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Environmental Microbial Diversity and Genomics

Exploration of Earth's microbial and viral diversity is a major scientific frontier. Sequencing DNA - the blueprint of life - collected directly from the environment provides a powerful way to access the uncatalogued microbial diversity on our planet. These uncharacterized lifeforms are ripe with novel functions, metabolisms, the potential for biotechnological and medical applications, and will inform us on the evolution of all life.

My previous work has explored the nature and extent of microbial life underground and below the seafloor using tools rooted in molecular biology, biogeochemistry, and microbiology. Now I am working to explore novel microbial diversity in additional environments through the leveraging of ultra-powerful computational resources and true access to massive genome databases (i.e. big data).

Check out my work featured in popular media outlets!

                                            

For a great overview of my deep biosphere research, check out a seminar I delivered as an invited participant of the C-DEBI Networked Speaker seminar series: Link to info about video

Twitter: @seanjungbluth

Twitter: @deepbiopubs

Curriculum Vitae

Short (3 pages)     Long (18 pages)

Professional Appointments

2017-present, Computational Biologist Postdoctoral Fellow, DOE Joint Genome Institute

2016-2017, Principal, Jungbluth Consulting

2015-2016, Postdoctoral Scholar - Research Associate, University of Southern California

2014-2015, Postdoctoral Scholar, University of Hawaii

Education

2014  PhD  Oceanography, University of Hawaii

2007  BS   Biology and Bacteriology, University of Wisconsin

Selected Awards and Honors

University-National Oceanographic Laboratory System Deep-Submergence Science Leadership Cruise, Invited Participant

Deep Carbon Observatory Origins and Movements of Subsurface Microorganisms Workshop, Invited Participant

Consortium for Ocean Leadership U.S. Science Support Program Marine Geoscience Leadership Symposium, Invited Participant

National Science Foundation Ecological Dissertations in the Aquatic Sciences Symposium, Invited Participant

Center for Dark Energy Biosphere Investigations Graduate Student Fellowship, Recipient

Consortium for Ocean Leadership U.S. Science Support Program Schlanger Ocean Drilling Fellowship, Recipient

Teaching

Fundamentals of Oceanography
Fundamentals of Microbiology

Selected Presentations

Rappe MS, Jungbluth SP, Lin H-T, Nigro OD, Steward GF (2016, March) The distribution, diversity, and function of microbial and viral communities inhabiting anoxic crustal fluids within deep subseafloor basalt. Presented at the Joint Genome Institute Users Meeting, Walnut Creek, CA.

Jungbluth SP, Glavina del Rio T, Tringe S, Stepanauskas R, Rappe MS (2015, December) Ecogenomic characterization of a marine microorganism belonging to a Firmicutes lineage that is widespread in both terrestrial and oceanic subsurface environments. Presented at the fall meeting of the American Geophysical Union, San Francisco, CA.

Nigro O, Jungbluth SP, Lin H-T, Rappe MS, Steward G (2015, December) Archaeal viruses contribute to the novel viral assemblage inhabiting oceanic, basalt-hosted deep subsurface crustal fluids. Presented at the fall meeting of the American Geophysical Union, San Francisco, CA.

Nigro O, Jungbluth SP, Lin H-T, Hsieh C-C, Mueller J, Schvarcz C, Rappe MS, Steward G (2015, February) A first look at a deep subsurface viral community from the basement fluids of the Juan de Fuca Ridge flank. Presented at the American Society for Limnology and Oceanography Aquatic Sciences Meeting, Grenada, Spain.

Lloyd KG, Bird J, Steen AD, Buongiorno J, Jungbluth SP (2015, January) Insights from the first deep subsurface single cell genomes and development of digestR, a new tool for metagenomic analysis. Presented at the Center for Dark Energy Biosphere Investigations NSF Site Visit, Los Angeles, CA.

Jungbluth SP, Lin H-T, Hsieh C-C, Rappe MS (2014, December) High-resolution temporal analysis of deep subseafloor microbial communities inhabiting basement fluids. Presented at the fall meeting of the American Geophysical Union, San Francisco, CA.

Carr S, Jungbluth SP, Lin H-T, Rappe MS (2014, December) Investigating chemotactic potential within crustal fluid communities. Presented at the fall meeting of the American Geophysical Union, San Francisco, CA.

