Karah Nazor: Departure from the San Francisco Bay and First Night of Fishing, May 29, 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 28-29, 2019


I departed Chattanooga, TN, for San Francisco, CA, on May 28th to participate as a NOAA Teacher at Sea on Leg 2 of NOAA’s Juvenile Rockfish Recruitment and Ecosystem Assessment Survey.  My job as a Teacher at Sea will be to share my experience and knowledge acquired over the next 10 days working alongside NOAA scientists with MY AUDIENCE. Who is my audience? You! I hope that you all can be my students!  You, my McCallie students and colleagues, my friends, my swimming community and my family members. My intention here is to explain in layman’s terms what I learned, and especially, what I thought was cool.

After tapas in North Beach with my San Francisco friends Cathy Delneo and Evan Morrison, they dropped me off at Pier 15 to sleep in my stateroom on the NOAA Ship Reuben Lasker. I felt rocking even while docked in the San Francisco Bay, but I slept great and am happy to report that my CVS brand “less drowsy” Dramamine tablets seem to be working as I am prone to motion sickness. This morning Evan and I got to explore the ship and take a bunch of photos of The City from the top deck of the ship, called the Flying Bridge. I imagine I will be spending many hours up here over the next 10 days!

Karah and Evan on the Flying Bridge
Karah and Evan on the Flying Bridge the morning of departure.


Meeting the Science Team

The first science team member I met was Kelly Goodwin, Ph.D., an environmental molecular biologist from NOAA National Marine Fisheries Service (NMFS), Southwest Fisheries Science Center (SWFSC) La Jolla, and NOAA Atlantic Oceanographic and Meteorological Laboratory.  Kelly is here along with Associate Researcher Lauren Valentino to collect environmental DNA (eDNA) from water collected at three depths (5 meters, the chlorophyll maximum, and 100 meters) during deployment of the Conductivity, Temperature and Depth (CTD) Rosette.  There will be more about these marine scientists and the cool biotechnology they will be employing to come in a future post!

Next, I met my stateroom bunkmate Flora Cordoleani, Ph.D., of NOAA NMFS, SWFSC,Fisheries Ecology Division (FED).   Her research lab at the University of California Davis focuses on the management of the endangered king salmon in the Central California Valley.  I will definitely interview her for a future blog!

Meet the rest of the team: Doctoral student Ilysa (Ily) Iglesias, NMFS SWFSC FED/ University of California Santa Cruz (UCSC), works in John Field’s Lab.  Ily will be analyzing the myctophids (one of the most abundant mesopelagic fish groups) collected on this survey and elucidating their role in the trophic cascade.  She was on the cruise last year as well and I can already tell is psyched about this opportunity and wants to teach everyone. 

John Field, Ph.D., was on the previous leg of the cruise and is the Principal Investigator for this project while Keith Sakuma, of NMFS SWFSC FED, is the Chief Scientist and has been working on this survey for 30 years as of this cruise!     

Kristin Saksa of NMFS SWFSC FED/ Moss Landing Marine Lab (MLML) and Kaila Pearson, NMFS SWFSC FED, of Scripps, who are both working on master’s degrees in marine science.  

Jarrod Santora, Ph.D., an ecologist from NMFS SWFSC FED/UCSC, will be on the day shift.  Brian Hoover, Ph.D., an ornithologist who works for the Farallon Institute for Advanced Ecosystem Research (FIAER), will be observing birds and marine mammals on the day shift. 

Keith Hanson is a NOAA Corps Officer representing NMFS SWFSC FED and is also a valuable member of the science team.

Night shift fish sorting crew
Night shift fish sorting crew. From left: Karah Nazor, Ph.D., Flora Cordoleani, Ph.D., Kristin Saksa, Keith Sakuma, Keith Hanson, Kaila Pearson, and Ilysa Iglesias.

After a welcome aboard orientation and safety briefing given by NOAA Corps Officer David Wang, we enjoyed a delicious reuben sandwich in the galley (cafeteria) of the Reuben Lasker.  Meals are served at 7 AM, 11 AM and 5 PM. Since I will be on night shift I can request to have meals put aside for me to eat whenever I want. Below is a typical menu.  The food is superb! See a menu from one of our last days below.

