Sampling the sediments in the deep seaBiogeochemistry examines the role of biological processes in mediating the chemical and geological dynamics of the Earth’s atmosphere, hydrosphere and lithosphere. It is an inherently interdisciplinary science and UGA Marine Sciences faculty are actively involved in areas of biogeochemical research including aquatic photochemistry, the exchange of trace gasses between the ocean and atmosphere, nutrient cycling, organic matter degradation, and the use of biomarkers. This work takes place in coastal environments such as salt marshes, extreme environments, the open ocean, and ocean sediments. The integrative nature of this work requires the application of tools from a wide range of disciplines such as microbiology, geochemistry, ecology, hydrology, mathematics and physics. 

Biogeochemistry Personnel

Biogeochemistry Labs

Publications under Biogeochemistry

Crespo-Medina M., Meile C.D., Hunter K.S., Diercks A.R., Asper V.L., Orphan V.J., Tavormina P.L., Nigro L.M., Battles J.J., Chanton J.P. et al..  2014.  The rise and fall of methanotrophy following a deepwater oil-well blowout. Nature Geoscience. 7:423-427.
Buck CS, Hammerschmidt CR, Bowman KL, Gill GA, Landing WM.  2015.  Flux of Total Mercury and Methylmercury to the Northern Gulf of Mexico from U.S. Estuaries. Environmental Science & Technology. 49(24):13992-13999.
Stubbins A.  2016.  A carbon for every nitrogen. Proceedings of the National Academy of Sciences. 113(39):10736-10738.
Alonso-Saez L., Waller A.S, Mende D.R, Bakker K., Farnelid H., Yager P.L, Lovejoy C., Tremblay J.-E., Potvin M., Heinrich F. et al..  2012.  Role for urea in nitrification by polar marine Archaea. Proceedings of the National Academy of Sciences. 109(44):17989-17994.
Delmont TO, Hammar KM, Ducklow HW, Yager PL, Post AF.  2014.  Phaeocystis antarctica blooms strongly influence bacterial community structures in the Amundsen Sea polynya. Frontiers in Microbiology. 5
Jaffe R., Ding Y., Niggemann J., Vahatalo A.V, Stubbins A., Spencer R.GM, Campbell J., Dittmar T..  2013.  Global Charcoal Mobilization from Soils via Dissolution and Riverine Transport to the Oceans. Science. 340(6130):345-347.
Stubbins A, Hood E, Raymond PA, Aiken GR, Sleighter RL, Hernes PJ, Butman D, Hatcher PG, Striegl RG, Schuster P et al..  2012.  Anthropogenic aerosols as a source of ancient dissolved organic matter in glaciers. Nature Geoscience. 5(3):198-201.
Bittar TB, Berger SA, Birsa LM, Walters TL, Thompson ME, Spencer RGM, Mann EL, Stubbins A, Frischer ME, Brandes JA.  2016.  Seasonal dynamics of dissolved, particulate and microbial components of a tidal saltmarsh-dominated estuary under contrasting levels of freshwater discharge. Estuarine, Coastal and Shelf Science. 182:72-85.
Baer SE, Connelly TL, Sipler RE, Yager PL, Bronk DA.  2014.  Effect of temperature on rates of ammonium uptake and nitrification in the western coastal Arctic during winter, spring, and summer. Global Biogeochemical Cycles. :n/a-n/a.
Fellman JB, Hood E, Spencer RGM, Stubbins A, Raymond PA.  2014.  Watershed Glacier Coverage Influences Dissolved Organic Matter Biogeochemistry in Coastal Watersheds of Southeast Alaska. Ecosystems. 17(6):1014-1025.
Helms JR, Stubbins A, E. Perdue M, Green NW, Chen H, Mopper K.  2013.  Photochemical bleaching of oceanic dissolved organic matter and its effect on absorption spectral slope and fluorescence. Marine Chemistry. 155:81-91.
Yager P, Sherrell R, Stammerjohn S, Alderkamp A-C, Schofield O, Abrahamsen P, Arrigo K, Bertilsson S, Garay L, Guerrero R et al..  2012.  ASPIRE: The Amundsen Sea Polynya International Research Expedition. Oceanography. 25(3):40-53.
Yeung LY, Berelson WM, Young ED, Prokopenko MG, Rollins N, Coles VJ, Montoya JP, Carpenter EJ, Steinberg DK, Foster RA et al..  2012.  Impact of diatom-diazotroph associations on carbon export in the Amazon River plume. Geophysical Research Letters. 39(18):n/a-n/a.
Van Stan JT, Stubbins A, Bittar T, Reichard JS, Wright KA, Jenkins RB.  2014.  Tillandsia usneoides (L.) L. (Spanish moss) water storage and leachate characteristics from two maritime oak forest settings. Ecohydrology.
Spencer RGM, Guo W, Raymond PA, Dittmar T, Hood E, Fellman J, Stubbins A.  2014.  Source and biolability of ancient dissolved organic matter in glacier and lake ecosystems on the Tibetan Plateau. Geochimica et Cosmochimica Acta.
Chen H, Stubbins A, E. Perdue M, Green NW, Helms JR, Mopper K, Hatcher PG.  2014.  Ultrahigh resolution mass spectrometric differentiation of dissolved organic matter isolated by coupled reverse osmosis-electrodialysis from various major oceanic water masses. Marine Chemistry. 164:48-59.
Helms JR, Mao J, Stubbins A, Schmidt-Rohr K, Spencer RGM, Hernes PJ, Mopper K.  2014.  Loss of optical and molecular indicators of terrigenous dissolved organic matter during long-term photobleaching. Aquatic Sciences. 76(3):353-373.
Burd AB.  2013.  Modeling particle aggregation using size class and size spectrum approaches. Journal of Geophysical Research: Oceans. 118(7):3431-3443.
Kitidis V, Stubbins AP, Uher ünther, Goddard RCUpstill, Law CS, E. Woodward MS.  2006.  Variability of chromophoric organic matter in surface waters of the Atlantic Ocean. Deep Sea Research Part II: Topical Studies in Oceanography. 53(14-16):1666-1684.
Stubbins A, Uher ünther, Law CS, Mopper K, Robinson C, Upstill-Goddard RC.  2006.  Open-ocean carbon monoxide photoproduction. Deep Sea Research Part II: Topical Studies in Oceanography. 53(14-16):1695-1705.
Stubbins A, Uher ünther, Kitidis V, Law CS, Upstill-Goddard RC, E. Woodward MS.  2006.  The open-ocean source of atmospheric carbon monoxide. Deep Sea Research Part II: Topical Studies in Oceanography. 53(14-16):1685-1694.
Spencer RGM, Vermilyea A, Fellman J, Raymond P, Stubbins A, Scott D, Hood E.  2014.  Seasonal variability of organic matter composition in an Alaskan glacier outflow: insights into glacier carbon sources. Environmental Research Letters. 9(5):055005.
Spencer RGM, Hernes PJ, Aufdenkampe AK, Baker A, Gulliver P, Stubbins A, Aiken GR, Dyda RY, Butler KD, Mwamba VL et al..  2012.  An initial investigation into the organic matter biogeochemistry of the Congo River. Geochimica et Cosmochimica Acta. 84:614-627.
