Karah Nazor: Myctophids, Rockfish, eDNA, and Interview with NOAA Lab Operation Officer Keith Hanson, June 1, 2019

NOAA Teacher at Sea

Karah Nazor

Aboard NOAA Ship Reuben Lasker

May 29 – June 7, 2019


Mission: Rockfish Recruitment & Ecosystem Assessment

Geographic Area: Central California Coast

Date: June 1, 2019

Game Plan and Trawling Line: Four trawls on the San Miguel Line in the Channel Islands.

Time Recap: 5:00 PM: Wake up and then Squat Challenge. 5:30 PM: Dinner. 8:30 PM: Report to fish lab.  Learn how to count to ten in French. Kristin sang France’s National Anthem (she learned in 7th grade). 10 PM: First Haul. 3AM: Kaila used her face flip app to turn us into the opposite sex and it was the most hilarious thing ever. 4AM: Latte made by Kaila. A lot of laughing. 6:20 AM: Finish fish lab clean up. 6:21 AM: Still heavily caffeinated so Team Red Hats headed up to the flying dock to watch the sunrise. The sea was very smooth and glassy as we approached Conception Point. We saw several dolphins and a humpback whale. 7:00 AM: To the Galley for a breakfast of blueberry pancakes. 7:45 AM: Lights out.

Part 1: How to distinguish between myctophid species in our catches

In this survey, we are conducting trawls at 30 meters, which is technically the epipelagic zone, so why do we catch deep sea creatures?   Many deep sea creatures, such as myctophids, participate in a daily vertical migration where they swim up into the upper layer of the ocean at night, likely following the migration of zooplankton on which they feed.  Myctophids are also known as lantern fish or lampfish and they feature photophore organs which bioluminesce. Around 250 species of mcytophids have been described. Graduate student Ily Iglesias is saving a lot of the myctophidae we catch on this cruise for her dissertation work.

Tonight most of the catches were small in volume (filling about 10% of a blue bucket), but had good species density. The catches consisted mostly of salps, anchovies and several species of myctophids. It is important to learn how to properly distinguish between the various myctophids in our catches. This is a daunting task for the novice fish sorter, such as myself, since these fish are small (1 to 2 inches long) and appear very similar to each other. It is worth noting that most of the myctophids lose their skin (scales) during the trawling operation. This exposes the underlying pink muscle tissue, however, their photophores remain intact. Fish collected in a bongo net deployment typically have better preserved scales.

Northern lampfish, Stenobrachius leucopsarus, have 3 photophores in a slanted line under the lateral line while the similar looking Mexican lampfish, Triphoturus mexicanus, have more streamlined bodies and have 3 photophores on the lateral line. Many of the Northern lumpfish had a heart parasite which is evident in the photo below. California lanternfish, Symbiophorus californiensis, are typically larger fish and have a distinguished lateral line. California headlight fish, Diaphus theta, have two photophores “headlights” on the front on their face. Blue lanternfish, Tartetonbeania crenularis, are easy to distinguish from the others because they have wider bodies and blue/silver scales.

Northern lampfish photophores
Northern lampfish, Stenobrachius leucopsarus, have three photophores in a row (circled).
Mexican lampfish
Mexican lampfish, Triphoturus mexicanus, are more narrow than Northern lampfish and have three photophores right on the lateral line.
California lanternfish, Symbiophorus californiensis, have a distinguished lateral line.
California headlight fish
California headlight fish, Diaphus theta, are easy to distinguish because of the two large photophores on the face.
Blue lanternfish
Blue lanternfish, Tartetonbeania crenularis, collected in a bongo net with intact scales. Photo courtesy of Lauren Valentino.
Blue lanternfish Photoorgans
Photoorgans lining ventral surface of Blue lanternfish, Tartetonbeania crenularis.


Part 2: Rockfish: why are we catching so few?

Last night there were 4 rockfish in the last haul, and the fish sorting team got excited because we have not seen very many.  The title of this survey is officially “Juvenile Rockfish Recruitment and Ecosystem Assessment Survey,” however, sampling for pelagic juvenile rockfish is only one of the project’s objectives. Other objectives include sampling for other epi-pelagic micronekton species, studying prevailing ocean conditions and examining prominent hydrographic features, mapping the distribution and abundance of krill (Euphausiacea), and observing seabird and marine mammal distribution and abundance.

