Publications by the Joye Research Group


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Recent Publications


Vertical marine snow distribution in the stratified, hypersaline, and anoxic Orca Basin (Gulf of Mexico). A Diercks, K Ziervogel, R Sibert, JP Montoya, SB Joye and V Asper. Elementa: Science of the Anthropocene, in press.

Generation and untilization of volatile fatty acids and alchohols in hydrothermally altered sediments in the Guaymas Basin, Gulf of California. G-C Zhuang, A Montgomery, VA Samarkin, M Song, J Liu, F Schubotz, APTeske, K-U Hinrichs, and SB Joye. Geophysical Research Letters, in press.

Significance of acetate as microbial carbon and energy source in the water column of Gulf of Mexico: implications for marine carbon cycling. G-C Zhuang, TD Peña-Montenegro, A Montgomery, and SB Joye. Global Biogeochemical Cycles, in press.

Biogeochemical Dynamics of Coastal Tidal Flats. CA Schutte, S Ahmerkamp, CS Wu, M Seidel, D de Beer, PLM Cook, SB Joye. Coastal Wetlands 407-440.


Long-term impact of the Deepwater Horizon oil well blowout on methane oxidation dynamics in the northern Gulf of Mexico. MK Rogener, A Bracco, KS Hunter, MA Saxton, SB Joye. Elementa; Science of the Anthropocene 6 (1).

Heterotrophic metabolism of C1 and C2 low molecular weight compounds in northern Gulf of Mexico sediments: controlling factors and implications for organic carbon degradation. GC Zhuang, A Montgomery, SB Joye. Geochimica et Cosmochimica Acta.

BP Gulf Science Data Reveals Ineffectual Subsea Dispersant Injection for the Macondo Blowout. CB Paris, I Berenshtein, ML Trillo, R Faillettaz, MJ Olascoaga, ZM Aman, M. Schlüter, S.B. Joye. Frontiers in Marine Science 5, 389.

Microbial metabolism of methanol and methylamine in the Gulf of Mexico: insight into marine carbon and nitrogen cycling. GC Zhuang, TD Peña‐Montenegro, A Montgomery, KS Hunter, SB Joye. Environmental Microbiology.

Effects of pressure, methane concentration, and temperature on the production of methane in marine sediments. GC Zhuang, A. Montgomery, R. Sibert, M.K. Rogener, V.A. Samarkin, S.B. Joye. Limnology and Oceanography, DOI:10.1002.

The impact of the Deepwater Horizon blowout on historic shipwreck-associated sediment microbiomes in the northern Gulf of Mexico. LJ Hamdan, JL Salerno, A Reed, SB Joye, M Damour. Scientific reports 8 (1), 9057.

Ocean deoxygenation: Time for action. SA Earle, DJ Wright, S Joye, D Laffoley, J Baxter, C Safina, P Elkus. Science 359 (6383), 1475-1476.

SnapShot: Microbial Hydrocarbon Bioremediation. SB Joye, S Kleindienst, TD Peña-Montenegro. Cell 172 (6), 1336-1336.

Relative importance of methylotrophic methanogenesis in sediments of the Western Mediterranean Sea. GC Zhuang, VB Heuer, CS Lazar, T Goldhammer, J Wendt, VA Samarkin, M Elvert, AP Teske, SB Joye, K Hinrichs. Geochimica et Cosmochimica Acta 244: 171-186.

Deep oxygen penetration drives nitrification in intertidal beach sands. CA Schutte, AM Wilson, T Evans, WS Moore, SB Joye. Limnology and Oceanography 63 (S1), S193-S208. DOI: 10.1002.

Carbon mineralization in Laptev and East Siberian sea shelf and slope sediment. V Brüchert, L Bröder, JE Sawicka, T Tesi, SB Joye, X Sun, IP Semiletov, VA Samarkin. Biogeosciences 15 (2), 471.

A unifying theory for top-heavy ecosystem structure in the ocean. CB Woodson, JR Schramski, SB Joye. Nature communications 9 (1), 23.


Hydrocarbon Seep Ecosystems. Joye, S.B., and S. Kleindienst. In: J. Kallmeyer, Ed., Life in Extreme Environments, DeGruyter Publishing, 311 pages. DOI:10.1515.

