C-MORE Publications

Newly Published


558. Shilova, I., J. Robidart, E. DeLong, J. Zehr, 2016. Genetic diversity affects the daily transcriptional oscillations of marine microbial populations. PLoS ONE 11(1): e0146706

560. Levine, N.M., Toole, D.A., Neeley, A., Bates, N.R., Doney, S.C., Dacey, J.W.H. 2016. Revising upper-ocean sulfur dynamics near Bermuda: new lessons from 3 years of concentration and rate measurements. Environmental Chemistry 3:302-313

561. Kavanaugh, M.T., Boersma, K., Close, S., Ganio, L., Hooven., L., Lachenbruch, B. 2015. Advancing Toward Professorship in Biology, Ecology and Earth System Sciences. In: Mavriplis, C., Sabila, P., Heller, S. FORWARD to Professorship in STEM: Inclusive Strategies That Work. pp -–-. Elsevier

562. Saunders, M., Brown, C., Foley, M.E., Febria,C., Albright,R., Mehling, M., Kavanaugh, M.T., Burfeind, D. 2015. Human impacts on connectivity in marine and freshwater ecosystems assessed using network measures. Marine and Freshwater Research 67:277-290

563. Moran, M.A., Kujawinski, E.B., Stubbins, A., Fatland, R., Aluwihare, L.I., Buchan, A., Crump, B.C., Dorrestein, P.C., Dyhrman, S.T., Hess, N., Longnecker, K., Medeiros, P.M., Niggemann, J., Obernosterer, I., Repeta, D.J., Waldbauer, J. 2016. Deciphering Ocean Carbon in a Changing World . Proc. Natl. Acad. Sci. 113:3143-3151

564. Alexander, H., Rouco, M., Haley, S.T., Wilson, S. T., Karl, D.M., Dyhrman, S.T. 2015. Functional group specific traits drive shift in ecosytem state in the oligotrophic ocean. Proc. Natl. Acad. Sci. 112:E5972-E5979

565. Diaz, J.M., Haley, S.T., Longo, A.F., Ingall, E.D., Björkman, K.M., Karl, D. M., Dyhrman, S. T. 2016. Polyphosphate content and dynamics at Station ALOHA, North Pacific Subtropical Gyre . Limnol. Oceanogr. 61:227-239

566. Dyhrman, S.T. 2016. Nutrients and Their Acquisition: Phosphorus Physiology in Microalgae. In: Borowitzka, M.A., Beardall, J., Raven, J.A. The Physiology of Microalgae. pp 155–183. Springer

567. Pereira N., Shilova, I.N., Zehr J.P. 2016. Molecular markers define progressing stages of phosphorus limitation in the nitrogen‐fixing cyanobacterium, Crocosphaera. Journal of Phycology 52:274-282

568. Cornejo-Castillo, F.M., Cabello, A.M., Salazar, G., Sánchez-Baracaldom, P., Lima-Mendez, G., Hingamp, P., Alberti, A., Sunagawa, S., Bork, P., De Vargas, C., Raes, J., Bowler, C., Wincker, P., Zehr, J.P., Gasol, J.P., Massana, R., Acinas S.G. 2016. Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton. Nature Communications 7:1-9

569. Rees, A.P., Turk-Kubo, K.A., Al-Moosawi, L., Alliouane, S., Gazeau, F., Hogan, M.E., Zehr, J.P. 2016. Ocean acidification impacts on nitrogen fixation in the coastal western Mediterranean Sea. Estuarine, Coastal and Shelf Science in press:in press-in press

570. Farnelid, H.M., Turk-Kubo, K.A., Zehr, J.P. 2016. Identification of Associations between Bacterioplankton and Photosynthetic Picoeukaryotes in Coastal Waters. Frontiers in Microbiology 7:1-16

571. Turk-Kubo, K.A., Frank, I.E., Hogan, M.E., Desnues, A., Bonnet, S., Zehr, J.P. 2015. Diazotroph community succession during the VAHINE mesocosm experiment (New Caledonia lagoon). Biogeosciences 12:7435-7452

572. Zehr, J.P. 2015. How single cells work together. Science 349:1163-1164

573. Hilton, J.A., Satinsky, B.M., Doherty, M., Zielinski,B., Zehr, J.P. 2015. Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume. ISME Journal 9:1557-1569

574. Bombar, D., Taylor, C.D., Wilson,S.T., Robidart,J.C., Rabines, A., Turk-Kubo, K.A., Kemp, J.N., Karl, D.M., Zehr, J.P. 2015. Measurements of nitrogen fixation in the oligotrophic North Pacific Subtropical Gyre using a free-drifting submersible incubation device. Journal of Plankton Research 37:727-739

575. Bonnet, S., Berthelot, H., Turk-Kubo, K., Fawcett, S., Rahav E., l’Helguen, S., Berman-Frank, I. 2015. Dynamics of N2 fixation and fate of diazotroph-derived nitrogen in a low nutrient low chlorophyll ecosystem: results from the VAHINE mesocosm experiment (New Caledonia). Biogeosciences Discussions 12:19579-19626

576. Bonnet, S., Rodier, M., Turk‐Kubo, K.A., Germineaud, C., Menkes, C., Ganachaud, A., Cravatte, S., Raimbault, P., Campbell, E., Quéroué, F., Sarthou, G., Desnues, A., Maes, C., Eldin, G. 2015. Contrasted geographical distribution of N2 fixation rates and nifH phylotypes in the Coral and Solomon Seas (southwestern Pacific) during austral winter conditions. Global Biogeochemical Cycles 29:1874-1892

577. Bang, M., Chisholm, P. submitted. Rivers of Sunlight: How the Sun moves water around the Earth. Blue Sky Press, Scholastic. 42 pp

578. Lea-Smith D., Biller S., Davey M., Cotton C., Perez-Sepulveda B., Turchyn A., Scanlan D., Smith A., Chisholm S., Howe C. 2015. Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle. Proc. Natl. Acad. Sci. 112(44):13591-13596

579. Biller S., Coe A., Martin-Cuadrado A., and Chisholm S. 2015. Draft genome sequence of Alteromonas macleodii strain MIT1002, isolated from an enrichment culture of the marine cyanobacterium Prochlorococcus. Genome Announcements 3(4):e00967-15

580. Coe, A., Ghizzoni, J., LeGault, K., Biller, S., Roggensack, S., Chisholm, S. 2016. Survival of Prochlorococcus in extended darkness. Limnol. Oceanogr. In press:x-x

581. Berube P., Coe A., Roggensack E., Chisholm S. 2016. Temporal dynamics of Prochlorococcus cells with the potential for nitrate assimilation in the subtropical Atlantic and Pacific oceans. Limnol. Oceanogr. 61(2):482-495

582. Casey, J.R., Falkowski, P.G., Karl, D.M. 2015. Substrate selection for heterotrophic bacterial growth in the sea. Marine Chemistry 177:349-356

583. Keffer, J.L., Sabanayagam, C.R., Lee, M.E. , DeLong, E.F., Hahn, M.W, Maresca, J.A. 2015. 2015. Identifying rhodopsin-containing cells using TIRF microscopy. Appl. Environ. Micrbiol. 81:3442-3450

584. Sosa, O., Gifford, S.M. , Repeta, D., DeLong, E.F. 2015. Dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures. ISME J. 9:2725-2739

585. Fontanez, K.M., Eppley, J.E., Samo, T.J., Karl, D.M. , DeLong, E.F. 6. Microbes and metabolic pathways on sinking particles in the North Pacific Subtropical Gyre. Frontiers in Microbiology 6:469-.

586. 4. Bryant, J.A., Aylward, F.O., Eppley, J.M., Karl, D.M., Church, M.J., DeLong, E.F. 2015. Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre. . ISME J. doi:10.1038/ismej.2015.221:.-.

587. 6. Mende D.R., Aylward F.O., Eppley J.M., Nielsen T.N., DeLong E.F. 2016. Improved environmental genomes via integration of metagenomic and single-cell assemblies. . Front Microbiol. 7:143-.

588. Bryant J.A., Clemente, T., Viviani, D.A., Fong, A.A., Thomas, K.A., Kemp, P., Karl D.M., White, DeLong E.F. 2016. Diversity and Activity of Communities inhabiting plastic debris in the North Pacific Gyre. mSystems 1:e00024-16-.

589. Nigro, O.D., Steward, G.F. 2015. Differential specificity of selective culture media for enumeration of pathogenic vibrios: advantages and limitations of multi-plating methods. Journal of Microbiological Methods 111:24-30

590. Miranda, J.A., Culley, A.I., Schvarcz, C.R., Steward, G.F. 2016. RNA viruses as major contributors to Antarctic virioplankton. Environmental Microbiology DOI: 10.1111/1462-2920.13291:1-14

591. Fitzsimmons, J., Boyle, E., Jenkins, W. 2014. Distal transport of dissolved hydrothermal iron in the deep South Pacific Ocean. Proc. Nat. Acad. Sci. 111:16654-16661

592. Fitzsimmons, J., Bundy, R., al-Subiai, S., Barbeau, K., Boyle, E. 2015. The composition of dissolved iron in the dusty surface ocean: an exploration using size-fractionated iron-binding ligands. Mar. Chem. 173:125-135

593. Hayes, C., Fitzsimmons, J., Boyle, E., McGee, D., Anderson, R., Weisend, R, Morton, P. 2015. Thorium isotopes tracing the iron cycle at the Hawaii Ocean Time-series Station ALOHA. Geochim. Cosmochim. Acta 169:1-16

594. Fitzsimmons, J., Hayes, C., al-Subiai, S., Zhang, R., Morton, P., Weisend, R., Ascani, F., Boyle, E. 2015. Daily to decadal variability of size-fractionated iron and iron-binding ligands at the Hawaii Ocean Time-series Station ALOHA. Geochim. Cosmochim. Acta 171:303-324

595. Wilson, S.T., Barone, B., Ascani, F., Bidigare, R.R., Church, M.J., del Valle, D.A., Dyhrman, S. T., Ferrón, S., Fitzsimmons, J.N., Juranek, L.W., Kolber, Z.S., Letelier, R. M., Martínez-Garcia, S., Nicholson, D., Richards, K. J., Rii, Y.M., Rouco, M., Viviani, D.A., White, A.E., Zehr, J.P., Karl D.M. 2015. Short-term variability in euphotic zone biogeochemistry and primary productivity at Station ALOHA: A case study of summer 2012. Global Biogeochemical Cycles 29:1-30

596. Yelton, A., Acinas, S., Sunagawa, S., Bork, P., Pedrós-Alió, C., Chisholm, S. 2016. Global genetic capacity for mixotrophy in marine picocyanobacteria. ISME Journal In Press:x-x

597. Biller, S., Coe, A., Chisholm, S. 2016. Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus. ISME Journal In Press:x-x

598. 4. Ferron, S., del Valle, D.A., Björkman, K.M., Quay, P.D., Church, M.J., Karl, D.M. 2016. Application of membrane inlet mass spectrometry to measure aquatic gross primary production by the 18O in vitro method. Limnology and Oceanography: Methods XX:XX-XX

599. Rii, Y.M., S. Duhamel, R.R. Bidigare, D.M. Karl, D.J. Repeta, M.J. Church 2015. Diversity and productivity of photosynthetic picoeukaryotes in biogeochemically distinct regions of the South East Pacific Ocean. Limnology and Oceanography doi: 10.1002/lno.10255:XX-XX

600. Björkman, K.M., M.J. Church, J.K. Doggett, D.M. Karl 2015. Differential assimilation of inorganic carbon and leucine by Prochlorococcus and non-pigmented bacteria in the oligotrophic North Pacific Subtropical Gyre. Frontiers in Marine Science doi: 10.3389/fmicb.2015.01401:XX-XX

601. Viviani, D.A., D.M. Karl, M.J. Church 2015. Photosynthetic production of dissolved and particulate organic carbon in the North Pacific Subtropical Gyre. Frontiers in Marine Science doi:10.3389/fmars.2015.00073:XX-XX

602. White, A.E., R.M. Letelier, A.L. Whitmire, B. Barone, R.R. Bidigare, M.J. Church, and D.M. Karl 2015. Phenology of particle size distributions and primary productivity in the North Pacific Subtropical gyre. Journal Geophysical Research – Oceans 120:7381-7399

603. Saito, Mak A., Matthew R. McIlvin, Dawn M. Moran, Tyler J. Goepfert, Giacomo R. DiTullio, Anton F. Post, and Carl H. Lamborg. 2014. Multiple Nutrient Stresses at Intersecting Pacific Ocean Biomes Detected by Protein Biomarkers. . Science 345:1173-1177

604. Saito, M. A., Dorsk, A., Post, A. F., McIlvin, M., Rappé, M. S., DiTullio, G., & Moran, D. 2015. Needles in the Blue Sea: Sub‐Species Specificity in Targeted Protein Biomarker Analyses Within the Vast Oceanic Microbial Metaproteome. PROTEOMICS 15:3521-3531

605. Mackey, K. R., Post, A. F., McIlvin, M. R., Cutter, G. A., John, S. G., & Saito, M. A. 2015. Divergent responses of Atlantic coastal and oceanic Synechococcus to iron limitation.. Proceedings of the National Academy of Sciences 112:9944-9949

606. Laufkötter, C., Vogt, M., Gruber, N., Aumont, O., Bopp, L., Doney, S.C., Dunne, J.P., Hauck, J., John, J.G., Lima, I.D., Seferian, R., C. Völker, C. 2016. Projected decreases in future marine export production: the role of the carbon flux through the upper ocean ecosystem. Biogeosciences 13:4023-4047

607. Barnypok 1985. polbTyvZksDTqiOUX. LgxuRzJooTwvqoWzzr. jasiypOuGZMTwub pp


Astorga-Eló, Marcia , Salvador Ramírez-Flandes, Edward F DeLong, and Osvaldo Ulloa 2015. Genomic potential for nitrogen assimilation in uncultivated members of Prochlorococcus from an anoxic marine zone.. ISME J. 9(5): 1264–1267.

Aylward, F.O., Eppley, J.M., Smith,J.M., Chavez, F.P., Scholin,C.A. & DeLong, E.F. 2015. Microbial Community Transcriptional Networks are Conserved in Three Domains at Ocean Basin Scales. Proc. Natl. Acad. Sci. U.S.A. 112(17) 5443-5448

Bagby, S., Chisholm, S.W 2015. Response of Prochlorococcus to varying CO2:O2 ratios. The ISME Journal 9(10):2232-45

Bench, S., I. Frank, J. Robidart, J. Zehr, 2015. Two subpopulations of Crocosphaera watsonii have distinct distributions in the North and South Pacific. Environmental Microbiology doi: 10.1111/1462-2920.13180

Biller, S.J., Berube, P.M., Lindell, D., Chisholm, S.W. 2015. Prochlorococcus: the structure and function of collective diversity. Nature Reviews Microbiology 13:13-27

Boyd, P.W., Lennartz, S.T., D.M. Glover, D.M., Doney, S.C. 2015. Biological ramifications of climate-change-mediated oceanic multi-stressors. Nature Climate Change 5:71-79

Collins, J.R., Edwards, B.R., Thamatrakoln, K., Ossolinski, J.E., DiTullio, G.R., Bidle, K.D., Doney, S.C., B.A.S. Van Mooy, B.A.S. 2015. The multiple fates of sinking particles in the North Atlantic Ocean. Global Biogeochemical Cycles 29:1471-1494

Cooper, S.D., H.M. Page, S.W. Wiseman, K. Klose, D.M. Bennett, T. Even, S. Sadro, C.E. Nelson, and T.L. Dudley 2015. Physicochemical and biological responses of streams to wildfire severity in riparian zones. Freshwater Biology 60: 2600–2619. doi:10.1111/fwb.12523

Doney, S. (committee member), National Research Council 2015. Climate Intervention: Carbon Dioxide Removal and Reliable Sequestratio. National Academies Press.

Doney, S. (committee member), National Research Council 2015. Climate Intervention: Reflecting Sunlight to Cool Earth. National Academies Press.