Rockfish, perch, or redfish are common names for the Sebastes genus of fish (with more than 100 species) which are abundant off of the California coast, and are a very important genus for the commercial fishing industry. Rockfish are benthic fish that live among rocks, and can be found in kelp forests or in the bathypelagic zone. One of the goals of this survey is to inform the fishing industry on the status of the population of rockfish so that reasonable catch limits can be set.

This year is proving to be a poor year for the rockfish pre-recruitment index, lower than the previous several years, says Chief Scientist, Keith Sakuma. He explains that one year of a weak young of year (YOY) rockfish class is not enough to have an impact on the fishing industry, but if the index was low for say, 10 years in a row, then this could potentially affect the exploitable population. He explains that since rockfish can live to be 100 years old or greater, they have many seasons to reproduce. Rockfish prefer cold water habitats. Keith’s research has demonstrated that most poor pre-recruitment index years are correlated to El Nino events which cause an increase in water temperatures and a reduction in cold water upwelling. This year’s slump in terms of rockfish numbers is not correlated to a strong El Nino event.

 young Cabazon Rockfish
Two young Cabazon Rockfish, Scorpaenichthys marmoratus.


Part 3: Environmental DNA (eDNA) Sampling on the Reuben Lasker

Last night Flora Cordoleani and I helped Dr. Kelly Goodwin collect water from the Conductivity, Temperature and Depth (CTD) bottles for the purpose of collecting environmental DNA (eDNA).  Kelly’s assistant, Lauren Valentino, is primarily on the day shift (see photo of Lauren with the CTD apparatus below). Isolation of eDNA from seawater is a newer technique used to determine which species swam through a particular location based on the DNA they left behind, through shedding of cells. This technique does not require that the organism be harvested to know that it had been present, and could be of value in detection of the presence of endangered species, for example.

For this CTD deployment, three bottles are filled at depths of 5 and 100 meters, and at the chlorophyll max somewhere between 5 – 20 meters. The water from each depth is run through a filter (pore size of 2 microns) in the eDNA lab on the ship (see photo below). The vacuum filtration procedure is a time-consuming process, as samples must be processed in triplicate, and in which aseptic technique is paramount so that human DNA does not contaminate the water.  Once the DNA is trapped on the filters, they are stored at -20C. The DNA will be purified from the filters back in the San Diego NOAA lab using a Qiagen kit. Species-specific regions of DNA known as bar-code regions will be amplified by Polymerase chain reaction (PCR) using 3 primers sets for analysis of DNA from bacteria, plankton, and fish. Illumina techology will be used to obtain DNA sequences, which are compared to DNA libraries for species determination.

The results from the eDNA study will give us a list of species that were present at each trawling station up to 48 hours prior to CTD deployment and fishing using the Cobb Trawl. We will be able to compare this list with the list of species that were physically caught in nets. Nighttime CTDs are deployed at the same station as bongo nets. Daytime CTD trawls occur at the same stations as night fishing.

Lauren with CTD
Lauren Valentino with the Conductivity, Temperature and Depth (CTD) Rosette on the Reuben Lasker.
Kelly Goodwin in the eDNA lab
Kelly Goodwin filtering water in the eDNA lab on the Reuben Lasker.


Part 4: Career Spotlight: NOAA Commissioned Officer Corps, Scientist Interview: Keith Hanson, NOAA Lab Operation Officer B.S. Marine Biology, University of Miami (UM) Hometown: Rye, New York

Keith H. and anchovies
NOAA Lab Operation Officer Keith Hanson with a large catch of anchovies.
Keith H sorting the catch
NOAA Lab Operation Officer Keith Hanson sorting the catch.

Keith Hanson joins this survey to assist with research and is a knowledgeable and experienced member of the science team.  Keith has taught me a lot about the fish we are collecting and was the first to show me around the ship.

Keith earned a Bachelor’s degree in Marine Biology from the University of Miami (UM) where he was vice president of the scuba club.   His favorite part of being a student at UM was being located so close to ocean and the many trips he took to Biscayne Beach and The Everglades.  While at UM, Keith worked as a Naturalist at the Biscayne Nature Center and with the Marine Operations Department at The Rosenstiel School of Marine and Atmospheric Science (RSMAS), where he managed boats and vehicles.  

After graduating from UM, Keith started the NOAA Corps Basic Officer Training Class (BOTC) at the U.S. Coast Guard Academy in New London, Connecticut.  His first assignment as a Junior Officer was on the NOAA Ship Nancy Foster in Charleston, SC which has a multi-mission platform with fish habitat and population studies, seafloor mapping surveys, oceanographic studies, and maritime heritage survey.  Keith enjoys the traveling opportunities afforded in this line of work. On the Nancy Foster, he got to travel to Cuba, the Caribbean, and Mexico. After 2.5 years of service, Keith advanced to OP Officer.