Orcutt BN, Sylvan J, Rogers D, Lee R, Girguis P, Carr S, Jungbluth SP, Rappe MS (2014, December) Carbon fixation in oceanic crust: does it happen, and is it important?. Presented at the fall meeting of the American Geophysical Union, San Francisco, CA. (Invited Presentation)

Jungbluth SP, Bowers R, Lin, H-T, Hsieh C-C, Cowen JP, Rappe MS (2012, December) Microbial diversity within Juan de Fuca ridge basement fluids sampled from oceanic borehole observatories. Presented at the fall meeting of the American Geophysical Union, San Francisco, CA. (Invited Presentation)

Invited Seminars

Jungbluth SP (2016, January) Investigating novel microbial life in the deep igneous oceanic crust. Seminar presented at the Department of Earth Sciences Paleoenvironmental Seminar Series. University of Southern California, Los Angeles, California

Jungbluth SP (2015, November) Microbial life in the deep subseafloor igneous basement: a frontier of exploration. Seminar presented at the Marine Environmental Biology Department Retreat. USC Wrigley Institute for Environmental Studies, Catalina Island, California

Jungbluth SP (2014, October) Juan de Fuca Ridge flank basement fluid microbiology. Seminar presented as part of the Center for Dark Energy Biosphere Investigations Networked Speaker Seminar Series. [Broadcast Online]

Jungbluth SP (2014, October) Microbial diversity in anoxic, subseafloor basaltic fluids. Seminar presented at the Astrobiology Seminar Series. University of Hawaii, Honolulu, Hawaii

Professional Activities

Member of: American Society for Microbiology, Association for the Sciences of Limnology and Oceanography, American Association for the Advancement of Science, American Geophysical Union, Astrobiology Society, International Society for Microbial Ecology, International Society for Subsurface Microbiology, The Oceanography Society

Reviewer for: Environmental Microbiology, Frontiers in Microbiology, The ISME Journal, National Science Foundation (Biological Oceanography), PLoS ONE

My research

Research

Google Scholar     PubMed     Github     LinkedIn     ResearchGate     ORCID     Mendeley     ResearcherID    

Exploration of the Deep Biosphere

Summary: For over seven years I worked on a team that was tasked with exploration of the deep subseafloor biosphere using manned and unmanned deep submersibles and ocean drilling program boreholes. In the deep-sea, we sampled fluids filling the spaces and microfractures in the basaltic rock using hundred meter long pipes installed into the seafloor. This technology provided an access point to the remote deep ocean volcanic rock and the extreme microbial lifeforms that live there.

CORK-infographic

Above: Infographic describing how we access microorganisms in the deep subseafloor. Full-size Version (6.7 MB)

Genomics of Subsurface Bacteria and Archaea

Summary: The genomic repertoire of bacteria and archaea inhabiting the subsurface are revealing clues to the adaptations required for life to survive in an environment devoid of sunlight. Cutting-edge DNA sequencing techniques and bioinformatics tools allow for recovery of near-complete genomes from environmental samples and are allowing for unprecedented investigations into the genomic potential of microbial communities.

genomics

Above: Genomic comparisons reveal clues to the metabolic features and adaptations of deep subsurface life.

Diversity of Microorganisms Inhabiting Igneous Rock

Summary: The diversity of microbial life inhabiting the rocky parts of Earth are poorly described. Microbes living on and inside rocks slowly eat the minerals and participate in the weathering of the Earth on global scales. Understanding the diversity of Bacteria and Archaea in the subsurface of the global ocean and basins and the role of this diversity in establishing community functioning is of high interest to me.

microbial-div

Above: Understanding the abundance and diversity of microbes in the environment helps to understand the hidden functions that occur there.

Viruses in the Deep Subsurface

Summary: The diversity of viruses on the planet is among the least catalogued of all life. I have been working to describe the diversity of novel viruses in the deep marine subseafloor and explore their genomic composition and potential for interaction with the other domains of life.

viruses

Above: Viral diversity investigations enabled by viral metagenomics are revealing novel thermophilic viruses. Analysis of microbial CRISPR sequences and spacers allows for understanding of virus-host dynamics in the environment.

Professional Development for Scientists

Summary: In addition to research, I believe it is important to promote diverse professional development opportuntities for young scientists. There are more professionally-trained scientists than academic positions allow, so additional useful modes of employment must be made available to trainees.

prof-dev

Above: Trainees are facing a harsh employment situation upon graduation and networking is key to success.