Menu for my last day.
Menu for my last day.

After a noon departure the engineers spent a couple of hours testing the dynamic positioning system just north of the Bay Bridge.  This system takes inputs from ocean conditions such as the tide, wind, waves and swell and uses the propulsion and thrusting instruments on board to maintain a fixed position on the global positioning system (GPS).   Most of the night shift science crew used this opportunity to nap since we had to stay up all night!

Kaila Pearson woke me up just in time as we exited San Francisco Bay to take in the spectacular view of passing under the Golden Gate Bridge.  It was a gorgeous sunny day in San Francisco and I felt super grateful to be a part of this research team, excited to get to know the team of amazing (mostly) female scientists I had just met, and ready to start fishing! It was fun to get to serve as a impromptu San Francisco tour guide as we departed the Bay, since I am quite familiar with this landscape. This body of water was my first open water swimming playground when I used to live in San Francisco during my postdoc at UCSF and was a member of the South End Rowing Club.  

Departing San Francisco Bay
Our departure from the San Francisco Bay. Photo taken on the flying bridge. From Left: Kaila Pearson, Flora Cordoleani, Ph.D., Lauren Valentino, and Ilysa Iglesia with Teacher at Sea Karah Nazor, Ph.D., in front.


Night 1 of Cobb Trawl and Fish Sorting

We arrived at our first trawl line, Monterey Bay, around 11:00 P.M.  My job as part of the night crew is to participate in marine mammal watches before and during fishing, and then to sort, count and measure the different species of animals collected, as well as bag and freeze specimens for various research organizations.  The fishing method used on this survey is a modified Cobb midwater trawl.  The net is deployed to fish at 30 meters depth and has a 9.5 mm codend liner (mesh at the end of the net where the fish gather).  Trawl operations commence just after dusk and conclude just before dawn, with the goal of conducting up to 5 trawls per night. The duration of fishing at target depth before “haul back” of the net can be either 5 minutes or 15 minutes.  Five minute trawls are used in areas of high abundance of gelatinous organisms such as jellyfish in order to reduce the size of the catch (e.g., fishing the additional 10 minutes would result in catches large enough to damage the net). 

catch from the first Cobb trawl
From left, Keith Hanson, NOAA Operations Officer, and Chief Scientist Keith Sakuma, help release the catch from the first haul of the survey.
first haul's catch
At first glance, it appeared the catch consisted mostly of Northern anchovies.
Graduate student Ilysa Iglesias
UCSC graduate student Ilysa Iglesias examines the first sort of the first haul, with the organisms arranged by species.

There are two marine mammal watches per trawl: the inside watch and the outside watch.  The inside watch goes to starboard side of the bridge 30 minutes prior to reaching the planned trawl station.  If any marine mammals such as sea lions, seals, dolphins or whales are spotted within one nautical mile of the planned trawl station, then the ship must move.  This protocol is employed for mitigating interaction with protected marine species.

If the inside watch does not see any marine mammals, then trawl operations can begin.  This is when the outside mammal watch takes over and looks for marine mammals during net deployment, trawling, and haul in.  The outside watch is conducted one floor above the fishing deck, and the person must wear foul weather gear, a life vest, and a helmet. This is summer, but it is the Pacific, and it is COLD out there.  If a marine mammal is spotted by the outside watch then the trawl net must immediately be reeled in.

I spotted a school of dolphins in Monterey Bay during haul back and reported the sighting via radio to the bridge officers and recorded my observations in the lab on the provided data sheet in the lab.

The duration of the entire fishing operation from net deployment, dropping the two “doors” (large metal plates weighing 900 pounds each) used to spread the net mouth open, fishing, haul in, properly wrapping the net on the winch, and finally, dispensing the harvested fish into the collection buckets, takes between 45 minutes to an hour and a half, depending on conditions.  

Our first catch consisted primarily of Northern anchovies (Engraulis mordax) and California market squid, Doryteuthis (Loligo) opalescens. Ily was excited by the presence of a few plainfin midshipman, Porichthys notatus, and showed us their beautiful pattern of large photophores located on their ventral surface.  These fish are quite hardy and survive the trawling procedure, so as soon as we saw one in the bucket, we placed it in a bowl of sea water for release after obtaining its length. Photophores are glandular organs that appear on deep sea or mesopelagic fish and are used for attracting prey or for confusing and distracting predators.  

