CV

Education

• PhD in Biology, Massachusetts Institute of Technology, 2009
  • HHMI Pre-doctoral Fellow
• BA(Hons) in Physiological sciences, Oxford University, 2002
  • Marshall Scholar
• BS in Biological chemistry, BA in Chemistry, BA in Philosophy, University of Chicago, 2000

Research

• 2009-2016: Postdoctoral research
  • UCSB Department of Earth Science, Marine Science Institute
  • Advisor: David L. Valentine
• 2002-2009: Graduate research
  • Massachusetts Institute of Technology Department of Biology
  • Advisors: Sallie W. Chisholm, David P. Bartel
• 2001-2002: Undergraduate research
  • Oxford University Department of Biochemistry
  • Advisor: James McDonnell
• 1998-2000: Undergraduate research
  • University of Chicago Department of Biochemistry & Molecular Biology
  • Advisor: Phoebe A. Rice

Field experience

• Lead scientist for ROV Jason lowerings J2-735 and J2-736, SEEPS2013 cruise (R/V Atlantis Leg 26-06, September-October 2013)
• Science crew, UNOLS Chief Scientist Training Cruise (R/V New Horizon Leg NH1212, November 2012)
• Lead scientist for ROV Jason lowerings J2-599 and J2-600, SEEPS2011 cruise (R/V Atlantis Leg 18-11, September 2011)
• Junior scientist for DSV Alvin dive 4542 (depth 3470 m), SEEPS2009 cruise (R/V Atlantis Leg 15-53, September 2009)
• Science crew, Hawaii Ocean Time-Series cruise 186 (R/V Kilo Moana Leg KM0627, October 2006)

Publications

Mobile Genetic Elements that Shape Microbial Diversity and Functions in Thawing Permafrost Soils

J Guo, S Aroney, G Dominguez-Huerta, DA Smith, D Vik, C Owusu-Ansah, AA Pratama, S Solonenko, F Tian, C Howard-Varona, Z Zhong, A Fofana, G Smith, SB Hodgkins, D Cronin, EMERGE Field Teams 2010--2019, EMERGE Coordinators, BJ Woodcroft, GW Tyson, VI Rich, MB Sullivan, S Roux, and SC Bagby. (2026). "Mobile Genetic Elements that Shape Microbial Diversity and Functions in Thawing Permafrost Soils." In review.

Stable States in an Unstable Landscape: Microbial Resistance at the Front Line of Climate Change

DR Cronin, H Holland-Moritz, DA Smith, STN Aroney, S Hodgkins, M Borton, Y-F Li, K Healy, IsoGenie Field and Analytic Teams 2010-2017, EMERGE Institute Coordinators, MM Tfaily, PM Crill, C McCalley, K Wrighton, RK Varner, GW Tyson, B Woodcroft, SC Bagby, J Ernakovich, and VI Rich. (2026). "Stable States in an Unstable Landscape: Microbial Resistance at the Front Line of Climate Change." In review.

Isolation and Characterization of TayeBlu, a Novel Bacteriophage of Azotobacter vinelandii

TM Akanbi, M Labat, T Sun, DA Smith, and SC Bagby. (2025). "Isolation and Characterization of TayeBlu, a Novel Bacteriophage of Azotobacter vinelandii." Microbiology Spectrum 14:e01286-25.

TaRTLEt: Transcriptionally-Active Riboswitch Tracer Leveraging Edge deTection

S Kshatriya and SC Bagby. (2025). "TaRTLEt: Transcriptionally-Active Riboswitch Tracer Leveraging Edge deTection." PeerJ 13:e19418.

A Framework for Integrating Genomics, Microbial Traits, and Ecosystem Biogeochemistry

Z Li, WJ Riley, GL Marschmann, U Karaoz, IA Shirley, Q Wu, NJ Bouskill, K-Y Chang , PM Crill, RF Grant, E King, SR Saleska, MB Sullivan , J Tang, RK Varner, BJ Woodcroft, KC Wrighton, EMERGE Biology Integration Institute Coordinators, and EL Brodie. (2025). "A Framework for Integrating Genomics, Microbial Traits, and Ecosystem Biogeochemistry." Nat Commun 16:2186.

A Climatically Significant Abiotic Mechanism Driving Carbon Loss and Nitrogen Limitation in Peat Bogs

AB Cory, RM Wilson, ME Holmes, WJ Riley, Y-F Li, MM Tfaily, SC Bagby, Isogenie Field Team, EMERGE Project Coordinators, PM Crill, JG Ernakovich, VI Rich, and JP Chanton. (2025). "A Climatically Significant Abiotic Mechanism Driving Carbon Loss and Nitrogen Limitation in Peat Bogs." Sci Rep 15:2560.

Microbiome-Metabolite Linkages Drive Greenhouse Gas Dynamics Over a Permafrost Thaw Gradient

V Freire-Zapata, H Holland-Moritz, DR Cronin, S Aroney, DA Smith, RM Wilson, JG Ernakovich, BJ Woodcroft, SC Bagby, EMERGE 2012 Field Team, EMERGE Coordinators, VI Rich, MB Sullivan, JC Stegen, and MM Tfaily. (2024). "Microbiome-Metabolite Linkages Drive Greenhouse Gas Dynamics Over a Permafrost Thaw Gradient." Nat Microbiol 9:2892.

What Is Microbial Dormancy?