Hydrocarbon composition and concentrations in the Gulf of Mexico sediments in the 3 years following the Macondo well blowout. L Babcock-Adams, JP Chanton, SB Joye, PM Medeiros. Environmental pollution 229, 329-338.

Characterization of a cold-active bacterium isolated from the South Pole “Ice Tunnel”. MT Madigan, ML Kempher, KS Bender, P Sullivan, WM Sattley, AC Dohnalkova, SB Joye. Extremophiles 21 (5), 891-901.

Genomic methods and microbiological technologies for profiling novel and extreme environments for the Extreme Microbiome Project (XMP). S Tighe, E Afshinnekoo, TM Rock, K McGrath, N Alexander, A McIntyre, S Ahsanuddin, D Bezdan, SJ Green, SB Joye, SS Johnson, DA Baldwin, N Bivens, N Ajami, JR Carmical, IC Herriott, R Colwell, M Donia, J Foox, N Greenfield, T Hunter, J Hoffman, J Hyman, E Jorgensen, D Krawczyk, J Lee, S Levy, N Garcia-Reyero, M Settles, K Thomas, F Gómez, L Schriml, N Kyrpides, E Zaikova, J Penterman, CE Mason. Journal of Biomolecular techniques: JBT 28 (1), 31.

Selective quantification of DOSS in marine sediment and sediment-trap solids by LC-QTOF-MS. MJ Perkins, SB Joye, JA Field. Analytical and bioanalytical chemistry 409 (4), 971-978.

Global aerobic degradation of hydrocarbons in aquatic systems. S Kleindienst, SB Joye. Aerobic Utilization of Hydrocarbons, Oils and Lipids, 1-18.

Agents of change and temporal nutrient dynamics in the Altamaha River Watershed. KK Takagi, KS Hunter, WJ Cai, SB Joye. Ecosphere 8 (1).


Biogeochemical and 16S rRNA gene sequence evidence supports a novel mode of anaerobic methanotrophy in permanently ice‐covered Lake Fryxell, Antarctica. MA Saxton, VA Samarkin, CA Schutte, MW Bowles, MT Madigan, SB Cadieux, LM Pratt, SB Joye. Limnology and Oceanography 61 (S1).

Environmental impacts of the deep-water oil and gas industry: a review to guide management strategies. EE Cordes, DOB Jones, TA Schlacher, DJ Amon, AF Bernardino, S Brooke, R Carney, DM DeLeo, KM Dunlop, EG Escobar-Briones, AR Gates, LGénio, JGobin, L Henry, S Herrera, S Hoyt, SB Joye, S Kark, NC Mestre, A Metaxas, S Pfeifer, K Sink, AK Sweetman, U Witte. Frontiers in Environmental Science 4, 58.

Distinct bacterial communities in surficial seafloor sediments following the 2010 Deepwater Horizon blowout. T Yang, K Speare, L McKay, BJ MacGregor, SB Joye, A Teske. Frontiers in microbiology 7, 1384.

Responses of microbial communities to hydrocarbon exposures. SB Joye, S Kleindienst, JA Gilbert, KM Handley, P Weisenhorn, WA Overholt, JE Kostka. Oceanography 29 (3), 136-149.

Microbial diversity and activity in seafloor brine lake sediments (Alaminos Canyon block 601, Gulf of Mexico). M Crespo‐Medina, MW Bowles, VA Samarkin, KS Hunter, SB Joye. Geobiology 14 (5), 483-498.

Differential effects of crude oil on denitrification and anammox, and the impact on N2O production. H Ribeiro, AP Mucha, I Azevedo, P Salgado, C Teixeira, CMR Almeida, SB Joye, C Magalhães. Environmental pollution 216, 391-399.

Multiple evidence for methylotrophic methanogenesis as the dominant methanogenic pathway in hypersaline sediments from the Orca Basin, Gulf of Mexico. GC Zhuang, FJ Elling, LM Nigro, V Samarkin, SB Joye, A Teske, K Hinrichs. Geochimica et Cosmochimica Acta 187, 1-20.

How Clonal Is Clonal? Genome Plasticity across Multicellular Segments of a “Candidatus Marithrix sp.” Filament from Sulfidic, Briny Seafloor Sediments in the Gulf of Mexico. V Salman-Carvalho, E Fadeev, SB Joye, A Teske. Frontiers in microbiology 7, 1173.