Nicholson, D.P., Wilson, S.T., Doney, S.C., Karl, D.M. 2015. Quantifying subtropical North Pacific gyre mixed layer primary productivity from Seaglider observations of diel oxygen cycles. Geophysical Research Letters 42:4032-4039

Paulot, F., Jacob, D.J., Johnson, M.T., Bell, T.G., Baker, A.R., Keene, W.C., Lima, I.D., Doney, S.C., Stock, C.A. 2015. Global oceanic emission of ammonia: Constraints from seawater and atmospheric observations. Global Biogeochemical Cycles 29:1165-1178

von Dassow, P., John, U., Ogata, H., Probert, I., Bendif, E.M., Kegel, J.U., Audic, S., Wincker, P., Da Silva, C., Claverie, J.-M., Doney, S., Glover, D.M., Flores, D.M., Herrera, Y., Lescot, M., Garet-Delmas, M.-J., de Vargas, C. 2015. Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton. The ISME Journal 9, 1365–1377

E.K. Wear, C.A. Carlson, A.K. James, M.A. Brzezinski, L.A. Windecker and C.E. Nelson 2015. Synchronous shifts in dissolved organic carbon bioavailability and bacterial community responses over the course of an upwelling-drivenphytoplankton bloom. Limnology & Oceanography 2015:1-32


Baker, L.J., Kemp, P.F. 2014. Exploring bacteria-diatom associations using single-cell whole genome amplification. Aquatic Microbial Ecology 72:73-88

Bang, M., Chisholm, S.W. 2014. Buried Sunlight: How fossil fuels have changed the Earth. Blue Sky Press, Scholastic. 48 pp

Bates, N.R., Astor, Y.M., Church, M.J., Currie, K., Dore, J.E., González-Dávila, M., Lorenzoni, L., Muller-Karger, F., Olafsson, J., Santana-Casiano, J.M. 2014. A time-series view of changing ocean chemistry due to ocean uptake of anthropogenic CO2 and ocean acidification. Oceanography 27:126-141

Becker, J.W., Berube, P.M., Follett, C.L., Waterbury, J.B, Chisholm, S.W., DeLong, E. F., Repeta, D.J. 2014. Closely related phytoplankton species produce similar suites of dissolved organic matter. Frontiers in Microbiological Chemistry 5:111

Berube, P.M., Biller, S.J., Kent, A.G., Berta-Thompson, J.W., Roggensack, S.E., Roache-Johnson, K.H., Ackerman, M., Moore, L.R., Meisel, J.D., Sher, D., Thompson, L.R., Campbell, L., Martiny, A.C., Chisholm, S.W. 2014. Physiology and evolution of nitrate acquisition in Prochlorococcus. The ISME Journal Advance Online:doi:10.1038/ismej.2014.211-

Biddle, J.F., Jungbluth, S.P., Lever, M.A., Rappé, M.S. 2014. Life in the oceanic crust. In: Kallmeyer, J., Wagner, D. Microbial Life of the Deep Biosphere. pp 1-20. De Gruyter

Bidigare, R.R., Buttler, F.R., Christensen, S.J., Barone, B., Karl, D.M., Wilson, S.T. 2014. Evaluation of the utility of xanthophylls cycle pigment dynamics for assessing upper ocean mixing processes at Station ALOHA. Journal of Plankton Research 36:1423-1433

Biller, S.J., Berube, P.M., Berta-Thompson, J.W., Kelly, L., Roggensack, S.E., Awad, L., Roache-Johnson, K.H., Ding, H., Giovannoni, S.J., Rocap, G., Moore, L.R., Chisholm, S.W. 2014. Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. Scientific Data 1:140034-

Biller, S.J., Schubotz, F., Roggensack, S.E., Thompson, A.W., Summons, R.E., Chisholm, S.W. 2014. Bacterial vesicles in marine ecosystems. Science 343:183-186

Bombar, D., Heller, P., Sanchez-Baracaldo, P., Carter, B. J., Zehr, J. P. 2014. Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria. ISME Journal 8:2530-2542

Böttjer, D., Jungbluth, S.P., Boiteau, R., Burkhardt, B., de Leo, F., Bruno, B.C. 2014. Career choices in marine and environmental sciences: navigating a sea of options. Oceanography 27:201-207

Böttjer, D., Karl, D.M., Letelier, R.M., Viviani, D.A., Church, M.J. 2014. Experimental assessment of diazotroph responses to elevated seawater pCO2 in the North Pacific Subtropical Gyre. Global Biogeochemical Cycles 28:601-616

Boyle, E.A., Lee, J.-M., Echegoyen, Y., Noble, A., Moos, S., Carrasco, G., Zhao, N., Kayser, R., Zhang, J., Gamo, T., Obata, H., Norisuye, K. 2014. Anthropogenic lead emissions in the ocean: The evolving global experiment. Oceanography 27:69-75

Bruno, B.C., Wren, J.L.K. 2014. Climate change, sea level rise, and ocean acidification. The Earth Scientist 30(1):9-11

Burkhardt, B., Watkins-Brandt, K.S., Defforey, D., Paytan, A., White, A.E. 2014. Remineralization of phytoplankton-derived organic matter by natural populations of heterotrophic bacteria. Marine Chemistry 163:1-9

Cameron Thrash J., Temperton B., Swan B.K., Landry Z.C., Woyke T., Delong E.F., Stepanauskas R., Giovannoni S.J. 2014. Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. The ISME Journal 8:1440-1451

Carini, P. A.E. White, E.O. Campbell and S. Giovanonni 2014. Aerobic methanogenesis by phosphate-starved SAR11 chemoheterotrophic marine bacteria. Nature Communications 5:doi:10.1038-ncomms5346.

Collavino, M.M, Tripp, H. J., Frank, I. E., Vidoz, M. L., Calderoli, P. A., Donato, M., Zehr, J.P., Aguilar, O. M. 2014. nifH pyrosequencing reveals the potential for location-specific soil chemistry to influence N2-fixing community dynamics. Environmental Microbiology 16:3211-3223

Culley, A.I., Mueller, J.A., Belcaid, M., Wood-Charlson, E.M., Poisson, G., Steward, G.F. 2014. The characterization of RNA viruses in tropical seawater using targeted PCR and metagenomics. mBio 5:e01210-14-e01210-14

Dalsgaard, T., Stewart, F.J., Thamdrup, B., De Brabandere, L., Revsbech,N.P., Ulloa,O., Canfield, D.E., DeLong E.F. 2014. Oxygen at nanomolar levels reversibly suppresses process rates and gene expression of anammox and denitrification in the oxygen minimum zone off northern Chile. MBio 5:e01966-doi: 10.1128/mBio.01966-14

del Valle, D.A., Karl, D.M. 2014. Aerobic production of methane from dissolved water-column methylphosphonate and sinking particles in the North Pacific Subtropical Gyre. Aquatic Microbial Ecology 73:93-105

DeLong, E.F. 2014. Alien invasions and gut “island biogeography” . Cell 159:233-235

Doney, S., Rosenberg, A.A., Alexander, M., Chavez, F., Harvell, C.D., Hofmann, G., Orbach, M., Ruckelshaus, M. 2014. Ch. 24: Oceans and Marine Resources. In: Melillo, J.M., Richmond, T.C., Yohe, G.W., Eds. Climate Change Impacts in the United States: The Third National Climate Assessment. pp 557-578. U.S. Global Change Research Program

Doney, S.C., Karnauskas, K.B. 2014. Oceanography: Oxygen and climate dynamics. Nature Climate Change 4:862-863

Dore, J.E., Church, M.J., Karl, D.M., Sadler, D.W., Letelier, R.M. 2014. Paired windward and leeward biogeochemical time series reveal consistent surface ocean CO2 trends across the Hawaiian Ridge. Geophysical Research Letters 41:6459-6467

Duhamel, S., Björkman, K.M., Doggett, J.K., Karl, D.M. 2014. Microbial response to enhanced phosphorus cycling in the North Pacific Subtropical Gyre. Marine Ecology Progress Series 504:43-58

Durham, B. P., J. Grote, K. A. Whittaker, S. J. Bender, H. Luo, S. L. Grim, J. M. Brown, J. R. Casey, A. Dron, L. R. Florez-Leiva, A. Krupke, C. M. Luria, A. H. Mine, O. Nigro, S. Pather, A. Talarmin, E. K. Wear, T. S. Weber, J. M. Wilson, M. J. Church, E. F. DeLong, D. M. Karl, G. F. Steward, J. M. Eppley, N. C. Kyrpides, S. Schuster, and M. S. Rappé 2014. Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter possessing an unusually small genome. Standards in Genomic Sciences 9:632-645

Fiechter, J., Curchitser, E.N., Edwards, C.A., Chai, F., Goebel, N.L., Chavez, F.P. 2014. Air-sea CO2 fluxes in the California Current: Impacts of model resolution and coastal topography. Global Biogeochemical Cycles 28:371-385

Fiedler, J. W., McManus, M. A., Tomlinson, M. S., De Carlo, E. H., Pawlak, G. R., Steward, G. F., Nigro, O. D., Timmerman, R. E., Drupp, P. S., Wells, J. R., Ostrander, C. E. 2014. Real-time observations of the February 2010 Chile and March 2011 Japan tsunamis in Honolulu, Hawaii as recorded by the Pacific Islands Ocean Observing System. Oceanography 2:186-200

Fitzsimmons, J.N., Boyle, E.A. 2014. Assessment and comparison of Anopore and cross flow filtration methods for the determination of dissolved iron size fractionation into soluble and colloidal phases in seawater. Limnology and Oceanography: Methods 12: 244-261

Fitzsimmons, J., Boyle, E. 2014. Both soluble and colloidal iron phases control dissolved iron variability in the tropical North Atlantic Ocean. Geochimica et Cosmochimica Acta 125:539-550

Ganesh S., Parris D.J., DeLong E.F., Stewart F.J. 2014. Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone. The ISME Journal 8:187-211

Gilbert JA, Dick GJ, Jenkins B, Heidelberg J, Allen E, Mackey KR, DeLong EF. 2014. Meeting report: Ocean 'omics science, technology and cyberinfrastructure: current challenges and future requirements. Stand Genomic Sci. 9:125-128

Goebel, N.L., Edwards, C.A., Follows, M.J., Zehr, J.P. 2014. Modeled diversity effects on microbial ecosystem functions of primary production, nutrient uptake, and remineralization. Ecology 95:153-163

Gradoville, M.R., A. E. White and R.M. Letelier 2014. Physiological effects of enhanced carbon dioxide on high density Crocosphaera cultures. PlosOne 9:doi:10.1371-/journal.pone.0110660

Gradoville, M.R., White, A.E., Böttjer, D., Church, M.J., Letelier, R.M. 2014. Diversity trumps acidification: No carbon dioxide enhancement of Trichodesmium community nitrogen or carbon fixation at Station ALOHA. Limnology and Oceanography 59:645-659

Heller, P., Tripp, H. J., Turk-Kubo, K., Zehr, J. P. 2014. ARBitrator: a software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank. Bioinformatics 30:2883-2890

Jungbluth, S.P., Lin, H.-T., Cowen, J.P., Glazer B.T., Rappé, M.S. 2014. Phylogenetic diversity of microorganisms in subseafloor crustal fluids from Holes 1025C and 1026B along the Juan de Fuca Ridge flank. Frontiers in Microbiology 5:doi:10.3389/fmicb.2014.00119.

Karl, D.M. 2014. Microbially mediated transformations of phosphorus in the sea: New views of an old cycle. Annual Reviews of Marine Science 6:279-337

Karl, D.M. 2014. Solar energy capture and transformation in the sea. Elementa doi:10.12952/journal.elementa.000021

Karl, D.M., Björkman, K.M. 2014. Dynamics of dissolved organic phosphorus. In: D. Hansell and C. Carlson Biogeochemistry of Marine Dissolved Organic Matter. pp 233–334. Elsevier

Karl, D.M., Schlesinger, W.H. (eds.) 2014. Biogeochemistry, 2nd edn., vol. 10 of Treatise on Geochemistry (Holland, H. D. and K. K. Turekian, Exec. Eds.). Elsevier. 649 pp

Karl, D. M. 2014. Roger Revelle Commemorative Lecture: The contemporary challenge of the sea: Science, society and sustainability. Oceanography 27:208-225

Karl, D.M., Church, M.J. 2014. Microbial oceanography and the Hawaii Ocean Time-series programme. Nature Reviews Microbiology 12:699-713

Kashtan, N., Roggensack, S.E., Rodrigue, S., Thompson, J.W., Biller, S.J., Coe, A., Ding, H., Marttinen, P., Stocker, R., Follows, M., Stephanauskas, R., Chisholm, S.W. 2014. Single cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344:416-420

Kavanaugh, M.T., Emerson, S.R., Hales, B., Lockwood, D.M., Quay, P.D., Letelier, R.M. 2014. Physicochemical and biological controls on primary and net community production across northeast Pacific seascapes. Limnology and Oceanography 59(6):2013-2027

Kavanaugh. M.T., Hales, B., Saraceno, M., Spitz, Y.H., White, A.E., Letelier, R.M. 2014. Hierarchical and dynamic seascapes: A quantitative framework for scaling pelagic biogeochemistry and ecology. Progress in Oceanography 120:291-304

Kelly, L.W., G. J. Williams, K.L. Barott, C.A. Carlson, E.A. Dinsdale, R.A. Edwards, A.F. Haas, M. Haynes, Y.W. Lim, T. McDole, C.E. Nelson, E. Sala, S.A. Sandin, J.E. Smith, M.J.A. Vermeij, M Youle and F.Rohwer 2014. Local genomic adaption of coral and algal-associated microbiomes to gradients of natural variability and anthropogenic stressors. Proceedings of the National Academy of Sciences of the United States of America 111:10227-10232

Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PS, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, et al. 2014. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.. PLoS Biol. 12:e1001920-.

Laws, E.A., Letelier, R.M., Karl, D.M. 2014. Estimating the compensation irradiance in the ocean: The importance of accounting for non-photosynthetic uptake of inorganic carbon. Deep-Sea Research 93:35-40

Lincoln, S.A., Wai, B., Eppley, J.M., Church, M.J., Summons, R.E., DeLong, E.F. 2014. Planktonic Euryarchaeota are a significant source of archaeal tetraether lipids in the ocean. Proceedings of the National Academy of Sciences USA 111:9858-9863

Luo, Y.W., Lima, I.D., Karl, D.M., Deutsch, C.A., Doney, S.C. 2014. Data-based assessment of environmental controls on global marine nitrogen fixation. Biogeosciences 11:691-708

Mackey, K., Culbertson, T. 2014. Science fairs for science literacy. Eos 95:10-10

Mansergh, S., Zehr, J.P. 2014. Vibrio diversity and dynamics in the Monterey Bay upwelling region. Frontiers in Microbiology 5:1-9

Moisander, P. H., Serros, T., Paerl, R.W., Beinart, R.A., Zehr, J.P. 2014. Gammaproteobacterial diazotrophs and nifH gene expression in surface waters of the South Pacific Ocean. ISME Journal 8:1962-1973

Mueller, J. A., Culley, A. I., Steward, G. F. 2014. Variables influencing extraction of nucleic acids from microbial plankton (viruses, bacteria, and protists) collected on nanoporous aluminum oxide filters. Applied and Environmental Microbiology 13:3930-3942

Muller-Karger, F.E., Kavanaugh, M.T., Montes, E., Balch, W.M., Breitbart, M., Chavez, F.P., Doney, S.C., Johns, E.M., Letelier, R.M., Lomas, M.W., Sosik, H.M., White, A.E. 2014. A framework for a marine biodiversity observing network within changing continental shelf seascapes. Oceanography 27:18-23

Nelson, C.E., Carlson, C.A., Ewart, C.S., Halewood, E.R. 2014. Community differentiation and population enrichment of Sargasso Sea bacterioplankton in the euphotic zone of a mesoscale mode-water eddy. Environmental Microbiology 16:871-887

Nelson, C.E. and Wear, E.K. 2014. Microbial diversity and the lability of dissolved organic carbon. Proceedings of the National Academy of Sciences of the United States of America 111:7166-7167

Nicholson, D., Stanley, R.H.R., Doney, S.C. 2014. The triple oxygen isotope tracer of primary productivity in a dynamic ocean model. Global Biogeochemical Cycles 28:538-552

Ottesen, E.A., Young, C.R., Gifford, S.M., Eppley, J.M., Marin, R. III, Schuster, S.C., Scholin, C.A., DeLong, E.F. 2014. Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages. Science 345:207-12

D. J. Parris, Sangita Ganesh, Virginia P. Edgcomb, Edward F. DeLong and Frank J. Stewart. 2014. Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile.. Front Microbiol. 5:543-doi: 10.3389/fmicb.2014.00543

R.J. Parsons, C.E. Nelson, C.A. Carlson, C.C. Denman, A.J. Andersson, A.L. Kledzik, K.L. Vergin, S.P. McNally, A.H. Treusch and S.J. Giovannoni 2014. Marine bacterioplankton community turnover within seasonally hypoxic waters of a sub-tropical sound: Devil’s Hole, Bermuda. Environmental Microbiology 17: 3481–3499. doi:10.1111/1462-2920.12445

Pei, S., Laws, E. A. 2014. Does the 14C method estimate net photosynthesis? II. Implications from cyclostat studies of marine phytoplankton. Deep-Sea Research 91:94-100

Pörtner, H.-O., D. M. Karl, P. W. Boyd, W. L. Cheung, S. E. Lluch-Cota, Y. Nojiri, D. N. Schmidt and P. O. Zavialov 2014. Ocean systems. In: Field, C.B. et al. Climate Change 2014: Impacts, Adaptation, and Vulnerability. Part A: Global and Sectoral Aspects. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. pp 000–000. Cambridge University Press

Robidart, J.C., Church, M.J., Ryan, J.P., Ascani, F., Wilson, S.T., Bombar, D., Marin III, R., Richards, K.J., Karl, D.M., Scholin, C.A., Zehr, J.P. 2014. Ecogenomic sensor reveals controls on N2-fixing microorganisms in the North Pacific Ocean. The ISME Journal 8:1175-1185

Rouco M., McGillicuddy D., Waterbury J.B., Dyhrman S.T. (2014). Trichodesmium sp. clade distributions in the North Atlantic Ocean. Limnology & Oceanography. 59: 1899-1909.

Sharma, A. K., J. W. Becker, E. A. Ottesen, J. A. Bryant, S. Duhamel, D. M. Karl, O. X. Cordero, D. J. Repeta and E. F. DeLong 2014. Distinct dissolved organic matter sources induce rapid transcriptional responses in coexisting populations of Prochlorococcus, Pelagibacter and the OM60 clade. Environmental Microbiology 16:2815-2830

Shilova, I.N., Robidart J.C, Tripp H.J., Turk-Kubo K., Wawrik B., Post A.F., et al 2014. A microarray for assessing transcription from pelagic marine microbial taxa. The ISME Journal 8:1476-1491

Siegel, D.A., Buesseler, K.O., Doney, S.C., Sailley, S.F., Behrenfeld, M.J., Boyd, P.W. 2014. Global assessment of ocean carbon export by combining satellite observations and food-web models. Global Biogeochemical Cycles 28: doi:10.1002/2013GB004743

Thompson, A., Carter, B.J., Turk-Kubo, K., Malfatti, F., Azam, F., Zehr, J.P. 2014. Genetic diversity of the unicellular nitrogen-fixing cyanobacteria UCYN-A and its prymnesiophyte host. Environmental Microbiology 16:3238-3249

Turk-Kubo, K.A., Karamchandani, M., Capone, D.G., Zehr, J.P. 2014. The paradox of marine heterotrophic nitrogen fixation: abundances of heterotrophic diazotrophs do not account for nitrogen fixation rates in the Eastern Tropical South Pacific. Environmental Microbiology DOI: 10.1111/1462-2920.12346

Turk-Kubo, K.A., Karamchandani, M., Capone, D.G., Zehr, J.P. 2014. The paradox of marine heterotrophic nitrogen fixation: abundances of heterotrophic diazotrophs do not account for nitrogen fixation rates in the Eastern Tropical South Pacific. Environmental Microbiology 16:3095-3114.