Stubbins A, Hubbard V, Uher G, Law CS, Upstill-Goddard RC, Aiken GR, Mopper K.  2008.  Relating Carbon Monoxide Photoproduction to Dissolved Organic Matter Functionality. Environmental Science & Technology. 42(9):3271-3276.
Green NW, E. Perdue M, Aiken GR, Butler KD, Chen H, Dittmar T, Niggemann J, Stubbins A.  2014.  An intercomparison of three methods for the large-scale isolation of oceanic dissolved organic matter. Marine Chemistry. 161:14-19.
Chong L.S., Berelson W.M., McManus J., Hammond D.E., Rollins N.E., Yager P.L..  2014.  Carbon and biogenic silica export influenced by the Amazon River Plume: Patterns of remineralization in deep-sea sediments. Deep Sea Research Part I: Oceanographic Research Papers. 85:124-137.
Stubbins A, Mann PJ, Powers L, Bittar TB, Dittmar T, McIntyre C, Eglinton TI, Zimov N, Spencer RGM.  2016.  Low photolability of yedoma permafrost dissolved organic carbon. Journal of Geophysical Research: Biogeosciences.
Tolar BB, King GM, Hollibaugh JT.  2013.  An Analysis of Thaumarchaeota Populations from the Northern Gulf of Mexico. Frontiers in Microbiology. 4
Stubbins A, Dittmar T.  2012.  Low volume quantification of dissolved organic carbon and dissolved nitrogen. Limnology and Oceanography: Methods. 10:347-352.
Stubbins A., Niggemann J., Dittmar T..  2012.  Photo-lability of deep ocean dissolved black carbon. Biogeosciences. 9(5):1661-1670.
Stubbins A., Law C.S, Uher G., Upstill-Goddard R.C.  2011.  Carbon monoxide apparent quantum yields and photoproduction in the Tyne estuary. Biogeosciences. 8(3):703-713.
Stubbins A, Spencer RGM, Chen H, Hatcher PG, Mopper K, Hernes PJ, Mwamba VL, Mangangu AM, Wabakanghanzi JN, Six J.  2010.  Illuminated darkness: Molecular signatures of Congo River dissolved organic matter and its photochemical alteration as revealed by ultrahigh precision mass spectrometry. Limnology and Oceanography. 55(4):1467-1477.
Spencer RGM, Hernes PJ, Ruf R, Baker A, Dyda RY, Stubbins A, Six J.  2010.  Temporal controls on dissolved organic matter and lignin biogeochemistry in a pristine tropical river, Democratic Republic of Congo. Journal of Geophysical Research. 115(G3)
Spencer RGM, Stubbins A, Hernes PJ, Baker A, Mopper K, Aufdenkampe AK, Dyda RY, Mwamba VL, Mangangu AM, Wabakanghanzi JN et al..  2009.  Photochemical degradation of dissolved organic matter and dissolved lignin phenols from the Congo River. Journal of Geophysical Research. 114(G3)
Burd AB, Jackson GA.  2009.  Particle Aggregation. Annual Review of Marine Science. 1(1):65-90.
Helms JR, Stubbins A, Ritchie JD, Minor EC, Kieber DJ, Mopper K.  2008.  Absorption spectral slopes and slope ratios as indicators of molecular weight, source, and photobleaching of chromophoric dissolved organic matter. Limnology and Oceanography. 53(3):955-969.
Stubbins A, Spencer RGM, Mann PJ, R. Holmes M, McClelland JW, Niggemann J, Dittmar T.  2015.  Utilizing colored dissolved organic matter to derive dissolved black carbon export by arctic rivers. Frontiers in Earth Science. 3
Chambers LR, Ingall ED, Saad EM, Longo AF, Takeuchi M, Tang Y, Benitez-Nelson C, Haley ST, Dyhrman ST, Brandes J et al..  2016.  Enhanced Dissolved Organic Matter Recovery from Saltwater Samples with Electrodialysis. Aquatic Geochemistry.
Dittmar T, de Rezende CEduardo, Manecki M, Niggemann J, Ovalle ARamon Coel, Stubbins A, Bernardes MCorrea.  2012.  Continuous flux of dissolved black carbon from a vanished tropical forest biome. Nature Geoscience. 5(9):618-622.
Stubbins A, Lapierre J-F, Berggren M, Prairie Y, Dittmar T, del Giorgio P.  2014.  What’s in an EEM? Molecular signatures associated with dissolved organic fluorescence in boreal Canada Environmental Science & Technology.
Buck CS, Landing WM, Resing JA, Lebon GT.  2006.  Aerosol iron and aluminum solubility in the northwest Pacific Ocean: Results from the 2002 IOC cruise. Geochemistry, Geophysics, Geosystems. 7(4):n/a-n/a.
Hawkes JA, Rossel PE, Stubbins A, Butterfield D, Connelly DP, Achterberg EP, Koschinsky A, Chavagnac érie, Hansen CT, Bach W et al..  2015.  Efficient removal of recalcitrant deep-ocean dissolved organic matter during hydrothermal circulation. Nature Geoscience.
Spencer RGM, Aiken GR, Dornblaser MM, Butler KD, R. Holmes M, Fiske G, Mann PJ, Stubbins A.  2013.  Chromophoric dissolved organic matter export from U.S. rivers. Geophysical Research Letters. 40(8):1575-1579.
Dornhoffer T, Waldbusser G, Meile C.  2012.  Burrow patchiness and oxygen fluxes in bioirrigated sediments. Journal of Experimental Marine Biology and Ecology. 412
Boetius A., Joye SB.  2009.  Thriving in Salt: Life in hypersaline habitats. Science. 324
Li L., Maher K., Navarre-Sitchler A., Druhan J., Meile C., others 20.  2016.  Expanding the Role of Reactive Transport Models in Earth Surface Processes. Earth-Science Reviews.
Seidel M, Dittmar T, Ward ND, Krusche AV, Richey JE, Yager PL, Medeiros PM.  2016.  Seasonal and spatial variability of dissolved organic matter composition in the lower Amazon River. Biogeochemistry. 131:281-302.
Buck CS, Landing WM, Resing J.  2013.  Pacific Ocean aerosols: Deposition and solubility of iron, aluminum, and other trace elements. Marine Chemistry. 157:117-130.
Fransson A, Chierici M, Yager PL, Smith WO.  2011.  Antarctic sea ice carbon dioxide system and controls. Journal of Geophysical Research. 116(C12)
Gallon C, Ranville MA, Conaway CH, Landing WM, Buck CS, Morton PL, A. Flegal R.  2011.  Asian Industrial Lead Inputs to the North Pacific Evidenced by Lead Concentrations and Isotopic Compositions in Surface Waters and Aerosols. Environmental Science & Technology. 45(23):9874-9882.
Kleindienst S, Seidel M, Ziervogel K, Grim S, Loftis K, Harrison S, Malkin SY, Perkins MJ, Field J, Sogin ML et al..  2015.  Chemical dispersants can suppress the activity of natural oil-degrading microorganisms. Proceedings of the National Academy of Sciences. 112:14900-14905.
