My motto for life is “always look down.” There’s so much around us, even the dirt under our toes, that is so full of life and beauty.

My art is on Axial Seamount, 1400 m below sea level, 300 miles off the coast of Oregon! I drew an octopus high-fiving ROPOS the ROV that placed it there!

Also, I’m a high school dropout who is now a straight-A senior in environmental science at the University of Washington, Tacoma. Other people’s perceptions of you don’t control your destiny.

Here are a couple pictures of some of the HABs Tracie has seen during this trip (she took these pictures from her microscope slides):

329 D. fortii — Algae under the microscope: D. fortii. Image by Tracie.

329 hobbit house 2 — Algae under microscope. Image by Tracie.

Personal Log:

Since today’s science log was about Tracie, I’ll feature her in the personal log too! She’s my partner in the ship-wide corn hole tournament, and we won our first-round game yesterday. Look at these awesome corn hole boards that were specially made for the Shimada!

IMG_20170822_153718727 — Shimada corn hole board!

We mostly credit our fabulous war paint for the win. Today we play against our fellow scientists Lance and Tim. Wish me luck!

Christine and Tracie celebrate corn hole victory

Another down-time activity that Tracie (and all the scientists) enjoy is decorating Styrofoam cups. The cool marine biologist thing to do is to sink them to very low ocean depths (3000+ meters). Apparently the pressure at that depth compresses the Styrofoam and shrinks it, making the cup tiny and misshapen but still showing all the designs that were put on it. I’m not kidding: this is a thing that all the marine biologists get really excited about. Tracie even decorated a Styrofoam head (the kind that cosmetologists use) in advance of this trip and brought it with her to sink. Look how cool it is – she’s an amazing artist!

IMG_20170824_171631958_HDR — Styrofoam head, decorated by Tracie, for shrinking

There are shrunken heads in the lab already from other people who have done this. Sinking Styrofoam is a legit marine biology hobby. Well, as the saying goes, “When in Rome…” so I worked on a Styrofoam cup today. I’m making a hake tessellation, which takes longer than you might think. Here’s what I’ve got so far:

IMG_20170823_051528993 — Styrofoam cup decorated with hake tesselation

We’re having lots of fun at sea on this beautiful day. Someone just came over the radio and said there’s been a marine mammal sighting off the bow…gotta go!

Special Shout-out:

A special shout-out to Mrs. Poustforoush’s class in Las Vegas, Nevada! I just found out you’ve been following this blog, and it’s great to have you aboard. If you have any questions about algae (from this post) or about life on a ship, please feel free to e-mail me. I can hopefully get your questions answered by the right people. Work hard in Mrs. Poustforoush’s class, okay? She’s a great teacher, you lucky kiddos. Learn a lot, and maybe one day you can be a scientist and live on a ship too!

May 17, 2016August 21, 2021

Dana Chu: May 17, 2016

NOAA Teacher at Sea
Dana Chu
On Board NOAA Ship Bell M. Shimada
May 13 – 22, 2016

Mission: Applied California Current Ecosystem Studies (ACCESS) is a working partnership between Cordell Bank National Marine Sanctuary, Greater Farallones National Marine Sanctuary, and Point Blue Conservation Science to survey the oceanographic conditions that influence and drive the availability of prey species (i.e., krill) to predators (i.e., marine mammals and sea birds).

Geographic area of cruise: Greater Farallones, Cordell Bank, and Monterey Bay National Marine Sanctuaries

Date: Tuesday, May 17, 2016

Weather Data from the Bridge
Clear skies, light winds at 0600 increased to 18 knots at 0900, 6-8 feet swells

Science and Technology Log

Ahoy from the Bell Shimada! Today, I will explain three of the tools that are deployed from the side deck to obtain samples of the water and the ocean’s prey species.

First off we have the Harmful Algal Bloom Net, also known as the HAB Net, which is basically a 10-inch opening with a 39-inch fine mesh netting attached to a closed end canister. The HAB net is deployed manually by hand to the depth of 30 feet three consecutive times to obtain a water sample. The top fourth of the water collected is decanted and the remaining water (approximately 80ml) is transferred to a bottle which is then sealed and labeled with the location (latitude, longitude), date, time, vertical or horizontal position, and any particular comments. The samples will eventually be mailed off to California Department of Health Services lab for analysis for harmful toxins from algae that can affect shellfish consumers.

Next we have the hoop net, which is pretty much similar in design to the HAB net, except for a larger opening diameter of 3 feet (think hula hoop) and a net length of nine feet. The net tapers off into a closed container with open slits on the sides to allow for water drainage. The purpose of the hoop net to collect organisms that are found at the various depth levels of the deployment. The hoop net is attached to a cable held by the winch. The hoop net is lowered at a specific angle which when calculated with the speed of the vessel equates to a certain depth. The survey crew reports the wire angle sighting throughout the deployment.