Northern anchovies
Northern anchovies, Engraulis mordax,, are one of the most abundant species we catch.
Photophores
Photophores on ventral surface of Plainfin midshipman, Porichthys notatus.

Mesopelagic depths start around 200 meters, a depth at where 99% of the sunlight can no longer penetrate, and extend down to 1000 meters below the ocean surface.  Above the mesopelagic zone is the epipelagic zone where sunlight reaches from the ocean surface down to 200 meters and, in California, corresponds to the ocean above the continental shelf.  

In this survey, we will conduct trawls at 30 meters, which is technically the epipelagic zone, so why do we catch deep sea creatures?   Many deep sea creatures participate in a daily vertical migration where they swim up into the upper layer of the ocean at night as that area is relatively rich in phytoplanktonic organisms.  Phytoplankton are the sun-powered primary producers of the food chain, single-celled photosynthetic organisms, which also provide the majority of the oxygen we breath.

After the first night of work I feel confident that I can identify around 10 species of mesopelagic fish and forage organisms, the California Headlight Fish (more to come on these amazing myctophids from my interview with Ily), a juvenile East Pacific red octopus, Octopus rubescens, (alive), and ctenophores!  Thanks to the Tennessee Aquarium’s Sharyl Crossly and Thom Demas, I get to culture ctenophores in my classroom.

Californian Headlightfish
Two large photophores in between the eyes of a Californian Headlightfish, Diaphus theta
Small octopus
Small octopus – Octopus rubescens.
Karah holding ctenophores
Karah Nazor with a handful of ctenophores! These are Hormiphora – Undescribed Species.


Scientist Spotlight: Ornithologist Brian Hoover

Brian Hoover, Ph.D., an ornithologist who works for the Farallon Institute for Advanced Ecosystem Research (FIAER) in Petaluma, CA, observes birds and marine mammals on the day shift of this NOAA research cruise.  

Brian Hoover
Brian Hoover, Ph.D., at his office in the San Francisco Bay
Brain and Jarred watching for birds
Brian Hoover, Ph.D., and Jarred Santora, Ph.D., watching for birds and marine mammals as we went underneath the Golden Gate Bridge.

Brian is from Colorado and earned his doctorate at UC Davis in 2018.  On this cruise we will be traversing through biological hotspots that occur near islands, underwater canyons, and where there is strong upwelling of the cold and nutrient rich deeper waters of the California Current.  Small fish feed on these nutrient rich waters, and birds feed on these fish. Hotspots on this cruise included the Gulf of the Farallons (just south of the Point Reyes upwelling plume) , the Channel Islands, and Monterey Bay with its submarine canyon. Brian’s hours on the ship are from 7am to 7pm.

Brian can be found perched on the flying bridge during the day shirt with a pair of binoculars in his hand and his laptop off to his right on a table.  Every time a bird or marine mammal is spotted within 300 yards of the ship to the right of the mid centerline of the bow, Brian records the species and numbers of animals observed in his database on his laptop. The objective of Brian’s work aboard the ship is to study how what is present underwater correlates with birds observed above the water.  In other words, he aims to find correlations between the distribution and abundance of seabirds and marine mammals to the species and abundance of prey we collect during our night trawls and data collected from the ship’s acoustic krill surveys which collect data during the day. Brian explains that such information teaches us about what is going on with the bird’s prey base and how well the ecosystem is functioning as a whole. His observations allow him to observe shifts in the system over time and how this affects tertiary and apex predators.  To find trends in these datasets, he used R software, Python, and ArcGIS mapping software to run spatial statistics and linear models.

Since 2010 Brian has been on 12 to 13 cruises and this is his third on the Reuben Lasker.  Brian is excited to perhaps spot the Cooks Petrel, Pterodroma cookii, or the Short-tailed albatross, Phoebastria albatrus, which only lives in a volcano in japan.  His favorite birds are the storm petrels because these birds are small and live in open ocean, only coming onshore to breed once a year.  His dissertation focus was on the reproduction and behavior of the leeches storm petrol. He explains that seabirds have an incredible sense of smell which they utilize to find a mate and food. Brian was able to collect blood samples from burrowing birds for genotyping. He found that the major histocompatibility complex (MHC) molecules located on antigen-presenting cells may play a role in odor detection and mate selection in these birds.  He found that males chose and avoided particular genotypes combinations and that healthier birds had more diverse MHCII complexes.