Wallhead, P., Garçon, V., Casey, J., Lomas, M. 2014. Long-term variability of phytoplankton carbon biomass in the Sargasso Sea. Global Biogeochemical Cycles 28:825-841

Walsh, J., Wuebbles, D., Hayhoe, K., Kossin, J., Kunkel, K., Stephens, G., Thorne, P., Vose, R., Wehner, M., Willis, J., Anderson, D., Doney, S., Feely, R., Hennon, P., Kharin, V., Knutson, T., Landerer, F., Lenton, T., Kennedy, J., Somerville, R. 2014. Ch. 2: Our Changing Climate. In: Melillo, J.M., Richmond, T.C., Yohe, G.W., Eds. Climate Change Impacts in the United States: The Third National Climate Assessment. pp 19–67. U.S. Global Change Research Program

Wilson, S.T., del Valle, D.A., Segura-Noguera, M., Karl, D.M. 2014. A role for nitrite in the production of nitrous oxide in the lower euphotic zone of the oligotrophic North Pacific Ocean. Deep Sea Research Part I 85:47-55

Yoshizawa S., Kumagai Y., Kim H., Ogura Y., Hayashi T., Iwasaki W., Delong E.F., Kogure K. 2014. Functional characterization of flavobacteria rhodopsins reveals a unique class of light-driven chloride pump in bacteria. Proceedings of the National Academy of Sciences USA 111:6732-6737


Aguirre, J.D., Clark, H.M., McIlvin, M., Vazquez, C., Palmere, S.L., Grab, D., Seshu, J., Saito, M.A., Culotta, V.C. 2013. A manganese-rich environment supports superoxide dismutase activity in the Lyme Disease pathogen, Borrelia burgdorferi. Journal of Biological Chemistry 12:8468-8478

Ascani, F., Richards, K.J., Firing, E., Grant, S., Johnson, K.S., Jia, Y., Lukas, R., Karl, D.M. 2013. Physical and biological controls of nitrate concentrations in the upper subtropical North Pacific Ocean. Deep Sea Research II 93:119-134

Beaulieu, C., Henson, S.A., Sarmiento, J.L., Dunne, J.P., Doney, S.C., Rykaczewski, R.R., Bopp, L. 2013. Factors challenging our ability to detect long-term trends in ocean chlorophyll. Biogeosciences 10:2711-2724

Behrenfeld, M.J., Doney, S.C., Lima, I., Boss, E.S., Siegel, D.A. 2013. Annual cycles of ecological disturbance and recovery underlying the subarctic Atlantic spring plankton bloom. Global Biogeochemical Cycles 27:526-540

Bench, S. R., Heller P., Frank I., Arciniega M., Shilova I. N., Zehr, J.P. 2013. Whole genome comparison of six Crocosphaera watsonii strains with differing phenotypes. Journal of Phycology 49:786-801

Bertrand, E.M., Moran, D.M., McIlvin, M.R., Hoffman, J.M. Allen, A.E., Saito, M.A. 2013. Methionine synthase interreplacement in diatom cultures and communities and the persistence of B12 use by eukaryotic phytoplankton. Limnology and Oceanography 58:1431-1450

Boiteau, R., Fitzsimmons, J., Repeta, D.J., Boyle, E.A. 2013. Detection of iron ligands in seawater and marine cyanobacteria cultures by high-performance liquid chromatography-inductively coupled plasma mass spectrometry. Analytical Chemistry 85:4357-4362

Bombar, D., Turk-Kubo K.A., Robidart J.C., Carter B.J., Zehr, J.P. 2013. Non-cyanobacterial nifH phylotypes in the North Pacific Subtropical Gyre detected by flow-cytometry cell sorting. Environmental Microbiology Reports 5:705-715

Bonnet, S., Dekaezemacker, J., Turk-Kubo, K.A., Moutin, T., Hamersley, R.M., Grosso, O., Zehr, J.P., Capone, D.G. 2013. Aphotic N2 fixation in the Eastern Tropical South Pacific Ocean. PLOS One 8:e81265-e81265

Briggs, R.A., Padilla-Gamiño, J.L., Bidigare, R.R. Gates, R.D., Ruttenberg, K.C. 2013. Impact of Montipora capitata coral spawning events on Hawaiian coastal biogeochemistry. Estuarine, Coastal and Shelf Science 134:57-68

Brum, J.R., Culley, A.I., Steward, G.F. 2013. Assembly of a marine viral metagenome after physical fractionation. PLoS ONE 8(4):e60604

Bruno, B.C., Rii, Y.M., Robidart, J.C., Viviani, D.A. 2013. The young scientist and the sea (of microbes). Current: The Journal of Marine Education 28:3-8

Bruno, B.C., Padilla-Gamiño, J., De Leo, F. 2013. C-MORE Professional Development Training Program for graduate students and post-doctoral researchers. The Earth Scientist XXIX(3):11-15

Buitenhuis, E.T., Li, W.K. W., Lomas, M.W., Karl, D.M., Landry, M.R., Jacquet, S. 2012. Picoheterotroph (Bacteria and Archaea) biomas distribution in the global ocean. Earth System Science Data 4:101-106

Buitenhuis, E.T., Vogt, M., Moriarty, R., Bednaršek, N., Doney, S.C., Leblanc, K., Le Quéré, C., Luo, Y.-W., O'Brien, C., O'Brien, T., Peloquin, J., Schiebel, R., Swan, C. 2013. MAREDAT: towards a world atlas of MARine Ecosystem DATa. Earth System Science Data 5:227-239

Casey, J., Aucan, J., Goldberg, S., Lomas, M. 2013. Changes in partitioning of carbon amongst photosynthetic pico- and nanoplankton groups in the Sargasso Sea in response to changes in the North Atlantic Oscillation. Deep Sea Research II 93:58-70.

Chen, B., Laws, E. A., Liu, H., Huang, B. 2013. Estimating microzooplankton grazing half-saturation constants from dilution experiments with nonlinear feeding kinetics. Limnology and Oceanography 59:639-644

Church, M.J., Böttjer, D. 2013. Diversity, ecology, and biogeochemical influence of N2 fixing microorganisms in the sea. In: Levin S.A. Encyclopedia of Biodiversity. pp 608–625. Academic Press

Church, M.J., Lomas, M., Karger, F.M. 2013. Sea Change: Charting the course for biogeochemical ocean time series research in a new millennium. Deep Sea Research II 93:2-15

Cox, A.D., Saito, M.A. 2013. Proteomic responses of oceanic Synechococcus WH8102 to phosphate and zinc scarcity and cadmium additions. Frontiers in Microbiological Chemistry 4:387- doi: 10.3389/fmicb.2013.00387

Crowe, S.A., Maresca, J.A., Jones, C.A., Sturm, A., Henny, C., Fowle, D.A., Cox, R.P., Delong, E.F., Canfield, D.E. 2013. Deep-water anoxygenic photosynthesis in a ferruginous chemocline. Geobiology 12:332-339.

DeLong, E.F. 2013. Editor Preface: Microbial metagenomics, metatranscriptomics, and metaproteomics. Methods Enzymology doi: 10.1016/B978-0-12-407863-5.09983-4:xxi-xxi

Doney, S.C. 2013. Marine ecosystems, biogeochemistry, and climate. In: Siedler, G., Griffies, S.M., Gould, J., Church, J.A., (Editors) Ocean Circulation and Climate, 2nd Ed. A 21st century perspective. pp 817–842. Academic Press

Ducklow, H.W., Doney, S.C. 2013. What is the metabolic state of the oligotrophic ocean? A debate. Annual Reviews in Marine Science 5:525-533

Dyhrman, S.T., White, A. 2013. The marine phosphorus cycle. Frontiers in Aquatic Microbiology 4:105-doi: 10.3389/fmicb.2013.00105

Fitzsimmons, J., Boyle, E. 2013. Both soluble and colloidal iron phases control dissolved iron variability in the tropical North Atlantic Ocean. Geochimica Cosmochimica Acta 125:539-550

Fitzsimmons, J.N., Zhang, R., Boyle, E.A. 2013. Dissolved iron in the tropical North Atlantic. Marine Chemistry 154:87-99

Flombaum, P., Gallegos, J.L., Gordillo, R.A., Rincón, J., Zabala, L.L., Jiao, N., Karl, D.M., Li, W.K.W., Lomas, M.W., Veneziano, D., Vera, C.S., Vrugt, J.A., Martiny, A.C. 2013. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proceedings of the National Academy of Sciences USA 110:9824-9829

Foley, J.M., Bruno, B.C., 2013. Plankton on the stage: Microscopes in middle schools. Current: The Journal of Marine Education 28(3):16-19

Foley, J.M., Bruno, B.C., Tolman, R.T., Kagami, R.S., Hsia, M.H., Mayer, B., Inazu, J.K. 2013. C-MORE Science Kits as a classroom learning tool. Journal of Geoscience Education 61(3):256-267

Franks, P.J.S., Di Lorenzo E., Goebel N.L., Chenillat F., Rivière P., Edwards C.A., Miller, A.J. 2013. Modeling physical-biological responses to climate change in the California Current System. Oceanography 26:26-33

Haas, A.F., Nelson, C.E., Rohwer, F., Kelly, L.W., Quistad, S.D., Carlson, C.A., Leichter, J.J., Hatay, M., Smith, J.E. 2013. Influence of coral and algal exudates on microbially mediated reef metabolism. PeerJ 1:e108-e135

Haley, S., Dyhrman, S., 2013. Microbial superheroes unite through the virtual world of Whyville. Current: The Journal of Marine Education 28(3):9-10

Hashioka, T., Vogt, M., Yamanaka, Y., Le Quéré, C., Buitenhuis, E.T., Aita, M.N., Alvain, S. Bopp, L., Hirata, T., Lima, I., Sailley, S., Doney, S.C. 2013. Phytoplankton competition during the spring bloom in four plankton functional type models, Biogeosciences, 10:6833-6850

Hilton, J.A., Foster, R.A., Tripp, H.J., Carter, B.J., Zehr, J.P., Villareal, T.A. 2013. Genomic deletions disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont. Nature Communications 4:1767-1767

Hunt, D. E., Lin, Y., Church, M. J., Karl, D. M., Tringe, S. G., Izzo, L. K., Johnson, Z. I. 2013. Relationship between abundance and specific activity of bacterioplankton in open ocean surface waters. Applied and Environmental Microbiology 79:177-184

Jones, V., Meador, T.B., Gogou, A., Penkman, KE.H, Collins, M.J., Repeta, D.J. 2013. Characterisation and dynamics of dissolved organic matter in the Northwestern Mediterranean Sea. Progress in Oceanography 119:78-89

Jungbluth, S. P., L. G. H. Johnson, J. P. Cowen, and M. S. Rappé 2013. Data report: microbial diversity in sediment nearby Grizzly Bare seamount from sites 1363B and 1363G. Proceedings of the Intergrated Ocean Drilling Program 327: doi:10.2204/iodp.proc.327.201.2013-.

Jungbluth, S., Grote, J., Lin, H.-T., Cowen, J., Rappé, M. 2013. Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank. The ISME Journal 7:161-172

Kelly, L., Ding, H., Huang, K.H., Osburne, M.S., Chisholm, S.W. 2013. Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent. The ISME Journal 7:1827-1841

Labrie, S.J., Frois-Moniz, K., Osburne, M.S., Kelly, L., Roggensack, S.E., Sullivan, M.B., Gearin, G., Zeng, Q., Fitzgerald, M., Henn, M.R., Chisholm, S.W. 2013. Genomes of marine cyanopodoviruses reveal multiple origins of diversity. Environmental Microbiology 15:1356-1367

Laws, E. A. 2013. Evaluation of in situ phytoplankton growth rates: A synthesis of data from varied approaches. Annual Review of Marine Science 5:247-268

Laws, E. A., Pei, S., Bienfang, P. 2013. Phosphate-limited growth of the marine diatom Thalassiosira weissflogii: Evidence of non-Monod growth kinetics. Journal of Phycology 49:241-247

Leichter, J.J., Alldredge, A.L., Bernardi, G., Brooks, A.J., Carlson, C.A., Carpenter, R.C., Edmunds, P.J., Fewings, M.R., Hanson, K.M., Hench, J.L., Holbrook, S.L., Nelson, C.E., Schmitt, R.J., Toonan, R.J., Washburn, L., Wyatt, A.S.J. 2013. Biological and physical interactions on a tropical island coral reef: Transport and retention processes on Moorea, French Polynesia. Oceanography 26:52-63

Li, B.L., Karl, D.M., Letelier, R.M., Bidigare, R.R., Church, M.J. 2013. Variability of chromophytic phytoplankton in the North Pacific Subtropical Gyre. Deep Sea Research II 93:84-95

Malmstrom, R., Rodrigue, S., Huang, K.H., Kelly, L., Kern, S., Thompson, A., Roggensack, S., Berube, P.M., Henn, M., Chisholm, S.W. 2013. Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis. The ISME Journal 7:184-198

Marinov, I., Doney, S.C., Lima, I.D., Lindsay, K., Moore, J.K., Mahowald, N. 2013. North-south asymmetry in the modeled phytoplankton response to climate change over the 21st century. Global Biogeochemical Cycles 27:1274-1290

Martínez A., Ventouras L.A., Wilson S.T., Karl D.M., Delong E.F. 2013. Metatranscriptomic and functional metagenomic analysis of methylphosphonate utilization by marine bacteria. Frontiers in Microbiology 4:340-doi: 10.3389/fmicb.2013.00340

Martínez-García, S., Fernández, E., del Valle, D.A., Karl, D.M., Teira, E. 2013. Experimental assessment of marine bacteria respiration. Aquatic Microbial Ecology 70:189-205

Michelou, V.K., Caporaso, J.G., Knight, R., Palumbi, S.R. 2013. The Ecology of Microbial Communities Associated with Macrocystis pyrifera. PLOS ONE 8:6-80

Misumi, K., Lindsay, K., Moore, J.K., Doney, S.C., Tsumune, D., Yoshida, Y. 2013. Humic substances may control dissolved iron distributions in the global ocean: Implications from numerical simulations. Global Biogeochemical Cycles 27:450-462

Moore, C.M., Mills, M.M., Arrigo, K.R., Berman-Frank, I., Bopp, L., Boyd,P.W., Galbraith, E.D., Geider, R.J., Guieu, C., Jaccard, S.L., Jickells, T.D., LaRoche, J., Lenton, T., Mahowald, N.M., Marañón, E., Marinov, I., Moore,J.K., Nakatsuka, T., Oschlies, A., Saito, M.A., Thingstad, T.F., Tsuda, A., and Ulloa, O. 2013. Processes and patterns of ocean nutrient limitation. Nature Geosciences 6:702-710

Noble, A.E., Moran, D.M., Allen, A.E., Saito, M.A. 2013. Dissolved and particulate trace metal micronutrients under the McMurdo Sound seasonal sea ice: basal sea ice communities as a capacitor for iron. Frontiers in Microbiological Chemistry 4:387-doi: 10.3389/fmicb.2013.00387

Ottesen E.A., Young C.R., Eppley J.M., Ryan J.P., Chavez F.P., Scholin C.A., DeLong E.F. 2013. Pattern and synchrony of gene expression among sympatric marine microbial populations. Proceedings of the National Academy of Sciences USA 110(6):E488-97

Padilla-Gamiño, J. Bidigare, R., Barshis, D., Alamaru, A., Hedouin, L., Hernandez-Pech, X., Kandel, F., Leon Soon, S., Roth, M., Rodrigues, L., Grottoli, A., Portocarrero, C., Wagenhouser, S., Buttler, F., Gates, R. 2013. Are all eggs created equal? A case study from the Hawaiian reef building coral Montipora capitata. Coral Reefs 32:137-152

Pasulka, A.L., Landry, M.R., Taniguchi, D.A.A., Taylor, A.G., Church, M.J. 2013. Temporal dynamics of phytoplankton and heterotrophic protists at station ALOHA. Deep Sea Research II 93:44-57

Pei, S., Laws, E. A. 2013. Does the 14C method estimate net photosynthesis? Implications from batchand continuous culture studies of marine phytoplankton. Deep-Sea Research 82:1-9

Peloquin, J., C. Swan, N. Gruber, M. Vogt, H. Claustre, J. Ras, J. Uitz, R. Letelier et al. 2013. The MAREDAT global database of high performance liquid chromatography marine pigment measurements. Earth System Science Data 5:109-123

Rappé, M. S. 2013. Stabilizing the foundation of the house that 'omics builds: the evolving value of cultured isolates to marine microbiology. Current Opinion in Microbiology 16:618-624

Ruckelshaus, M., Doney, S.C., Galindo, H.M., Barry, J.P., Chan, F., Duffy, J.E., English, C.A., Gaines, S.D., Grebmeier, J.M., Hollowed, A.B., Knowlton, N., Polovina, J., Rabalais, N.N., Sydeman, W.J., Talley, L.D. 2013. Securing ocean benefits for society in the face of climate change. Marine Policy 40:154-159

Sailley, S., Vogt, M., Doney, S.C., Aita, M.N., Bopp, L., Buitenhuis, E.T., Hashioka, T., Lima, I., Le Quéré, C., Yamanaka, Y. 2013. Comparing food web structures and dynamics across a suite of global marine ecosystem models, Ecological Modeling, 261-262:43-57

Saito, M.A., Noble, A.E., Tagliabue, A., Goepfert, T.J., Lamborg, C.H., Jenkins, W.J. 2013. A Large Hydrothermal Iron Plume in the South Atlantic and Implications for Global Iron Cycling. Nature Geosciences 6:775-779

Sharma, A.K., Becker, J.W., Ottesen, E.A., Bryant, J.A., Duhamel, S., Karl, D.M., Cordero, O.X., Repeta, D.J., Delong, E.F. 2013. Distinct dissolved organic matter sources induce rapid transcriptional responses in coexisting populations of Prochlorococcus, Pelagibacter and the OM60 clade. Environmental Microbiology doi: 10.1111/1462-2920.12254

Shilova, I. N., Thompson A, Hewson I., Zehr, J.P. 2013. Ocean Gyres, Metagenomics of. In: Nelson K. Encyclopedia of Metagenomics: SpringerReference. pp xx–xx. Springer-Verlag Berlin Heidelberg

Siegel, D.A., Behrenfeld, M.J., Maritorena, S., McClain, C.R., Antoine, D., Bailey, S.W., Bontempi, P.S., Boss, E.S., Dierssen, H.M., Doney, S.C., Eplee Jr., R.E., Evans, R.H., Feldman, G.C., Fields, E., Franz, B.A., Kuring, N.A., Mengelt, C., Nelson, N.B., Patt, F.S., Robinson, W.D., Sarmiento, J.L., Swan, C.M., Werdell, P.J., Westberry, T.K., Wilding, J.G., Yoder, J.A. 2013. Regional to global assessments of phytoplankton dynamics from the SeaWiFS mission. Remote Sensing Environ. 135:77-91

Smith, J.E., Price, N.N., Nelson, C.E., Haas, A.F. 2013. Coupled changes in oxygen concentration and pH caused by metabolism of benthic coral reef organisms. Marine Biology 160:2437-2447

Steward, G.F., Culley, A.I., Wood-Charlson, E.M. 2013. Marine Viruses. In: Levin, S. Encyclopedia of Biodiversity 2nd Edition. Vol. 5, pp 127–144. Elsevier Inc.