Every time the hoop net is brought back up there is a sense of anticipation at what we will find once the canister is open. Coloring is a good indicator. Purple usually indicates a high concentration of doliolids, while a darker color may indicate a significant amount of krill. Phytoplankton usually have a brownish coloring. Many of the hoop net collections from today and yesterday include doliolids and colonial salps, neither are very nutrient dense. Yesterday we also found pyrosomes, which are transparent organisms that resemble a sea cucumber with little bumps and soft thorns along their body. The smallest pyrosome we came upon was two and a half inches with the largest over six inches long. A few small fish of less than one inch in length also showed up sporadically in these collections as well.

The Scientific team is looking for the presence of krill in the samples obtained. The Euphausia pacifica is one of the many species of krill found in these waters. Many tiny krill were found in the various hoop net deployments. On the last hoop net deployment for today and yesterday, larger sized krill of approximately 1 inch) were found. This is good news because krill is the dominant food source for marine mammals such as whales. Ideally it would be even better if the larger krill appeared more frequently in the hoop net samples.

Finally, we have the Tucker Trawl, which is the largest and most complex of the three nets discussed in today’s post. The Tucker Trawl consists of three separate nets, one for sampling at each depth: the top, middle, and bottom of the water column. Like the hoop net, the tucker trawl nets also have a canister with open slits along the side covered with mesh to allow water to drain. All three nets are mounted on the same frame attached to a wire cable held by the winch. As the Tucker Trawl is towed only one net is open at a time for a specific length of time. The net is closed by dropping a weight down along the tow. Once the weight reaches the net opening, it triggers the net to shut and sends a vibration signal up the cable line back to the surface which can be felt by the scientist holding the cable. The net is then towed at the next depth for ten minutes. Once the last net tow has been completed, the Tucker Trawl is brought back up to surface. Similar to the hoop net, the survey tech reads the wire angle throughout the deployment to determine the angle the cable needs to be at in order for the net to reach a certain depth. This is where all the Geometry comes in handy!

As mentioned already, with three nets, the Tucker Trawl yields three separate collections of the nutrients found within the top, middle and bottom of the water column. Once the nets are retrieved, each collection container is poured into a different bucket or tub, and then into a sieve before making it into a collection bottle. If there is a large quantity collected, a subsample is used to fill up a maximum of two bottles before the remainder is discarded back into the ocean. Once the samples are processed, an outside label is attached to the bottle and an interior label is dropped inside the bottle, formalin is added to preserve the sample organisms collected so that they can be analyzed later back in the lab.

Personal Log

It is so good to finally get my sea legs! I am glad I can be of use and actively participate. Cooperative teamwork is essential to getting everything to flow smoothly and on time. The Bell Shimada’s deck crew and NOAA team work hand in hand with the scientists to deploy and retrieve the various instruments and devices.

In the past two days I am getting a lot of hands on experience with deploying the HAB net to assisting with processing samples from the HOOP Net and Tucker Trawl. It’s always exciting to see what we might have collected. I can’t wait to see what the rest of the week may bring. I wonder what interesting finds we will get with the midnight Tucker Trawl samples.

Lesson Learned: Neatness and accuracy are imperative when labeling samples! Pre-planning and preparing labels ahead of time helps streamline the process once the samples are in hand.

Word of the Day: Thermocline – This is the depth range where the temperature of the water drops steeply. The region above the thermocline has nutrient depleted waters and while the region below has nutrient rich waters.

August 13, 2009April 6, 2021

Bryan Hirschman, August 13, 2009

NOAA Teacher at Sea
Bryan Hirschman
Onboard NOAA Ship Miller Freeman (tracker)
August 1 – 17, 2009

Mission: 2009 United States/Canada Pacific Hake Acoustic Survey
Geographical area: North Pacific Ocean; Newport, OR to Port Angeles, WA
Date: August 13, 2009

Weather Data from Bridge (0800)
Visibility: 10 nautical miles
Wind: 6 knots
Wave Height: 1 ft
Wave Swell: 1-2 ft
Ocean temperature: 15.2⁰C
Air Temperature: 14.2⁰C

Science and Technology Log

This is the net reel. The unit attaches with four bolts in each corner

Life at sea can be very unpredictable. One minute everything is working great, and the next minute problems occur. Last evening a problem occurred with the net reel. The net reel is a large bull wheel that the nets roll into and out of when lowered in the water. The reel is spun by a huge engine that pulls the nets in when they are loaded with fish. This net reel is anchored to the boat with 16 huge bolts and nuts. Four of the bolts were found last night to be weakened during one of the daily inspections of ship’s mechanical instruments. The crew is constantly inspecting each piece of equipment to ensure the safest working conditions. Once this problem was seen all fish tows were canceled. We will be heading into port four days early to fix the problem.

An incorrect assembly of the bolts on the net reel

A correct assembly of the bolts on the net reel

Once in port the entire net reel will have to be lifted by crane and all the bolts will be replaced. The reel will then be lowered back in place and locked in place with nuts. Even though we are not fishing, other work on the ship is still occurring. The XBT (Expendable Bathythermograph) is deployed at regular intervals. This device sends depth and temperature data to a science laboratory to be recorded and used later (discussed in more detail in log 2).

Toxin-producing phytoplankton pseudo-nitzschia.

