Sarah C. Bagby

Sarah C. Bagby

Environmental microbiologist at Case Western Reserve University

Publications

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

Published in bioRxiv preprint, 2026

Comprehensive profiling of the mobile genetic elements in a natural soil system. MGEs, bioinformatics, microdiversity.

Recommended citation: 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

Published in bioRxiv preprint, 2026

Integrative analysis of community structure and function in long-term observation of permafrost peatland soils. Metagenomics, metabolism, community assembly, network analysis.

Recommended citation: 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.

TaRTLEt: Transcriptionally-Active Riboswitch Tracer Leveraging Edge deTection

Published in PeerJ, 2025

A novel bioinformatic approach for predicting riboswitches that act by modulating transcription termination. Riboswitches, transcriptomics.

Recommended citation: 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

Published in Nat Commun, 2025

A trait-based approach to genome-informed microbial ecosystem modeling. Genome-to-ecosystem scaling, ecosys, DEBmicroTrait.

Recommended citation: 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

Published in Sci Rep, 2025

Browning reactions sequester nitrogen in peat bogs, shaping carbon cycling. Carbon flux, abiotic processes.

Recommended citation: 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

Published in Nat Microbiol, 2024

Molecular ecology of a climate-critical permafrost peatland. Metabolomics, assembly modeling.

Recommended citation: 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?

Published in Trends Microbiol, 2024

A new conceptual framework for microbial dormancy across environments. Opinion, acclimation, dormancy.

Recommended citation: 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

Published in PLoS Comput Biol, 2022

Modeling constraints on the production of public goods in the context of co-limitation. Theory, evolutionary ecology, metabolic interactions.

Recommended citation: 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

Published in Nat Commun, 2021

Global survey of diversity-generating retroelements in public genomes and metagenomes. Diversification, mobile genetic elements, bioinformatics.

Recommended citation: 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

Published in Frontiers in Microbiology, 2017

Microbial mats from a shallow hydrocarbon seep field are among the most diverse communities yet characterized, with multiple avenues of primary production. Stable isotope probing, metagenomics, lipid analysis.

Recommended citation: 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

Published in Proceedings of the National Academy of Sciences, 2016

A novel chemical fingerprint identifies sediment samples contaminated with oil from Deepwater Horizon, and the loss rates of 125 hydrocarbon analytes in these samples show that contamination level strongly influences chemical structure-based trends in biodegradation kinetics. Hydrocarbon geochemistry, statistics, more statistics.

Recommended citation: 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

Published in Ecosphere, 2015

Ecologists need to change the way we do our work, to make open, reproducible research the norm. Opinion.

Recommended citation: 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

Published in The ISME Journal, 2015

Minimal marine phototrophs use oxygen reduction as a safety valve when CO2 limitation makes ordinary light levels stressful. Growth curves, flow cytometry, transcriptomics.

Recommended citation: 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

Published in Nature Communications, 2015

A genomic cassette with more diversity-generating potential than the vertebrate immune system is active in archaea and archaeal viruses, not just in bacteria and bacteriophage. Metagenomics, single-cell genomics, evolution.

Recommended citation: 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

Published in Proceedings of the National Academy of Sciences, 2014

Spill response teams found, and then lost, a plume of oil that had been trapped ~1 km deep in the Gulf of Mexico. We found its 3200-km2 contamination footprint on the seafloor. Hydrocarbon geochemistry, statistics, GIS.

Recommended citation: 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

Published in Nature Structural & Molecular Biology, 2011

Entropy drives the high-affinity receptor interaction underlying asthma and allergy. X-ray crystallography, surface plasmon resonance, thermodynamics.

Recommended citation: 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

Published in Nature Geoscience, 2010

A newly discovered cluster of extinct asphalt volcanoes on the Santa Barbara Basin seafloor may explain historical methane anomalies. Submarine exploration, hydrocarbon geochemistry, paleoclimate.

Recommended citation: 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

Published in RNA, 2009

A ribozyme selected for rapid catalysis shows changes to a network of structural interactions that contribute to metal-binding. In vitro evolution, statistics, structural biochemistry.

Recommended citation: 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

Published in Science, 2009

An RNA enzyme evolved from random sequence relies on familiar Mg2+-dependent chemistry to catalyze phosphodiester bond formation. X-ray crystallography, enzymology, structural biochemistry.

Recommended citation: 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

Published in Journal of Molecular Biology, 2009

A previously unrecognized component of bacterial microcompartments shows potential for dynamic gating. Bioinformatics, x-ray crystallography, expression analysis.

Recommended citation: 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

Published in Current Biology, 2008

Auxiliary metabolic genes in cyanophage exploit a non-host-derived mechanism of pigment biosynthesis. Enzymology, metagenomics, qRT-PCR.

Recommended citation: 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.