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Jarrod J. Scott
I study microbial diversity. My approach is holistic, spanning marine & terrestrial systems to understand how simple organisms coalesce into complex communities & how these communities affect host biology, biogeochemical cycles, & ecosystem-level processes. I also work to make my research more accessible & exciting, transparent & reproducible. I use & teach open-source tools to create web products that communicate science more effectively.
Current Appointment
Research Associate
Smithsonian Tropical Research Institute
Panama
2022 -
Education
PhD Microbiology
University of Wisconsin
Madison, Wisconsin USA
2011 - 2006
BSc Aquatic Biology, Minor in Archaeology
University of Texas
Austin, Texas USA
2002 - 1998
Prior Research Positions
STRI/Moore Foundation Postdoctoral Fellow
Smithsonian Tropical Research Institute
Panama
2017 - 2022
- Microbial ecology of coral reefs & mangrove ecosystems across the Isthmus of Panama. The Eastern Pacific & Western Atlantic.
Postdoctoral Research Associate
Bigelow Laboratory for Ocean Sciences
East Boothbay, Maine USA
2016 - 2012
Graduate Fellow
University of Wisconsin
Madison, Wisconsin USA
2011 - 2010
Predoctoral Fellow
Smithsonian Tropical Research Institute
Gamboa, Panama
2010 - 2009
Research Technician
University of Texas
Austin, Texas USA
2005 - 2002
Marine Field Experience
Caribbean Field Work
Smithsonian Tropical Research Institute
Bocas del Toro, Panama
2020 - 2017
Extensive field work around the Bocas del Toro archipelago.
Expeditions to Isla Coiba
Smithsonian Tropical Research Institute
Isla Coiba, Panama
2020 - 2017
5 expeditions over the past 3 years
Use this link to learn more about Isla Coiba.
R/V Revelle & ROV Jason II (cruise RR1413)
Submarine Ring of Fire - Ironman Cruise
Mariana BackArc Basin
2014
November 23 – December 21
All research cruises from 2012 - 2014 were to study the microbial ecology of deep-sea hydrothermal systems, specifically iron-oxidizing communities.
R/V Atlantic Explorer (cruise AE1410)
Chief Scientist Training Cruise
Barbados to Bermuda
2014
May 31 – June 10
R/V Thompson, ROV Jason II, & AUV Sentry (cruise TN293)
Lo’ihi Seamount, Hawaii
2013
March 4 – April 1
R/V Knorr & ROV Jason II (cruise KN209-02)
Woods Hole Oceanographic Institution
Mid-Atlantic Ridge
2012
October 16 – November 14
I’ve also worked on a lobster boat in Maine & a seine boat in Alaska.
R/V Longhorn
University of Texas
Gulf of Mexico
2001
Terrestrial Field Experience
Microbial Ecology of Fungus-Growing Ants
Smithsonian Tropical Research Institute
Panama
2010 - 2008
- Four expeditions to Panama
- 15-month residency at STRI
- Field & lab experiments with fungus-growing ants
A lot of my field experience in terrestrial systems is on fungus-growing ants in the Neotropics.
Biogeography of Fungus-Growing Ants
University of Texas
Mexico & Panama
2004 - 2001
Multiple field expeditions to understand the biogeography of fungus-growing ants & their fungal symbionts.
Molecular Ecology of Cichlids in Northern Mexico
University of Texas
Coahuila, Mexico
2001 - 2000
Molecular analysis of cichlid fish endemic to aquifer fed pools of the Cuatro Cienegas Basin.
Mayan Archaeological Surveys
University of Texas
Northwestern Belize
2000
Extensive surveys & excavations of Mayan archaeological sites in lowland tropical rain forests.
Recent Teaching Experience
Instructor
STRI-McGill NEO Tropical Biology Field Course
Panama
2024
- Guide project design & implementation.
- Reproducible analytical workflows using R Markdown.
- Assist students with field work.
- Natural history of neotropical marine & terrestrial ecosystems.
Data Specialist & Project Coordinator
STRI-McGill NEO Tropical Biology Field Course
Panama
2022
- Guide project design & implementation.
- Reproducible analytical workflows using R Markdown.
- Assist students with field work.
- Natural history of neotropical marine & terrestrial ecosystems.
Click here for the course tutorial site
Field sites incl. Barro Colorado Island, Bocas del Toro, Agua Salud, & Isla Coiba.
Instructor & Course Creator
Panama
2020
Click here for the course website.
Online course about creating web-based reproducible workflows using open source software tools and platforms. The course website can be found here.