The HABS (Harmful Algal Bloom Sampling) research is also still being completed by Nick Adams, an oceanographer with NOAA. He takes water samples approximately every 10 nautical miles (1 nautical mile = 1.15 miles). After collecting the samples, he filters them for toxin and chlorophyll analysis. He also collects seawater for phytoplankton numeration and identification. His main focus is on toxin-producing genera, such as Pseudo-nitzschia and Alexandrium which are responsible for Amnesic Shellfish Poisoning and Paralytic Shellfish Poisoning, respectively. At the end of the cruise, Nick will be able to create a map of the concentrations and locations of toxin- producing phytoplankton. This will then be compared with data from years past to determine patterns and trends.

Toxin-producing phytoplankton Alexandrium

The phytoplankton themselves are not harmful to humans, but as they accumulate in the food chain there can be human-related sickness. If we eat the organisms that are eating the plankton that produce toxins, we can become ill. Not much is known about the cause of the toxin producers, but with more research like Nick’s, scientists continually increase their understanding and ultimately hope to prevent human sickness from these phytoplankton.

Personal Log

I am saddened to be cutting my journey earlier then expected, but I will leave the ship with fond memories of Pacific Hake, Humboldt Squid, and all the wonderful people who work on the ship. I am particularly grateful to the seven scientists who have gone out of their way to make me feel at home on the ship and have answered all of my questions. They are: the acoustic scientists: Dr. Dezhang Chu, Larry Hufnagle, and Steve de Blois; the fish biologists: Melanie Johnson and John Pohl; the oceanographers: Steve Pierce and Nick Adams. They are each extremely dedicated and passionate about their research and equally passionate about protecting our oceans and the organisms living there.

Scientists Steve de Blois, Larry Hufnagle, Dr. Dezhang Chu, and John Pohl

Challenge Yourself
Volunteers play an integral role in supporting the environmental stewardship conducted every day by the National Oceanic and Atmospheric Administration. Across the United States and its coastal waters, opportunities exist for volunteers to take part in research, observation and educational roles that benefit science, our citizens and our planet.

Visit this website to see where you can help

August 12, 2009April 6, 2021

Justin Czarka, August 12, 2009

NOAA Teacher at Sea
Justin Czarka
Onboard NOAA Ship McArthur II (tracker)
August 10 – 19, 2009

Mission: Hydrographic and Plankton Survey
Geographical area of cruise: North Pacific Ocean from San Francisco, CA to Seattle, WA
Date: August 12, 2009

Weather Data from the Bridge

Sunrise: 06:25 a.m.
Sunset: 20:03 (8:03 p.m.)
Weather: isolated showers/patchy coastal fog
Sky: partly cloudy
Wind direction and speed: North 10-15 knots (kt)
Visibility: unrestricted to less than 1 nautical mile (nm) in fog
Waves: northwest 4-6 feet
Air Temperature: 17.3 °C
Water Temperature: 16.6 °C

Science and Technology Log

Justin Czarka collects water samples to use in nutrient and chlorophyll research. While on the deck during “ops” (operation) all personnel must wear a life jacket and hardhat.

This log discusses the purpose behind the scientific cruise aboard the McArthur II. The cruise is titled, “Hydrographic and Plankton Survey.” The cruise is part of a larger study by many scientists to, in the words of chief scientist, Bill Peterson, “understand the effects of climate variability and climate change on biological, chemical and physical parameters that affect plankton, krill, fish, bird and mammal populations in Pacific Northwest waters.” This specific cruise focuses on hydrology, harmful algal blooms, zooplankton, krill, fish eggs, fish larvae, and bird and mammal observations.

I will provide an overview of these aspects of the cruise. The McArthur II is set up with sensors for salinity, temperature, and fluorescence that provide a continuous monitoring of the ocean (hydrology) throughout the cruise. In addition at various points along the transect lines (see the dots on the diagram of the cruise route on page 2), the CTD is deployed into the water column at specific depths to determine salinity (via measuring conductivity), water temperature, and depth (via pressure), and collect water samples (which we use to measure chlorophyll and nutrient levels at specific depths). The transects (predetermined latitudes that forms a line of sampling stations) have been selected because they have been consistently monitored over time, some since the late 1980s. This provides a historical record to monitor changes in the ocean environment over time.

The dots represent planned sampling station. Due to sea conditions, these have been slightly modified.

One scientist, Morgaine McKibben from Oregon State University, is researching harmful algal blooms (HAB). HABs occur when certain algae (the small plants in the ocean that are the basis of the food web) produce toxins that concentrate in animals feeding on them. As these toxins move up the food web through different species, they cause harmful effects in those species, including humans. Bill Peterson (NOAA/ Northwest Fisheries Science Center) and Jay Peterson (OSU/Hatfield Marine Science Center) are studying copepod reproduction. They are collecting data on how many eggs are laid in a 24 hour period, as well as how the copepod eggs survive in hypoxic (low oxygen) conditions. Mike Force, the bird and marine mammal observer is keeping a log of all species spotted along the cruise route, which is utilized by scientists studying the species.

Personal Log

Tiny squid collected in a vertical net and viewed under microscope on Crescent City transect line at 41 deg 54 min North.