Brian is a sensory ecologist and studies how seabirds interact with their environment  through observations of their behavior and physiology. When Ily asked Brian how do the seabirds know where the fish are in the open ocean, he explained that birds have a sense of smell that is as good or better than any commercial sensor that detects sulfur.  Why have some seabirds evolved to be so good at sniffing out traces of sulfur in the ocean breeze up to 10 miles away from its source? Brian explained that sulfur is an important part of the photosynthetic pathway for phytoplankton (algal cells) and that when krill eat the algae, the algae releases the chemical dimethyl sulfide (DMS).  Marine plastic debris floating on the sea surface also release DMS and provides an explanation as to why seabirds eat plastic.

Carol Schnaiter, Science is Not Always in a Lab! June 18, 2014

NOAA Teacher at Sea

Carol Schnaiter

Aboard NOAA Ship Oregon II

June 7 – 21, 2014

sunrise

Thursday morning!

Mission: SEAMAP Summer Groundfish Survey

Gulf of Mexico

Date: June 18, 2014

Winds: 20 knots

Waves: 3-4 ft

Latitude: 2804.78N

Longitude: 09440.95W

 

Science and Technology Lab:

Well, by the title you probably guessed that we will be discussing the reason we are on this ship. The NOAA Ship Oregon II is involved with SEAMAP (Southeast Area Monitoring and Assessment Program) which is a state/federal program to collect, manage, and disseminate fishery independent data. This program has been around for a very long time and the commercial fishermen depend on the information to plan where they will sail.

NOAA Fisheries does surveys of sharks, groundfish, plankton, and reeffish in the Gulf of Mexico. NOAA uses the data collected on the ship and it is sent to the Gulf States Marine Fisheries Commission. This information is sent out to everyone that would like to see it. To see the first preliminary data for the 2014 SEAMAP summer shrimp go to this site:

http://www.gsmfc.org/default.php?p=realtime/smr_t.htm

The real-time plots on the website show the station locations and total catches for the pink, white, and brown shrimp . The number of shrimp found and the size of the shrimp is important data that goes out to the public.  The stations that are tested are randomly selected by the depth strata (<20 fathoms, and >20 fathoms) and by statistical zone (aka:area).

map reading

Taniya showing me where the stations are on the map.

There are many species of shrimp. The three species of Penaeid shrimp that NOAA collects data for are the white, pink, and brown shrimp. Shrimp is one of the most valuable products, with 97% of brown shrimp harvested in the Gulf.

All of the shrimpers are waiting to hear when the shrimp season will begin. The date will be determined based on the data collected here on the NOAA Ship Oregon II and from the State vessels.

 

 

Scientists aboard the NOAA Ship Oregon II:

There are five scientists aboard the ship, two are NOAA scientists and three are contractors. They work 12 hour shifts, either noon to midnight or midnight to noon, seven days a week

Kim Johnson

Lead Scientist Kim Johnson at work.

Kim Johnson is the Chief Scientist, which means she is the one in charge of the other scientists. She is a residential fishery biologist for NOAA. Chief Scientist Johnson graduated with a degree in Marine Fishery, which focuses on fish, and has her Master’s Degree in Marine Biology, which focuses on everything in the water.

scientists on the NOAA Oregon II

Andre, Kim, and Taniya in the “dry” lab.

She started as a contractor for NOAA in 2001 and was hired by NOAA in 2003. At the beginning of her career she would spend up to 200 days out at sea, but now goes out for groundfish survey only.

As the Chief Scientist, she is responsible for all the data that is being collected. She needs to know what is happening at each station and sometimes she needs to “clean” up the data. That means Kim looks for any errors in entering the data and checks to see what it should be. Her job requires her to have a vast knowledge of computer programs to enter the information and be able to work with people under all types of situations. (She was my main nurse while I was seasick!)

Kim's children

Here are three of Kim’s children before we sailed.