Instructor
STRI-McGill NEO Tropical Biology Field Course
Panama
2020
- Guide project design & implementation.
- Reproducible analytical workflows using R Markdown.
- Assist students with field work.
- Natural history of neotropical marine & terrestrial ecosystems.
Field sites incl. Barro Colorado Island, Ft Sherman Canopy Crane, Pipeline Road Forests, Agua Salud & Isla Coiba.
I teach the way I learn. My goal is to create a venue where students can be curious, get their hands dirty, make mistakes, & explore. I’m here to help students see what’s possible, not tell them what to do.
Marine Biology Instructor
STRI-McGill Tropical Biology Field Course
Isla Coiba, Panama
2019
- Guide project design & implementation.
- Assist students with field work.
- Snorkeling class for inexperienced students.
Click here for the course blog & here for the course website.
Workshop Creator & Organizer
Marine Microbiome Workshop
Bocas del Tora, Panama
2018
From model organisms to ecosystems: scaling-up our understanding of host-microbe symbiosis in the sea.
- Conceived, created & designed workshop.
- Handled workshop logistics & organization.
- Led discussions & working groups.
Click here for the workshop website & here for the publication written by workshop participants.
Web Products
R Markdowng Fielduide
Web project guide book for 2022 STRI-McGill NEO Tropical Biology Field Course.
Panama
2022
SWELTR
Reproducible bioinformatic workflows for the study Soil Warming Experiment in Lowland Tropical Rainforest.
Barro Colorado Island, Panama
2022
Reproducible Workflows
Hypocolypse
Reproducible bioinformatic workflows for the study Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean reef.
Bocas del Toro, Panama
2021
Reproducible Workflows
Istmobiome Project
Reproducible bioinformatic workflows for the Istmobiome microbiome project.
Panama
2021
BocasBiome
Reproducible bioinformatic workflows for the study The gut microbiome stability of a butterflyfish is disrupted on severely degraded Caribbean reef habitats..
Bocas del Toro, Panama
2020
ProjectDIGEST
Reproducible bioinformatic workflows for the study Intestinal microbes: an axis of functional diversity among large marine consumers.
Pickles Reef, Florida USA
2020
Cacao Fermentation
Talk about the microbiology of cacao fermentation.
Bocas del Toro, Panama
2020
Public Presentations
Rethinking the Diversity of Life
Talk about understanding diversity through a molecular lens.
Bocas del Toro, Panama
2020
How the Isthmus of Panama Changed the World
Talk about how life changed on land & in the sea after the closure of the Isthmus of Panama.
Bocas del Toro, Panama
2019
R Markdown Fieldguide
Web project tutorial site for the 2022 STRI-McGill NEO Tropical Biology Field Course.
Panama
2022
Courses & Workshops
Web Products & Data Curation
Website for course on using open-source software tools to create web-based reproducible workflows.
Panama
2020
Web Project Guide
Web project guide book for 2020 STRI-McGill NEO Tropical Biology Field Course.
Panama
2020
Workshop Guide
Web site for the first STRI/Moore Foundation Marine Microbiome Workshop.
Bocas del Toro,
2018
Additional Training & Certifications
PADI Rescue Diver Certification Course
Panama Dive School
Bocas del Toro, Panama
2018
PADI Advanced Open Water Diver Certification Course
Panama Dive School
Bocas del Toro, Panama
2017
PADI Open Water Diver Certification Course
Panama Dive School
Bocas del Toro, Panama
2017
PoreCamp
University of Exeter Sequencing Center
Penryn, England
2016
1-week hands-on training bootcamp on deploying Oxford Nanopore’s portable sequencing platform, the MinION.
Click here to learn more.
Complex Systems Summer School
Santa Fe Institute
Santa Fe, New Mexico USA
2015
4-week intensive course on complex systems.
Click here for the 2015 CSSS proceedings.
UNOLS Chief Scientist Training Cruise
The University-National Oceanographic Laboratory System
Barbados to Bermuda.
2014
2-week course on how to effectively plan for, acquire, utilize, & report on time at sea for multi-disciplinary research & education.
Click here for the final report from the 2014 UNOLS training cruise.
Fire Fighter I & II. NFPA 1001-2006
Southern Maine Community College
Portland, Maine USA
2013
Year-long training course for Fire Fighter I & II Certification.
Microbial Diversity Course
Marine Biological Labs
Woods Hole, Massachusetts USA
2007
6-week intensive course. Cultivating, & isolating diverse microbes. Molecular & computational analyses.
Click here to learn more.