Who said you never find the end of the rainbow? All you have to do is go out to sea (or become a leprechaun!). We have been going through patches of fog today, putting the foghorn into action. When it clears out above, yet is foggy to the horizon, you get these white rainbows which arc down right to the ship. We have become the pot of gold at the end of the rainbow. Who knew it was the McArthur II! If you follow the entire rainbow, you will notice that it makes a complete 360° circle, half on top the ocean and half in the atmosphere near the horizon.

I enjoyed using the dissecting microscope today.

The water collected from the vertical net is stored in a cooler on the deck to be used in experiments. I was able to collect a sample of the water, which contained a diverse group of organisms, from tiny squids to copepods to euphausiids. These tiny organisms from the size of a pinhead to a centimeter long are critical to the diets of large fish populations, such as salmon. Under magnification, one can see so much spectacular detail. I have learned how essential it is to have an identification guide in order to identify the names of each copepod and euphausiid. On the other hand the scientists tend to specialize and become very adept at identifying the different species.

Animals Seen Today

Arrow worms (long clear, with bristles)
Shrimp Copepods
Tiny rockfish (indigo colored eyes)
Fish larvae

August 4, 2009April 6, 2021

Bryan Hirschman, August 4, 2009

NOAA Teacher at Sea
Bryan Hirschman
Onboard NOAA Ship Miller Freeman (tracker)
August 1 – 17, 2009

Mission: 2009 United States/Canada Pacific Hake Acoustic Survey
Geographical area: North Pacific Ocean; Newport, OR to Port Angeles, WA
Date: August 4, 2009

Weather Data from the Bridge (0800)
Visibility: 10 miles
Wind: 2 knots
Wave Height: <1 ft
Wave Swell: 3 ft
Ocean temperature: 15.5⁰C
Air Temperature: 15.5⁰C

Science and Technology Log

We will be conducting several types of oceanographic sampling during our cruise: 2-3 Pacific hake tows per day (weather permitting), an open net tow where fish are viewed through a camera, XBTs: Expendable Bathythermograph (take temperatures at various depths), HABS: Harmful Algal Bloom Sampling, CTD: Conductivity, Temperature, and Density (also at various depths), and a Multiple Opening Plankton Net (collects living organisms at various depths). We will also release a Surface Drifter: floats with currents and sends information about currents via satellite.

The tows, XBTs and HABS are done from 7:00 am to 9:00 pm, while the CTD and plankton net are used during nighttime hours. By working in daytime and nighttime shifts the scientists are maximizing the boat’s usage. I was fortunate enough to help with the plankton net last night. Five samples were collected while I observed. Each sample was labeled and preserved for later use in a laboratory. Observed were amphipods, copepods, shrimp, and crab larvae.

Can you identify the animal I’m holding?

Our first Pacific hake tow came at approximately 8:00 am. The acoustic scientists use four transducers that are attached to the bottom of the boat. Each transducer sends out pulses of sound at a different frequency toward the bottom of the sea floor. The sound pulse then travels back to the boat and is recorded onto graphs. Fish and other biological organisms also reflect sound pulses. Each type of fish gives off a different signal depending on its size, shape, and orientation. The fish are then identified on a computer using acoustic analysis software. The strength of the sonar signal helps determine the biomass and number of fish. When the chief scientist see an interesting aggregation of fish to tow on, he calls the bridge (the brains of the boat–this is where the boat is controlled) and reports the latitude and longitude of where he wishes to fish. The ship then turns about and the deck hands work to lower the tow net and prepare to collect fish at the depth the scientists observed the fish.

After the fish are collected, the Pacific hake are weighed and counted. A sub-sample of about 300 Pacific hake is sexed and lengthed. Another sub-sample of about 50 Pacific hake is weighed, sexed, and lengthed; sexual maturity is determined by observation of the gonads, and ear bones are removed – this will enable scientists to determine the age of the fish. About 10 Pacific hake have their stomach contents sampled as well. All this information is collected and used by Fishery Biologists to determine the population dynamics of the overall Pacific hake stock. The acoustic scientists also save all their data in an acoustic library. This will help scientists to analyze the Pacific hake biomass (population) while minimizing how many live specimens they need to collect. In total we completed three tows today. That’s a lot of Pacific hake to measure, weigh, and sex.

Personal Log

The ship is loud. Sleep was hard to come by last night. Living in quiet Vermont has made me a light sleeper. I need to work on adjusting to the constant noise. The food and staff are great. Everyone takes pride in their ship and the work which is done on the ship.

Question of the Day
Can you identify the beast in the picture to the picture?

Animals Seen Today
Pacific Hake, Humboldt Squid, Myctophids, Breaching Whale (too far away to identify; most likely a Humpback)

July 26, 2009April 5, 2021

Jennifer Fry, July 26, 2009

NOAA Teacher at Sea
Jennifer Fry
Onboard NOAA Ship Miller Freeman (tracker)
July 14 – 29, 2009

Mission: 2009 United States/Canada Pacific Hake Acoustic Survey
Geographical area of cruise: North Pacific Ocean from Monterey, CA to British Columbia, CA.
Date: July 26, 2009

Weather Data from the Bridge
Wind speed: 10 knots
Wind direction: 100° [from the east]
Visibility: fog
Temperature: 13.5°C (dry bulb); 13.5°C (wet bulb)
Sea water temperature: 10°C
Wave height: 1ft.
Swell direction: 315° Swell height: 6 ft.