Thompson, A., Bench S., Carter B., Zehr, J. 2013. Coupling FACS and genomic methods for the characterization of uncultivated symbionts. Methods in Enzymology 531:45-60

Thompson, A.W., Zehr, J.P. 2013. Cellular interactions: lessons from the nitrogen-fixing cyanobacteria. Journal of Phycology 49:1024-1035

Ussler, W. III, Tavormina, P., Preston, C., Marin III, R., Pargett, D., Jensen, S, Roman, B., Shah, S., Girguis, P.R., Birch, J.M., Orphan, V. Scholin, C. 2013. Autonomous in situ quantitative PCR amplification of aerobic methanotroph genes in the deep sea. Environmental Science Technology 47:9339-9346

White, A.E., Dyhrman, S. 2013. The marine phosphorus cycle. Frontiers in Microbiology 4:doi: 10.3389 -/fmicb.2013.00105

Wilson, S.T., del Valle, D.A., Robidart, J.C., Zehr, J.P. and Karl, D.M. 2013. Dissolved hydrogen and nitrogen fixation in the oligotrophic North Pacific Subtropical Gyre. Environmental Microbiology Reports 5:697-704

Wilson, S.T., Karl, D.M., 2013. A high-resolution insight into microbial biogeochemistry in the North Pacific Ocean. Current: The Journal of Marine Education 28(3):20-21

Wood-Charlson, E.M. 2013. Marine Symbioses: Metazoans and Microbes. In: Levin, S.A. Encyclopedia of Biodiverity, 2nd ed. pp 116–126. Academic Press: Waltham

Yeo, S. K., Eiler, A., Huggett, M., Rappé, M. S. 2013. Coastal bacterioplankton community dynamics in response to a natural disturbance.. PLoS ONE doi:10.1371/journal.pone.0056207.


Apprill, A., Marlow, H.Q., Martindale, M.Q., Rappé, M.S. 2012. The specificity of associations between bacteria and the coral Pocillopora meandrina during early development. Applied and Environmental Microbiology 78:7467-7475

Bang, M., Chisholm, P. 2012. Ocean Sunlight: How Tiny Plants Feed the Seas. Scholastic, Inc. 48 pp

Björkman, K.M., Duhamel, S., Karl, D.M. 2012. Microbial group specific uptake kinetics of inorganic phosphate and adenosine-5’-triphosphate (ATP) in the North Pacific Subtropical Gyre. Frontiers in Microbiology 3:1-17

Blomquist, B.W., Fairall, C.W., Huebert, B.J., Wilson S.T. 2012. Direct measurement of the oceanic carbon monoxide flux by eddy correlation. Atmos. Meas. Tech. Discuss. 5:4089-4825

Boyle, E., John, S., Abouchami, W., Adkins, J., Echegoyen-Sanz, Y., Ellwood, M., Flegal, A., Fornace, K., Gallon, C., Galer, S., Gault-Ringold, M., Lacan, F., Radic, A., Rehkamper, M., Rouxel, O., Sohrin, Y., Stirling, C., Thompson, C., Vance, D., Xue, Z., Zhao, Y. 2012. GEOTRACES IC1 (BATS) Contamination-Prone Trace Element Isotopes Cd, Fe, Pb, Zn, Cu, Mo) Intercalibration. Limnology and Oceanography Methods 10:653-665

Bryant, J. A., Stewart, F. J., Eppley, J. M., Delong, E. F. 2012. Microbial community phylogenetic and trait diversity declines steeply with depth in a marine oxygen minimum zone. Ecology 93:1659-1673

Buitenhuis, E. T., Li, W. K. W., Vaulot, D., Lomas, M. W., Landry, M., Partensky, F., Karl, D. M., Ulloa, O., Campbell, L., Jacquet, S., Lantoine, F., Chavez, F., Macias, D., Gosselin, M., McManus, G. B. 2012. Picophytoplankton biomass distribution in the global ocean. Earth System Science Data 4:37-46

Cassman, N., Prieto-Davó, A., Walsh, K., Silva, G.G.Z., Angly, F., Akhter, S., Barott, K., Busch, J., McDole, T., Haggerty, J.M., Willner, D., Alarcón, G., Ulloa, O., DeLong, E.F., Dulith, B., Rohwer, F., Dinsdale, E. A. 2012. Oxygen minimum zones harbour novel viral communities with low diversity. Environmental Microbiology 14:3043-3065

Cordero, O.X., Ventouras, L.A., Delong, E.F., Polz, M. 2012. Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations. Proceedings of the National Academy of Sciences USA 109:20059-20064

Danhorn, T., Young C.R., DeLong, E.F. 2012. Comparison of large-insert, small-insert, and pyrosequencing libraries for metagenomic analysis. The ISME Journal 6:2056-2066

DeLong, E.F. 2012. Microbial evolution in the wild. Science 336:422-424

del Valle, D.A., Kiene, R.P., Karl, D.M. 2012. Effect of visible light on dimethylsulfoniopropionate assimilation and conversion to dimethylsulfide in the North Pacific Subtropical Gyre. Aquatic Microbial Ecology 66:47-62

Ditchfield A.K., Wilson, S.T., Hart, M.C., Purdy, K.J., Green, D.H., Hatton, A.D. 2012. Identification of putative methylotrophic and hydrogenotrophic methanogens within sedimenting material and copepod faecal pellets. . Aquatic Microbial Ecology 67:151-160

Duhamel, S., Björkman, K.M., Karl, D.M. 2012. Light dependence of phosphorus uptake by microorganisms in the North and South Pacific subtropical gyres. Aquatic Microbial Ecology 67:225-238

Dyhrman, S.T., Haley, S.T. 2012. Arsenate resistance in the marine diazotroph Crocosphaera watsonii. Frontiers in Microbiology 2:214-doi:10.3389/fmicb.2011.00214

Dyhrman, S.T., Jenkins, B.D., Rynearson, T.A., Saito, M.A., Mercier, M.L. and others 2012. The Transcriptome and Proteome of the Diatom Thalassiosira pseudonana reveal a Diverse Phosphorus Stress Response. PLoS ONE 7:e3376-doi:10.1371/journal.pone.0033768

Fitzsimmons, J., Boyle, E. 2012. An intercalibration between the GEOTRACES GO-Flo and the MITESS/Vanes sampling systems for dissolved iron concentration analyses (and a closer look at adsorption effects). Limnology and Oceanography Methods 10:437-450

Friedrich, T., Timmermann, A., Abe-Ouchi, A., Bates, N.R., Chikamoto, M.O., Church, M.J., Dore, J.E., Gledhill, D.K., Gonzalez-D´avila, M., Heinemann, M., Ilyina, T., Jungclaus, J.H., McLeod, E., Mouchet, A., Santana-Casiano, J.M. 2012. Detecting regional anthropogenic trends in ocean acidification against natural variability. Nature Climate Change 2:167-171

Gibson, B.A., Bruno, B.C. 2012. The C-MORE Scholars Program: Motivations for an academic-year Research Experiences for Undergraduates program. Journal of College Science Teaching 41:12-18

Grote, J., Thrash, J. C., Huggett, M.J., Landry, Z.C., Carini, P., Giovannoni, S.J., Rappé, M.S. 2012. Streamlining and core genome conservation among highly divergent members of the SAR11 clade. mBio 3(5):e00252-12

Grote, J., Schott, T., Bruckner, C.G., Glockner, F.O., Jost, G., Teeling, H., Labrenz, M., Jürgens K. 2012. Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones. Proceedings of the National Academy of Sciences USA 109:506-510

Guidi, L., Calil, P.H.R., Duhamel, S., Björkman, K.M., Doney, S.C., Jackson, G.A., Li, B., Church, M.J., Tozzi, S., Kolber, Z.S., Richards, K.J., Fong, A.A., Letelier, R.M., Gorsky, G., Stemmann, L., Karl, D.M. 2012. Does eddy-eddy interaction control surface phytoplankton distribution and carbon export in the North Pacific Subtropical Gyre? J. Geophys. Res. Biogeosci. 117:G02024 -doi:10.1029/2012JG001984

Hsia, M.H., Bruno, B.C. 2012. Hands-on family science program stimulates interest in ocean science careers. Current: The Journal of Marine Education 28:16-25

Huggett, M. J., Hayakawa, D. H., Rappé, M. S. 2012. Genome sequence of strain HIMB624, a cultured representative from the OM43 clade of marine Betaproteobacteria. Standards in Genomic Sciences 6:doi:10.4056/sigs.2305090-.

Huggett, M.J., Rappé, M.S. 2012. Genome sequence of strain HIMB55, a novel marine gammaproteobacterium of the OM60/NOR5 clade. J. Bacteriology 194:2393-2394

Huggett, M.J., Rappé, M.S. 2012. Genome sequence of strain HIMB30, a novel member of the marine Gammaproteobacteria. J. Bacteriology 194:732-733

Hynes, A.M., Webb, E.A., Doney, S.C., Waterbury, J.B. 2012. Comparison of cultured Trichodesmium (Cyanophyceae) with species characterized from the field. J. Phycology 48:196-210

Juranek, L., Quay, P., Feely, R., Lockwood, D., Karl, D., Church, M. 2012. Biological production in the NE Pacific and its influence on air-sea CO2 flux: Evidence from dissolved oxygen isotopes and O2/Ar. J. Geophysical Research, Oceans 117:C05012

Kahng, S., Hochberg, E., Apprill, A., Wagner, D., Luck, D., Perez, D., Bidigare, R. 2012. Efficient light harvesting in deep-water, zooxanthellate corals. Marine Ecology Progress Series 455:65-77

Karl, D.M., Church, M.J., Dore, J.E., Letelier, R.M., Mahaffey, C. 2012. Predictable and efficient carbon sequestration in the North Pacific Ocean supported by symbiotic nitrogen fixation. Proceedings of the National Academy of Sciences USA 109:1842-1849

Levine, N.M., Varaljay, V.A., Toole, D.A., Dacey, J.W.H., Doney, S.C., Moran, M.A. 2012. Environmental, biochemical and genetic drivers of DMSP degradation and DMS production in the Sargasso Sea. Environmental Microbiology 14:1210-1223

Lomas, M., Moran, S., Casey, J., Bell, D., Tiahlo, M., Whitefield, J., Kelly, R., Mathis, J., Cokelet, E. 2012. Spatial and seasonal variability of primary production on the Eastern Bering Sea shelf. Deep Sea Research II 65-70:126-140

Luo, Y.-W., Ducklow, H.W., Friedrichs, M.A.M., Church, M.J., Karl, D.M., Doney, S.C. 2012. Interannual variability of primary production and dissolved organic nitrogen storage in the North Pacific Subtropical Gyre. , J. Geophysical Research Biogeosci. 117:G03019-doi:10.1029/2011JG001830

Luo, Y.-W., S.C. Doney, L.A. Anderson, M. Benavides, I. Berman-Frank, A. Bode, S. Bonnet, K.H. Boström, D. Böttjer, D.G. Capone, E.J. Carpenter, Y.L. Chen, M.J. Church, J.E. Dore, L.I. Falcón, A. Fernández, R.A. Foster, K. Furuya, F. Gómez, K. Gundersen, A.M. Hynes, D.M. Karl, S. Kitajima, R.J. Langlois, J. LaRoche, R.M. Letelier, E. Marañón, D.J. McGillicuddy Jr., P.H. Moisander, C.M. Moore, B. Mouriño-Carballido, M.R. Mulholland, J.A. Needoba, K.M. Orcutt, A.J. Poulton, E. Rahav, P. Raimbault, A.P. Rees, L. Riemann, T. Shiozaki, A. Subramaniam, T. Tyrrell, K.A. Turk-Kubo, M. Varela, T.A. Villareal, E.A. Webb, A.E. White, J. Wu, and J.P. Zehr, 2012: Database for diazotrophs in global ocean: abundances, biomass and nitrogen fixation rates. Earth Syst. Sci. Data, 4:47-73

Mackey, K., Buck, K., Casey, J., Cid, A., Lomas, M., Sohrin, Y., Paytan, A. 2012. Phytoplankton responses to atmospheric metal deposition in the coastal and open-ocean Sargasso Sea. Frontiers in Microbiology 3:1-15

Mahaffey, C., Bjorkman, K.M., Karl, D.M. 2012. Phytoplankton response to deep seawater nutrient addition in the North Pacific Subtropical Gyre. Marine Ecology Progress Series 460:13-34

McSorley, F.R., Wyatt, P., Martinez, A., DeLong, E.F., Hove-Jensen, B., Zechel, D.L. 2012. PhnY and PhnZ comprise a new oxidative pathway for enzymatic cleavage of a carbon-phosphorus bond. J. Am. Chem. Soc. 134:8364-8367

Mouw, C.B., Yoder, J.A., Doney, S.C. 2012. Impact of phytoplankton community size on a linked global ocean optical and ecosystem model. J. Marine Systems 89:61-75

Nicholson, D.P., Stanley, R.H.R., Barkan, E., Karl, D.M., Luz, B., Quay, P.D., Doney, S.C. 2012. Evaluating triple oxygen isotope estimates of gross primary production at the Hawaii Ocean Time-series and Bermuda Atlantic Time-series Study sites . J. Geophys. Res. Oceans 117:C05012-doi:10.1029/2010JC006856

Nigro, O.D., Culley, A.I., Steward, G.F. 2012. Complete genome sequence of bacteriophage VvAW1, which infects Vibrio vulnificus. Standards in Genomic Sciences 6:415-426

Noble, A.E., Lamborg, C.H., Ohnemus, D., Lam, P.J., Goepfert, T.J., Measures, C.I., Frame, C.H., Casciotti, K.L., DiTullio, G.R., Jennings, J., Saito, M.A. 2012. Basin-scale plumes of cobalt, iron, and manganese emanating from the Benguela-Angola front in the South Atlantic Ocean. Limnology and Oceanography 57:989-1010

Paerl, R. W., Tozzi, S., Kolber, Z., Zehr, J.P. 2012. Variation in Synechococcus sp. CC9311 narB mRNA abundance relative to changes in light, nitrogen growth conditions and nitrate assimilation. J Phycology 48:1028-1039

Paerl, R.W., Turk, K.A., Beinart, R., Chavez, F.P., Zehr, J.P. 2012. Seasonal change in the abundance of Synechococcus and multiple distinct phylotypes at Monterey Bay determined by rbcL and narB quatitative PCR. Environmental Microbiology 14:580-593

Robidart, J.C, Preston, C.M., Paerl, R.W., Turk, K.A., Mosier, A.C., Francis, C.A., Scholin, C.A., Zehr, J.P. 2012. Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation. The ISME Journal 6:513-523

Robidart, J., Shilova, I.N., Zehr, J.P. 2012. ‘Omics’-enabled microbial sensors on ocean platforms. In: Tiquia-Arashiro, S.M. Molecular Biological Technologies for Ocean Sensing. pp 1-32. Humana Press, The University of Michigan-Dearborn

Saito, M.A. 2012. The rise of oxygen and aerobic biochemistry. Structure 20:1-2

Sanudo-Wilhelmy, S.A., Cutter, L.S., Duraxo, R., Smail, E.A., Gomez-Consarnau, L., Webb, E.A., Prokopenko, M.G., Berelson, W.M., Karl, D.M. 2012. Multiple B-vitamin depletion in large areas of the coastal ocean. Proceedings of the National Academy of Sciences USA 109:14041-14045

Steward, G.F., Culley, A.I., Mueller, J.A., Wood-Charlson, E.M., Belcaid, M., Poisson, G. 2012. Are we missing half of the viruses in the ocean? The ISME Journal 7:672-679.

Stewart, F. J., Dalsgaard, T., Young, C.R., Thamdrup, B., Revsbech, N.P., Ulloa, O., Canfield, D.E., DeLong, E.F. 2012. Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton. PLoSOne 7:e37118-.

Stewart, F.J., Ulloa, O., DeLong, E.F. 2012. Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environmental Microbiology 14:23-40

Thompson, A., Foster, R.A., Krupke, A., Carter, B.J., Vaulot, D., Kuypers, M.M.M., Zehr, J.P. 2012. Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga. Science 337:1546-1550

Turk-Kubo, K.A., Achilles, K.M., Cote, T., Ochiai, M., Montoya, J. P., Zehr, J.P. 2012. Nitrogenase (nifH) gene expression in diazotrophic cyanobacteria in the Tropical North Atlantic in response to nutrient amendments. Frontiers in Aquatic Microbiology 3:386

Ulloa, O., Canfield, D.E., DeLong, E.F., Letelier, R.M., Stewart, F.J. 2012. Microbial oceanography of oxygen minimum zones. Proceedings of the National Academy of Sciences USA 109:15996-156003

Van Mooy, B.A.S., Hmelo, L.R., Soffen, L.E., Campangna, S.R., May, A.L., Dyhrman, S.T., Heithoff, A., Webb, E.A., Momper, L., Mincer, T.J. 2012. Quorum sensing control of phosphorus acquisition in Trichodesmium consortia. The ISME Journal 6:422-429

Varaljay, V.A., Gifford, S.M., Wilson, S.T., S. Sharma, Karl, D.M., Moran, M.A. 2012. Bacterial dimethylsulfoniopropionate-degrading genes in the oligotropic North Pacific Subtropical Gyre. Applied and Environmental Microbiology 78:2775-2782

Waldbauer, J.R., Rodrigue, S., Coleman, M.L., Chisholm, S.W. 2012. Transcriptome and proteome dynamics of a light-dark synchronized bacterial cell cycle. PLoS One 7:e43432-

White, A.E., Foster, R.A., Benitez-Nelson, C.R., Masqué, P., Verdeny, E., Popp, B.N. et al. 2012. Nitrogen fixation in the Gulf of California and the Eastern Tropical North Pacific. Progress in Oceanography 109:1-17.

Wilson, S.T., Bottjer, D., Church, M.J., Karl, D.M. 2012. Comparative assessment of nitrogen fixation methodologies conducted in the oligotrophic North Pacific Ocean. Applied and Environmental Microbiology 78:6516-6523

Wilson, S.T., Kolber, Z.S., Tozzi, S., Zehr, J.P., Karl, D.M. 2012. Nitrogen fixation, hydrogen cycling and electron transport kinetics in Trichodesmium erythraeum (Cyanobacteria) Strain IMS101. J. Phycology 48:595-606

Zeng, Q., Chisholm, S.W. 2012. Marine viruses exploit their host's two-component regulatory system in response to resource limitation.. Current Biology 22:124-128


Anderson, L.A., McGillicuddy, D.J. Jr., Maltrud, M.E., Lima, I.D., Doney, S.C. 2011. Impact of eddy-wind interaction on eddy demographics and phytoplankton community structure in a model of the North Atlantic. Dynamics Atmos. Oceans 52:80-94

Bench, S.R., Ilikchyan, I.N., Tripp, H., James, H., Zehr, J.P. 2011. Two strains of Crocosphaera watsonii with highly conserved genomes are distinguished by strain-specific features. Frontiers in Microbiol. 2:261

Bienfang, P., DeFelice, S., Laws, E.A. 2011. Quantitative Environmental Benchmarking in a Hydrologically Driven Hawaiian Coastal System. Marine Technology Society Journal 45:88-100

Bombar, D., Moisander, P.H., Dippner, J.W., Foster, R.A., Voss, M., Karfeld, B., Zehr, J.P. 2011. Distribution of diazotrophic microorganisms and nifH gene expression in the Mekong River Plume during intermonsoon. Marine Ecology Progress Series 424:39-55

Brum, J.R., Steward, G.F. 2011. Evaluation of methods for physical fractionation of aquatic viral assemblages. Limnology and Oceanography Methods 9:150-163

Bruno, B. C., Tice, K. A., Puniwai, N., Achilles, K. 2011. Ocean acidification: hands-on experiments to explore the causes and consequences. Science Scope 34:23-30

Bruno, B.C., Wiener, C.W., Kimura, A., Kimura, R. 2011. Ocean FEST: Families Exploring Science Together. Journal of Geoscience Education 59:13-21

Bruno, B.C., Thomas, S.E., Frazier, M.M., James, L. 2011. Student perspectives on facilitating positive undergraduate research experiences. Council of Undergraduate Research Quarterly 32 (2):37-40

Brzezinski, M.A., Krause, J.W., Church, M.J., Karl, D.M., Li, B., Jones, J.L., Updyke, B. 2011. The annual silica cycle of the North Pacific subtropical gyre. Deep Sea Research I 58:988-1001

Calil, P.H.R., Doney, S.C., Yumimoto, K., Eguchi, K., Takemura, T. 2011. Episodic upwelling and dust deposition as bloom triggers in low nutrient low chlorophyll (LNLC) regions. J. Geophys. Res. Oceans 116:C06030-doi:10.1029/2010JC006704

Chisholm, S.W. 2011. Unveiling Prochlorococcus. Microbe 6:280-283

Culley, A.I. 2011. Virophages to viromes: a report from the frontier of viral oceanography. Current opinion in virology 1:52-57

Duhamel, S., Björkman, K.M., Van Wambeke, F., Moutin, T., Karl, D.M. 2011. Characterization of alkaline phosphatase activity in the North and South Pacific Subtropical Gyres: Implications for phosphorus cycling. Limnology and Oceanography 56:1244-1254

Eiler, A., Hayakawa, D. H., Rappé, M. S. 2011. Non-random assembly of bacterioplankton communities in the subtropical North Pacific Ocean. Frontiers in Aquatic Microbiology 2:140-140

Farnelid, H., Andersson, A.F., Bertilsson, S. Al-Soud, W.A., Hansen, L.H., Sorensen, S., Steward, G.F., Hagstrom, A., Riemann, L. 2011. Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria. PLoS ONE 6:e19223

Fawcett, S., Lomas, M., Casey, J., Ward, B., Sigman, D. 2011. Assimilation of upwelled nitrate by small eukaryotes in the Sargasso Sea. Nature Geoscience 4:1-6

Feely, R.A., Doney, S.C. 2011. Ocean acidification: the other CO2 problem. ASLO Limnology and Oceanography: e-Lectures website

Field D, Sansone S, DeLong E.F., Sterk P, Friedberg I, Kottmann R, Hirschman L, Garrity G, Cochrane G, Wooley J, Meyer F, Hunter S, White O. 2010. Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB.. ISMB 3:232-234

Field D, Sansone S, DeLong E.F., Sterk P, Friedberg I, Gaudet P, Lewis S, Kottmann R, Hirschman L, Garrity G, Cochrane G, Wooley J, Meyer F, Hunter S, White O, Bramlett B, Gregurick S, Lapp H, Orchard S, Rocca-Serra P, Ruttenberg A, Shah N, Taylor C, Thessen A. 2010. Meeting Report: BioSharing at ISMB. Stand Genomic Science. 3:3:254-258

Finzi, A.C., Cole, J.J., Doney, S.C., Holland, E.A., Jackson, R.B. 2011. Research frontiers in the analysis of coupled biogeochemical cycles. Frontiers Ecology and the Environment 9:74-80

Foster, R.A., Kuypers, M.M.M., Vagner, T., Paerl, R.W., Musat, N., Zehr, J.P. 2011. Nitrogen fixation and transfer in open ocean diatom-cyanobacterial symbioses. The ISME Journal 5:1484-1493

Glover, D.M., Jenkins, W.J., Doney, S.C. 2011. Modeling Methods for Marine Science. Cambridge University Press. 592 pp

Grote, J., et al. (including Y.M. Rii, M.J. Church, G.F. Steward, D.M. Karl, E.F. DeLong and M.S. Rappé) 2011. Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria. Stand. Genomic Sci. 5:269-278

Hamersley, M.R., Turk K.A., Leinweber A., Gruber N., Zehr J.P., Gunderson, T, Capone, D.G. 2011. Nitrogen fixation within the water column associated with two hypoxic basins within the Southern California Bight. Aquatic Microbial Ecology 63:19

Hayakawa, D. H., Huggett, M. J., Rappé, M. S. 2011. Ecology and cultivation of marine oligotrophic bacteria. In: Horikoshi, K., Antranikian, G., Bull, A. T., Robb, F., Stetter, K. Extremophiles Handbook. pp 1161–1178. Springer-Verlag

Hsia, M.H., Thomas, K.A., Bruno, B.C. 2011. What microbe are you? An activity designed for our youngest scientists. American Society for Microbiology Classroom and Outreach Activities (online) July 2011:1-11

John, S.G., Mendez, C.B., Deng, L., Poulos, B., Kauffman, A.K.M., Kern, S., Brum, J., Polz, M.F., Boyle, E.A. Sullivan, M.B. 2011. A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environmental Microbiology Reports 3:195-202

Johnsen, G., A. Bricaud, N. Nelson, B. B. Prézelin and R. R. Bidigare. 2011. In vivo bio-optical properties of phytoplankton pigments. In: Phytoplankton Pigments: Characterization, Chemotaxonomy and Applications in Oceanography. Cambridge Environmental Chemistry Series, Cambridge, pp. 496-537.

Jouandet, M.P., Trull, T.W., Guidi, L., Picheral, M., Ebersbach, F., Stemmann, L., Blain. S. 2011. Optical imaging of mesopelagic particles indicates deep carbon flux beneath a natural iron-fertilized bloom in the Southern Ocean. Limnology and Oceanography 56:1130-1140

Kelly, L., Huang, K.H., Ding, H., Chisholm, S.W. 2011. ProPortal: A resource for integrated systems biology of Prochlorococcus and its phage. Nucleic Acids Res 40:D632-D640

Kim, J.-M., Lee, K., Shin, K., Yang, E.J., Engel, A., Karl, D.M., Kim, H.-C. 2011. Shifts in biogenic carbon flow from particulate to dissolved forms under high carbon dioxide and warm ocean conditions. Geophysical Research Letters 38: L08612, doi:10.1029/2011GL047346

Kimura, H., Young, CR, Martinez, A., DeLong, E.F. 2011. Light induced transcriptional responses associated with proteorhodopsin enhanced growth in a marine flavobacterium. The ISME Journal 5:1641-1651

Landry, M. R., Selph, K.E, Taylor, A. G., Décima, M., Balch, W. M., Bidigare, R.R. 2011. Phytoplankton growth, grazing and production balances in the HNLC equatorial Pacific . Deep Sea Research II 58:524-535

Laws, E. A., Pei, S., Bienfang, P., Grant, S. 2011. Phosphate-limited growth and uptake kinetics of the marine prasinophyte Tetraselmis suecica (Kylin) Butcher. Aquaculture 323:117-121

Laws, E.A., Pei, S. F.,Bienfang, P., Grant, S., Sunda, W.G. 2011. Phosphate-limited growth of Pavlova lutheri (prymnesiophyceae) in continuous culture: determination of growth-rate-limiting substrate concentrations with a sensitive bioassay procedure. Journal of Phycology 47:1089-1097

Laws, E.A., D'Sa, E., Naik, P. 2011. Simple equations to estimate ratios of new or export production to total production from satellite-derived estimates of sea surface temperature and primary production. Limnology and Oceanography:Methods 9:593-601

Lee, J.-M., Boyle, E.A., Echegoyen-Sanz, Y. , Fitzsimmons, J.N., Zhang, R., Kayser, R.A. 2011. Analysis of trace metals (Cu, Cd, Pb, and Fe) in seawater using single batch Nitrilotriacetate resin extraction and isotope dilution inductively coupled plasma mass spectrometry. Analytica Chimica Acta 686:93-101

Li, B., Karl, D.M., Letelier, R.M., Church, M.J. 2011. Size-dependent photosynthetic variability in the North Pacific Subtropical Gyre. Marine Ecology Progress Series 440: 27-40.

Martinez, A., Osbourne, M., DeLong, E.F., Chisholm, S.W. 2011. Phosphite utilization by the marine picocyanobacterium Prochlorococcus marinus MIT9301. Environmental Microbiology 14:1363-1377

Mayer, B., Bruno, B.C. 2011. C-MORE and Science Buzz: Where students and scientists meet. The Earth Scientist 27 (4):27-30

McQuatters-Gollop, A., Reid, P.C., Edwards, M., Burkill, P.H., Castellani, C., Batten, S., Gieskes, W., Beare, D., Bidigare,R.R., Head, E., Johnson, R., Kahru, M., Koslow J.A., Pena, A. 2011. Is there a decline marine phytoplankton? Nature 472:E6-E7

Misumi, K., Tsumune, D., Yoshida, Y., Uchimoto, K., Nakamura, T., Nishioka, J., Mitsudera, H. Bryan, F.O., Lindsay, K., Moore, J.K., Doney, S.C. 2011. Mechanisms controlling dissolved iron distribution in the North Pacific: A model study. J. Geophys. Res. Biogeosci 116:G03005-doi:10.1029/2010JG001541

Moisander P.H., Zhang, R., Boyle, E.A., Hewson, I., Montoya, J.P., Zehr, J.P. 2011. Analogous nutrient limitations in unicellular diazotrophs and Prochlorococcus in the South Pacific Ocean. The ISME Journal 6:733-744

Osburne, M.S., Holmbeck, B.M., Coe, A., Chisholm, S.W. 2011. The spontaneous mutation frequency in the marine cyanobacterium is commensurate with that of other bacteria. Environmental Microbiology Reports 3:744-749

Ottesen, E.A., Marin III, R., Preston, C.M., Young, C.R., Ryan, J.P., Scholin, C.A., DeLong, E.F. 2011. Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. The ISME Journal 5:1881-1895

Paerl, R.W., Johnson, K.S., Welsh, R.M., Worden, A.Z., Chavez, F.P., Zehr, J.P. 2011. Differential distributions of Synechococcus subgroups across the California Current System. Frontiers in Microbolgy 2:59

Preston, C.M., Harris, A., Ryan, J.P., Roman, B.,, Marin III, R., Jensen, S., Everlove, C., Birch, J., Dzenitis, J.M., Pargett, D., Adachi, M., Turk, K., Zehr, J.P., Scholin, C.A. 2011. Underwater application of quantitative PCR on an ocean mooring. PLoS ONE 6(8): e22522. doi:10.1371/journal.pone.0022522

Quigg, A., Sylvan, J. B., Gustafson, A. B., Fisher, T. R., Tozzi, S., and J. W. Ammerman 2011. Going west: role of phosphorus limitation in expanding the primary production across the Louisiana shelf. Aquatic Geochemistry 17:519-544

Rich, V.R., Pham, V., Eppley, J., Shi, Y., DeLong, E.F. 2011. Time-series analyses of Monterey Bay coastal microbial picoplankton using a "genome proxy" microarray. Environmental Microbiology 13:116-134

Robidart, J.C, Preston, C.M., Paerl, R.W., Turk, K.A., Mosier, A.C., Francis, C.A., Scholin, C.A., Zehr, J.P. 2011. Seasonal dynamics of Synechococcus and Thaumarchaeal microbial populations in Monterey Bay resolved in real time with remote in situ instrumentation. The ISME Journal 6:513-523

Ryan, J., Greenfield, D., Marin III, R., Preston, C., Roman, B., Jensen, S., Pargett, D., Birch, J., Mikulski, C., Doucette, G., Scholin, C. 2011. Harmful phytoplankton ecology studies using an autonomous molecular analytical and ocean observing network. Limnology and Oceanography 56:1255-1272

Saito, M.A., Bertrand, E.M., Bulygin, V., Moran, D., Dutkiewicz, S., Monteiro, F.M., Follows, M.J., Valois, F.W., Waterbury, J.B. 2011. Iron Conservation by Reduction of Metalloenzyme Inventories in the Marine Diazotroph Crocosphaera watsonii. Proceedings of the National Academy of Sciences USA 108:2184-2189

Saito, M.A. , Bulygin, V., Moran, D. , Taylor, C., Scholin, C. 2011. Examination of Microbial Proteome Preservation Techniques Applicable to Autonomous Environmental Sample Collection. Frontiers in Aquatic Microbiology doi: 10.3389/fmicb.2011.00215:1-10

Salerno, J.L., Reineman, D.R., Gates, R.D., Rappé, M.S. 2011. The effect of a sub-lethal temperature elevation on the structure of bacterial communities associated with the coral Porites compressa. Journal of Marine Biology doi:10.1155/2011/969173:.-.

Salter, I., Bottjer, D., Christaki, U. 2011. The effect of inorganic particle concentration on bacteria-virus-nanoflagellate dynamics. Environmental Microbiology 13:2768-2777

Scholin, C.2013. Ecogenomic Sensors. In: Levin S.A. (ed.) Encyclopedia of Biodiversity, second edition, Volume 2, pp. 690-700. Waltham, MA: Academic Press.

Selph, K.E., Landry, M.R., Taylor, A., Yang, E.J., Measures, C.I., Yang, J., Stukel, M., Christensen, S., Bidigare, R.R. 2011. Spatially-resolved taxon-specific phytoplankton production and grazing dynamics in the equatorial Pacific between 110°W and 140°W. Deep Sea Research II 58:358-377

Sher, D., Thompson, J.W., Kashtan, N., Croal, L., Chisholm, S.W. 2011. Response of Prochlorococcus ecotypes to co-culture with diverse marine bacteria. The ISME Journal 1:1-8

Shi, Y., Tyson, G. W, Eppley, J., DeLong. E.F. 2011. Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. The ISME Journal 5:999-1013

Smith Jr., W. O., Asper, V. A., Tozzi, S., Liu. X. 2011. Surface layer variability in the Ross Sea, Antarctica as assessed by in situ fluorescence measurements. Progress in Oceanography 88:28-45

Sohm, J. A., Hilton, J., Noble, A., Zehr, J.P., Saito, M.A., Webb, E.A. 2011. Nitrogen fixation in the South Atlantic Gyre and Benguela Upwelling System. Geophysical Research Letters 38:L16608

Steward, G.F., Preston, C.M. 2011. Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct cloning. Virology Journal 8:287

Stewart F.J., Dmytrenko O., Delong E.F., Cavanaugh C.M. 2011. Metatranscriptomic analysis of sulfur oxidation genes in the endosymbiont of solemya velum. Front Microbiol. 2:134-144

Stewart, F., Sharma, A. Bryant, J., Eppley, J.M., DeLong, E.F. 2011 Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities, Genome Biology, 12:R26, doi:10.1186/gb-2011-12-3-r26

Swan, B. K, Martinez-Garcia, M., Preston, C. M., Sczyrba, A., Woyke, T., , Lamy, D., Reinthaler, T., Poulton,N. J., Masland, E. D. P. , Lluesma Gomez, M., Sieracki, M.E., DeLong, E. F., Herndl,G.J., Stepanauskas, R. 2011. Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333:1296-1300

Sylvan, J. B., Quigg, A., Tozzi, S., Ammerman, J.W. 2011. Mapping phytoplankton community physiology on a river impacted continental shelf: testing a multifaceted approach. Estuaries and Coasts 34:1220-1233

Talarmin A., Van Wambeke F., Duhamel S., Catala P., Moutin T., Lebaron P. 2011. Improved methodology to measure taxon-specific phosphate uptake in live and unfiltered samples. Limnology and Oceanography: Methods 9:443-453

Thomas, K.A., Bruno, B.C., Achilles, K., Sherman, S.B., 2011. A watery whodunit: the case of the missing zooxanthellae. Science Scope 34:44-54

Thompson, L.R., Zeng, Q., Kelly, L., Huang, K.H., Coleman, M.L., Singer, S.U., Stubbe, J., Chisholm, S. W. 2011. Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. Proceedings of the National Academy of Sciences USA 108:E757-E764

Thompson, A.W., Huang, K., Saito, M.A., Chisholm, S.W. 2011. Transcriptome response of high- and low-light adapted Prochlorococcus strains to changing iron availability. The ISME Journal 49:1-15

Thrash, J. C., Boyd, A., Huggett, M. J., Grote, J., Carini, P., Yoder, R. J., Robbertse, B., Spatafora, J. W., Rappé, M. S., Giovannoni, S. J. 2011. Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade. Scientific Reports 1:13-13

Tripp, H. J., I. Hewson, S. Boyarsky, J. Stuart, and J. P. Zehr 2011. Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies. Nucleic Acids Research 39:8792

Viviani, D.A., Bjorkman, K.M., Karl, D.M., Church, M.J. 2011. Plankton metabolism in surface waters of the tropical and subtropical Pacific Ocean. Aquatic Microbial Ecology 62:1-12

Wiener, C., Bruno, B., Foley, J. 2011. Monitoring coral reefs using quadrats. Green Teacher 92:31-34

Ye, S. Y., Laws, E. A., Ding, X. G., Yuan, H. M., Zhao, G. M., Wang, J. 2011. Trace metals in porewater of surface sediments and their bioavailability in Jiaozhou Bay, Qingdao, China. Environmental Earth Sciences 64:1641-1646

Ye, S. Y., Laws, E. A., Zhong, S. J., Ding, X. G., Pang, S. J. 2011. Sequestration of metals through association with pyrite in subtidal sediments of the Nanpaishui Estuary on the Western Bank of the Bohai Sea, China. Marine Pollution Bulletin 62:934-941

Zehr, J.P. Kudela, R.M. 2011. Nitrogen cycle of the open ocean: from genes to ecosystems. Annual Review of Marine Science 3:197-225

Zehr, J.P., Robidart, J.C., Scholin, C.A. 2011. Marine microorganisms, biogeochemical cycles, and global climate change. Microbe 6:169-175


Aller, J.Y., Aller, R.C., Kemp, P.F., Chistoserdov, A.Y., Madrid, V.M. 2010. Fluidized muds, a novel setting for the generation of biosphere diversity through geologic time. Geobiology 8:169-178

Beversdorf, L.J., White, A.E., Bjorkman, K.M., Letelier, R.M., Karl, D.M. 2010. Phosphonate metabolism by Trichodesmium IMS101 and the production of greenhouse gases. Limnology and Oceanography 55:1768-1778

Bonnet, S, Webb, E.A., Paneza, C., Karl, D.M., Capone, D.G., Sanudo-Wilhelmy, S.A. 2010. Vitamin B12 excretion by cultures of the marine cyanobacteria Crocosphaera and Synechococcus. Limnology and Oceanography 55:1959-1964

Brum, J.R., Steward, G.F. 2010. Morphological characterization of viruses in the stratified water column of alkaline, hypersaline Mono Lake. Microbial Ecology 60:636-643

Bruno, B., Tice, K., Achilles, K. and Matsuzaki, J. 2010. Quantifying marine microbes: a simulation to introduce random sampling. American Society of Microbiology- Online Microbial Discovery Activity : -

Calil, P.H.R., Richards, K.J. 2010. Transient upwelling hot spots in the oligotrophic North Pacific. Journal of Geophysical Research, Oceans 115:C02003

Church, M.J., Wai, B., Karl, D.M., DeLong, E.F. 2010. Distributions of crenarchaeal amoA genes and transcripts in the Pacific Ocean. Environmental Microbiology 12: 679-688

Coleman, M.L., Chisholm, S.W. 2010. Ecosystem-specific selection pressures revealed by comparative population genomics. Proceedings of the National Academy of Sciences USA 107:18634-18639

Culley, A.I., Suttle C.A., Steward G.F. 2010. Characterization of the diversity of marine RNA viruses. In: Suttle C.A., Wilhelm S.W., Weinbauer, M.G. Methods in aquatic virus ecology. ASLO

DeLong, E.F. 2010. Interesting things come in small packages: Population metagenomics reveals the stripped-down genome of an unusual marine nitrogen-fixing cyanobacterium. Genome Biology 11:118

Delong E.F., Beja, O. 2010. The light-driven proton pump proteorhodopsinenhance bacterial survival during tough times. PLoS Biology 8(4):e1000359-e1000359

Doney, S. 2010. The Growing Human Footprint on Coastal and Open-Ocean Biogeochemistry. Science 328:1512-1516

Doney, S. 2010. Solutions to environmental threats: ocean acidification. Scientific American 302:60-60

Duhamel, S., Dyhrman, S.T., Karl, D.M. 2010. Alkaline phosphatase activity and regulation in the North Pacific Subtropical Gyre. Limnology and Oceanography 55:1414-1425

Foster, R.A., Goebel, N.L., Zehr, J.P. 2010. Isolation of Calothrix rhizosoleniae (CYANOBACTERIA) strain SC01from Chaetoceros (BACILLARIOPHYTA) spp. Diatoms of the subtropical north Pacific Ocean. Journal of Phycology 46:1028-1037.

Gleick, P.H. et al. 2010. Climate change and the integrity of science. Science 328:689-690

Goebel, N.L., Turk, K.A., Achilles, K.M., Paerl, R.W., Hewson, I., Morrison, A. E., Montoya, J.P., Edwards, C.A., Zehr, J.P. 2010. Abundance and distribution of major groups of diazotrophic cyanobacteria and their potential contribution to N2 fixation in the tropical Atlantic Ocean. Environmental Microbiology 12:3272-3289

Goebel, N.L., Edwards, C.A., Zehr, J.P., Follows, M.J. 2010. An emergent community ecosystem model applied to the California Current System. Journal of Marine Systems 83:221-224

Guidi, L., Calcagno, V., Ibanez, F., Beaugrand, G. 2010. Reply to Comment on "A new procedure to optimize the selection of groups in a classification tree: Applications for ecological data". Ecological Modelling 221:2739-2740

Henn, M. R., Sullivan, M. B., Stange-Thomann, N., Osburne, M. S., Berlin, A. M., Kelly, L., Yandava, C., Kodira, C., Zeng, Q., Weiand, M., Sparrow, T., Saif, S., Giannoukos, G., Young, S. K., Nusbaum, C., Birren, B. W., Chisholm, S. W. 2010. Analysis of high-throughput sequencing and anotation strategies for phage genomes. PLoS ONE 5:e908-e908

Henson, S.A., Sarmiento, J.L., Dunne, J.P., Bopp, L., Lima, I., Doney, S.C., John, J., Beaulieu, C. 2010. Detection of anthropogenic climate change in satellite records of ocean chlorophyll and productivity. Biogeosciences 7:621-640

Hewson, I., Poretsky, R.S., Tripp, H.J., Montoya, J.P., Zehr, J.P. 2010. Spatial patterns and light-driven variation of microbial population gene expression in surface waters of the oligotrophic open ocean. Environmental Microbiology 12:1940-1956

Joint, I., Doney, S.C., Karl, D.M. 2011. Will ocean acidification affect marine microbes? The ISME Journal 5:1-7

Karl, D.M. 2010. Oceanic ecosystem time-series programs: ten lessons learned. Oceanography 23:104-125

Lawrence, J.L., Steward, G.F. 2010. Purification of viruses by centrifugation in density gradients. In: Suttle C.A., Wilhelm S.W., Weinbauer, M.G. Methods in aquatic virus ecology. ASLO

Li, B., Sher, D., Kelly, L., Huang, K., Joewono, I., Rusch, D., Chisholm, S.W., van der Donk, W. A. 2010. Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria. Proceedings of the National Academy of Sciences USA 107:10430-10435

Liu, X., Zhang, Q., Murata, K., Baker, M.L., Sullivan, M.B., Fu, C., Schmid, M.F., Osburne, M.S., Chisholm, S.W., Chiu, W. 2010. Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Nature Structural and Molecular Biology 17:830-836

Luo, Y., Ducklow, H.W., Friedrichs, M.A.M., Doney, S.C., Church, M.J. 2010. Oceanic heterotrophic bacterial nutrition by semilabile DOM as revealed by data assimilative modeling. Aquatic Microbial Ecology 60:273-287

Moloney, C.L., St. John, M.A., Denman, K.L., Karl, D.M., Koster, F.W., Sundby, S. and Wilson, R.P. 2010. Weaving marine food webs from end-to-end under global change. Journal of Marine Systems 84:106-116

Marinov, I., Doney, S.C., Lima, I.D. 2010. Response of ocean phytoplankton community structure to climate change over the 21st century: partitioning the effects of nutrients, temperature and light. Biogeosciences 7:3941-3959

Malmstrom, R., Coe, A., Kettler, G.C., Martiny, A.C., Frias-Lopez, J., Zinser, E., and Chisholm, S.W. 2010. Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans. The ISME Journal 4:1252-1264

McCarren, J., Becker, J.W., Repeta, D.J., Shi, Y., Young, C.R., Malmstrom, R.R. Chisholm, S.W.., DeLong, E.F. 2010. Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proceedings of the National Academy of Sciences USA 107:16420-16427

Moisander, P.H., Beinart, R.A., Hewson, I., White, A.E., Johnson, K.S., Carlson, C.A., Montoya, J.P., Zehr, J.P. 2010. Unicellular cyanobacterial distributions broaden the oceanic N2 fixation domain. Science 327:1512-1514

Orchard, E.D., Ammerman, J.W., Lomas, M.W., Dyhrman, S.T. 2010. Dissolved inorganic and organic phosphorus uptake in Trichodesmium and the microbial community: The importance of phosphorus ester in the Sargasso Sea. Limnology and Oceanography 55:1390-1399

Orchard, E.D., Benitez-Nelson, C., Pellechia, P.J., Lomas, M.W., Dyhrman, S.T. 2010. Polyphosphate in Trichodesmium from the low-phosphorus Sargasso Sea. Limnology and Oceanography 55:2161-2169

Padilla Gamino, J.L., Bruno, B. 2010. El mar y sus microbios. Helix, Ciencia y Desarrollo October:1-6

Pennebaker, K., Mackey, K., Smith, R.M., Williams, S.B., Zehr, J.P. 2010. Diel cycling of DNA-staining and nifH gene regulation in the unicellular cyanobacterium Crocosphaera watsonii Strain WH8501 (CYANOPHYTA). Environmental Microbiology 12:1001-1010

Picheral, M., Guidi, L., Stemmann, L., Karl, D., Iddaoud, G., Gorsky, G. 2010. The underwater Vision Profiler 5: An advanced instrument for high spatial resolution studies of particle size spectra and zooplankton. Limnology and Oceanography Methods 8:462-473

Quay, P. D., Peacock, C., Bjorkman, K., Karl, D. M. 2010. Measuring primary production rates in the ocean: enigmatic results between incubation and non–incubation methods at Station ALOHA. Global Biogeochemical Cycles 24: GB3014, doi:10.1029/2009GB003665

Riemann, L., Farnelid, H., Steward, G.F. 2010. Nitrogenase genes in non-cyanobacterial plankton: prevalence, diversity, and regulation in marine waters. Aquatic Microbial Ecology 61:225-237

Rodrigue, S., Materna, A.C., Timberlake, S.C., Blackburn M.C., Malmstrom, R.R., Alm, E.J., Chisholm, S.W. 2010. Unlocking short read sequencing for metagenomics. PLoSONE 5:e11840-e11840

Saba, V.S., M.A.M. Friedrichs, M.-E. Carr, D. Antoine, R.A. Armstrong, I. Asanuma, O. Aumont, N.R. Bates, M.J. Behrenfeld, V. Bennington, L. Bopp, J. Bruggeman, E.T. Buitenhuis, M.J. Church, A.M. Ciotti, S.C. Doney, M. Dowell, J. Dunne, S. Dutkiewicz, W. Gregg, N. Hoepffner, K.J.W. Hyde, J. Ishizaka, T. Kameda, D.M. Karl, I. Lima, M.W. Lomas, J. Marra, G.A. McKinley, F. Mélin, J.K. Moore, A. Morel, J. O'Reilly, B. Salihoglu, M. Scardi, T.J. Smyth, S. Tang, J. Tjiputra, J. Uitz, M. Vichi, K. Waters, T.K. Westberry, and A. Yool 2010. Challenges of modeling depth-integrated marine primary productivity over multiple decades: A case study at BATS and HOT. Global Biogeochem. Cycles 24:GB3020-doi:10.1029/2009GB003655

Scholin, C. 2010. What are "ecogenomic sensors?" A review and thoughts for the future. Ocean Science 6:51-60

Shi, T., Ilikchyan, I., Rabouille, S., Zehr, J.P. 2010. Genome-wide analysis of diel gene expression in the unicellular N2-fixing cyanobacterium Crocosphaera watsonii WH 8501. The ISME Journal 4:621-632

Steglich, C. Futschik, M., Lindell, D., Rector, T., Steen, R., Chisholm, S.W. 2010. Short RNA half–lives in the slow–growing marine cyanobacterium Prochlorococcus. Genome Biology 11:R54

Steward, G.F., Culley, A.I. 2010. Extraction and purification of nucleic acids from viruses. In: Suttle C.A., Wilhelm S.W., Weinbauer, M.G. Methods in aquatic virus ecology. ASLO

Stewart, F.J., Ottesen E.A., DeLong, E.F. 2010. Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics. The ISME Journal 18:1-12

Sullivan, M.B., Huang, K.H., Ignacio–Espinoza, J.C., Berlin, A., Kelly, L., Weigele, P.R., DeFrancesco, A.S., Kern, S.E., Thompson, L.R., Young, S., Yandava, C., Fu1, R., Krastins, B., Chase, M., Sarracino, D., Osburne, M.S., Henn, M.R., Chisholm, S.W. 2010. Genomic analysis of oceanic cyanobacterial myoviruses compared to T4–like myoviruses from diverse hosts and environments. Environmental Microbiology 12:3035-3056

Tripp, H.J., Bench, S., Turk, K., Foster, R.A., Desany, B., Niazi, F., Affourtit, J. P., Zehr, J.P. 2010. Metabolic streamlining in an open ocean nitrogen-fixing cyanobacterium. Nature 464:90-94

Turk, K., Rees, A. P., Zehr, J. P., Pereira, N. A., Swift, P., Shelley, R., Lohan, M., Woodward, E. M. S., Gilbert, J. 2010. Nitrogen fixation and nitrogenase (nifH) expression in tropical waters of the eastern North Atlantic. The ISME Journal 7:1201-1212

Weersing, K., Padilla-Gamino, J., Bruno, B. 2010. What microbe are you? The Science Teacher 77:40-44

White, A. E., Karl, D. M., Bjorkman, K. M., Beversdorf, L.J., Letelier, R. M. 2010. Production of organic matter by Trichodesmium IMS101 as a function of phosphorus source. Limnology and Oceanography 55:1755-1767

White, A. E., Bjorkman, K., Grabowski, E., Letelier, R. M., Poulos, S., Watkins, B., Karl, D. M. 2010. An open ocean trial of controlled upwelling using wave pump technology. Journal of Atmospheric and Oceanic Technology 27:385-396

Wilson, S.T., Foster, R.A., Zehr, J.P., Karl, D.M. 2010. Hydrogen production by Trichodesmium, Cyanothece and Crocosphaera spp. Aquatic Microbial Ecology 59:197-206

Wilson S.T., Tozzi, S., Foster, R.A., Ilikchyan, I., Kolber, Z.S., Zehr, J.P., Karl, D.M. 2010. Hydrogen cycling by the unicellular marine diazotroph Crocosphaera watsonii strain WH8501. Applied and Environmental Microbiology 76:6797-6803

Wood-Charlson, E.M., Markell, D.A. 2010. Immunocytochemical evidence that symbiotic algae secrete potential recognition signal molecules in hospite. Marine Biology 157:1105-1111

Zehr, J.P. 2010. Nitrogen fixation by marine cyanobacteria. Trends Microbiology 19:162-173


Apprill, A.M., Rappé, M.S. 2009. Response of the microbial community to coral spawning in lagoon and reef flat environments of Hawaii, USA. Aquatic Microbial Ecology 62:251-266

Bang, M, Chisholm, P. 2009. Living Sunlight: How plants bring life to the Earth (a children's book on Photosynthesis). Blue Sky Press, Scholastic. 43 pp

Bidigare, R.R., Chai, F., Landry, M.R., Lukas, R., Hannides, C.C.S., Christensen, S.C., Karl, D.M., Shi, L. and Chao, Y. 2009. Subtropical ocean ecosystem structure changes forced by North Pacific climate variations. J. Plankton Research 31:1131–1139

Bowler, C., Karl, D.M., Colwell, R.R. 2009. Microbial oceanography in a sea of opportunity. Nature 459:180-184.

Bragg. J., Dutkiewicz, S., Jahn, O., Follows, M.J., Chisholm, S.W. 2009. Modeling selective pressures on phytoplankton in the global ocean. PLoS ONE 5(3):e9569i

Church, M.J. 2009. The trophic tapestry of the sea. Proceedings of the National Academy of Sciences USA 106:15519-15520

Church, M.J., Mahaffey, C., Letelier, R.M., Lukas, R., Zehr, J.P., Karl, D.M. 2009. Physical forcing of nitrogen fixation and diazotroph community structure in the North Pacific Subtropical Gyre. Global Biogeochemical Cycles 23: GB2020, doi:10.1029/2008GB003418.

Cooley, S.R., Doney, S.C. 2009. Ocean acidification's impact on fisheries and societies: a U.S. perspective. Current–the Journal of Marine Education 25:15-19

Culley A.I., Asuncion, B., Steward, G.F. 2009. Detection of inteins among diverse DNA polymerase genes of uncultivated members of the Phycodnaviridae. The ISME Journal 3: 409-413

DeLong, E.F. 2009. The microbial ocean from genomes to biomes. Nature 459:200-206

Doney, S.C., Fabry, V.J., Feely, R.A., Kleypas, J.A. 2009. Ocean acidification: the other CO2 problem. Annual Review Marine Science 1:169-192

Doney, S.C., Feely, R.A. 2009. Ocean acidification. Education in Chemistry (Royal Society of Chemistry) 46:182-187

Doney, S.C., Lima, I., Moore, J.K., Lindsay, K., Behrenfeld, M.J., Westberry, T.K., Mahowald, N., Glover, D.M., Takahashi, T. 2009. Skill metrics for confronting global upper ocean ecosystem–biogeochemistry models against field and remote sensing data. J. Marine Systems 76:95-112

Doucette, G.J., Mikulski, C.M., Jones K.L., King, K.L., Greenfield D.I., Marin III R., Jensen S., Roman B., Elliott C.T., Scholin, C.A. 2009. Remote, subsurface detection of the algal toxin domoic acid onboard the Environmental Sample Processor: assay development and initial field trials. Harmful Algae 8:880-888

Ducklow, H., Doney, S.C., Steinberg, D.K. 2009. Contributions of long–term research and time–series observations to marine ecology and biogeochemistry. Ann. Rev. Mar. Sci. 1:279-302

Duhamel, S., Gregori, G., Van Wambeke, F., Nedoma, J. 2009. Detection of extracellular phosphatase activity at the single–cell level by enzyme–labeled fluorescence and flow cytometry: The importance of time kinetics in ELFA labeling. Cytometry Part A 75A:163-168

Dyhrman, S. T., Benitez–Nelson, C.R., Orchard, E.D., Haley, S.T., Pellechia, P.J. 2009. A microbial source of phosphonates in oligotrophic marine systems. Nature Geoscience 2:696-699

Eiler, A., Hayakawa, D.H., Church, M.J., Karl, D.M. Rappé, M.S. 2009. Dynamics of the SAR11 bacterioplankton lineage in relation to environmental conditions in the oligotrophic North Pacific subtropical gyre. Environmental Microbiology 11:2291-2300.

Foster, R.A., Paytan, A., Zehr, J.P. 2009. Seasonality of N2 fixation and nifH diversity in the Gulf of Aqaba (Red Sea). Limnology and Oceanography 54:219-223

Frias–Lopez, J., Thompson, A., Waldbauer, J., Chisholm, S.W. 2009. Use of stable isotope labeled cells to identify active grazers of picocyanobacteria in ocean surface waters. Environmental Microbiology 11:512-525

Friedrichs, M.A.M., Carr, M.–E., Barber, R.T, Scardi, M., Antoine, D., Armstrong, R.A., Asanuma, I., Behrenfeld, M.J., Buitenhuis, E.T., Chai, F., Christian, J.R., Ciotti, A.M., Doney, S.C., Dowell, M., Dunne, J., Gentili, B., Gregg, W., Hoepffner, N., Ishizaka, J., Kameda, T., Lima, I., Marra, J., Mélin, F., Moore, J.K., Morel, A., O'Malley, R.T., O'Reilly, J., Saba, V.S., Schmeltz, M., Smyth, T.J., Tjiputra, J., Waters, K., Westberry, T.K., Winguth, A. 2009. Assessing the uncertainties of model estimates of primary productivity in the tropical Pacific Ocean. J. Marine Systems 76:113-133

Gregg, W.W., Friedrichs, M.A.M., Robinson, A.R., Rose, K.A., Schlitzer, R., Thompson, K.R., Doney, S.C. 2009. Skill assessment in ocean biological data assimilation. J. Mar. Systems 76:16–33

Gruber, N., Doney, S.C. 2009. Modeling of ocean biogeochemistry and ecology. In: ed. Steele, J., Turekian, K.K., Thorpe, S.A. Encyclopedia of Ocean Sciences . pp 4105-4120. Elseiver

Guidi, L., Ibanez, F., Calcagno, V., Beaugrand, G. 2009. A new procedure to optimize the selection of groups in a classification tree: Applications for ecological data. Ecological Modelling 220:451-461

Guidi, L., Stemmann, L., Jackson, G., Ibanez, F., Claustre, H., Legendre, L., Picheral, M., Gorsky, G. 2009. Effects of phytoplankton community on production, size, and export of large aggregates: A world–ocean analysis. Limnology and Oceanography 54:1951-1963

Haley, S., Dyhrman, S.T. 2009. The Artistic Oceanographer Program "Enhancing Ocean Science Literacy through Multidisciplinary Learning". Science and Children, a Journal of the National Science Teachers Association April/May:31-35

Hewson, I., R. W. Paerl, H. J. Tripp, J. P. Zehr and D. M. Karl. 2009. Metagenomic potential of microbial assemblages in the surface waters of the central Pacific Ocean tracks variability in oceanic habitat. Limnology and Oceanography 54:1981-1994

Hewson, I., R. S. Poretsky, S. T. Dyhrman, B. Zielinski, A. E. White, H. J. Tripp, J. P. Montoya, and J. P. Zehr 2009. Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean. . The ISME Journal 3:1286-1300

Hewson, I., R. Poretsky, R. Beinart, A. White, T. Shi, S. R. Bench, P. H. Moisander, R. W. Paerl, H. J. Tripp J. P. Montoya, M. A. Moran , and J. P. Zehr. 2009. In situ transcriptomic analysis of the globally important keystone N2–fixing taxon Crocosphaera watsonii. The ISME Journal 3:618-631

Hynes, A.M., Chappell, P.D., Dyhrman, S.T., Doney, S.C., Webb, E.A. 2009. Cross–basin comparison of phosphorus stress and nitrogen fixation in Trichodesmium Limnology and Oceanography 54:1438–1448

Ilikchyan, I.N., McKay, R.M., Zehr, J.P., Dyhrman, S.T., Bullerjahn, G.S. 2009. Detection and expression of the phosphonate transporter gene phnD in marine and freshwater picocyanobacteria. Environmental Microbiology 11:1314-1324.

Karl, D.M., Letelier, R. 2009. Marine habitats and conditions for microbial growth. In: M. Schaechter (Ed.), Encyclopedia of Microbiology, Third edition, Elsevier, Oxford, pp. 258–277.

Karl, D.M., Letelier, R.M. 2009. Seascape microbial ecology: Habitat structure, biodiversity and ecosystem function. In: S. A. Levin (Ed.), Guide to Ecology, Princeton University Press, Princeton, New Jersey, pp. 488–500.

Kavanaugh, M.T., Menge, B.A., Nielsen, K.J., Chan, F.T., Letelier, R.M., Goodrich, L.M. 2009. Experimental assessment of the effects of shade on an intertidal kelp: do phytoplankton blooms inhibit growth of open coast macroalgae? Limnology and Oceanography 54:276-288

Kelly, A.E., Reuer, M.K., Goodkin, N.F., Boyle, E.A. 2009. Lead Concentrations and Isotopes in Corals and Water near Bermuda, 1780-2000. Earth Planet. Sci. Lett. 283:93-100

Klein, M.G., Zward, P., Bagby, S.C., Cai, F., Chisholm, S.W., Heinhorst, S., Cannon, G.C., Kerfeld, C.A. 2009. Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport. J. Mol. Biol 392:319–333

Konstantinidis, K., Braff, J., Karl, D.M., DeLong. E.F. 2009. Comparative metagenomic analysis of an abyssal microbial community from 4000 m deep at Station ALOHA in the North Pacific Ocean. Appl. Environ. Microbiol. 75:5345–5355

Krishnamurthy, A., Moore, J.K., Mahowald, N., Luo, C., Doney, S.C., Lindsay, K., Zender, C.S. 2009. Impacts of increasing anthropogenic soluble iron and nitrogen deposition on ocean biogeochemistry. Global Biogeochemical Cycles 23:GB3016–

Laney, S.R., Letelier, R.M., Abbott, M.R. 2009. Using a nonanalytical stochastic approach to model nonlinear dynamics in photosynthesis at the photosystem level. Journal of Phycology 45:298-310

Lang, A.S., Rise, M.L., Culley, A.I., Steward, G.F. 2009. RNA viruses in the sea. FEMS Microbiology Reviews 33:295-332

Maresca, J., Braff, J.C., DeLong, E. F. 2009. Characterization of canthaxanthin biosynthesis genes from an uncultured marine bacterium. Environmental Microbiology 1: 524-534

Martinez, A., Tyson, G.W., DeLong, E.F. 2009. Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses. Environmental Microbiology 12 : 222-238

Martiny, A. S. Kathuria, and P.M. Berube 2009. Widespread metabolic potential for nitrite and nitrate assimilation among Prochlorococcus ecotypes. Proceedings of the National Academy of Sciences USA 106:10787-10792

Moore, R.M., Punshon, S., Mahaffey, C., Karl, D. 2009. The relationship between dissolved hydrogen and nitrogen fixation in ocean waters. Deep Sea Research I 56:1449-1458.

Orchard, E.D., Webb, E.A., Dyhrman, S.T. 2009. Molecular analysis of the phosphorus starvation response in Trichodesmium spp. Environmental Microbiology 11:2400-2411

Osburne, M.S., Holmbeck, B.M., Frias–Lopez, J., Steen, R., Huang, K., Waraska, K., Gagne, A., Chisholm, S.W. 2009. UV resistance in Prochlorococcus MED4 results from a single base pair deletion just upstream of an operon encoding nudix hydrolase and photolyase. Environmental Microbiology 12:1978-1988

Paytan, A., Mackey, K.R.M., Chen, Y., Lima, I.D., Doney, S.C., Mahowald, N., Labiosa, R., Post, A.F. 2009. Toxicity of atmospheric aerosols on marine phytoplankton. Proceedings of the National Academy of Sciences USA 106:4601-4605

Preston, C., Marin III, R., Jenson, S., Feldman, J., Massion, E., DeLong, E., Suzuki, M., Wheeler, K., Cline, D., Alvarado, N., Scholin, C. 2009. Near real–time, autonomous detection of marine bacterioplankton on a coastal mooring in Monterey Bay, California using rRNA–targeted DNA probes. Environmental Microbiology 11:1168-1180.

Rappé, M. S., Brandon, M.L. 2009. Diversity among bacteria from the coastal subtropical Pacific Ocean determined by high-throughput culturing and small-subunit rRNA gene clone libraries. Environmental Microbiology in review

Rodrigue, S., Malmstrom, R.R., Berlin, A.M., Birren, B.W., Henn, M.R., Chisholm, S.W. 2009. Whole genome amplification and de novo assembly of single bacterial cells. PLoS ONE 4(9):e6864. doi:10.1371/journal.pone.0006864

Saito, M.A. 2009. Less nickel for more oxygen. Nature 458:714-715

Scholin, C. 2009. What are ecogenomic sensors? Ocean Science Discussions 6:191-213

Scholin, C, Doucette, G., Jensen, S., Roman, B., Pargett, D., Marin III, R., Preston, C., Jones, W., Feldman, J., Everlove, C., Harris, A., Avarado, N., Massion, E., Birch, J., Greenfield, D., Wheeler, K., Vrijenhoek, R., Mikulski, C., Jones, K. 2009. Remote detection of marine microbes, small invertebrates, harmful algae and biotoxins using the Environmental Sample Processor (ESP). Oceanography 22:158-167

Shi, Y., Tyson, G.W., DeLong, E.F. 2009. Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column. Nature 459:266-269

Sigman, D.M., DiFiore, P.J., Hain, M.P., Deutsch, C., Karl, D.M. 2009. Sinking organic matter spreads the nitrogen isotope signal of pelagic denitrification in the North Pacific. Geophysical Research Letters 36: L08605, doi:10.1029/2008GL035784.

Sigman, D.M., DiFiore, P.J., Hain, M.P., Deutsch, C., Wang, Y., Karl, D.M., Knapp, A.N., Lehmann, M.F., Pantoja, S. 2009. The dual isotopes of deep nitrate as a constraint on the cycle and budget of oceanic fixed nitrogen. Deep Sea Research I 56:1419-1439

St. John, M.A., Moloney, C.L., Denman, K.L., Karl, D.M., Koster, F.W., Sundby, S., Wilson, R. P. submitted. Newton and Kelvin meet Darwin in the complex sea of global change: developing a pragmatic understanding of marine food webs end to end. Theoretical Ecology in press

Stow, C., Jolliff, A.J., McGillicuddy, D.J. Jr., Doney, S.C., Allen, J.I., Friedrichs, M.A.M., Rose, K.A., Wallhead, P. 2009. Skill assessment for coupled biological/physical models of marine systems. J. Marine Systems 76:4-15

Strong, A.L., Chisholm, S., Miller, C., Cullen, J. 2009. Ocean fertilization: time to move on. Nature 461:347-348

Strong, A.L., Cullen, J.J., Chisholm, S.W. 2009. Ocean fertilization: Science, policy and commerce. Oceanography Magazine 22:236-261

Sullivan, M.B., Krastins, B., Hughes, J.L., Kelly, L., Chase, M., Sarracino, D., Chisholm, S.W. 2009. The genome and structural proteome of an ocean cyanobacterial siphovirus: A new window into the cyanobacterial 'mobilome' Environmental Microbiology 11:2935-2951

Van Mooy, B.A.S., Fredricks, H.F., Pedler, B.E., Dyhrman, S.T., Karl, D.M., Koblizek, M., Lomas, M.W., Mincer, T., Moore, L.R., Moutin, T., Rappé, M.S., Webb, E.A. 2009. Phytoplankton in the ocean use non–phosphorus lipids in response to phosphorus scarcity. Nature 458:69-72

Weersing, K., Toonen, R. 2009. Population genetics, larval dispersal, and demographic connectivity in marine systems. Marine Ecology Progress Series 393:1-15

White, A. 2009. New insights into bacterial acquisition of phosphorus in the surface ocean. Proceedings of the National Academy of Sciences USA 106:21013-21014

Wood–Charlson, E.M., Weis, V.M. 2009. The diversity of C–type lectins in the genome of a basal metazoan, Nematostella vectensis. Developmental and Comparative Immunology 33:881-889

Zehr, J.P. 2009. From microbes to global environmental change: thinking big about small things. Environmental Microbiology Reports 1:24-26

Zehr, J.P. 2009. New twist on nitrogen cycling in oceanic oxygen minimum zones. Proceedings of the National Academy of Sciences USA 106:4575-4576.

Zehr, J.P., Kudela, R.M. 2009. Photosynthesis in the open ocean. Science 326:945-946.

Zinser, E.R., Lindell, D., Johnson, Z.I., Futschik, M.E., Steglich, C., Coleman, M.L., Wright, M.A., Rector, T., Steen, R., McNulty, N., Thompson, L.R., Chisholm, S.W. 2009. Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, Prochlorococcus. PLoS ONE 4(4):e5135


Aller, J.Y., Kemp, P.F. (2008) Are Archaea inherently less diverse than Bacteria in the same environments? FEMS Microbiology Ecology 65:74-87

Bragg, J. G., Chisholm, S.W. 2008. Modeling the fitness consequences of a cyanophage–encoded photosynthesis gene. PLoS ONE 3:e3550 doi: 10.1371/journal.pone.0003550

Bruno, B.C., K. Achilles, K. Weersing, G. Walker, P. Kemp (2008), Professional Development at the Center for Microbial Oceanography: Research and Education (C–MORE), The Earth Scientist XXVII (2):7–10.

Buesseler, K.O., Trull, T.W., Steinberg, D.K., Silver, M.W., Siegel, D.A., Saitoh, S.–I., Lamborg, C.H., Lam, P.J., Karl, D.M., Jiao, N.Z., Honda, M.C., Elskens, M., Dehairs, F., Brown, S.L., Boyd, P.W., Bishop, J.K.B., Bidigare, R.R. 2008. VERTIGO (VERtical Transport In the Global Ocean): a study of particle sources and flux attenuation in the North Pacific. Deep Sea Research II 55:1522-1539

Buessler, K.O., Doney, S.C., Karl, D.M., Boyd, P.W., Caldiera, K., Chai, F., Coale, K.H., H., de Baar, J.W., Falkowski, P.G., Johnson, K.S., Lampitt, R.S., Michaels, A.F., Naqvi, S.W.A., Smetacek, V., Takeda, S., Watson, A.J. 2008. Ocean iron fertilization – Moving forward in a sea of uncertainty. Science 319:162-162

Church, M.J. 2008. Resource control of bacterial dynamics in the sea. In: Kirchman, D.L. Microbial Ecology of the Oceans. pp 335-382. Wiley Liss.

Church, M.J., Bjorkman, K.M., Karl, D.M., Saito, M.A., Zehr, J.P. 2008. Regional distributions of nitrogen-fixing bacteria in the Pacific Ocean. Limnology and Oceanography 53:63-77

Corno, G., Letelier, R.M., Abbott, M.R., Karl, D.M. 2008. Temporal and vertical variability in photosynthesis in the North Pacific Subtropical Gyre. Limnology and Oceanography 53:1252-1265

Dammeyer, T.S., Bagby, S.C., Sullivan, M.B., Chisholm, S.W., Frankenberg-Dinkel, N. 2008. Efficient phage–mediated pigment biosynthesis in oceanic cyanobacteria. Current Biology 18:442-448

Doney, S.C. 2008. Ocean Acidification. In: Earle, S.A., Glover, L.K. Ocean: An Illustrated Atlas (National Geographic Atlas). pp 39-39. National Geographic

Dore, J.E., Letelier, R.M., Church, M.J., Lukas, R., Karl, D.M. 2008. Summer phytoplankton blooms in the oligotrophic North Pacific Subtropical Gyre: Historical perspective and recent observations. Progress in Oceanography 76:2-38

Duhamel, S., Gregori, G., Van Wambeke, F., Mauriac, R., Nedoma, J. 2008. A method for analysing phosphatase activity in aquatic bacteria at the single cell level using flow cytometry. J. Microbiol. Methods 75:269-278

Falkowski, P.G., Fenchel, T. DeLong E.F. 2008. The microbial engines that drive Earth's biogeochemical cycles. Science 320:1034-1039

Fong, A.A., Karl, D.M., Lukas, R., Letelier, R.M., Zehr, J.P., Church, M.J. 2008. Nitrogen fixation in an anticyclonic eddy in the oligotrophic North Pacific Ocean. The ISME Journal 2:663-676

Foster, R.A., Subramaniam, A., Zehr, J.P. 2008. Distribution and activity of diazotrophs in the Eastern Equatorial Atlantic. Environmental Microbiology 11:741-750

Frias–Lopez, J., Shi, Y., Tyson, G.W.,. Coleman, M.L., Schuster, S.C., Chisholm, S.W., DeLong, E.F. 2008. Microbial community gene expression in ocean surface waters. Proceedings of the National Academy of Sciences USA 105:3805-3810

Giovannoni, S.J., Hayakawa, D.H.U. Stingl, H. J. Tripp, S. Givan, J.-C. Cho, H-M. Oh, J. Kitner, K. L. Vergin and M. S. Rappé 2008. The small genome of an abundant coastal ocean methylotroph. Environmental Microbiology 10:1771-1782

Goebel, N. L., Edwards, C.A., Carter, B.J., Achilles, K.M., Zehr, J.P. 2008. Growth and carbon content of three different sized diazotrophic cyanobacteria observed in the subtropical North Pacific. J. Phycology 44:1212-1220

Grabowski, M., Church, M.J., Karl, D.M. 2008. Nitrogen fixation rates and controls at Station ALOHA. Aquatic Microbial Ecology 52:175-183

Greenfield, D., Marin III, R., Doucette, G., Mikulski, C., Jensen, S., Roman, B., Alvarado, N., Scholin, C.A. 2008. Field applications of the second–generation Environmental Sample Processor (ESP) for remote detection of harmful algae: 2006–2007. Limnology and Oceanography: Methods 6:667-679

Hannides, C.C.S., Landry, M.R., Benitez-Nelson, C.R., Styles, R.M., Montoya, J.P., Karl, D.M. 2008. Export stoichiometry and migrant–mediated flux of phosphorus in the North Pacific subtropical gyre. Deep Sea Research I 56:73-88

Hynes, A. 2008. A most ingenious paradoxical plankton. Oceanus 47:36-39

Jin, X., Gruber, N., Frenzel, H., Doney, S.C., McWilliams, J.C. 2008. The impact on atmospheric CO2 of iron fertilization induced changes in the ocean's biological pump. Biogeosciences 5:385-406

Karl, D.M., Beversdorf, L., Bjorkman, K.M., Church, M.J., Martinez, A., DeLong, E. F. 2008. Aerobic production of methane in the sea. Nature Geoscience 1:473-478

Karl, D.M., Letelier, R.M. 2008. Nitrogen fixation-enhanced carbon sequestration in low nitrate, low chlorophyll seascapes. Marine Ecology Progress Series 364:257-268

Karl, D.M., Bidigare, R.R., Church, M.J., Dore, J.E., Letelier, R.M., Mahaffey, C., Zehr, J.P. 2008. The nitrogen cycle in the North Pacific trades biome: An evolving paradigm, p. 705-769. In, Nitrogen in the Marine Environment, D. G. Capone, D. A. Bronk, M. R. Mulholland and E. J. Carpenter (ed.), Academic Press, New York, NY.

Konstantinidis, K., DeLong, E. F. 2008. Genomic patterns of recombination, clonal divergence, and environment in marine microbial populations. ISME Journal 2:1062–1065

Lamborg, C.H., Buesseler, K.O., Valdes, J., Bertrand, C.H., Bidigare, R.R., Manganini, S., Pike, S., Steinberg, D., Trull, T., Wilson, S. 2008. The flux of bio– and lithogenic material associated with sinking particles in the mesopelagic "Twilight Zone" of the Northwest and North Central Pacific Ocean. Deep Sea Research II 55:1540-1563

Laney, S.R., Letelier, R.M. 2008. Artifacts in measurements of chlorophyll fluorescence transients, with specific application to fast repetition rate fluorometry. Limnology and Oceanography Methods 6:40-50

Letelier, R.M., Strutton, P.G., Karl, D.M. 2008. Physical and ecological uncertainties in the widespread implementation of controlled upwelling in the North Pacific Subtropical Gyre. Marine Ecology Progress Series 371:305-308

Mahaffey, C., Benitez–Nelson, C.R., Bidigare, R.R., Rii, Y., Karl, D.M. 2008. Nitrogen dynamics within a wind–driven eddy. Deep Sea Research II 55:1398-1411

McAndrew, P.M., Bidigare, R.R., Karl, D.M. 2008. Primary production and implications for metabolic balance in Hawaiian lee eddies. Deep Sea Research II 55:1300-1309

Martiny, A.C., Tai, A.P.K., Veneziano, D., Primeau, F., Chisholm, S.W. 2008. Taxonomic resolution, ecotypes, and the biogeography of Prochlorococcus. Environmental Microbiology 11:823-832

Moisander, P.H., Beinart, R.A., Voss, M., Zehr, J.P. 2008. Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon. The ISME Journal 2:254-267

Moisander, P.H., Paerl, H.W., Zehr, J.P. 2008. Effects of inorganic nitrogen on taxa-specific cyanobacterial growth and nifH expression in a subtropical estuary. Limnology and Oceanography 53:2519-2532

Moutin, T., Karl, D.M., Duhamel, S., Rimmelin, P., Raimbault, P., Van Mooy, B.A.S., Claustre, H. 2008. Phosphate availability and the ultimate control of new nitrogen input by nitrogen fixation in the tropical Pacific Ocean. Biogeosciences 5:95-109

Noble, A.E., Saito, M.A., Maiti, K., Benitez-Nelson C. 2008. Cobalt, manganese, and iron near the Hawaiian Islands: A potential concentrating mechanism for cobalt within a cyclonic eddy and implications for the hybrid-type trace metals. Deep Sea Research II 55: 1473-1490

Paerl, R.W., Foster, R.A., Jenkins, B.D., Montoya, J.P., Zehr, J. P. 2008. Phylogenetic diversity of cyanobacterial narB genes from various marine habitats. Environmental Microbiology 10:3377-3387

Pham, V., Konstantinidis, K.T., Palden, T., DeLong, E.F. 2008. Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre. Environmental Microbiology 10:2313-30

Paul, J., Scholin, C., van den Engh, G., Perry, M.J. 2007. In situ instrumentation. Oceanography 20:58-66

Pidgeon, E., Doney S.C. 2008. The role of the oceans (Chapter 8). In: R.A. Mittermeier et al., A Climate for Life, Meeting the Global Challenge. pp 246-276. CEMEX Conservation Book Series, with Conservation International and the International League of Conservation Photographers

Rappé, M. S., Brandon, M.L., Becker, J.W. 2008. Isolation of aquatic microorganisms via high throughput cultivation methods. In G. A. Kowalchuk, F. J. de Bruijn, I. M. Head, and A. D. Akkermans [eds], Molecular Microbial Ecology Manual, update to 2nd Edition. Springer Netherlands, pp. 1838-1862

Rich, V. I., Konstantinidis, K., DeLong, E.F. 2008. Design and testing of "genome–proxy" microarrays to profile marine microbial communities. Environmental Microbiology 10:506-521

Rii, Y., Brown, S.L., Nencioli, F., Kuwahara, V., Dickey, T., Karl, D.M., Bidigare, R.R. 2008. The transient oasis: Nutrient–phytoplankton dynamics and particle export in Hawaiian lee cyclones. Deep Sea Research II 55:1275-1290

Saito, M.A., Goepfert, T.J. 2008. Zinc-cobalt colimitation in Phaeocystis antarctica. Limnology and Oceanography 53:266-275

Saito, M.A., Goepfert, T.J., Ritt, J.T. 2008. Some thoughts on the concept of co-limitation: Three definitions and the importance of bioavailability. Limnology and Oceanography 53:276-290

Scholin, C.A., Doucette, G.J., Cembella, A.D. 2008. Prospects for developing automated systems for in situ detection of harmful algae and their toxins. In: M. Babin, C.S. Roesler and J.J. Cullen (eds.) Real–Time Coastal Observing Systems for Ecosystem Dynamics and Harmful Algal Blooms, UNESCO Publishing, Paris, France. pp 413-462

Steinberg, D.K., Van Mooy, B.A.S., Buesseler, K.O., Boyd, P.W., Kobari, T., Karl, D.M. 2008. Bacterial vs. zooplankton control of sinking particle flux in the ocean's twilight zone. Limnology and Oceanography 53:1327-1338

Steglich, C. Futschik M.E., Lindell, D., Voss, B., Chisholm, S.W., Hess, W.R. 2008. The challenge of regulation in a minimal photoautotroph: Non–coding RNAs in Prochlorococcus. PLoS Genetics 4:e1000173–

Sullivan, M.B., Coleman, M.L., Quinlivan,V., Rosenkrantz, J.E., DeFrancesco, Alicia S., Tan, G., Fu, R., Lee, J.A., Waterbury, J.B., Bielawski, J.P., Chisholm, S.W. 2008. Portal protein diversity and phage ecology. Environmental Microbiology 10:2810-2823

Venegas, R.M., Strub, P.T., Beier, E., Letelier, R.M., Thomas, A.C., Cowles, T., James, C., Soto–Mardones, L., Cabrera, C. 2008. Satellite–derived variability in chlorophyll, wind stress, sea surface height, and temperature in the northern California Current system. Journal of Geophysical Research 113:C03015–doi:10.1029/2007JC004481

Webb, E.A., Ehrenreich,I.M., Brown, S.L., Valois, F.W., Waterbury, J.B. 2008. Phenotypic and genotypic characterization of multiple strains of the diazotrophic cyanobacterium, Crocosphaera watsonii, isolated from the open ocean. Environmental Microbiology 11:338-348

Zehr, J.P., Bench, S.R., Carter, B.J., Hewson, I., Niazi, F., Shi, T., Tripp, H.J., Affourtit, J.P. 2008. Globally distributed uncultivated oceanic N2–fixing cyanobacteria lack oxygenic photosystem II. Science 322:1110-1112

Zehr, J.P., Montoya, J.P. 2008. Measuring N2 fixation in the field, p. 193–205. In, H. Bothe, S. Ferguson, and W. E. Newton (ed.), Biology of the nitrogen cycle. Elsevier B.V., Amsterdam, The Netherlands

Zehr, J.P., Paerl, H.W. 2008. Molecular ecological aspects of nitrogen fixation in the marine environment. p. 481-525 In, D. L. Kirchman (ed.), Microbial Ecology of the Oceans. 2nd Edition. Wiley-Liss, Inc. Durham, NC.


Becker, J. W., Brandon, M.L., Rappé, M.S. 2007. Cultivating microorganisms from dilute aquatic environments: melding traditional methodology with new cultivation techniques and molecular methods. In C. J. Hurst et al. [eds], Manual of Environmental Microbiology, 3rd Edition. ASM Press, pp. 399-406

Bertrand, E.M., Saito, M.A., Rose, J.M., Riesselman, C.R., Lohan, M.C., Noble, A.E., Lee, P.A., DiTullio, G.R. 2007. Vitamin B12 and iron co-limitation of phytoplankton growth in the Ross Sea. Limnology and Oceanography 52:1079-1093.

Bane, J.M., Spitz, Y.H., Letelier, R.M., Peterson. W.T. 2007. Jet stream intraseasonal oscillations drive dominant ecosystem variations in Oregon's summertime coastal upwelling system. Proceedings of the National Academy of Sciences USA 104:13,262-13,267

Buesseler, K.O., Lamborg, C.H., Boyd, P.W., Lam, P.J., Trull, T.W., Bidigare, R.R., Bishop, J. K.B., Casciotti, K.L., Dehairs, F., Elskens, M., Honda, M., Karl, D.M., Siegel, D., Silver, M.W., Steinberg, D.K., Valdes, J., Van Mooy, B., Wilson, S. 2007. Revisiting carbon flux through the ocean’s twilight zone. Science 316:567-570

Coleman, M.L., Chisholm, S.W. 2007. Code and Context: Prochlorococcus as a model for cross–scale biology. Trends in Microbiology 15:398-407

Corno, G., Karl, D.M., Abbott, M.A., Church, M.J., Lukas, R., Letelier, R.M. 2007. Impact of climate forcing on ecosystem processes in the North Pacific subtropical gyre. J. Geophysical Research 112:C04021–doi:10.1029/2006JC003730

Culley, A.I., Steward G.F. 2007. New genera of RNA viruses in subtropical seawater, inferred from polymerase gene sequences. Applied and Environmental Microbiology 73:5937-5944

DeLong, E.F. 2007. Microbial domains in the ocean: A lesson from the Archaea. Oceanography 20:124-129

Desiderio, R., Laney, S., Letelier, R., Giovannoni, S. 2007. Using lasers to probe the transient light absorption by proteorhodopsin in marine bacterioplankton. Applied Optics 46:7329-7336

Dhadwal, H.S., Mukherjee, B., Kemp, P., Aller, J., Liu, Y., Radway, J. 2007. A dual detector Capillary Waveguide Sensor for detection and quantification of hybridized target species. Analytica Chimica Acta 598:147-154

D’Hondt, S., Inagaki, F., Ferdelman, T., Jørgensen, B.B., Kato, K., Kemp, P., Sobecky, P., Sogin, M., Takai, K. 2007. Exploring subseafloor life with the Integrated Ocean Drilling Program. Scientific Drilling 5:58-69

Follows, M., Dutkiewicz, S., Grant, S., Chisholm, S.W. 2007. Emergent biogeography of microbial communities in a model ocean. Science 315:1843-1846

Giaquinto L., Curmi P.M., Siddiqui K.S., Poljak A., DeLong E. F., Dassarma S., Cavicchioli R. 2007. Structure and function of cold shock proteins in archaea. J Bacteriology 189:5738-5748

Giovannoni, S.J., Foster, R.A., Rappé, M.S., Epstein, S. 2007. New cultivation strategies bring more microbial plankton species into the laboratory. Oceanography 20:24-30

Goebel, N. L., Edwards, C.A., Church, M.J., Zehr, J.P. 2007. Modeled contributions of three types of diazotrophs to nitrogen fixation at Station ALOHA. The ISME Journal 1:606-619

Hallam, S.J., Konstantinidis, K.T., Putnam, N., Schleper, C., Watanabe, Y., Sugahara, J., Preston, C.M., de la Torre, J, Richardson, P.R., DeLong, E.F. 2007. Genomic analysis of the uncultivated marine crenarchaeote, Cenarchaeum symbiosum. Proceedings of the National Academy of Sciences USA 103:18296-18301

Hewson, I., Moisander, P.H., Morrison, A.E., Zehr, J.P. 2007. Diazotrophic bacterioplankton in a coral reef lagoon: phylogeny, diel nitrogenase expression, and response to phosphate enrichment. The ISME Journal 1:78-91

Huyer, A., Kosro, M., Letelier, R., Smith, R.L., Wheeler, P.A. 2007. The Newport Line off Oregon: Studies in the North East Pacific. Progress in Oceanography 75:126-160

Karl, D.M., Proctor. L. 2007. Foundations of microbial oceanography. Oceanography 20:16-27

Karl, D.M. 2007. Microbial oceanography: paradigms, processes and promise. Nature Reviews Microbiology 5:759-769

Karl, D.M. 2007. Plastics-irradiated-etched: The Nuclepore filter turns 45 years old. Limnology and Oceanography Bulletin 16:49-54

Karl, D., Proctor, L. 2007. A Sea of Microbes, Oceanography 20 (2), special issue.

Karl, D., DeLong, E., Rocap, G. 2007. Microbial Oceanography: Challenges and Opportunities, a report commissioned and published by The Agouron Institute.

Karl, D.M. 2007. Microbial nucleotide fingerprints in nature. In: C. A. Reddy, T. Beveridge, J. A. Breznak, S. Maloy, G. A. Marzluf, T.M. Schmidt (eds.). Methods for General and Molecular Microbiology, ASM Press, Washington, D.C. pp. 869–878

Karl, D.M. The marine phosphorus cycle. 2007. In: Manual of Environmental Microbiology, Third Edition, ed. by J. L. Garland, American Society of Microbiology, pp. 523–539.

Kettler, G., Martiny, A.C., Huang, K., Zucker, J., Coleman, M.L., Rodrigue, S., Chen, F., Lapidus, A., Ferriera, S., Johnson, J., Steglich, C., Church, G., Richardson, P., Chisholm, S.W. 2007. