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.

Alex Miller, Heading for Home, June 11, 2015

NOAA Teacher at Sea
Alexandra (Alex) Miller, Chicago, IL
Onboard NOAA Ship Bell M. Shimada
May 27 – June 10, 2015

Mission: Rockfish Recruitment and Ecosystem Assessment
Geographical area of cruise: Pacific Coast
Date: Thursday, June 11, 2015

Front row from left: Paul Chittaro, Brittney Honisch, Tyler Jackson; Back row from left: Alexandra Miller, Will Fennie, Toby Auth

Front row from left: Paul Chittaro, Brittney Honisch, Tyler Jackson; Back row from left: Alexandra Miller, Will Fennie, Toby Auth

 

To conclude the discussion of the research on board the Shimada, I would like to profile the remaining scientists: the four fishermen of the night shift, and give a general report of the results of the cruise.

____________________________

Toby Auth, fisheries biologist with Pacific States Marine Fisheries Center (PSMFC), oversees most of the operations of the sorting, measuring and counting of the trawls. He works as a contractor to NOAA under the guidance of Ric Brodeur. Toby holds a BA in Fisheries and Wildlife from the University of Minnesota and he did both his MA and Ph.D. at the University of Maryland in Fisheries Management and he specialized in studying the early life of fish–egg, larval and juvenile stages, collectively called ichthyoplankton, basically anything fish-related that is small enough to sort of float along in the water.

As a researcher, he is most interested in understanding spawning success and food chain interactions of the Pacific coast species that come up in the trawls. Typically, Toby is at sea 30 – 40 days a year, but this year, due to the anomalous warm blob, he expects to be at sea about 50 – 60 days. The anomaly has implications for all fields of marine biology and oceanography.

In the far left of the image stands Dr. Paul Chittaro, of Ocean Associates in Seattle, WA. Paul is at sea on a research cruise for the first time in 10 years, and he’s very happy to be here. He was on board collecting fish in order to examine their otoliths, which are ear bones. Otoliths grow every day, laying down rings, almost like a tree. Analyzing these rings can give information about the fishes travels, diet and ocean conditions when they were alive.

The big guy in the back is Will Fennie, who will begin his Ph.D. at Oregon State University in the fall. The entire cruise he has been eagerly awaiting some juvenile rockfish to come up in the net and finally, in the last few nights, some did. Overall, we caught much less rockfish than in previous years. This could be for any number of reasons.

You can hear interviews with Paul and Will below.

____________________________

I have to give a HUGE thank you to Ric Brodeur, Chief Scientist of this mission, for supporting me as a Teacher at Sea and for reading each and every blog post!

Listen to my interview with Ric to learn more about the impacts of the research done on board the Shimada for these 13 DAS and possibilities for the future.

 

Thanks to XO Sarah Duncan as well, both she and Ric had to read and edit each one!

 

IMG_9442

Front row from left: Yours Truly, Emily Boring, Ric Brodeur; Back row from left: Jason Phillips, H.W. Fennie, Brittney Honisch, Toby Auth, Dr. Paul Chittaro, Amanda Gladics, Samantha Zeman, Curtis Roegner, Tyler Jackson

____________________________

It would take quite some time to tell all the stories of the marine wildlife we have seen on our 13 day cruise, but I would still like to share with you some of the photos and video I and others were lucky enough to capture. Enjoy!

All photos in these two galleries are courtesy of Amanda Gladics, Oregon State University, Seabird Oceanography Lab.

 

 

Personal Log

My experiences on board the Shimada have taught me a lot about myself and my abilities. I’ve done more writing, media processing and chatting with new people in the last two weeks than I have in the last two years. I have a greater understanding of how scientists work in the field and the importance of fisheries to the health of our oceans and the commercial fishing industry and I plan to apply that understanding in my classroom to increase students’ understanding of marine science and awareness of possible careers. To my students: “Get ready, dudes!”

Hopefully, you all have learned a lot about fisheries research, the process of science and the fascinating cast of characters who sailed with the NOAA Ship Bell M. Shimada. Maybe you’re even feeling a little inspired. Now, I know I’m an inland city kid, but I’ve loved the sea since I first saw Free Willy at the age of 7 and I’m not the only one who can trace their love of the sea to a starting point.

All the scientists on board have an origin story: one salient memory that they can credit with being the moment of inspiration for pursuing a life of study and research and a career in the field of science. If you’re curious about the world, you have the potential to be a great scientist. Science is for all people, no matter what age or situation, and these ones just happen to do theirs at sea. So, I want to know: Where will you do yours?

That’s all for now. Thank you for reading and listening and, maybe, sea you again soon!

Alex Miller, Teacher at Sea, signing off.

output_mgo8L7

Bye!

One last huge THANK YOU to the crew and officers of the Shimada for a wonderful cruise!!!