Science and Technology Log

We conducted a number of HAB, Harmful Algal Bloom sample tests. The Harmful Algal Bloom test takes samples at predetermined location in our study area. The water is filtered to identify the presence of toxic plants (algae) and animals (zooplankton). The plankton enter the food chain specifically through clams and mussels and can be a possible threat to human health.

We also conducted XBTs, Expendable Bathythermograph; and one fishing trawl net. The trawling was successful, catching hake, squid, and Myctophids. Fishery scientist, Melanie Johnson collected specific data on the myctophids’ swim bladder. The swimbladder helps fish regulate buoyancy. It acts like a balloon that inflates and deflates depending on the depth of the fish. Sharks on the other hand have no swim bladder. They need to swim to maintain their level in the water. Marine mammals such as dolphins and whales have lungs instead of a swimbladder. Most of the sonar signal from the fish comes from their swimbladder. The study of the swimbladder’s size helps scientists determine how deep the fish are when using the sonar signals and how strong their sonar signal is likely to be.

Commander Mike Hopkins, LTjg Oliver Brown, and crewmember John Adams conduct a marine mammal watch on the bridge before a fishing trawl.

The scientists tried to conduct a “swim through” camera tow, but each time it was aborted due to marine mammals in the area of the net. During the “Marine Mammal Watch” held prior to the net going in the water, we spotted humpback whales. They were observed breeching, spouting, and fluking. The humpback then came within 30 feet of the Miller Freeman and swam around as if investigating the ship.

Animals Seen Today
Fish and animals trawled: Hake, Squid (Cephalopod), and Myctophids.
Marine Mammals: Humpback whale.
Birds: Albatross, Fulmar, and Shearwater.

July 23, 2009April 5, 2021

Jennifer Fry, July 23, 2009

NOAA Teacher at Sea
Jennifer Fry
Onboard NOAA Ship Miller Freeman (tracker)
July 14 – 29, 2009

Mission: 2009 United States/Canada Pacific Hake Acoustic Survey
Geographical area of cruise: North Pacific Ocean from Monterey, CA to British Columbia, CA.
Date: July 23, 2009

Here I am in the lab helping with the HAB samples.

Weather Data from the Bridge
Wind speed: 15 knots
Wind direction: 350°from the north
Visibility: clear
Temperature: 12.0°C (dry bulb); 11.8°C (wet bulb)
Sea water temperature: 9.7°C
Wave height: 2 ft.
Swell direction: 000°
Swell height: 4 ft.

Science/Technology Log

We began the day conducting 2 HAB (Harmful Algal Bloom) sample tests of the ocean. This tests the amount of plankton in the water. Scientists test this because some plankton can carry harmful toxins that can get into the fish and sea life we eat, such as clams. Later we sighted numerous marine mammals including: 2 humpback whales (breaching), 12 Pacific white-sided dolphins, and California sea lions.

We made two trawls which provided plenty of hake for us to observe, measure, and collect data. Acoustic Judging: One important aspect of the acoustic hake survey is what scientists do when not trawling. There is a process called judging that fishery biologist, Steve De Blois spends most of his day doing. While looking at acoustic data, he draws regions around schools of fish or aggregations of other marine organisms and assigns species identification to these regions based on what he sees on the acoustic display and catch information gathered from trawls. He uses 4 different frequencies to “read” the fish signals—each shows different fish characteristics. Having started at the Alaska Fishery Science Center in 1991, this is Steve’s 19^th year of participating in integrated acoustic and trawl surveys and his eighth acoustic survey studying Pacific hake. He’s learned how to read their signs with the use of sonar frequencies and his database. Steve tells us about the importance of science: “Science is a methodology by which we understand the natural world.”

New Term/Phrase/Word Pelagic: relating to, living, or occurring in the waters of the ocean opposed to near the shore. In terms of fish, this means primarily living in the water column as opposed to spending most of their time on the sea floor.

Steve De Blois, NOAA Research Fishery Biologist, shares acoustic datawith Julia Clemons, NOAA Oceanographer, aboard the Miller Freeman. — Steve De Blois, NOAA Research Fishery Biologist, shares acoustic data
with Julia Clemons, NOAA Oceanographer, aboard the Miller Freeman.

Did You Know?
Northern fur seals are pelagic for 7-10 months per year. Pelagic Cormorant birds live in the ocean their entire life.

Animals Seen Today
Humpback whales (2), Pacific white-sided dolphin (12), California sea lions (6), and Northern fur seal.

In Praise of…Harmful Algal Bloom Samples
Crystal cold ocean water running through clear plastic pipes
Be patient as containers are carefully rinsed out three times.
The various sized bottles are filled with the elixir of Poseidon
Accurate measuring is essential.
Consistency ensures accurate results.
Once the water is filtered, tweezers gently lift plankton-laden filter papers.
All samples await analysis in the 20°F freezer.
Data from each test is later recorded;
Levels of domoic acid, Chlorophyll,
And types, populations, and species of phytoplankton and zooplankton.