Keith is currently on his land assignment in Santa Cruz NOAA working as the Vessel Operations Coordinator and he manages a fleet of small boats from kayaks to a 28 foot barge.  Most vessels are used for river salmon work and groundfish research. His favorite vessel is the Egret offshore fishing boat which is used for rockfish hook and line sampling.

When asked what advice he has for undergraduate students wanting to purse degrees and careers in marine biology, he suggests getting involved in a research lab early on to gain a competitive edge.

Karah Nazor: The Glowing Dolphins of the Channel Islands and Interview with UCSC Graduate Student Ilysa “Ily” Iglesias, May 31, 2019

NOAA Teacher at Sea

Karah Nazor

Aboard NOAA Ship Reuben Lasker

May 29 – June 7, 2019


Mission: Rockfish Recruitment & Ecosystem Assessment

Geographic Area: Central California Coast

Date: May 31, 2019

Game Plan and Trawling Line: Channel Islands San Nicolas Line

I am up on the flying bridge and I just saw two humpback whales spouting, an albatross soaring and a large Mola Mola on the sea surface.  In this blog I will write about an amazing once in a lifetime experience that from last night- May 31, 2019. The first haul was called off due to an abundance of Pacific White-Sided Dolphins, Lagenorhynchus obliquidens, (as reported by the inside marine mammal watch prior to net deployment), so we motored on ahead to the second station, but dolphins chased the ship all the way there, too.  One strategy to encourage marine mammals to leave is for the ship to stop moving with the hope that the dolphins become disinterested and vacate the area. This pod was intent on having a party at the ship so Keith Sakuma encouraged everyone to just go outside to observe and enjoy the dolphins! 

Fishing on this survey takes place at nighttime (so the fish do not see the net) and Scripps graduate student Kaila Pearson and I stepped outside on the side deck into the darkest of dark nights. Kaila and I carefully placed one foot in front of the other because we couldn’t see our feet and where to step next. I was afraid I would trip. When I asked Keith Hanson if we should use a flashlight to safely make our way up to the top deck, he suggested that we stay in place for a few minutes to allow our eyes to adjust. Within 5 minutes or so objects around us started to present themselves to us within the black void.  We could eventually see our feet, each others faces, the dolphins, and even the finer features of the sea surface.

Within a few minutes Ily Iglesias reported seeing bioluminescence, a type of chemiluminescence that occurs in living things, such as the familiar green glow of lightening bugs in the Summer in the South.   This glow results from oxidation of the protein luciferin (present in photophore cells/organs) by the enzyme luciferase.  It its excited state, lucifern emits light.  This reaction is known to occur in some marine bacteria, dinoflagellates (single celled photosynthetic organisms), squid, deep sea fish, pyrosomes and jellyfish, and I am fortunate to have observed many of these creatures already on this research cruise (see photos below).  Some animals have photophore organs and generate their own luciferin, while others are hosts to bioluminescent bacteria.

deepsea longfin dragonfish
The large photo organ is a large green circle under the eye of the deepsea longfin dragonfish, Tactostoma macropus.
California lanternfish
California lanternfish, Symbolophorus californiensis, with photophores under the lateral line and the ventral surface.
California lanternfish photophores
California lanternfish photophores
Blue lanternfish
Blue lanternfish, Tarletonbeania crenularis, collected from a bongo net at 265 meters. Photophores line the ventral surface of the body.
Cranchia scabra
Cranchia scabra “baseball squid” with large photophores lining the eyes.
Chiroteuthis veranii squid
Chiroteuthis veranii squid

When dinoflagellates floating on the sea surface are agitated, they glow.  At first when I was trying really hard to see this, I noticed a couple of tiny flashes of green light, sort of like lightening bugs, but it wasn’t anything super obvious. In time, I noticed clouds of faint light, sort of like a glowing mist floating the water’s surface, that moved up and down with the swell.  I hypothesized that dinoflagellates on the sea surface were being agitated by the passage of waves through them and Ily suggested that it was caused by schools of anchovies.

Since the dolphins were intent on staying, we decided to head to the next station.  I knew that as the ship began to move that the bow would be breaking through surface water that had previously been undisturbed, and I predicted the bioluminescence would be much more intense.