Kim said the important parts of her job are checking the health of the environment and the fish, and the population of many different species. The best part of her job is the fishing time and the worst part is leaving her husband and wonderful four small children. (I had the pleasure of meeting Kim’s family before we sailed and her children are ADORABLE!)

Taniya Wallace is the NIght Shift. She works for Riverside and is a contractor worker for NOAA. She has been doing this for four years. Taniya  graduated with a major in biology and a minor in chemistry. She enjoys the adventure of this job and likes to try new things. In the future she hopes to advance in this field. Taniya is great at identifying fish, crabs, and shrimp. She uses her computer skills to enter information and must be able to read a map to know where the stations are located. During her watch she is in constant communication with the Bridge and the Lead Fisherman on duty.

Taniya Wallace

Taniya entering data into the computer.

Andre DeBose is a NOAA employee. He graduated with honors with a Major in Biology. Right after college he worked for a company called Sea Chick for six months in the aquaculture business before being hired as a contractor for NOAA. After four years as a contractor, Andre was hired full-time by NOAA. He came on to the reef fish team and worked with them for three years. He then moved to the trawl team and is happy where he is now.

 

Andre and Robin

Andre and Robin on deck.

Andre said the best part of the job is working with people, and the worst part is being away from home. Andre said for his job you need science, math, English and good writing skills in order to communicate with others. He feels that in his job he is using every aspect of his biology degree.

Andre is a great singer and has entertained us with songs when the night gets long.

I only see the day team for a few minutes at noon or midnight as we switch jobs, but they all seem to work well together.

the day crew

Lee, Trisha, Rebecca, and my bunk mate, Chrissy.

Personal Log

working in the chem lab

Here I am working in the chem lab. Photo by Robin Gropp

Each day on the ship I am learning more and more. Taniya and Andre are very encouraging and patient with me asking a million times, “What is this again?”

The deck crew all have been very helpful explaining how and why everything is done the way it is. You really can not believe how much team work there is on this ship!

It is hard to believe that in just a few days I will be leaving the ship. I am already missing the people that I have met and the wonderful learning experience that NOAA Teacher at Sea has allowed me to experience. What a great learning adventure this has been….from learning to identify fish, crabs, shrimp…to measuring species….to doing transfers… I have learned so much!

ear of salmon

Fish ear’s, called an Otolith, can be used to age the fish.

Lion fish

I’m not lying, this is a Lion Fish!

Paul Ritter: Teamwork, July 20, 2013

NOAA Teacher at Sea
Paul Ritter
Aboard the NOAA Ship Pisces
July 16– August 1, 2013 

Mission: Southeast Fishery-Independent Survey (SEFIS)
Geographical area of cruise: southeastern US Atlantic Ocean waters (continental shelf and shelf-break waters ranging from Cape Hatteras, NC to Port St. Lucie, FL)
Date: July 20, 2013

Weather Data from the Bridge

7-20-13 ship data

Science and Technology Log

OLYMPUS DIGITAL CAMERAEach day the fish traps aboard the NOAA Ship Pisces are baited and prepared with cameras, and sent to the ocean floor where they must sit for ninety minutes.  It is necessary to keep this time consistent for all locations and traps so we can compare apples to apples.  We call this a “control variable”.  The particular parameter that someone measures that is a constant and non-changing point of comparison in an experiment or scientific observation is a controlled variable for consistency.

After being on the bottom for the time allotted, the officers on the bridge drive the ship back to the number one trap and drives alongside the trap’s buoys.  Approximately, half way down the ship is the side sampling deck.  From the side sampling station, approximately halfway down the ship, we take a grappling tied to a long rope and hurl it over the side, aiming between the two buoys. It is important that we hit it on the first attempt.

If we miss, the ship has to take vital time to maneuver around to make another attempt at the buoys.  Have we missed?  Honestly, yes but only a couple of times.  If we have done our job correctly, we pull in the grappling hook and with it the buoys, and rope.  The buoys are then unhooked from the rope and the rope is threaded into a pot hauler, which is a large tapered wheel that grabs onto the rope without slipping.  The pot hauler then hydraulically pulls the rope and trap up to the surface.  Once at the surface, another hook and winch is connected to the trap and the entire rig is pulled up on the side sampling deck.  It is at this time that our team attacks the trap by taking off the cameras and unloading its cargo of fish.  If we have fish, they are taken to the wet lab and all the measurements are taken.  Once empty, the trap is carried to the main aft deck and prepared for the next round of trapping.  It really is a lot of heavy work but it is all worth it to understand the ecology of our ocean reefs.

