Michelle Jungbluth, PhD main menu

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Biological Oceanographer

I am an ecologist, naturalist, and marine biologist interested in the diversity of zooplankton and in the phenomena occurring at the base of the food web.

In my career as a scientist I have focused on a variety of studies of zooplankton - the animals that drift in the sea.

Microscope work at sea, common for any zooplankton ecologist

My technical expertise is primarily in DNA barcoding, quantitative PCR-based methods, and next-generation sequencing. I have also dabbled in DNA barcoding of deep-sea larval invertebrates - a location where we know almost nothing about organism diversity and even less about larval ecology.

I am currently wrapping up a project using DNA metabarcoding or community eDNA sequencing to study the larval diet of a threatened species of fish in the San Francisco Estuary - the longfin smelt (Spirinchus thaleichthyes). This fish is one of many struggling fishes in the San Francisco Estuary ecosystem and my work will help us to understand what food resources they need to survive and whether food is what is limiting their populations.

We have a NEW bioRxiv pre-print available on my larval diet metabarcoding work! doi: 10.1101/2020.10.18.344440

I am also interested in the cryptic interactions that occur in marine plankton (Millette et al.,2018 Limnology and Oceanography Letters)


As well as what goes on in places like the deep sea.

Kersten et al., 2019 "Larval assemblages over the abyssal plain in the Pacific are highly diverse, novel, and spatially patchy" https://doi.org/10.7717/peerj.7691

In order to study copepod populations at a finer scale, I have further developed a DNA-based method that allows me to estimate animal abundance using a combination of size-based separation and quantification of species-specific DNA (Jungbluth et al., 2013 Marine Biology doi: 10.1007/s00227-013-2300-y).


I have also dabbled in diet studies marine copepods and their offspring (Jungbluth et al., 2017 Marine Ecology Progress Series, doi: 10.3354/meps12139)


and am now using high-throughput DNA sequencing to investigate the phytoplankton and microzooplankton food that supports copepods in the San Francisco Estuary.

Check out my Publications for more info on my past work

Twitter: @ShellyFish311

Curriculum Vitae

Full CV

Professional Appointments

2018-present, Adjunct Assistant Professor of Biology, San Francisco State University, Estuary & Ocean Science Center

2017-2019, Postdoctoral Research Fellow, San Francisco State University, Estuary & Ocean Science Center

2016, Postdoctoral Research Associate, Hawaii Pacific University


2016  PhD  Oceanography, University of Hawaii

2012 MS Oceanography, University of Hawaii

2007  BS   Biology, University of Wisconsin

Selected Awards and Honors

Delta Science Postdoctoral Research Fellowship, NOAA-Sea Grant California, May 2017-May 2019

Invited to speak during the closing session of the 6th international ICES/PICES Zooplankton Production Symposium, Bergen, Norway, May 2016

Awarded funding to hold a professional development workshop: Improvisation for Scientists, Honolulu, HI, April 2015

Outstanding Student Presentation Award, 2014 Ocean Sciences Conference, Honolulu, HI, February 2014

Teaching & Mentorship

Mentor and Committee Member Graduate student M.S. Thesis Project, 2018-present

Research mentor, STAR Stem Teacher and Researcher program at SFSU, 2019

Research mentor, NSF REU-BREED program at SFSU, 2019

Guest lecturer, MSCI 709: Case studies in the San Francisco Estuary, San Francisco State University, Estuary & Ocean Science Center, 2019

Introduction to Oceanography, Lead Teaching Assistant, University of Hawaii at Manoa

Mentor for graduates and undergraduates in the laboratory


One of the perks of being a scientist is attending conferences and being invited to present about my work! I have been lucky enough to present in locations like Honolulu, San Francisco, New Orleans, Bergen Norway, and Naples Italy!

Check out my Full CV for more details!