As we took off, the dolphins began to bow surf and, as I predicted, the dinoflagellates were activated and this time their glow was a bright white.  As the dolphins surfaced to breath, their skin became coated with the glowing algal cells, creating an effect as if they were swimming in an X-ray machine.  The dolphins were literally glowing white swimming in a black sea! We were so entranced and excited by the beauty, we screamed in delight. I am sure the dolphins heard us cheering for them. They too, seemed excited and could see each other glowing as well.

Next we saw the faint cloud of dinoflagellates caused by Northern anchovies (Ily was right) up ahead of us. As the ship encountered the school of small (~ 3-6 inch) fish, they also started to glow really bright and it was easy to see all of the individual fish in the school. The dolphins could also see the glowing fish and split off in different directions to hunt them.  There were hundreds of fish that dispersed as they were being chased creating a pattern of short white glowing lines somewhat like the yellow lane markers on the highway.

The display was unlike anything I have ever witnessed. It was like the Aurora Borealis of the sea.  Despite our best efforts, our cell phone cameras were unable to pick up the bioluminescent signal, however, we do not need photos because the patterns of light will be forever embedded in our minds. The dolphins eventually tired from the surf and chase and departed. Ily said the experience was “an explosion of light that overwhelmed the senses” while Flora said it was “better than fireworks.”

With no marine mammal sightings at the third station, we completed a five minute haul in the deep channel and collected a huge white bin of anchovies (see photo of Keith Hanson with this catch below). In this catch we found a few Mexican lampfish, 3 king of the salmon, a lot of of large smooth tongues, a lot of salps, a few pyrosomes and one purple striped jellyfish.  The purple-striped jelly (Chrysaora colorata) is is primarily preyed upon by Leatherback turtles. Haul 2 was conducted over shallower water near San Nicolas Island and we only found salps and four small rockfish in the catch.  After these two hauls, we called it a night and wrapped up at 4:15 a.m.

Scientist Spotlight: Ilysa Iglesias, NMFS SWFSC FED/ University of California Santa Cruz (UCSC)

Ilysa “Ily” is a doctoral student who works in John Field’s Lab at UCSC.  She is studying the fish we are collecting on this cruise as part of her research. She is very knowledgeable about all of the survey research objectives. She is also one of the most positive and gregarious people I have every met. Ily grew up in Santa Cruz, CA, and enjoys surfing, hiking, gardening and raising chickens.   Ily is a fan of early marine explorer Jacques Cousteau, who often wore a red beanie/toboggan and a blue shirt. Ily came prepared and brought six red hats (that she knit herself) for each of the members of the sorting team. Ily’s favorite fish is the hatchetfish. She was thrilled when we found on in the catch!

Ilysa with hatchetfish
Ilysa Iglesias with deepsea marine hatchetfish
deepsea marine hatchetfish
A deepsea marine hatchetfish caught in the bongo which was deployed to depth of 265 meters.

Ily obtained a Bachelor’s degree from UC Berkeley in integrated biology and a Masters Degree from the University of Hawaii in Zoology with a specialization in marine biology.  Her thesis was on the function of intertidal pools as a nursery habitat for near-shore reef fish. She compared otoliths (fish bone ears) of fish reared inside and outside of tide pools and compared their growth rates.  Otoliths can be used to the age of the fish much like counting rings on a tree and stable isotope analysis reveals information about where the fish were reared.

Ily, Flora and Kristin have all used otoliths in their research and taught me how to locate and collect the sagittal otolith from anchovies and myctophids. It is a tiny ear bone (one of three) that is positioned near the hindbrain of fish.  See photos below of the otoliths we collected. This is a technique that I will definitely take back to my classroom and teach my McCallie students.

Otoliths
Otoliths we collected and observed under the dissecting microscope.
Photomicrograph of otoliths
Photomicrograph of otoliths we collected from blue lanternfish (top) and Northern Anchovy (bottom) and observed under the dissecting microscope.

After obtaining her masters degree, Ily was Conservation Fellow for the Nature Conservancy in HI and worked in octopus fisheries before returning home to join NOAA’s salmon team and then the rockfish team as a Research Associate.  Ily has just completed the first year of her doctoral work in the Field Lab and expects to complete the program within 5 years.

On this cruise, Ily is collecting small fish called Myctophids for her research. These are small bioluminescent fish that live at depths of 300 and 1,500 m in the bathypelagic zone. In this survey, we encounter these deep sea dwellers during their nightly vertical migration up to the edge of the photic zone at depths we are targeting.  They are likely chasing their prey (krill) on this upward journey. It is amazing to me they are able to withstand the pressure change. Mcytophids are also known as lanternfishes and have bioluminescent photophores dispersed on their bodies. The fish sorting team analyzes the position of these organs to help distinguish between the different species. There are 243 known species of myctophids, making these little fishes one of the most diverse vertebrates on Earth.  They are so abundant in the sea that they make up 65% of the ocean’s biomass, but most people have never heard of them!