Image Portfolio

Science communication relies on the art of figure design. Here are some example figures I've designed for research publications - please enjoy!

Publications

Google Scholar     PubMed     ResearchGate     ORCID     Mendeley     ResearcherID    

Published

Momper L, Jungbluth SP, Lee M, Amend JP. (2017) Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community. The ISME Journal 1-15.

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Marlow J, Borrelli C, Jungbluth SP, Hoffman C, Marlow H, Girguis P, AT-36 Team. (2017) Telepresence is a potentially transformative tool for field science. PNAS 114: 4841-4844.

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Jungbluth SP, Glavina del Rio T, Tringe SG, Stepanauskas R, Rappé MS. (2017) Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems. PeerJ 5:e3134.

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Jungbluth SP, Amend JP, Rappé MS. (2017) Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids. Scientific Data 4:170037.

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Nigro OD, Jungbluth SP, Lin H-T, Hsieh C-C, Miranda J, Schvarcz C, Rappé MS, Steward GF. (2017) Viruses in the oceanic basement. mBio 8: e02129-16.

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Robador A, LaRowe, DE, Jungbluth SP, Lin H-T, Rappé MS, Nealson KH, Amend JP (2016) Nanocalorimetric characterization of microbial activity in deep subsurface oceanic crustal fluids. Frontiers in Microbiology 7: 454.

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Jungbluth SP, Bowers RM, Lin H-T, Cowen JP, Rappé MS. (2016) A novel microbial assemblage inhabits fluids within mid-ocean ridge flank subsurface basalt. The ISME Journal 10: 2033-2047.

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Robador A, Jungbluth SP, LaRowe DE, Bowers RM, Amend JP, Rappé MS, Cowen JP. (2015) Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust. Frontiers in Microbiology 5: 748.

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Biddle JF, Jungbluth SP, Lever MA, Rappé MS. (2014) Life in the ocean crust. In: Kallmeyer J (ed). Life in Extreme Environments: The Deep Biosphere. DeGruyter. [Book Chapter; No Peer-Review]

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Böttjer D, Jungbluth SP, Boiteau R, Burkhardt B, De Leo F, Bruno BC. (2014) Career choices in marine and environmental sciences: navigating a sea of options. Oceanography 27(4): 37-43. [NON PEER-REVIEWED]

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Lin H-T, Cowen JP, Olson EJ, Lilley MD, Jungbluth SP, Wilson ST, Rappé MS. (2014) Dissolved hydrogen and methane in the oceanic basaltic biosphere. Earth and Planetary Science Letters 405: 62-73.

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Jungbluth SP, Lin H-T, Cowen JP, Glazer BT, Rappé MS. (2014) Phylogenetic diversity of microorganisms in subseafloor crustal fluids from boreholes 1025C and 1026B along the Juan de Fuca Ridge flank. Frontiers in Microbiology 5: 119.

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Jungbluth SP, Johnson LGH, Cowen JP, Rappé MS. (2013). Data report: microbial diversity in sediment near Grizzly Bare Seamount from Holes U1363B and U1363G. Proceedings of the Integrated Ocean Drilling Program 327: pp. 1-27.

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Jungbluth SP, Grote J, Lin H-T, Cowen JP, Rappé MS. (2013). Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank. The ISME Journal 7(1): 161-172.

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Fisher AT, Tsuji T, Petronotis K, Wheat CG, Becker K, Clark JF, Cowen J, Edwards K, Jannasch H, IODP Expedition 327 and Atlantis Expedition AT18-07 Shipboard Parties (2012). IODP Expedition 327 and Atlantis Expedition AT18-07: Observatories and Experiments on the Eastern Flank of the Juan de Fuca Ridge. Scientific Drilling 13: 4-11.

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Published PrePrints

Jungbluth SP, Amend JP, Rappé MS. (2016) Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids. PeerJ PrePrints.

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Jungbluth SP, Glavina del Rio T, Tringe SG, Stepanauskas R, Rappé MS. (2016) Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems. PeerJ PrePrints.