MD McDonald, C Owusu-Ansah, JB Ellenbogen, ZD Malone, MP Ricketts, SE Frolking, JG Ernakovich, M Ibba, SC Bagby, and JL Weissman. (2024). "What Is Microbial Dormancy?." Trends Microbiol vol(num):page.

How Public Can Public Goods Be? Environmental Context Shapes the Evolutionary Ecology of Partially Private Goods

BA Lerch and DA Smith and T Koffel and SC Bagby and KC Abbott. (2022). "How Public Can Public Goods Be? Environmental Context Shapes the Evolutionary Ecology of Partially Private Goods." PLoS Comput Biol 18(11):e1010666.

Ecology and Molecular Targets of Hypermutation in the Global Microbiome

S Roux, BG Paul, SC Bagby, S Nayfach, MA Allen, G Attwood, R Cavicchioli, L Chistoserdova, RJ Gruninger, SJ Hallam, ME Hernandez, M Hess, W-T Liu, TA McAllister, MA OMalley, X Peng, VI Rich, SR Saleska, and EA Eloe-Fadrosh. (2021). "Ecology and Molecular Targets of Hypermutation in the Global Microbiome." Nat Commun 12(1):3076.

Methane-oxidizing bacteria shunt carbon to microbial mats at a marine hydrocarbon seep

BG Paul, H Ding, SC Bagby, MY Kellermann, MC Redmond, GL Andersen, and DL Valentine. (2017). "Methane-oxidizing bacteria shunt carbon to microbial mats at a marine hydrocarbon seep." Front Microbiol 8:186. DOI: 10.3389/fmicb.2017.00186.

Persistence and biodegradation of oil at the ocean floor following Deepwater Horizon

SC Bagby, CM Reddy, C Aeppli, GB Fisher, and DL Valentine. (2016). "Persistence and biodegradation of oil at the ocean floor following Deepwater Horizon." PNAS 114(1):E9. DOI: 10.1073/pnas.1610110114.

The Tao of open science for ecology

SE Hampton, SS Anderson, SC Bagby, C Gries, X Han, EM Hart, MB Jones, WC Lenhardt, A MacDonald, WK Michener, J Mudge, A Pourmokhtarian, M Schildhauer, KH Woo, and N Zimmerman (2014). "The Tao of open science for ecology." Ecosphere 6:art120. DOI: 10.1890/ ES14-00402.1.

Response of Prochlorococcus to varying CO₂:O₂ ratios

SC Bagby and SW Chisholm. (2015). "Response of Prochlorococcus to varying CO₂:O₂ ratios." ISME J 9(10):2232.

Targeted diversity generation by intraterrestrial archaea and archaeal viruses

BG Paul, SC Bagby, E Czornyj, D Arambula, S Handa, A Sczyrba, P Ghosh, JF Miller, and DL Valentine (2015). "Targeted diversity generation by intraterrestrial archaea and archaeal viruses." Nature Comm 6:6585. DOI: 10.1038/ncomms7585.

Fallout plume of submerged oil from Deepwater Horizon

DL Valentine, GB Fisher, SC Bagby, RK Nelson, CM Reddy, SP Sylva, and MA Woo (2014). "A fallout plume of submerged oil from Deepwater Horizon." PNAS 111:15906.

Conformational changes in IgE contribute to its uniquely slow dissociation rate from receptor FcεRI

MD Holdom, AM Davies, JE Nettleship, SC Bagby, B Dhaliwal, E Girardi, J Hunt, HJ Gould, AJ Beavil, JM McDonnell, RJ Owens, and BJ Sutton (2011). "Conformational changes in IgE contribute to its uniquely slow dissociation rate from receptor FcεRI." Nature Struct Mol Biol 18:571.

Asphalt volcanoes as a potential source of methane to late Pleistocene coastal waters

DL Valentine, CM Reddy, C Farwell, TM Hill, O Pizarro, DR Yoerger, R Camilli, RK Nelson, E Peacock, SC Bagby, BA Clark, CN Roman, and M Soloway. (2010). "Asphalt volcanoes as a potential source of methane to late Pleistocene coastal waters." Nature Geosci 3:345.

A class I ligase ribozyme with reduced Mg²⁺ dependence: selection, sequence analysis, and tertiary-structure mapping

SC Bagby,¹ NH Bergman,¹ DM Shechner, C Yen, and DP Bartel (2009). "A class I ligase ribozyme with reduced Mg²⁺ dependence: selection, sequence analysis, and tertiary-structure mapping." RNA 15:2129. (¹joint first authors)

Crystal structure of the catalytic core of an RNA-polymerase ribozyme

DM Shechner, SC Bagby, R Grant, Y Koldobskaya, J Piccirilli, and DP Bartel (2009). "Crystal structure of the catalytic core of an RNA-polymerase ribozyme." Science 326:1271.

Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport

M Klein, P Zwart, SC Bagby, F Cai, SW Chisholm, S Heinhorst, G Cannon, and CA Kerfeld (2009). "Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport." J Mol Biol 392(2):319.

Efficient phage-mediated pigment biosynthesis in oceanic cyanobacteria

TD Dammeyer, SC Bagby, MB Sullivan, SW Chisholm, and N Frankenbert-Dinkel. (2008). "Efficient phage-mediated pigment biosynthesis in oceanic cyanobacteria." Curr Biol 18(6):442.