In 2014- 2015 there was an anonymously high sea surface temperatures off of the Pacific Coast known as The Blob.  Marine scientists are still elucidating the effect of the hot water had on fish populations and ecosystems. Ily explains that “atmospheric forcing caused changes in oxygen and temperature resulting in variability in the California current.”  The water was less nutrient dense and caused a reduction in phytoplankton. This disruption of primary production propagated up the trophic cascade resulting in die offs of zooplankton, fish, marine mammals and birds.  

Ily is using the catch records and acoustics data from the rockfish survey to study changes in distribution and abundance of myctophids from before, during and after The Blob (2013-2019).  She aims to understand if and how their trophic position of myctophids was affected by the unusually high sea surface temperatures.   Using elemental analysis isotope ratio mass spectrometry to analyze the Carbon and Nitrogen atoms incorporated into fish muscle, Ily can determine what the myctophids were eating each year.

Amanda Dice: Using Light for Survival, September 13, 2017

NOAA Teacher at Sea

Amanda Dice

Aboard Oscar Dyson

August 21 – September 2, 2017

 

Mission: Juvenile Pollock Fishery Survey

Geographic area of cruise: Western Gulf of Alaska

Date: September 13, 2017

Weather Data: Rainy, 76 F

Baltimore, MD

Science and Technology Log

Now that I am back home, I have some time to think about the variety of animals I saw on the cruise and do a little more research about them. Many of the animals we caught in our net have the ability to light up. This adaptation is known as bioluminescence. Different species use bioluminescence in different ways to help them survive.

 

Myctophids are a type of fish also known as a lantern fish. These small fish can occupy the same habitat as juvenile pollock, and we caught several of them at our sampling stations. I got a chance to look at them closely and I could see small spots, called photophores, along the sides of their bodies. In dark waters, these spots have bioluminescent properties. Lantern fish can control when to light them up and how bright the spots will glow.

 

There are many different species of lantern fish. Scientists have learned that each species has a unique pattern of bioluminescent photophores along the sides of their bodies. For this reason, it is believed that lantern fish use their bioluminescent properties to help them find a mate.

myctophid

The photophores can be seen as white spots on this lantern fish. Image courtesy of NOAA.

Lantern fish also have bioluminescent areas on the underside of their bodies. This adaptation helps them achieve what is known as counter-illumination. In the ocean, a predator can be lurking in the dark waters below its prey. Since many things feed on lantern fish, it is important for them to have a way to camouflage into the environment. When a predator looks up, during the day, a fish that is lit up on the bottom will blend in with the lighter waters above it, making it hard to see.

counterillumination 2

The camouflaging effect of counter-illumination can be seen when this bioluminescent fish lights up its underside. Image courtesy of the Smithsonian.

Lots of animals use this technique to help them hide from predators, including squid. We pulled in many small squid in with our samples that had patterns of photophores on them. Depending on the species, squid also use bioluminescence to attract mates and to confuse predators.

squid NOAA 2

The pattern of lighted photophores can be seen on this squid. Image courtesy of NOAA.

In addition to fish and crustaceans, we also pulled in a variety of jellyfish. Jellyfish also have bioluminescence characteristics. Many jellyfish use light as a way to protect themselves from predators. When a jellyfish is threatened by a predator, it flashes in a rapid pattern. This signals other fish nearby that it is being hunted. This can alert larger predators, who may be hunting the predator of the jellyfish. The larger predator will then swoop in after the jellyfish’s predator, allowing the jellyfish to escape!

Jellyfish NOAA

Many jellyfish use bioluminescence to protect themselves from predators. Image courtesy of NOAA.

Personal log

I have been home for over a week and I think I finally have my land legs back again. Looking back on the experience, there were so many little surprises that came with living onboard a ship. One thing I noticed is that I got much better at walking around the longer I was there. I learned to always have one hand available to grab a railing or brace myself during any sudden movements. However, I never quite mastered getting a decent workout in on the treadmill! Another surprise is how relaxing the rocking of the ship could be when I laid down. I thought the movement would be distracting, but it actually helped me drift off to sleep!

Did you know?

There are many superstitions surrounding life on a ship. It is considered bad luck to have bananas on board and whistling is discouraged. Whistling onboard a ship is thought to bring on wind and storms!