July 16, 2009April 5, 2021

Jennifer Fry, July 16, 2009

NOAA Teacher at Sea
Jennifer Fry
Onboard NOAA Ship Miller Freeman (tracker)
July 14 – 29, 2009

Mission: 2009 United States/Canada Pacific Hake Acoustic Survey
Geographical area of cruise: North Pacific Ocean from Monterey, CA to British Columbia, CA.
Date: July 16, 2009

Here is Dr. Chu using a sonar readout to determine where the hake are located.

Weather Data from the Bridge
Wind speed: 20 knots
Wind direction: 358°from the north
Visibility: foggy
Temperature: 15.2°C (dry bulb); 13.4°C (wet bulb)

Science and Technology Log

We conducted several sea trawls for hake and other various fish species. First, the scientists conduct an acoustic survey using 4 different frequencies. Then the nets are lowered and drug at depth. The fun begins when we don our rubber overalls, gloves, and galoshes and count, identify and, weigh the fish. The most numerous fish in the trawls were myctophids (see photo), bioluminescent fish with some species having 2 headlights in front of their eyes to help attract prey.

HAB/ Harmful Algal Blooms Test: Throughout the day we took HAB samples, “harmful algae blooms”, which measures the toxins, domoic acid, and chlorophyll levels in the water (which correspond to the amount of plankton present). The HAB sample entails collecting sea water and putting it through a filtering process. Julia Clemons, a NOAA Oceanographer, and I conducted the HAB survey (pictured below). Fifty milliliters of sea water is measured into a graduated cylinder then filtered.

This is a type of fish called a myctophid. They are bioluminescent.

Sea water is collected at specific times during each transect or line of study. The sea water goes through a filtering process testing domoic acid and chlorophyll levels. These results will be evaluated later in the lab. One thing that strikes me is the importance of careful and accurate measurement in the lab setting. The harmful algal bloom samples are conducted 5-6 times daily and accuracy is essential for precise and definitive results. Later scientists will review and evaluate the data that was collected in the field. It is very important that the scientists use the same measurements and tools so that each experiment is done the same way. Making accurate data collection makes for accurate scientific results.

Animals Seen Today
Numerous albatross circling the stern of the ship, Viper fish, Octopi (approx. 6 inches in length), Squid (approx. 3 inches in length), and Myctophidae (see photo).

Here I am observing Julia as she filters a HAB sample.

July 15, 2009April 5, 2021

Jennifer Fry, July 15, 2009

NOAA Teacher at Sea
Jennifer Fry
Onboard NOAA Ship Miller Freeman (tracker)
July 14 – 29, 2009

Mission: 2009 United States/Canada Pacific Hake Acoustic Survey
Geographical area of cruise: North Pacific Ocean from Monterey, CA to British Columbia, CA.
Date: July 15, 2009

Weather Data from the Bridge
Wind Speed: 19 kts.
Wind direction: 355° north
Temperature: 15.4°C (dry bulb); 13.2°C (wet bulb)

Science and Technology Log

This picture shows the Miller Freeman in Alaskan waters. On our cruise, it’s working off the coast of California.

Our cruise was delayed for a day due to poor weather conditions and heavy seas. We began with a meeting of the scientific team which consists of 8 members all with their specific scientific knowledge and expertise. We will be conducting several types of oceanographic sampling during our cruise: 2-3 hake tows per day, weather permitting, an open net tow where fish are viewed through a camera, XBTs: Expendable Bathythermograph, HABS: Harmful Algal Bloom Sampling, and CTD: Conductivity, Temperature, and Density. The ship conducted Man Overboard and Fire drills.

The research vessel Miller Freeman set sail from Eureka, California on Wednesday, July 15^th at approximately 12:30. Each person aboard is assigned a specific job and place to report on the Miller Freeman during such an event. Our assignments are posted on our stateroom door. During a Fire/Emergency Drill the signal is a 10 second blast of the general alarm and/or ship’s whistle. I am to report or muster to the Chemical Lab.

In the event of an Abandon Ship Drill, I am assigned to life raft #2 and muster on the O-1 deck, port (left) side. The Abandon Ship signal is more than 6 short blasts followed by one long blast of the general alarm and/or ship’s whistle. If a Man Overboard Drill is called, we will hear 3 prolonged blasts of the general alarm and/or ship’s whistle. The muster station is the Chemical Lab. If we personally see a person go overboard the ship there are three things to do immediately: Throw a life ring overboard, call the bridge, and keep your eyes on the person.

These things all need to be done as simultaneously as possible to assure the safety and recovery of the person who is in the sea. It is important to conduct these emergency drills so that everyone is ready and prepared in the case of an emergency event.

Personal Log

I am sharing a stateroom with Julia Clemons, an oceanographer on board the Miller Freeman. She works for NOAA Fisheries in Newport, Oregon. Her educational background includes a Bachelors’ degree in Oceanography and a masters’ degree in Geology. The scientists and crew on board are so professional and willing to teach and tell about their job. They are an amazing group of people.

New Term/Phrase/Word
Domoic acid

Questions of the Day?
What does a hake look like in person?