Personal Log

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Patrick and I Working on a Red Snapper

7-20-13

Today started around 12:30 am.  It was not something that I intended to do.  The night before we went to bed around 10:00 pm.  I was sore and very tired from the long and hard day we had fishing.  For some reason I woke up and looked out the window and saw that it was very bright outside.  I thought it was daybreak and it was time to get up.  I looked at my clock and it said it was 12:30.  But that could not be.  It was too light outside for just pass midnight.  I actually thought my clock was broke so I fired up my computer to check the time.  Sure enough, it was 12:30.

The moon was so bright and reflecting off of the water in a way that the light was coming right into my room.  Crazy.  After the confusion, I finally made it back to sleep.  Around 5:30 my internal alarm clock went off.  I actually never need an alarm clock to wake up, ever.  For some reason I always have been able to just think about when I want to get up and I do.  Anyway, I got up, brushed my teeth and headed to work.

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Our Team in the Wet Lab

At 6:15, I met up with my brothers and sisters of the trap setting team which consists of Doug Devries – NOAA Scientist; Patrick Raley – NOAA Scientist; Jenny Ragland – NOAA Scientist; Julie Vecchio – volunteer Scientist; Zach Gillum – graduate student / Scientist, and me – the new guy scientist.  Have you ever watched Star Trek?  Usually each show’s scientific mission consists of Captain Kirk, Mr. Spock, Bones, Lt. Uhura, who are all in one color uniform, and a new guy who is in the red shirt.  The mission goes something like this.  Captain Kirk will say “Mr. Spock go check out the nondescript rock.  Bones see if you can get some readings on that green flower over there, Uhura please open up a channel to the ship, and New Guy, go check out that purple pulsating blob over next to the cliff.”  I really hope these guys don’t watch Star Trek…..

To be completely honest, it is nothing like Star Trek at all.  Our team is amazing.  I am very humble that they have accepted me into their family.  They are so fun to be around and I could not be more thankful for their friendship and guidance.  Each of us has to play many vital roles in the mission. This expedition would not work if we did not have each other to rely on.  I don’t want to let my teammates down, and I will do anything to make sure that does not happen.

Anyway, back to the traps…..  We set our first set of traps of the day and ninety minutes later we discovered that our return was not very good.  Our second set of traps, on the other hand, were much better and netted many fish.  Some of the fish included Black Sea Bass, Grey Trigger, Tomtate, White Grunt, and one of the most desirable fish on the market, the Red Snapper.  Red Snapper is a fish that can grow upwards of 40 lbs. and live as long as 50 years if it can escape being caught.  This amazingly beautiful red fish has had much pressure from commercial and sport fishermen and as a result their numbers have dwindled.  After speaking with Zeb Schobernd, our mission’s Chief Scientist, it is his hope that due to strict regulation of the harvest of the species, we will see an increase of the population.  The data we are collecting will help develop a better survey for reef fish populations in the future, especially grouper and red snapper..  Lunch was at 11:00 and what a lunch it was.  Crab legs, and prime rib.  Man, the crew of the Pisces eats very well and I am thankful.  My wife is a great cook, and I would say that the ship’s chief steward is a close second.  After lunch, we quickly we set our third series of traps and were able to increase our catch exponentially.  Dinner consisted of Jamaican jerk chicken, pork roast, green beans, lettuce salad, and cheese cake.  After dinner I took a little time to visit the team in the acoustics lab.  The acoustics lab is responsible for mapping out the ocean floor to determine where we should put traps out the next day.  I will probably touch more on them in my next blog.

Swabbing the deck

Swabbing the deck

Did you know?

Did you know that NOAA ships do not just stay in one particular location of the world?

The Pisces has sailed from Canada, to the Gulf of Mexico, and down to Venezuela and back.  Not to mention the Pisces is one of the fastest ships in the NOAA fleet capable of reaching speeds greater than 17 knots with a following current.