Sherrell R.M., Lagerström M.E., Forsch K.O., Stammerjohn S.E., Yager P.L..  2015.  Dynamics of dissolved iron and other bioactive trace metals (Mn, Ni, Cu, Zn) in the Amundsen Sea Polynya, Antarctica. Elementa: Science of the Anthropocene. 3:000071.
Mu L., Stammerjohn S.E, Lowry K.E, Yager P.L.  2014.  Spatial variability of surface pCO2 and air-sea CO2 flux in the Amundsen Sea Polynya, Antarctica. Elementa: Science of the Anthropocene. 2:000036.
Ingall ED, Diaz JM, Longo AF, Oakes M, Finney L, Vogt S, Lai B, Yager PL, Twining BS, Brandes JA.  2013.  Role of biogenic silica in the removal of iron from the Antarctic seas. Nature Communications. 4
Buck CS, Paytan A.  2012.  Evaluation of commonly used filter substrates for the measurement of aerosol trace element solubility. Limnology and Oceanography: Methods. 10:790-806.
Barrett PM, Resing JA, Buck NJ, Buck CS, Landing WM, Measures CI.  2012.  The trace element composition of suspended particulate matter in the upper 1000m of the eastern North Atlantic Ocean: A16N. Marine Chemistry. 142-144:41-53.
Lowell RP, Houghton J, Farough A, Craft K, Larson B, Meile C.  2015.  Mathematical modeling of diffuse flow in seafloor hydrothermal systems: The potential extent of the subsurface biosphere at ocean ridges. Earth and Planetary Science Letters.
Dornhoffer T, Waldbusser G, Meile C.  2015.  A modeling study of lugworm irrigation behavior effects on sediment nitrogen cycling. Marine Ecology Progress Series. 534
Hoelker F, Vanni MJ, Kuiper JJ, Meile C, others 10.  2015.  Tube-dwelling invertebrates: tiny ecosystem engineers have large effects in lake ecosystems. Ecology Monographs.
Larson B, Houghton J, Lowell RP, Farough A, Meile C.  2015.  Subsurface conditions in hydrothermal vents inferred from diffuse flow composition, and models of reaction and transport. Earth and Planetary Science Letters.
Joye SB.  2015.  Deepwater Horizon, Five Years On. Science. 349(6248)
Kleindienst S, Grim S, Sogin M, Bracco ALisa, Crespo-Medina M, Joye SB.  2015.  Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume. The ISME Journal. doi:10.1038/ismej.2015.121
Helms JR, Mao J, Chen H, E. Perdue M, Green NW, Hatcher PG, Mopper K, Stubbins A.  2015.  Spectroscopic characterization of oceanic dissolved organic matter isolated by reverse osmosis coupled with electrodialysis. Marine Chemistry.
Medeiros P.M, Seidel M, Dittmar T, Whitman WB, Moran MA.  2015.  Drought-induced variability in dissolved organic matter composition in a marsh-dominated estuary. Geophysical Research Letters. 42:6446-6453.
Kujawinski EB, Moran M.A., Stubbins A, Fatland R.  2016.  The ocean microbiome: metabolic engine of the marine carbon cycle. Microbe Magazine. 11(6):262-267.
Joye SB, Samarkin VA, Schutte C., Bowles M.W., Madigan M.T., Cadieux SB, Pratt LM, Saxton M..  2016.  Biogeochemical and 16S rRNA sequences evidence supports a novel mode of anaerobic methanotrophy in permanently ice- covered Lake Fryxell, Antarctica. Limnology and Oceanography. 61(S1):S119–S130.
Fellman JB, Hood E, Raymond PA, Stubbins A, Spencer RGM.  2015.  Spatial Variation in the Origin of Dissolved Organic Carbon in Snow on the Juneau Icefield, Southeast Alaska. Environmental Science & Technology. 49(19):11492-11499.
Seidel M, Yager PL, Ward ND, Carpenter EJ, Gomes HR, Krusche AV, Richey JE, Dittmar T, Medeiros PM.  2015.  Molecular-level changes of dissolved organic matter along the Amazon River-to-ocean continuum. Marine Chemistry. 177:218-231.
Han Q, Zender CS, J. Moore K, Buck CS, Chen Y, Johansen A, Measures CI.  2012.  Global estimates of mineral dust aerosol iron and aluminum solubility that account for particle size using diffusion-controlled and surface-area-controlled approximations. Global Biogeochemical Cycles. 26(2):n/a-n/a.
Buck CS, Landing WM, Resing JA.  2010.  Particle size and aerosol iron solubility: A high-resolution analysis of Atlantic aerosols. Marine Chemistry. 120(1-4):14-24.
Doherty M, Yager PL, Moran MAnn, Coles VJ, Fortunato CS, Krusche AV, Medeiros PM, Payet JP, Richey JE, Satinsky BM et al..  2017.  Bacterial biogeography across the Amazon River-ocean continuum. Frontiers in Microbiology. 8:882. doi:10.3389/fmicb.2017.00882
Xavier M, Passow U, Migon C, Burd AB, Legendre L.  2017.  Transparent Exopolymer Particles: Effects on carbon cycling in the ocean. Progress in Oceanography.
Seidel M, Kleindienst S, Dittmar T, Joye SB, Medeiros PM.  2016.  Biodegradation of crude oil and dispersants in deep seawater from the Gulf of Mexico: Insights from ultra-high resolution mass spectrometry. Deep Sea Research Part II: Topical Studies in Oceanography. 129:108-118.
Ducklow HW, Wilson SE, Post AF, Stammerjohn SE, Erickson M, Lee SH, Lowry KE, Sherrell RM, Yager PL.  2015.  Particle flux on the continental shelf in the Amundsen Sea Polynya and Western Antarctic Peninsula. Elementa: Science of the Anthropocene. 3:000046.
Spencer RGM, Mann PJ, Dittmar T, Eglinton TI, McIntyre C, R. Holmes M, Zimov N, Stubbins A.  2015.  Detecting the signature of permafrost thaw in Arctic rivers. Geophysical Research Letters.
Medeiros PM, Seidel M, Ward ND, Carpenter EJ, Gomes HR, Niggemann J, Krusche AV, Richey JE, Yager PL, Dittmar T.  2015.  Fate of the Amazon River dissolved organic matter in the tropical Atlantic Ocean. Global Biogeochemical Cycles. 29:677-690.
Barrett PM, Resing JA, Buck NJ, Feely RA, Bullister JL, Buck CS, Landing WM.  2014.  Calcium carbonate dissolution in the upper 1000 m of the eastern North Atlantic. Global Biogeochemical Cycles. :n/a-n/a.
Medeiros PM, Seidel M, Gifford SM, Ballantyne F, Dittmar T, Whitman WB, Moran MAnn.  2017.  Microbially-mediated transformations of estuarine dissolved organic matter. Frontiers in Marine Science. 4:69. doi: 10.3389/fmars.2017.00069
Loick-Wilde N, Weber SC, Conroy BJ, Capone DG, Coles VJ, Medeiros PM, Steinberg DK, Montoya JP.  2016.  Nitrogen sources and net growth efficiency of zooplankton in three Amazon River plume food webs. Limnology and Oceanography. 61:460-481.