Marine Botany & the Biology of Fish
University of Texas Marine Science Institute.
Port Aransas, Texas USA
2001
Archaeological Field Techniques
The Programme for Belize Archaeological Project
Orange Walk District, Belize
2000
Intensive field course on Mayan art, architecture, & iconography.
Learn more on the course website.
Fellowships
Smithsonian Institution Genomics Postdoctoral Fellowship
declined
Panama
2014 - 2012
Wisconsin Distinguished Graduate Fellowship
College of Agriculture & Life Science
University of Wisconsin
2011 - 2010
Smithsonian Institution Predoctoral Fellowship
Smithsonian Tropical Research Institute
Panama
2010 - 2009
Peer Reviewed Publications
Contrasting drivers of abundant phage and prokaryotic communities revealed in diverse coastal ecosystems.
ISME Communications 3, 127 (2023)
N/A
2023
Weinheimer AR, Aylward FO, Leray M, Scott JJ
Microbial diversity declines in warmed tropical soil and respiration rise exceed predictions as communities adapt.
Nature Microbiology 7, 1650–1660 (2022)
N/A
2022
Nottingham AT, Scott JJ, Saltonstall K, Broders K, Montero-Sanchez M, Püspök J, Bååth E, Meir P.
Click here for the project website & reproducible workflows from this paper.
The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs
Communications Biology 5, 770 (2022)
N/A
2022
Clever F, Sourisse JM, Preziosi RF, Eisen JA, Rodriguez Guerra EC, Scott JJ, Wilkins LGE, Altieri AH, McMillan WO, Leray M.
Click here for the project website & reproducible workflows from this paper.
Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean reef
Nature Communications 12, 4522 (2021)
N/A
2021
Johnson MD, Scott JJ, Leray M, Lucey N, Lucia Rodriguez L, Wied W, Altieri AH.
Click here for the project website & reproducible workflows from this paper. Johnson, Scott, Leray, & Lucey contributed equally to the work.
Intestinal microbes: an axis of functional diversity among large marine consumers
Proceedings of the Royal Society B: Biological Sciences 287:(20192367)
N/A
2020
Scott JJ, Adam TC, Duran A, Burkepile DE, Rasher DB.
Click here for the project website & reproducible workflows from this paper.
Biological rejuvenation of iron oxides in bioturbated marine sediments.
The ISME Journal. 12(2018):1389-1394.
N/A
2018
Beam JP, Scott JJ, McAllister SM, Chan CS, McManus J, Meysman FJ, Emerson D.
Bringing microbial diversity into focus: high‐resolution analysis of iron mats from the Lō‘ihi Seamount.
Environmental Microbiology. 19(2017):301-316.
N/A
2017
Scott JJ, Glazer BT, Emerson D.
Physiological and ecological implications of an iron-or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. nov.
The ISME Journal. 11(2017):2624-2636.
N/A
2017
Mori JF, Scott JJ, Hager KW, Moyer CL, Küsel K, Emerson D.
Biogeography of mutualistic fungi cultivated by leafcutter ants.
Molecular Ecology. 26(2017):6921-6937.
N/A
2017
Mueller UG, Ishak HD, Bruschi SM, Smith CC, Herman JJ, Solomon SE, Mikheyev AS, Rabeling C, Scott JJ, Cooper M, Rodrigues A.
In situ estimates of iron-oxidation and accretion rates for iron-oxidizing bacterial mats at Lō’ihi Seamount.
Deep Sea Research Part I: Oceanographic Research Papers. 126(2017):31-39.
N/A
2017
Emerson D, Scott JJ, Leavitt A, Fleming E, Moyer C.
Exploring the “SHARKCANO”: biogeochemical observations of the Kavachi Submarine Volcano (Solomon Islands).
Oceanography. 29(2016):160-169.
N/A
2016
Phillips BT, Dunbabin M, Henning B, Howell C, DeCiccio A, Flinders A, Kelley KA, Scott JJ, Albert S, Carey S, Tsadok R.
Microbial iron mats at the Mid-Atlantic Ridge and evidence that Zetaproteobacteria may be restricted to iron-oxidizing marine systems.
N/A
2015
Scott JJ, Breier JA, Luther III GW, Emerson D.
Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores.
Nature Communications. 6(2015):8285.
N/A
2015
Sanders JG, Beichman AC, Roman J, Scott JJ, Emerson D, McCarthy JJ, Girguis PR.
Microbial iron oxidation in the arctic tundra and its implications for biogeochemical cycling.
Applied & Environmental Microbiology. 81(2015):8066-8075.