Patterns and variability in geochemical signatures and microbial activity within and between diverse cold seep habitats along the lower continental slope, Northern Gulf of Mexico. M Bowles, KS Hunter, V Samarkin, SB Joye. Deep Sea Research Part II: Topical Studies in Oceanography 129, 31-40.

Pulsed blooms and persistent oil-degrading bacterial populations in the water column during and after the Deepwater Horizon blowout. T Yang, LM Nigro, T Gutierrez, SB Joye, R Highsmith, A Teske. Deep Sea Research Part II: Topical Studies in Oceanography 129, 282-291.

Response of anaerobic ammonium oxidation to inorganic nitrogen fluctuations in temperate estuarine sediments. C Teixeira, C Magalhães, SB Joye, AA Bordalo. Journal of Geophysical Research: Biogeosciences 121 (7), 1829-1839.

The Gulf of Mexico ecosystem, six years after the Macondo oil well blowout. SB Joye, A Bracco, TM Özgökmen, JP Chanton, M Grosell, IR MacDonald, EE Cordes, JP Montoya, U Passow. Deep Sea Research Part II: Topical Studies in Oceanography 129, 4-19.

The Gulf of Mexico ecosystem-Before, during and after the Deepwater Horizon oil well blowout. SB Joye. Deep Sea Research Part II: Topical Studies in Oceanography 129, 1-1.

Hercules 265 rapid response: Immediate ecosystem impacts of a natural gas blowout incident. SC Weber, L Peterson, JJ Battles, BJ Roberts, RN Peterson, DJ Hollander, JP Chanton, SB Joye, JP Montoya. Deep Sea Research Part II: Topical Studies in Oceanography 129, 66-76.

Enhanced particle fluxes and heterotrophic bacterial activities in Gulf of Mexico bottom waters following storm-induced sediment resuspension. K Ziervogel, C Dike, V Asper, J Montoya, J Battles, U Passow, A Diercks, M Esch, SB Joye, C Dewald, C Arnosti. Deep Sea Research Part II: Topical Studies in Oceanography 129, 77-88.

Biodegradation of crude oil and dispersants in deep seawater from the Gulf of Mexico: Insights from ultra-high resolution mass spectrometry. M Seidel, S Kleindienst, T Dittmar, SB Joye, PM Medeiros. Deep Sea Research Part II: Topical Studies in Oceanography 129, 108-118.

Microbial enzymatic activity and secondary production in sediments affected by the sedimentation pulse following the Deepwater Horizon oil spill. K Ziervogel, SB Joye, C Arnosti. Deep Sea Research Part II: Topical Studies in Oceanography 129, 241-248.

Methanotrophy controls groundwater methane export from a barrier island. CA Schutte, AM Wilson, T Evans, WS Moore, SB Joye. Geochimica et Cosmochimica Acta 179, 242-256.

Reply to Prince et al.: Ability of chemical dispersants to reduce oil spill impacts remains unclear. S Kleindienst, M Seidel, K Ziervogel, S Grim, K Loftis, S Harrison, SY Malkin, MJ Perkins, J Field, ML Sogin, T Dittmar, U Passow, P Medeiros, SB Joye. Proceedings of the National Academy of Sciences 113 (11), E1422-E1423.

Linking Heterotrophic Microbial Activities with Particle Characteristics in Waters of the Mississippi River Delta in the Aftermath of Hurricane Isaac. K Ziervogel, C Osburn, A Brym, J Battles, S Joye, N D'souza, J Montoya, U Passow, C Arnosti. Frontiers in Marine Science 3, 8.

Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume. S Kleindienst, S Grim, M Sogin, A Bracco, M Crespo-Medina, SB Joye. The ISME journal 10 (2), 400.

Protocols for Radiotracer Estimation of Methane Oxidation Rates at In Situ Methane Concentrations in Marine Sediments. R Sibert, VA Samarkin, SB Joye. Hydrocarbon and Lipid Microbiology Protocols, 277-303.

Protocols for Radiotracer Estimation of Primary Hydrocarbon Oxidation in Oxygenated Seawater. R Sibert, S Harrison, SB Joye. Hydrocarbon and Lipid Microbiology Protocols, 263-276.