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Submitted/In Revison/Accepted/In Press

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Schulz F, Doud D, Reddy TBK, Jarett J, Rivers A, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Schriml L, Podar M, Bork P, Weinstock GM, Banfield JF, Garrity GM, Hugenholtz P, Parks DH, Tyson GW, Rinke C, Dodsworth JA, Yooseph S, Sutton GG, Yilmaz P, Glockner FO, Meyer F, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema T, Tighe S, Konstantinidis KT, Liu W-T, Baker BJ, Rattei T, Eisen J, Hedlund BP, McMahon KD, Fierer N, Knight R, Finn RD, Mizrachi I, Eren AM, Woyke T. Genome standards for single amplified genomes and genomes from metagenomes of Bacteria and Archaea. Accepted to Nature Biotechnology.

Teehara KB, Jungbluth SP, Acosta TE, Hellebrand E, Misra AK, Onac PB, Pflitsch A, Smith SM, Rappe MS, Telus M, Schorghofer N. Cryogenic minerals in Hawaiian lava tubes: A geochemical and microbiological survey. Submitted to Geomicrobiology.

McVeigh D, Skarke A, Dekas A, Borrelli C, , Hong W-L, Marlow J, Pasulka A, Jungbluth SP, Barco R, Djurhuus. Characterization of benthic biogeochemistry and ecology at three methane seep sites on the Northern US Atlantic Margin. Submitted to Deep-Sea Research Part II.

In Prep

Jungbluth SP, Paver S, Carreira C, Fong A, Maier M, Tolar B, Williams A. Toward predictive microbial ecology: how we do, don’t, and should study aquatic microbial communities. Submitted.

Jungbluth SP, Chadwick G, Orphan V, Amend JP, Rappé MS. A novel methanogenic Archaea. In prep.

Robador A, Jungbluth SP, LaRowe DE, Amend JP. Invited review: Microbial activity in deep subseafloor crustal fluids. In prep for Frontiers in Microbiology. (Anticipated submission: Q3, 2017)

Consulting

Computational biology is a rapidly developing field, and so the best workflow or required suite of packages that you may need for your analysis needs necessitates an understanding of biology and scripting. That's where my knowledge of molecular biology, genetics and informatics can help! Bioinformatic consultation services I can provide will allow you to construct fully-customized informatic pipelines.

Academic and commercial clients are provided consultation for an hourly or fixed price fee. Rates are negotiable and are on a case-by-case basis. Please contact me if interested.

Oceanographic Expeditions and Field Work

Above: Map of locations where I've embarked on oceanographic expeditions and other field work.

Atlantic Continental Shelf, URI Inner Space Center shore-based participant, AT36 (Aug 3 – Aug 8, 2016)

Atlantic Continental Shelf, R/V Atlantis – HOV ALVIN-II and AUV Sentry cruise participant, AT36 (July 28 – Aug 2, 2016)

Juan de Fuca Ridge flank, R/V Atlantis – HOV ALVIN-II cruise participant, AT26-18 (August 10 – August 24, 2014)

Juan de Fuca Ridge flank, R/V Atlantis – ROV JASON-II cruise participant, AT26-03 (July 13 – July 26, 2013)

North Pacific Subtropical Gyre, R/V Kilo Moana cruise participant, KM12-23 & HOT 247 (October 6-10, 2012)

North Pacific Subtropical Gyre, R/V Kilo Moana cruise participant, KM12-18 & HOT 245 (August 16-20, 2012)

North Pacific Subtropical Gyre, R/V Kilo Moana cruise participant, KM12-16 & HOT 244 (July 30 – August 3, 2012)

North Pacific Subtropical Gyre, R/V Kilo Moana cruise participant, KM12-13 & HOT 243 (June 25-29, 2012)

North Pacific Subtropical Gyre, R/V Ka’Imikai-O-Kanaloa cruise participant, KOK12-05 & HOT 242 (May 29 – June 2, 2012)

North Pacific Subtropical Gyre, R/V Ka’Imikai-O-Kanaloa cruise participant, KOK12-02 & HOT 241 (April 30 – May 4, 2012)

North Pacific Subtropical Gyre, R/V Kilo Moana cruise participant, KM12-05 & HOT 240 (March 23-27, 2012)

North Pacific Subtropical Gyre, R/V Ka’Imikai-O-Kanaloa cruise participant, KOK12-01 & HOT 239 (January 17-21, 2012)

Juan de Fuca Ridge flank, R/V Atlantis – ROV JASON-II cruise participant, AT18-07 (June 28 – July 14, 2011)

Juan de Fuca Ridge flank, D/V JOIDES Resolution shore-based participant, IODP Expedition 327