N/A
2015
Emerson D, Scott JJ, Benes J, Bowden WB.
Unique honey bee (Apis mellifera) hive component-based communities as detected by a hybrid of phospholipid fatty-acid and fatty-acid methyl ester analyses.
N/A
2015
Grubbs KJ, Scott JJ, Budsberg KJ, Read H, Balser TC, Currie CR.
Convergent bacterial microbiotas in the fungal agricultural systems of insects.
N/A
2014
Aylward FO, Suen G, Biedermann PH, Adams AS, Scott JJ, Malfatti SA, del Rio TG, Tringe SG, Poulsen M, Raffa KF, Klepzig KD.
Using in situ voltammetry as a tool to identify and characterize habitats of iron-oxidizing bacteria: from fresh water wetlands to hydrothermal vent sites.
Environmental Science: Processes & Impacts 16(2014):2117-2126.
N/A
2014
MacDonald DJ, Findlay AJ, McAllister S, Barnett JM, Hredzak-Showalter P, Krepski ST, Cone SG, Scott JJ, Bennett SK, Chan CS, Emerson D, GW Luther III.
Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens.
Applied & Environmental Microbiology 79(2013):3770-3778.
N/A
2013
Aylward FO, Burnum-Johnson KE, Tringe SG, Teiling C, Tremmel DM, Moeller JA, Scott JJ, Barry KW, Piehowski PD, Nicora CD, Malfatti SA.
A phylogenetic analysis of the phylum Fibrobacteres.
Systematic & Applied Microbiology. 36(2013):376-382.
N/A
2013
Jewell KA, Scott JJ, Adams SM, Suen G.
Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens.
The ISME Journal. 6(2012):1688-701.
N/A
2012
Aylward FO, Burnum KE, Scott JJ, Suen G, Tringe SG, Adams SM, Barry KW, Nicora CD, Piehowski PD, Purvine SO, Starrett GJ.
The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle.
PLoS Genetics. 7(2011):e1002007.
N/A
2011
Suen G, Teiling C, Li L, Holt C, Abouheif E, Bornberg-Bauer E, Bouard P, Caldera EJ, Cash E, Cavanaugh A, Denas O, Elhaik E, Fav MJ, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Harkins TT, Helmkampf M, Hu H, Johnson BR, Kim J, Marsh SE, Moeller JA, Muoz-Torres MC, Murphy MC, Naughton MC, Nigam S, Overson R, Rajakumar R, Reese JT, Scott JJ Smith CR, Tao S, Tsutsui ND, Viljakainen L, Wissler L, Yandell MD, Zimmer F, Taylor J, Slater SC, Clifton SW, Warren WC, Elsik CG, Smith CD, Weinstock GM, Gerardo NM, Currie CR.
Microbial community structure of leaf-cutter ant fungus gardens and refuse dumps.
N/A
2010
Scott JJ, Budsberg KJ, Suen G, Wixon DL, Balser TC, Currie CR.
An insect herbivore microbiome with high plant biomass-degrading capacity.
PLoS Genetics. 6(2010): e1001129.
N/A
2010
Suen G, Scott JJ, Aylward FO, Adams SM, Tringe SG, Pinto-Tomás AA, Foster CE, Pauly M, Weimer PJ, Barry KW, Goodwin LA.
Monoculture of leafcutter ant gardens.
N/A
2010
Mueller UG, Scott JJ, Ishak HD, Cooper M, Rodrigues A.
Polymorphic microsatellite markers for the symbiotic fungi cultivated by leaf cutter ants (Attini, Formicidae).
Molecular Ecology Resources. 9(2009):1391-1394.
N/A
2009
Scott JJ, Kweskin MK, Cooper M, Mueller UG.
Mycangimycin, a polyene peroxide from a mutualist Streptomyces.
Organic Letters. 11(2009):633-636.
N/A
2009
Oh DC, Scott JJ, Currie CR, Clardy J.
Bionectriol A, a polyketide glycoside from the fungus Bionectria sp. associated with the fungus-growing ant, Apterostigma dentigerum.
Tetrahedron Letters. 50(2009):6834-6837.
N/A
2009
Freinkman E, Oh DC, Scott JJ, Currie CR, Clardy J.
Bacterial protection of beetle-fungus mutualism
Scott JJ, Oh DC, Yuceer MC, Klepzig KD, Clardy J, Currie CR.
N/A
2008
See accompanying Perspective: Bugs Bugs. Berenbaum MR, Eisner T. 2008. Science. 322:52-53.