Animals Seen Today
5 Egrets
1 great blue heron
Numerous gulls

April 23, 2008April 2, 2021

Scott Donnelly, April 23, 2008

NOAA Teacher at Sea
Scott Donnelly
Onboard NOAA Ship McArthur II
April 20-27, 2008

Mission: Assembly of Science Team and Movement of Science Gear/Equipment
Geographical Area: Coos Bay to Astoria, Oregon
Date: April 23, 2008

Weather Data from the Bridge
Sunrise: 0620 Sunset: 2010
Wind: 10 kts, 30 kt gusts
Seas: 4-7 ft
Light rain showers

Low resolution radar image of the storm system that postponed cruise operations

Science and Technology Log

My fourth (0100 to 0500, 1am to 5am) and fifth (1300 to 1700, 1pm to 5pm) 4-hour shifts are postponed due to the continued inclement weather. Seas are turbulent (combined seas 16 feet) and the winds blow non-stop (30 knots with gusts near 40 knots) from all directions it seems. Standing on deck both port and starboard, the howling wind throws sharp sea spray darts at my unprotected face. For a seasoned mariner these conditions are probably routine, if not prosaic. But for a newbie like me, with a little more than 48 hours of sea time experience, they are impressive and awe-inspiring, especially so given that I’m watching

it all from in the midst of the storm and not from the relative safety of the shore as I’ve done at times in San Diego. I climb the stairs to the ship’s bridge to watch and videotape this grand spectacle. The captain is calm and seems unimpressed with the temperamental, chaotic happenings outside. As I make my way to the bridge’s front viewing window he says to me, “Crummy weather isn’t it.” Without thinking, I nod my head in agreement. Also, a gale warning remains in effect until 1400 (2pm) this afternoon. A gale force wind has sustained surface speeds greater than 34 knots (39mph).

CTD deployment and biological sampling with the nets are postponed until the weather subsides and is more conducive to on deck activity. If the weather cooperates and the night forecast is accurate, the plan is to resume water sampling with the CTD and collection of marine organisms around 2000 (8pm) tonight. In the meantime the CTD has been securely fastened to the fantail deck. The coordinates for today’s postponed longitudinal sampling (constant latitude, changes in longitude) are 43^O07’N, 124^O29’W to 125^O15’W.

With the postponement in work activity in today’s log I’ll discuss a number of topics. In the following paragraphs I’ll discuss some of the nautical terms used in marine weather conditions as found in today’s forecast (see beginning of log, top) and what a low pressure system is. In yesterday’s log I described what a bongo net is and how it works. Today I’ll talk about the marine organisms that a bongo net collects and also describe the other three zooplankton nets used on this cruise- the Manta, ring, and HAB nets. Let’s begin with nautical terms used in marine weather forecasts.

Winds are identified with respect to the direction from which the wind originates. Surface water currents on the other hand are identified with respect to the direction they are flowing. So for example, today’s morning forecasted southeast (SE) winds originate from the southeast and blow toward the northwest (NW) since in general winds travel in a straight line path when not disrupted. Conversely, today’s forecasted morning southwest (SW) swells are traveling in the southwest direction. Marine wind and ship speeds are measured in terms of knots (kts). One knot (one nautical mile per hour, nm/hr) equals 1.15 statuary (or land) miles per hour, mph. Today’s forecasted morning wind speed of 25kts then equals 29mph, with morning gusts (G) forecasted at 30kts or 35mph and subsiding by mid-afternoon.

A change in winds from the SE to the E and then NW as forecasted from AM to PM indicates that the storm system is moving in a northeast direction onto land.

What is a swell? A swell is a mature wind wave of a given wavelength (distance between successive wave crests, i.e. the highest point of a wave) that forms orderly undulations seen on the ocean surface. Swells are described with respect to their height and period. Wave height is self-explanatory. What about wave period? Notice in the weather forecast that a wave period is defined in terms of time (typically seconds). Let’s use a hypothetical situation to explain a wave period. Suppose you are standing on deck, looking out across the vast sea, and a wave passes across your line of sight. Seven seconds later another wave crosses your line of sight, which remains unchanged. Seven seconds later another wave passes; your line of sight is still unchanged. The wave period then is the time elapsed for successive waves to pass a fixed point. In general, the longer the period, the calmer the sea.

Since my arrival in Oregon on Friday, April 18 a low pressure system has been positioned off the Oregon coast bringing clouds and precipitation. Today’s stormy seas are a result of a low pressure system. The winds and clouds in a low pressure system rotate in a counter-clockwise direction when viewed from satellites above. So if the winds blow from the southeast (SE) and are sustained, this indicates that the northern region of the low pressure system is south of the observer. In yesterday’s log I wrote briefly about how a bongo net is deployed and its function. So what marine organisms are collected in a bongo net? On this cruise at the depths the bongo net is deployed, it’s mostly a thumb-sized, shrimplike crustacean called krill. Krill are an important and central component of the oceans’ food chains and webs. In the northeastern Pacific the predominant species of krill is Euphausia pacifica. They are prolific consumers of microscopic marine organisms too small to see with the naked eye. But they too are consumed in enormous quantities by seabirds, squid, fishes, whales, and more recently, humans.