Juan de Fuca Ridge flank, R/V Atlantis – ROV JASON-II cruise participant, AT15-66 (June 13 – July 1, 2010)

Juan de Fuca Ridge and ridge flank, R/V Atlantis – DSV Alvin cruise participant, AT15-51 (August 20 – September 6, 2009)

West Coast of Oahu, Hawaii, R/V Kilo Moana cruise participant, KM09-06 (February 12 – February 15, 2009)

Juan de Fuca Ridge flank, R/V Atlantis – DSV Alvin cruise participant, AT15-35 (July 24 – August 14, 2008)

Data

Subseafloor Biosphere

BCO-DMO

Link to BCO-DMO Data Entree

Download BCO-DMO Data (.xlsx)

The BCO-DMO link will help you access data related to my publications. Please let me know if you can't find some data or information that you need.

Jungbluth et al. 2013 The ISME Journal

NCBI Genbank Sequences (n=501)

This link takes you to the SSU rRNA sequence data from borehole crustal fluid and seawater microbial communities. These sequences were published with the paper.

NCBI Genbank Sequences (n=27) from unpublished data.

This link takes you to the SSU rRNA sequence data from borehole crustal fluid microbial communities. These data are unpublished but generated with different gene primers from an identical sample used in the publication.

Jungbluth et al. 2013 Proceedings of the Integrated Ocean Drilling Program

NCBI Genbank Sequences (n=80)

This link takes you to the SSU rRNA sequence data from sediment microbial communities.

Jungbluth et al. 2014 Frontiers in Microbiology

NCBI Genbank Sequences (n=99)

This link takes you to the SSU rRNA sequence data from borehole crustal fluid microbial communities.

Robador et al. 2015 Frontiers in Microbiology

NCBI Genbank Sequences (n=31)

This link takes you to the dsrAB sequence data from borehole crustal fluid microbial communities.

NCBI BioProject entree

This link takes you to the SSU rRNA amplicon sequence data from borehole crustal fluid microbial communities.

Jungbluth et al. 2016 The ISME Journal

NCBI Genbank Sequences (n=192)

This link takes you to the SSU rRNA sequence data from borehole crustal fluid, sediment, and seawater microbial communities.

NCBI BioProject entree

This link takes you to the SSU rRNA amplicon sequence data from borehole crustal fluid, sediment, and seawater microbial communities.

Jungbluth et al. 2017 Scientific Data

NCBI BioProject entree for samples used for metagenomics.

IMG/MER sample entree for U1362A metagenome data.

IMG/MER sample entree for U1362B metagenome data.

Files needed to isolate scaffold sets for all 98 metagenome-assembled genomes (MAGs) in IMG/M.

FASTA files containing the contigs of all 98 metagenome-assembled genomes (MAGs).

FASTA file containing 54 SSU rRNA genes with length >300 base pairs extracted from the 98 metagenome-assembled genomes (MAGs).

IMG/M annotations associated with the scaffolds of all 98 metagenome-assembled genomes (MAGs).

Jungbluth et al. 2017 PeerJ

EMIRGE reconstructed SSU rRNA genes from U1362A and U1362B metagenome data.

Basaltic Ice Cave

Unpublished data

NCBI BioProject entree unpublished samples used for SSU rRNA amplicon sequencing.

This link takes you to the SSU rRNA amplicon sequence data from Hawaii ice cave microbial communities.

News

2017, Mar 7: A new publication lead by Olivia Nigro is now published! Check out the first description of the virosphere in Earth's deep subseafloor aquifers!

2017, Feb 1: I'm excited to be starting as a Computational Biology Postdoctoral Fellowship at the DOE Joint Genome Institute! Here I'll be working with Dr. Emiley Eloe-Fadrosh and others to explore new lineages of life!

Contact

jungbluth dot sean at gmail dot com

Fun Science Stuff

Photos

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Under Construction

Rank Country Population % of world population Date
1 中华人民共和国 (People's Republic of China) 1,370,570,000 18.9% June 24, 2015
2 India 1,273,140,000 17.6% June 24, 2015
3 United States "USA" 321,268,000 4.43% June 24, 2015
4 Indonesia 255,461,700 3.52% July 1, 2015
5 Brazil 204,503,000 2.82% June 24, 2015
6 Pakistan 190,156,000 2.62% June 24, 2015
7 Nigeria 183,523,000 2.53% July 1, 2015
8 Bangladesh 126,880,000 2.19% June 24, 2015