Leadership Training

Exhibit Leader California Academy of Sciences Women in Science Night, 2019

Exhibit Leader School of Ocean Earth Science and Technology Open House outreach event- Zooplankton: Microscopic Ocean Drifters, 2013, 2015, 2017

Officer Professional Development and Training Program, 2015-2016

Chair Science Communicators ‘Ohana, 2014-2015

President Na Kama Kai oceanography graduate student organization, 2014-2015

Member Mentoring Network, 2014-2015

Organizer Student committee member representative of The Oceanography Society, for the 2014 Ocean Sciences Meeting, 2013-2014

Vice President Na Kama Kai Oceanography graduate student organization, 2013-2014

Founder and regular contributor, Real Science at SOEST Blog, 2013-2016

Professional Activities

Member of: Association for the Sciences of Limnology and Oceanography, The Oceanography Society, World Association of Copepodologists, American Microscopical Society, The Crustacean Society, Graduate Women in Science, American Association for Advancement of Science

Reviewer for: Marine Biology, Journal of Plankton Research, Bioinvasions Records

My research


Google Scholar     LinkedIn     ResearchGate    

My Research

Current Research

I am continuing my work on exciting projects as a Researcher at the San Francisco State University Estuary & Ocean Science Center with Dr. Wim Kimmerer. Our current project will utilize my experience in zooplankton ecology, plankton identification, and molecular biological methods to reveal the prey that are important to copepods in the San Francisco Estuary using next-generation sequencing techniques. Stay tuned, I will be very active in the San Francisco Estuary research community over the next few years - and hopefully beyond!

Prior Research

I am continuing to investigate foodweb interactions of larval and juvenile fishes in the San Francisco Estuary using high-throughput DNA sequencing, primarily DNA metabarcoding. We currently (Oct 2020) have a pre-print available where you can read about the results from the larval longfin smelt and Pacific herring diet study!

Link to bioRxiv pre-print, soon to be submitted for peer-review.

ZooplanktonJars Longfin smelt

In the Oceanography department at UH Manoa I studied the role of copepod nauplii in marine ecosystems, including their response to storm events in Kane'ohe Bay, Hawaii. My work will give us a better understanding of how important nauplii are as grazers of algae and whether they can have an impact on their prey populations(See Pubs & Presentations - Jungbluth et al 2017 MEPS). Using a novel DNA-based technique that I developed during my master's degree (See Pubs & Presentations- Jungbluth et al. 2013), I could estimate the abundance or biomass of nauplii by species. This was not possible in a diverse ecosystem when armed with only a microscope and no species-specific larval-identifying characteristics.


I also have worked with Dr. Eric Vetter at Hawaii Pacific University on a short-term, collaborative project describing the molecular-taxonomic diversity of larval invertebrate species present near the abyssal seafloor. My work on that project was published in PeerJ:

Kersten, O., Vetter, E. W., Jungbluth, M. J., Smith, C. R., & Goetze, E. (2019). Larval assemblages over the abyssal plain in the Pacific are highly diverse and spatially patchy. PeerJ, 7:e7691, 36. https://doi.org/10.7717/peerj.7691


All Aboard!

A large portion of my dissertation focused on plankton dynamics in a large, productive subtropical embayment on Oahu, Hawaii, so I have spent a lot of time on a 12-foot Boston Whaler, rain or shine, collecting my precious zooplankton to look at what lies below the surface. But I also love ship-based research, and have been lucky enough to spend over 80 days at sea on 5 different ships with scientists from many countries getting to contribute to studies on zooplankton around the worlds oceans. Thankfully I do NOT get seasick!


Google Scholar     ResearchGate     LinkedIn    


Oceanographic Expeditions and Field Work

R/V Questuary, USGS Arcoplites, and USGS Munson - Longfin smelt 24-h sampling series for juvenile fishes in San Pablo Bay, 2 nights, chief scientist of night operations, 2017

NOAA Oscar Elton Sette - Leeward Oahu Pelagic Ecosystem Characterization, 10 days at sea, 2017

RRS James Clark Ross – Naupliar studies across the Atlantic (and the equator!), North to South, 46 days at sea, 2014

R/V Falkor – Naupliar grazing in the open ocean, Station ALOHA North of Oahu, HI, and the Molokai channel, 6 days at sea, 2014

R/V Kilo Moana -Zooplankton and mesopelagic fish diet studies, Station ALOHA, 6 days at sea, 2011

R/V Kilo Moana - Student cruise, West Oahu, 2 days at sea, 2011

R/V AtlantisROV JASON-II cruise volunteer, Juan de Fuca Ridge, 18 days at sea, 2010

Field sampling time series, Kaneohe Bay, HI, over 75 days of coastal work, 2010-2013


Coastal Plankton Ecology


Link to BCO-DMO Data Entry

Photos of my Research and Science Adventures

Under construction! Apologies for any wonky-ness.