As seen in the upper right photo Euphausia pacifica krill have red “spots” along the entire length of their transparent, tubular bodies. These “spots” are photophores (light emitting organs) that emit blue light when a krill is agitated. During the 0100 to 0500 shift when it’s relatively dark on deck, one can see the blue emitted light from individual krill (but not all simultaneously) when the detached cod end of the bongo net is shaken. The emission of light from living organisms is called bioluminescence. Remember the scene in the 2003 Academy Award winning, computer-animated family film Finding Nemo when Nemo’s iconic clownfish father, Marlin, and his absent-minded blue tang friend Dory descend into the pitch-black deep water to find the scuba mask dropped when Marlin’s colorful, curious son Nemo was captured by the scuba diver. Dory is mesmerized by a glowing light that suddenly appears. Both eventually escape becoming a meal for a deep water fish that uses bioluminescence to attract and then eat unsuspecting prey.

A sub-category of bioluminescence is chemiluminescence, which refers to the emission of visible light on account of a chemical reaction. In the krill’s photophores is a creatively named molecule called luciferin, which combines with its complementary enzyme called luciferase, to emit blue light. Of all the known bioluminescence in the natural, biological world, an overwhelming majority is found in marine organisms, especially those found in deep water where light from the sun does not penetrate.

In yesterday’s log I wrote briefly about the function of a bongo net in collecting marine organisms (zooplankton) in a horizontal water column below the ocean’s surface. How are the nearly weightless, free-floating zooplankton found at the ocean’s surface and a few inches below collected? In the following paragraphs I’ll answer this question and also describe the nets used to collect marine organisms in a water column vertical (or perpendicular) to the surface.

A Manta net (also called a Neuston net) collects zooplankton at and a few inches below the ocean’s surface. Like a bongo net it too collects marine organisms found in a horizontal column of seawater. This requires the ship to be moving forward. Since a Manta net collects marine organisms at the surface and a few inches below, weights are not attached to the Manta net’s metal rectangular frame which also serves as its mouth. Floats are permanently attached to the right and left of the net’s mouth. A rotary flowmeter is suspended in the net’s mouth so the water volume can be determined. Like a bongo net the biomass density (number of organisms per volume water) then can be estimated. For our cruise the Manta net was deployed starboard once every shift for a total of ten minutes for each cast.

NOAA TAS Scott Donnelly (green helmet) retrieving a Manta net — Scott Donnelly (green helmet) retrieving a Manta net

Two other nets used on this cruise are a ring net and a HAB (Harmful Algal Bloom) net, both of which are used to collect samples in a column of water vertical or perpendicular to the ocean surface. Consequently, the ship must not be moving and the net weighted for vertical sampling of a water column to occur since the nets themselves are not dense enough to sink. Deployment and retrieval of both nets are simple enough. Basically, the net is attached to a winch cable and a weight, is slowly lowered into the water to the desired depth and kept there for the desired time before it’s slowly lifted upward through the water, brought alongside the ship and suspended, washed with seawater, lifted onto the ship’s deck, and the collected sample removed from the cod end. The organisms collected represent those found in the vertical column of water through which the net ascended. On account of their small, compact size and weight, both the ring and HAB nets can be managed with one person, thereby freeing the other to take care of other sampling tasks.

Manta net skimming the surface for zooplankton

What is Harmful Algal Bloom (HAB)? HAB is caused by the elevated levels of toxins produced by certain marine algae that proliferate when seawater conditions are favorable for increased rates of reproduction. The microscopic algae are consumed by the ocean’s voracious eaters called phytoplankton. One of the toxins released by these certain marine algae is domoic acid, which accumulates in the phytoplankton that consume the algae. The phytoplankton are eaten by shellfish and fish such as anchovies and sardines. Domoic acid is poisonous to the shellfish and other fish thereby increasing mortality rates. If the toxin levels are elevated, massive die-offs occur, beaches are closed, and the sale and human consumption of shellfish, etc. are prohibited. The biological, social, and economic impacts are painful.

Personal Log

In spite of the ship’s constant pitching and rolling in these unsettled, stormy seas, I slept well Tuesday night, taking two hour catnaps, waking for ten minutes or so, and then falling back to sleep for another two hours or so before waking after midnight to get ready for the 1am shift. About mid-morning I made a visit to the bridge where ship operations are carried out. According to ship’s radar the low pressure system and local squalls causing the inclement weather shows signs of letting up.

HAB net deployment as seen from above

Almost three full days on the ship and I have shown no indications or symptoms of sea sickness in spite of the constantly changing seas. According to the NOAA crew I’ve earned my sea legs and it’s not likely that I’ll get sea sick. So much for all the tablets of Dramamine I brought. I took some memorable video from the bridge (both inside and outside) of the ship’s bow rising and falling between waves, some of them smashing violently into the McARTHUR’s bow on both the port (left) and starboard (right) sides, sending seawater spray up to the bridge window and all about the bow’s deck. I felt like a true mariner. Still no sightings of whales, orca, or the Black Pearl of Pirates of the Caribbean film fame.