Kleindienst S, Seidel M, Ziervogel K, Grim S, Loftis K, Harrison S, Malkin SY, Perkins MJ, Field J, Sogin ML et al..  2016.  Reply to Prince et al.: Ability of chemical dispersants to reduce oil spill impacts remains unclear. Proceedings of the National Academy of Sciences. 113(11):E1422-E1423.
Siegel DA, Buesseler KO, Behrenfeld MJ, Benitez-Nelson CR, Boss E, Brzezinski MA, Burd A, Carlson CA, D'Asaro EA, Doney SC et al..  2016.  Prediction of the Export and Fate of Global Ocean Net Primary Production: The EXPORTS Science Plan. Frontiers in Marine Science. 3
Grand MM, Buck CS, Landing WM, Measures CI, Hatta M, Hiscock WT, Brown MT, Resing JA.  2014.  Quantifying the impact of atmospheric deposition on the biogeochemistry of Fe and Al in the upper ocean: A decade of collaboration with the US CLIVAR-CO2 Repeat Hydrography Program. Oceanography. 27(1):62-65.
Ranville MA, Cutter GA, Buck CS, Landing WM, Cutter LS, Resing JA, A. Flegal R.  2010.  Aeolian Contamination of Se and Ag in the North Pacific from Asian Fossil Fuel Combustion. Environmental Science & Technology. 44(5):1587-1593.
Ward ND, Bianchi TS, Medeiros PM, Seidel M, Richey JE, Keil RG, Sawakuchi HO.  2017.  Where carbon goes when water flows: Carbon cycling across the aquatic continuum. Frontiers in Marine Science (Review article). 4:7. doi:10.3389/fmars.2017.00007
Moran MAnn, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, Buchan A, Crump BC, Dorrestein PC, Dyhrman ST, Hess NJ et al..  2016.  Deciphering ocean carbon in a changing world. Proceedings of the National Academy of Sciences. 113(12):3143-3151.
Moran M.A, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, Buchan A, Crump BC, Dorrestein PC, Dyhrman ST, Hess NJ et al..  2016.  Deciphering ocean carbon in a changing world. Proceedings of the National Academy of Sciences. 113(12):3143-3151.
Morton PL, Landing WM, Hsu S-C, Milne A, Aguilar-Islas AM, Baker AR, Bowie AR, Buck CS, Gao Y, Gichuki S.  2013.  Methods for the sampling and analysis of marine aerosols: results from the 2008 GEOTRACES aerosol intercalibration experiment. Limnology and Oceanography: Methods. 11:62-78.
Cawley KM, Murray AE, Doran PT, Kenig F, Stubbins A, Chen H, Hatcher PG, McKnight DM.  2016.  Characterization of dissolved organic material in the interstitial brine of Lake Vida, Antarctica. Geochimica et Cosmochimica Acta.
Repeta DJ, Aluwihare L, Carlson C, Liu Z, Nelson C, Stubbins A.  2015.  Introduction to the special issue on the Biogeochemistry of Dissolved Organic Matter. Marine Chemistry. 177:203-204.
Wilson SE, Swalethorp R, Kjellerup S, Wolverton MA, Ducklow HW, Yager PL.  2015.  Meso- and macro-zooplankton community structure of the Amundsen Sea Polynya, Antarctica (Summer 2010–2011). Elementa: Science of the Anthropocene. 3:000033.
Medeiros PM, Seidel M, Ward ND, Carpenter EJ, Gomes HR, Niggemann J, Krusche AV, Richey JE, Yager PL, Dittmar T.  2015.  Fate of the Amazon River dissolved organic matter in the tropical Atlantic Ocean. Global Biogeochemical Cycles. 29(5):677-690.
Ward ND, Krusche AV, Sawakuchi HO, Brito DC, Cunha AC, é Moura MSousa, da Silva R, Yager PL, Keil RG, Richey JE.  2015.  The compositional evolution of dissolved and particulate organic matter along the lower Amazon River—Óbidos to the ocean. Marine Chemistry.
Rossel PE, Stubbins A, Hach PF, Dittmar T.  2015.  Bioavailability and molecular composition of dissolved organic matter from a diffuse hydrothermal system. Marine Chemistry.
Seidel M, Yager PL, Ward ND, Carpenter EJ, Gomes HR, Krusche AV, Richey JE, Dittmar T, Medeiros PM.  2015.  Molecular-level changes of dissolved organic matter along the Amazon River-to-ocean continuum. Marine Chemistry.
Logvinova CL, Frey KE, Mann PJ, Stubbins A, Spencer RGM.  2015.  Assessing the potential impacts of declining arctic sea ice cover on the photochemical degradation of dissolved organic matter in the Chukchi and Beaufort seas. Journal of Geophysical Research: Biogeosciences. :n/a-n/a.
Rushdi AI, Oros DR, Al-Mutlaq KF, He D, Medeiros PM, Simoneit BRT.  2016.  Lipid, sterol and saccharide sources and dynamics in surface soils during an annual cycle in a temperate climate region. Applied Geochemistry. 66:1-13.
Carini S.A., Orcutt B.N, Joye SB.  2003.  Interactions between nitrification and methane oxidation in estuarine sediments. Geomicrobiology. 20(4):355-374.
Craft C., Clough J., Ehman J., Guo H., Joye SB, Machmuller M., Park D., Pennings S..  2009.  Effects of accelerated sea level rise on ecosystem services provided by tidal marshes: A simulation of the Georgia Coast. Frontiers in Ecology and Environment. 7(2):73-78.
Orcutt B.N., Barco R.A., Joye SB, Edwards K.J..  2012.  Summary of carbon, nitrogen, and iron leaching characteristics and fluorescence properties of materials considered for IODP Expedition 336 subseafloor observatory assembly. Proceedings of the Integrated Ocean Drilling Program. 336:doi:10.2204/iodp.proc.336.108.2012.
Joye SB, Samarkin VA, MacDonald IR, Hinrichs K-U, Elvert M, Teske AP, Lloyd KG, Lever MA, Montoya JP, Meile CD et al..  2009.  Metabolic variability in seafloor brines revealed by carbon and sulphur dynamics. Nature Geoscience. 2:349–354.
Sansone F.J.,.T.Hollibaugh J, Vink S.M., Chambers R.M., Joye SB.  1994.  Diver-operated piston corer for nearshore use. Estuaries. 17:716-720.
Feller I.C., Lovelock C., McKee K., Berger U., Joye SB, Ball M..  2010.  Biocomplexity in Mangrove Ecosystems. Annual Review of Marine Science. 2:395-417.
Rivers AA, Sharma S., Tringe S., Martin J., Joye SB, Moran MA.  2013.  Transcriptional response of bathypelagic marine bacteria to the Deepwater Horizon Oil Spill. The ISME Journal. 10:doi:10.1038/ismej.2013.129.
Currin C.A., Joye SB, Paerl H.W..  1996.  Nitrogen fixation and denitrification in a transplanted Spartina marsh: Implications for nitrogen budgets. Estuarine Coastal and Shelf Science. 42:597-616.
Weston N.B., Joye SB.  2006.  Microbial and geochemical ramifications of salinity intrusion into tidal freshwater sediments. Journal of Geophysical Research: Biogeosciences. 111:G1:G01009,10.1029/2005JG00007.
Bowles M.W., Joye SB.  2010.  High rates of denitrification and nitrate consumption in cold seep sediments. The ISME Journal. 5:565-567.