Research Adventures

Sette1   Sette2   Sette3
Microscope ID of zooplankton on the R/V Sette        
sette4   sette5   sette7
Filtering size-fractionated copepods on the R/V Sette   A seahorse we saw in a plankton collection off West Oahu on the R/V Sette    
    Scenic views from Sea, off West Oahu, on the R/V Sette    
LFS1   LFS2   LFS3
View of San Pablo Bay from a small research vessel   Tools of the trade: A 500 µm and a 150 µm net for collection of plankton and micronekton   Spring samples tend to have a lot of suspended sediment in them in the San Francisco Estuary
LFS4   falkor1   Falkor2
Field work selfie, in San Pablo Bay   Amazing shot of the net being submerged for sampling from the R/V Falkor, go pro attached to the tow line    
Falkor3   Falkor4   Falkor5
Me picking nauplii at the microscope at sea   Working in the live lab on the R/V Falkor   R/V Falkor
Falkor6   Moc1   Moc2
    10 m MOCNESS net - it is truly a beast to wrangle and collects lots of really exciting samples from different depths of interest    
JDF1   KM1123   KBay2010
My first oceanographic research cruise ever - on the R/V Atlantis, 2010       My territory - Kaneohe bay, Oahu, Hawaii. Where I spent my dissertation studies.
Amt1   AMT2   AMT3
THE most beautiful sunrise I've ever seen: Somewhere in the middle of the Atlantic Ocean on the RRS James Clark Ross, 2014   We are LITERALLY at the equator, on the Atlantic, at this moment!   RRS James Clark Ross, a British Antarctic Survey vessel, an icebreaker!
AMT4   AMT4   AMT6
Rough seas on the JCR        
AMT7   AMT8   AMT9
AMT10   AMT11   AMT12
Crossing the line.   Tools of the trade.   Group on deck to admire our first sight of land, the Falkland Islands, after 46 days at sea

Sea Life Images

This is just a small subsample of the creatures I love to see and often take photos of while at sea! Feel free to contact me if you have any questions or want to know more!

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Spoils of San Francisco Estuary sampling for fish larvae, you can see them! (2017)   Larval squid of many sizes (aww)   Billfish larvae from offshore Oahu, Hawaii
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Barreleye fish from Falkor cruise, offshore Oahu, Hawaii   Vellela vellela, AMT cruise   Pteropod.
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Flying fish on Atlantic Ocean (photo: Ian Brown)       Pelagic polychaete worm, Atlantic Ocean, 2014
Sette1   Sette2   Sette3
Mesopelagic fish   Heteropod (a type of mollusk)   Annelid worm? This one is a mystery! Atlantic Ocean 2014


mjjungbluth @ gmail(dot)com

You can also find me on Facebook, Twitter, or Instagram


Communicating our work to a broad audience, including the general public, policymakers, and scientific peers, is critical to making progress in the fast-paced world we live in.

That is why colleagues and I in Hawaii created the Science Communicators 'Ohana, a Registered Independent Organization at UH Mānoa, created for scientists to get together and explore effective methods for communicating our science with each other and the public.

Through workshops organized with the 'Ohana, we have provided the University of Hawaii community with opportunities to improve their non-scientific writing, oral presentation, public speaking, and "elevator pitches". This was important to me before the 'Ohana; A collaborator and I decided we, as early career scientists and stewards of our Earth, really needed an outlet for the students to practice outreach writing, so we created a Real Science at SOEST Blog . The blog, recently renamed to align with the Science Communicators 'Ohana, was created as a platform through which graduate scientists in the University at Manoa could improve their communication skills.

Outreach Event Photos

I'm sharing some photos of biannual outreach event held at UH Manoa, School of Ocean Earth Science and Technology called the SOEST Open House. In 2013, Katherine Hanson and I joined forces to create an collaborative exhibit between the zooplankton labs of Dr. Erica Goetze and Dr. Petra Lenz.

Since then I have led the exhibit in 2013, 2015 and 2017, and it is always popular amongst the students. For purposes of privacy I have not included photos of the room FILLED with curious and excited kids from all across Hawaii - trust me that it is always a success!

OH13_1   OH15_1   OH15_2
SOEST Open House 2013   SOEST Open House 2015   2015
OH17_6   OH17_1   OH17_2
SOEST Open House 2017 - gets better and better every year!        
OH17_3   OH17_4   OH17_5
    Chalkboard before the madness...   Chalkboard after! Kids love drawing "plankton" on the chalkboard
Sette1   Sette2   Sette3
    A fun addition to our exhibit this year. Holy chum bucket!