A marine bacteriumMicrobes play many vital roles in the oceans. They are crucial in the transformation and cycling of elements such as carbon, nitrogen, and sulfur; they are fundamental components of marine food webs, and although small, their activities affect global biogeochemical cycles and help regulate the global climate. Using cutting-edge technologies, faculty in the department study the diversity, structure, and function of microbial communities; how microbes affect the transformations and cycling of elements such as nitrogen and sulfur; and the ecological interactions between viruses, bacteria, and phytoplankton. 

Microbial Ecology Personnel

Microbial Ecology Labs

Publications under Microbial Ecology

Ghiglione J.-F., Galand P.E, Pommier T., Pedros-Alio C., Maas E.W, Bakker K., Bertilson S., Kirchman D.L, Lovejoy C., Yager P.L et al..  2012.  Pole-to-pole biogeography of surface and deep marine bacterial communities. Proceedings of the National Academy of Sciences. 109(43):17633-17638.
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.
Hollibaugh JT, Gifford SM, Moran MA, Ross MJ, Sharma S, Tolar BB.  2014.  Seasonal variation in the metratranscriptomes of a Thaumarchaeota population from SE USA coastal waters. The ISME Journal. 8(3):685-698.
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
Luo H, Tolar BB, Swan BK, Zhang CL, Stepanauskas R, Moran MA, Hollibaugh JT.  2014.  Single-cell genomics shedding light on marine Thaumarchaeota diversification. The ISME Journal. 8(3):732-736.
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.
Vila-Costa M, Rinta-Kanto JM, Poretsky RS, Sun S, Kiene RP, Moran MA.  2014.  Microbial controls on DMSP degradation and DMS formation in the Sargasso Sea. Biogeochemistry. 120(1-3):295-305.
King GM, Smith CB, Tolar B, Hollibaugh JT.  2013.  Analysis of Composition and Structure of Coastal to Mesopelagic Bacterioplankton Communities in the Northern Gulf of Mexico. Frontiers in Microbiology. 3
Tolar BB, King GM, Hollibaugh JT.  2013.  An Analysis of Thaumarchaeota Populations from the Northern Gulf of Mexico. Frontiers in Microbiology. 4
Smith CB, Tolar BB, Hollibaugh JT, King GM.  2013.  Alkane hydroxylase gene (alkB) phylotype composition and diversity in northern Gulf of Mexico bacterioplankton. Frontiers in Microbiology. 4
Hopkinson BM, Barbeau KA.  2012.  Iron transporters in marine prokaryotic genomes and metagenomes. Environmental Microbiology. 14(1):114-128.
Boetius A., Joye SB.  2009.  Thriving in Salt: Life in hypersaline habitats. Science. 324
Moran M.A.  2015.  The Global Ocean Microbiome. Science. 350
Luo H, Moran MA.  2014.  Evolutionary ecology of the marine roseobacter clade. Microbiology and Molecular Biology Reviews. 78
Alivisatos A.P, Blaser M.J, Brodie E.L, Chun M., Dangl J.L, Donohue T.J, Dorrestein P.C, Gilbert J.A, Green J.L, Jansson J.K et al..  2015.  A unified initiative to harness Earth's microbiomes. Science. 350(6260):507-508.
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
Amin S.A, Hmelo L.R, van Tol H.M, Durham B.P, Carlson L.T, Heal K.R, Morales R.L, Berthiaume C.T, Parker M.S, Djunaedi B. et al..  2015.  Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria. Nature. 522(7554):98-101.
Kleindienst S, Paul JH, Joye SB.  2015.  Using dispersants after oil spills: impacts on the composition and activity of microbial communities. Nature Reviews Microbiology.
Williams C.M., Dupont A.M., Loevenich J., Post A.F., Dinasquet J., Yager P.L..  2016.  Pelagic microbial heterotrophy in response to a highly productive bloom of Phaeocystis antarctica in the Amundsen Sea Polynya, Antarctica. Elementa: Science of the Anthropocene. 4:000102.
Alderkamp A-C, van Dijken GL, Lowry KE, Connelly TL, m Mö, Sherrell RM, Haskins C, Rogalsky E, Schofield O, Stammerjohn SE et al..  2015.  Fe availability drives phytoplankton photosynthesis rates during spring bloom in the Amundsen Sea Polynya, Antarctica. Elementa: Science of the Anthropocene. 3:000043.
Richert I, Dinasquet J, Logares R, Riemann L, Yager PL, Wendeberg A, Bertilsson S.  2015.  The influence of light and water mass on bacterial population dynamics in the Amundsen Sea Polynya. Elementa: Science of the Anthropocene. 3:000044.
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.
Burns AS, Bullock HA, Smith C, Huang Q, Whitman WB, Moran M.A.  2016.  Small RNAs expressed during dimethylsulfoniopropionate degradation by a model marine bacterium. Environmental Microbiology Reports.
Satinsky BM, Fortunato CS, Doherty M, Smith CB, Sharma S, Ward ND, Krusche AV, Yager PL, Richey JE, Moran MA et al..  2015.  Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011. Microbiome. 3:39.
Luo H, Moran MA.  2015.  How do divergent ecological strategies emerge among marine bacterioplankton lineages? Trends in Microbiology. 23(9):577-584.
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.
Varaljay VA, Robidart J, Preston CM, Gifford S, Durham BP, Burns AS, Ryan JP, Marin R, Kiene RP, Zehr J et al..  2015.  Single-taxon field measurements of bacterial gene regulation controlling DMSP fate. ISME Journal. 9
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. :http://dx.doi.org/10.1016/j.dsr2.2014.04.003.
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.
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.
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.
Cuvelier ML, Allen AE, Monier A, McCrow JP, Messie M, Tringe SG, Woyke T, Welsh RM, Ishoey T, Lee J-H et al..  2010.  Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 107:14679-14684.
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..
Beier S, Rivers A, Moran MA, Obernosterer I..  2015.  Phenotypic plasticity in heterotrophic marine microbial communities in continuous cultures. ISME Journal. 9
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, 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.
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:http://dx.doi.org/10.1016/j.marpolbul.2012.11.004.
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.
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.
Newton RJ, Griffin LE, Bowles KM, Meile C, Gifford S, Givens CE, Howard EC, King E, Oakley CA, Reisch CR et al..  2010.  Genome characteristics of a generalist marine bacterial lineage. The ISME journal. 4:784–798.
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.
Durham BP, Sharma S, Luo H, Smith CB, Amin S, Bender SJ, Dearth SP, Van Mooy BAS, Campagna S, Kukawinski EB et al..  2015.  Cryptic carbon and sulfur cycling between surface ocean plankton. Proceedings of the National Academy of Sciences. 112
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.
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.
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.
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.
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.
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.
Moran MA, Belas R, Schell MA, Gonzalez JM, Sun F, Sun S, Binder BJ, Edmonds J, Ye W, Orcutt B et al..  2007.  Ecological genomics of marine roseobacters. Applied and environmental microbiology. 73:4559–4569.
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
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.
Joye SB, Hollibaugh J.T..  1995.  Sulfide inhibition of nitrification influences nitrogen regeneration in sediments. Science. 270:623-625.
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.
Chan L-K, Newton RJ, Sharma S, Smith CB, Rayapati P, Limardo AJ, Meile C, Moran MA.  2012.  Transcriptional changes underlying elemental stoichiometry shifts in a marine heterotrophic bacterium. Frontiers in Microbiology. 3
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.
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.
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:http://dx.doi.org/10.1016/j.marchem.2013.02.008.
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.
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.
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.