Ziervogel K, Joye SB, Arnosti C.  2014.  Microbial enzymatic activity and secondary production in sediments affected by the sedimentation pulse following the Deepwater Horizon oil spill. Deep Sea Research. :
Fisher C.R., MacDonald I.R., Sassen R., Young C.M., Macko S.A., Hourdez S., Carney R.S., Joye SB, McMullin E..  2000.  Methane ice worms: Hesiocaeca methanicola colonizing fossil fuel reserves. Naturwissenschaften. 87(4):184-187.
Krüger M., Wolters H., Gehre M., Joye SB, Richnow H.H..  2008.  Tracing the slow growth of anaerobic methane oxidizing communities by 15N-labeling techniques. FEMS Microbiology Ecology. 63 (3):401-411.
Peterson C.H., Anderson S, Cherr G., Ambrose R., Anghera S., Bay S., Blum M., Condon R., Dean T.A., Graham M. et al..  2012.  A Tale of Two Spills. BioScience. 62:461-469.
Chanton J.P., Zhao T., Rosenheim B., Joye SB, Bosman S., Brunner C., Yeager K., Hollander D.  2014.  Radiocarbon Tracing of the Flux of Petrocarbon to the Sea Floor associated with the Deepwater Horizon Event. Environmental Science and Technology. 10:DOI:10.1012/es5046524.
Pallud C, Kausch M, Fendorf S, Meile C.  2009.  Spatial patterns and modeling of reductive ferrihydrite transformation observed in artificial soil aggregates. Environmental science & technology. 44:74–79.
Joye SB, Boetius A., Orcutt B.N., Montoya J.P., Schulz H.N., Erickson M., Lugo S.K..  2004.  The anaerobic oxidation of methane and sulfate reduction in sediments from Gulf of Mexico cold seeps. Chemical Geology. 205(3/4):219-238.
House C.H., Orphan V.O., Turk K.A., Thomas B., Pernthaler A., Vrentas J.M., Joye SB.  2009.  Extensive carbon isotopic heterogeneity among methane seep microbiota. Environmental Microbiology. 11(7):1632-1645.
Segarra K.E.A., Samarkin V., King E., Meile C., Joye SB.  2013.  Seasonal variations of methane fluxes from a tidal, freshwater sediment (Hammersmith Creek, GA). Biogeochemistry. 10:DOI10.1007/s10533-013-9840-6.
Measures CI, Landing WM, Brown MT, Buck CS.  2008.  A commercially available rosette system for trace metal-clean sampling. Limnology and Oceanography: Methods. 6
Ginn BR, Habteselassie MY, Meile C, Thompson A.  2014.  Effects of sample storage on microbial Fe-reduction in tropical rainforest soils. Soil Biology and Biochemistry. 68:44-51.
Weston N.B., Joye SB.  2005.  Temperature driven accumulation of labile dissolved organic carbon in marine sediments. Proceedings of the National Academy of Sciences (US). 102:17036-17040.
Wankel S.D., Joye SB, Samarkin V.A., Shah S., Friderich G., Melas-Kryiazi J., Girguis P.R..  2010.  New constraints on diffusive methane fluxes and rates of anaerobic methane oxidation in a Gulf of Mexico brine pool through the use of a deep sea in situ mass spectrometer. Deep Sea Research. 10:doi:10.1016/j.dsr2.2010.05.009.
Schutte C.A., Hunter K.S., McKay P., DiIorio D., Joye SB, Meile CD.  2013.  Patterns and controls on nutrient levels in a southeastern United States tidal river.. Oceanography. 26(3):132-139.
Mayer L.M., Keil R.G., Macko S.A., Joye SB, Ruttenberg K.C., Aller R.C.  1998.  The importance of suspended particulates in riverine delivery of bioavailable nitrogen to coastal zones. Global Biogeochemical Cycles. 12:573-580.
Bailey J.V., Joye SB, Kalanetra K.M., Flood B.E., Corsetti F.A..  2007.  Evidence for giant sulfur bacteria in Neoproterozoic phosphorites. Nature. 445:198-201.
Joye SB, MacDonald I.R., Leifer I., Asper V..  2011.  Magnitude and oxidation potential of hydrocarbon gases released from the BP blowout. Nature Geoscience. 4:160-164.
Avrahamov N.G., Antler Y, Yechieli Y., Gavrieli I., Saxton M., Joye SB, Sivan O.  2014.  Anaerobic oxidation of methane by sulfate in hypersaline groundwater in the Dead Sea aquifer. Geobiology. 10:1111.
Porubsky W.P., Velasquez L., Joye SB.  2008.  Nutrient replete benthic microalgae as a source of labile dissolved organic carbon to coastal waters. Estuaries and Coasts. 31:860-876.
Palomo L., Meile C.D., Joye SB.  2012.  Drought impacts on biogeochemistry and microbial processes in salt marsh sediments: a flow-through reactor approach. Biogeochemistry. :doi10.1001/s10533-012-9734-z..
Joye SB, Leifer I, MacDonald IR, Chanton JP, Meile CD, Teske AP, Kostka JE, Chistoserdova L, Coffin R, Hollander D et al..  2011.  Comment on “A Persistent Oxygen Anomaly Reveals the Fate of Spilled Methane in the Deep Gulf of Mexico”. Science. 332:1033.
Hollibaugh J.T., Carini S., Jellison R., Joye SB, LeCleir G., Meile C., Vasquez L., Gürleyük H., Wallschläger D..  2005.  Distribution of arsenic species in an alkaline, hypersaline, meromictic lake in response to the seasonal stratification. Geochimica et Cosmochimica Acta. 69(8):1925-1937.
Bailey J.V., Orphan V.J., Joye SB, Corsetti F.A..  2009.  Chemotrophic microbial mats and their potential for preservation in the rock record. Astrobiology. 9:843-859.
Adams MM, Hoarfrost A.L., Bose A., Joye SB, Girguis P.R..  2013.  Anaerobic short-chain alkanes in hydrothermal sediments: influences on sulfur cycling and microbial diversity. Frontiers in Microbiology. 10:doi:10.3389/fmicb.2013.00110.
Joye SB, MacDonald I.R..  2010.  Offshore oceanic impacts from the BP oil spill.. Nature Geoscience. 38:446.
Treude T, Levin L., Smith C., Joye SB.  2014.  Marine ecosystems associated with near surface methane gas hydrate. Frozen Heat: A global outlook on methane gas hydrates. In: Beaudoin, Y.C., W. Waite, and R. Boswell (Eds.), UPEP Global Outlook on Methane Hydrates, Volume 1. UNEP
Ward B.B., Martino D., Diaz C., Joye SB.  2000.  Analysis of ammonia-oxidizing bacteria from hypersaline Mono Lake, California on the basis of 16S rRNA sequences. Applied and Environmental Microbiology. 66(7):2873-2881.
Edmonds J.W, Weston N.B., Joye SB, Moran M.A..  2008.  Variation in prokaryotic community composition as a function of resource availability in tidal creek sediments. Applied and Environmental Microbiology. 74:1836-1844.
Wade T.L., Sweet S.T., Sericano J.L., Guinasso N.L., Diercks A.R., Highsmith R.C., Asper V.L., Joung D., Shiller A.M., Lorehnz S.E. et al..  2011.  Analyses of water samples from the Deepwater Horizon Oil Spill: Documentation of the Sub-Surface Plume. Journal of Geophysical Research: Oceans, Geophysical Monograph. 195:77-82.
Kostka JE, Teske A.P., Joye SB, Head I.M..  2014.  The metabolic pathways and environmental controls of hydrocarbon biodegradation in marine ecosystems. Frontiers in Microbiology. 10:doi:10.3389/fmicb.2014.00471.
Orcutt B.N., Boetius A., Lugo S.K., MacDonald I.R., Samarkin V., Joye SB.  2004.  Life at the edge of methane ice: methane and sulfur cycling in Gulf of Mexico gas hydrates. Chemical Geology. 205(3/4):219-251.
Joye SB, Samarkin V.A, Orcutt B.N., MacDonald I.R., Hinrichs K.-U., Elvert M., Teske A.P., Lloyd K.G., Lever M.A., Montoya J.P. et al..  2009.  Surprising metabolic variability in seafloor brines revealed by carbon and sulfur cycling. Nature Geoscience. 2:349-354.
Teixeira C., Magalhaes C., Joye SB, Bordalo A.A..  2012.  The role of salinity in shaping dissolved inorganic nitrogen and N2O fluxes at the estuarine sediment-water interface. Marine Pollution Bulletin. 10:
Joye SB, Mozzotta M.L., Hollibaugh J.T..  1996.  Community metabolism in intertidal microbial mats: the importance of iron and manganese reduction. Estuarine Coastal and Shelf Science. 43:747-766.
Lin J.L., Joye SB, Schafer H., Scholten C.M., McDonald I., Murrell J.C..  2005.  Analysis of methane monooxygenase genes in Mono Lake suggests that increased methane oxidation activity may correlate with a change in methanotroph community structure. Applied and Environmental Microbiology. 71:6458-6462.
Joye SB, Bowles M.W., Samarkin V.A., Hunter K.S., Niemann H..  2010.  Biogeochemical signatures and microbial activity of different cold seep habitats along the Gulf of Mexico lower slope. Deep Sea Research. 10:doi:10.1016/j.dsr2.2010.06.001.
Baas P, Hester M.W., Joye SB.  2013.  Benthic primary production and nitrogen cycling in Spartina alterniflora marshes impacted by acute dieback. Biogeochemistry. :DOI10.1007/s10533-013-9897-2.
Lee R., Joye SB, Valiala I..  1997.  Release of N2 and N2O from salt marsh sediments subject to different land-derived N loads. The Biological Bulletin. 193:292-293.
Howard E.C., Henricksen J.R., Buchan A., Reisch C.R., Burgmann B., Welsh R., Ye W., Gonzalez J.M., Joye SB, Keine R.P. et al..  2006.  Bacterial taxa that limit sulfur flux from the ocean. Science. 314:649-652.
Wilson A., Moore W.S., Joye SB, Anderson J., Schutte C..  2010.  Storm-driven groundwater flow in a salt marsh. Water Resources Research. 10:doi:10.1029/2010WR009496.
Peters BK, Samarkin V.A., Madigan M., Schutte C., Joye SB.  2014.  Stable isotope analysis of NO2-, NO3-, and N2O in hypersaline ponds and soils of the McMurdo Dry Valleys, Antarctica. Geochimica et Cosmochimca Acta. 135:87-101.
Sun M.Y., Cai W.J., Joye SB, Ding H., Dai J., Hollibaugh J.T..  2002.  Degradation of algal lipids in microcosm sediments with different mixing regimes. Organic Geochemistry. 33:445-159.
Wankel S., Adams M., Johnstone D., Joye SB, Girguis P.R..  2012.  Anaerobic methane oxidation in metalliferous hydrothermal sediments: influence on carbon flux and decoupling from sulfate reduction. Environmental Microbiology. 14:2726-2740.
Porubsky WP, Joye SB, Moore WS, Tuncay K, Meile C.  2011.  Field measurements and modeling of groundwater flow and biogeochemistry at Moses Hammock, a backbarrier island on the Georgia coast. Biogeochemistry. 104:69–90.
Paerl H.W., Bebout B.M., Joye SB.  1993.  Microscale characterization of dissolved organic matter production and uptake in marine microbial mat communities. Limnology & Oceanography. 38:1150-1161.
Carini SA, LeCleir G., Bano N., Joye SB.  2005.  Activity, abundance and diversity of aerobic methanotrophs in an alkaline, hypersaline lake (Mono Lake, CA, USA). Environmental Microbiology. 7(8):1127-1937.
Edmonds J.E., Weston N.B, Joye SB, Mou X., Moran M.A..  2009.  Microbial Community Response to Seawater Amendment in Low-Salinity Tidal Sediments. Microbial Ecology. 58:558-568.
Shah S.R., Joye SB, Brandes J., McNichol A.P..  2013.  Carbon isotopic evidence for microbial control of carbon supply to Orca Basin, Gulf of Mexico. . Biogeosciences. 10:3175-3183.
Schutte C., Hunter K.S., McKay P., Di Iorio D., Joye S.B, Meile C.  2013.  Patterns and controls of nutrient concentrations in a southeastern United States tidal creek. Oceanography. 26(3):132-139.
Roberts H.H., Feng D., Joye SB.  2010.  Cold seep carbonates of the middle and lower continental slope, northern Gulf of Mexico. Deep Sea Research. 10:doi:10.1016/j.dsr2.2010.09.003.
Yang T, Nigro L., Gutierrez T., Joye SB, Highsmith R.C., Teske AP.  2014.  Bacterial community signatures of the Deepwater Horizon Oil spill reflect inherent metabolic potential and rapid physiological adaptability. Deep Sea Research. 10:10.1016/j.dsr2.2014.01.014.
Sassen R., Joye SB, Sweet S.T., DeFrietas D.A., Milkov A.V., MacDonald I.R..  1999.  Thermogenic gas hydrates and hydrocarbon gases in complex chemosynthetic communities, Gulf of Mexico, Continental Slope. Organic Geochemistry. 30:485-497.
Roberts H.H., Fisher C., Bernard B., Brooks J., Bright M., Carney R., Cordes E., Hourdez S., Hunt J., Joye SB et al..  2007.  ALVIN Explores the Deep Northern Gulf of Mexico Slope. EOS Transactions of the American Geophysical Union. 88:341-342.
Bowles M.W., Samarkin V.A., Joye SB.  2001.  Improved measurement of microbial activity in deep-sea sediments at in situ pressure and methane concentration. Limnology and Oceanography: Methods. 9:499-506.
Joye SB, Montoya J.P., Murawski S.A., zgökmen T.M.Ö, Wade T.L., Montuoro R., Roberts B.J., Hollander D.J., Jeffrey W.H., Chanton J.P..  2014.  A Rapid Response Study of the Hercules Gas Well Blowout. EOS Transactions of the American Geophysical Union. 95(38):341-342.
Meile C, Tuncay K.  2006.  Scale dependence of reaction rates in porous media. Advances in water resources. 29:62–71.
Osburn CL, Stedmon CA, Spencer RGM, Stubbins A.  2013.  Emerging Issues Workshop Report: Linking optical and chemical properties of dissolved organic matter in natural waters. Limnology and Oceanography Bulletin. (22):78-82.
Arvidson R.L., Morse J.W., Joye SB.  2004.  The Sedimentary Biogeochemistry of Chemosynthetic Cold Seep Communities, Gulf of Mexico, USA. Marine Chemistry. 87:97-119.
Weston N.B., Hollibaugh J.T., Joye SB.  2009.  Population growth away from the coastal zone: Thirty years of land use change and nutrient export from the Altamaha River, GA.. Science of the Total Environment. 407:3347-3356.
Joye SB.  2012.  A piece of the methane puzzle. Nature. 491:538-539.
Chen H, Stubbins A, Hatcher PG.  2011.  A mini-electrodialysis system for desalting small volume samples for Fourier transform ion cyclotron resonance mass spectrometry. Limnol. Oceanogr.: Methods. (9):582-592.
Joye SB, Smith S.V., Hollibaugh J.T., Paerl H.W..  1996.  Estimating denitrification in estuarine sediments: comparisons of stoichiometric and acetylene based methods. Biogeochemistry. 33:197-766.
Kalanetr K.M., Joye SB, Sunseri N.R., Nelson D.C..  2005.  Novel, large, vacuolate, nitrate-accumulating sulfur bacteria discovered in the Gulf of Mexico reproduce by reductive division in three dimensions. Environmental Microbiology. 7(9):1451-1460.
Samarkin V.A., Madigan M.T., Bowles M.W., Casciotti K.L, Priscu J., McKay C., Joye SB.  2010.  Abiotic brine-rock reactions produce nitrous oxide in a cold, hypersaline. Nature Geoscience. 3:341-344.
Dekas AE, Chadwick G., Connon S., Bowles M., Joye SB, Orphan V.J..  2013.  Investigating methane seep nitrogen fixation at Mound 12, Costa Rica: Spatial distribution of diazotrophy and significance of the ANME archaea. Environmental Microbiology. 10:DOI10.1007/s10533-013-9897-2.
Connell T., Joye SB, Miller L.G., Oremland R.S..  1997.  Bacterial oxidation of methyl bromide in Mono Lake, California. Environmental Science and Technology. 31:1489-1495.
Moore W.S., Blanton J., Joye SB.  2006.  Estimates of flushing times, submarine groundwater discharge, and nutrient fluxes to Okatee Estuary, South Carolina. Journal of Geophysical Research. 111:No.C9,C09006,10.1029/2005JC003041.
.R.Diercks A, Highsmith R.C., Asper V.L., Joung D., Guo L., Zhou Z., Shiller A.M., Joye SB, Teske A.P., Lohrenz S.E..  2010.  Characterization of subsurface polycyclic aromatic hydrocarbons at the Deepwater Horizon site. Geophysical Research Letters. 37:doi:10.1029/2010GL045046.
Joye SB, Teske A.P., Kostka JE.  2014.  Microbial dynamics following the Macondo Oil Well Blowout across Gulf of Mexico environments. BioScience. 64(9):766-777.
Moore W.S., Krest J., Taylor G., Roggenstein E., Joye SB, Lee R.Y..  2002.  Thermal evidence of water exchange through a coastal aquifer: Implications for nutrient fluxes. Geophysical Research Letters. 10:1029/2002GL014923.
Lee R.Y., Porubsky W.P., Feller K.L.IC, McKee K.L., Joye SB.  2008.  Porewater biogeochemistry and soil metabolism in dwarf red mangrove habitats (Twin Cays, Belize). Biogeochemistry. 87:181-198.
Mendelssohn I.A., Anderson G., Baltz D., Caffey R., Carman K., Fleegar J., Joye SB, Maltby E., Overton E., Rozas L..  2012.  Oil impacts to coastal wetland systems: Implications for the Mississippi River Delta Plain Ecosystem after the Deepwater Horizon Oil Discharge. BioScience. 62:562-574.
Crespo-Medina M, Bowles M.W., Samarkin V.A., Hunter K.S., Joye SB.  2015.  Microbial diversity and activity in seafloor brine lake sediments (Alaminos Canyon 601, Gulf of Mexico). Geobiology. in press
Meile C, Porubsky WP, Walker RL, Payne K.  2010.  Natural attenuation of nitrogen loading from septic effluents: Spatial and environmental controls. Water research. 44:1399–1408.
Paerl H.W., Joye SB, Fitzpatrick M.W..  1993.  An evaluation of nutrient limitation of carbon and nitrogen fixation in marine microbial mats.. Marine Ecology Progress Series. 105:23-36.
Magalhães C.M., Joye SB, Moreira R.M., Wiebe W.J., Bordalo A.A..  2005.  Salinity and inorganic nitrogen effects on nitrification and denitrification rates in intertidal sediments and rocky biofilms: Douro River estuary, Portugal. Water Research. 39(9):1783-1794.
Segarra K.E.A., Comerford C., Slaughter J., Joye SB.  2013.  Impact of electron acceptor availability on the anaerobic oxidation of methane in coastal freshwater and marine sediments. Geochimica et Cosmochimica Acta. 115:15-30.
Loftis KM, Meile C.  2014.  Isotopes and elemental ratios in multi-parameter mixing models. Limnology and Oceanography: Methods. 12:694–702.
Nercession O., Kalyuzhnaya M.G., Joye SB, Lidstrom M.E., Chistoserdova L..  2005.  Analysis of fae and fhcD genes in Mono Lake, California. Applied and Environmental Microbiology. 71:8949-895.
Porubsky W.P, Joye SB, Moore W.S., Tuncay K., Meile C..  2010.  Hammock groundwater flow and biogeochemistry: Field measurements, laboratory assays and predictive modeling. Biogeochemistry. 10:DOI:10.1007/s10533-010-9484-8.
Porubsky W.P., Weston N.B., Moore W.S., Ruppel C.D., Joye SB.  2014.  Groundwater as a potential source of nutrients, organics and trace gases to the Okatee River estuary (South Carolina, USA). Geochimica et Cosmochimica Acta . 131:81-97.
Joye SB, Connell T.M., Miller L.G., Oremland R.S..  1999.  Oxidation of ammonia and methane in an alkaline, saline lake. Limnology & Oceanography. 44(1):178-188.
Kniemer O., Musat F., Sievert S.M., Knittel K., Wilkes H., Blumenberg M., Michaelis W., Classen A., Joye SB, Widdel F..  2007.  Anaerobic oxidation of propane and ethane by novel marine sulphate-reducing bacteria. Nature. 449:898-902.
Joye SB, Leifer I., MacDonald I.R, Chanton J.P, Meile C.D, Teske A.P, Kostka E., Chistoserdova L., Coffin R., Hollander D. et al..  2011.  Technical Comment on “A Persistent Oxygen Anomaly Reveals the Fate of Spilled Methane in the Deep Gulf of Mexico". Science. :27May2011,1033.DOI:10.1126/science.1203307.
Wilson AM, Evans T., Anderson J., Hughes A.H., Moore W.S., Schutte C.A., Joye SB.  2014.  Groundwater controls ecological zonation of macrophytes in salt marshes. Ecology. 10:doi/abs/10.1890/13-2183.1.
Lasher C., Dyszynski G., Everett K., Ye W., Sheldon W., Joye SB, Moran M.A., Whitman W.B..  2009.  The diverse bacterial community in intertidal, anaerobic sediments at Sapelo Island, Georgia. Microbial Ecology. 58:244-261.
Bowles M.W., Nigro L.M., Teske A.P., Joye SB.  2012.  Denitrification and the environmental factors influencing nitrate removal in Guaymas Basin hydrothermally-altered sediments. Frontiers of Microbiology. 10:doi:10.3389/fmicb.2012.00377.
Joye SB, Hollibaugh J.T..  1995.  Sulfide inhibition of nitrification influences nitrogen regeneration in sediments. Science. 270:623-625.
Orcutt B.N., Samarkin V., Boetius A., Elvert M., Joye SB.  2005.  Molecular biogeochemistry of sulfate reduction, methanogenesis and the anaerobic oxidation of methane at Gulf of Mexico methane seeps. Geochimica et Cosmochimica Acta. 69:4267-4281.
Tavormina P.L., Ussler W., Joye SB, Giovannoni S., Orphan V.J..  2010.  Intergenic spacer length of particulate methane monooxygenases reveals distributions of microbial methane oxidizers in the mesopelagic ocean. The ISME Journal. :doi:10.1038/ismej.2009.155.
Feng D, Roberts H.H., Joye SB, Heydari E.  2013.  Formation of low-magnesium calcite at cold seeps in an aragonite sea. Terra Nova . 10:doi:10.111/ter.12081.
Smith V., Joye SB, Howarth R.W..  2006.  Eutrophication in aquatic ecosystems. Eutrophication in aquatic ecosystems. 51(2):351-355.
Bowles M.W., Samarkin V.A., Bowles K.L.M., Joye SB.  2010.  Weak coupling between sulfate reduction and the anaerobic oxidation of methane in methane-rich seafloor sediments in ex situ incubations. Geochimica et Cosmochimica Acta. 75:500-519.
Crespo-Medina M, Meile C.D., Hunter K.S., Orphan V.J., Tavormina P., Nigro L.M., Battles J.J., Diercks A.R., Asper V., Chanton J.P. et al..  2014.  The rise and fall of methanotrophy following a deepwater oil-well blowout. Nature Geoscience. 7:423-427.
Orcutt B.N., Samarkin V., Boetius A., Joye SB.  2008.  On the relationship between methane production and oxidation by anaerobic methanotrophic communities from cold seeps of the Gulf of Mexico. Environmental Microbiology. 10(5):1108-1117.
Teixeira C., Magalhaes C., Joye SB, Bordalo A.A..  2012.  Rates and environmental controls of anaerobic ammonium oxidation in estuarine sediments. Aquatic Microbial Ecology. :doi:10.3354/ame01548.
Teixiera C, Magalhaes C., Joye SB, Bordalo AA.  2015.  The contribution of anaerobic ammonium oxidation to nitrogen loss in temperate eutrophic estuaries. Estuarine Coastal and Shelf Science. 143:41-47.
King EL, Tuncay K, Ortoleva P, Meile C.  2009.  In silico Geobacter sulfurreducens metabolism and its representation in reactive transport models. Applied and environmental microbiology. 75:83–92.
Joye SB, MacDonald I.R., Montoya J.P., Peccini M..  2005.  Geophysical and geochemical signatures of Gulf of Mexico seafloor brines. Biogeosciences. 2:637-671.
Porubsky W.P., Weston N.B., Joye SB.  2009.  Interactions between benthic primary production, denitrification and dissimilatory nitrate reduction to ammonium in intertidal sediments. Estuarine Coastal and Shelf Science. 83:392-402.
Peterson R.N., Viso R.F., MacDonald I.R., Joye SB.  2013.  On the utility of radium isotopes as tracers of seafloor hydrocarbon discharge. Marine Chemistry. 10:
Tishchenko V, Meile C, Scherer MM, Pasakarnis TS, Thompson A.  2015.  Fe2+ catalyzed iron atom exchange and re-crystallization in a tropical soil. Geochimica et Cosmochimica Acta. 148:191-202.
Niemann H., Elvert M., Damm E., Gutt J., Orcutt B., Suck I., Wendt G., Wunderlich J., Joye SB, Finster K. et al..  2005.  Methane emission and consumption at a North Sea pockmark (Tommeliten area). Biogeosciences. 2:335-351.
Orcutt B.N., Joye SB, Kleindienst S., Knittel K., Ramette A., Reitz A., Samarkin V.A., Truede T., Boetius A..  2010.  Impact of natural oil and higher hydrocarbons on microbial diversity, distribution and activity in Gulf of Mexico cold seep sediments. Deep Sea Research. 10:doi:10.1016/j.dsr2.2010.05.014.
Bose A., Rogers D.R., Adams M.M., Joye SB, Girguis P.R..  2013.  Rates of sulfate reduction and alkane oxidation in cold seep sediments and their contribution to the dissolved inorganic carbon pool. . Frontiers in Microbiology . 10:10.3389/fmicb.2013.00386.
Sassen R., MacDonald I.R., Guinasso N.L., Joye SB, Requejo A.G., Sweet S.T., Alcala-Herrera J., DeFrietas D.A., Schink D.R..  1998.  Bacterial methane oxidation in sea-floor gas hydrate: Significance to life in extreme environments. Geology. 26:851-854.
Bailey J.V., Joye SB, Kalanetra K.M., Flood B.E., Corsetti F.A..  2007.  Undressing and redressing Ediacaran embryos. Nature. 446:E10-E11.
Dohm J.M, Miyamoto H., Ori G.G., Fairen A.G., Davila A.F., Komatsu G., Mahaney W.C., Williams P., Joye SB, others 27.  2011.  Prime candidate environments for life detection on Mars. Geological Society of America, Frontiers Volume, “Analogs for Planetary Exploration. Special Paper:486.
Feng D, Birgel D., Roberts H.H., Peckman J., Joye SB, Fisher C.R., Sassen R., Liu X-L., Hinrichs K.U., Chen D.  2014.  Time integrated variation of sources of fluids and seepage dynamics archived in authigenic carbonates from Gulf of Mexico Gas Hydrate Seafloor Observatory. Chemical Geology. 385:129-139.
Dittmar T., Stubbins A..  2014.  Dissolved Organic Matter in Aquatic Systems. Treatise on Geochemistry.
Mopper K, Kieber DJ, Stubbins A.  2015.  Marine Photochemistry of Organic Matter: Processes and Impacts. Biogeochemistry of Dissolved Organic Matter.
Dittmar T., Stubbins A.  2014.  Dissolved Organic Matter in Aquatic Systems. Treatise on geochemistry, ed. H. D. Holland, and K. K. Turekian, 25-156. Oxford: Elsevier. :125-156.
Spencer RGM, Gaillardet J, Stubbins A.  2013.  Geochemistry of the Congo River, Estuary and Plume. Biogeochemical Dynamics at Major River-Coastal Interfaces: Linkages with Global Change. :554-583.
Meile C., Jones C..  2016.  A mathematical perspective on microbial processes in Earth’s biogeochemical cycles. Mathematical paradigms of climate science. 15:3-14.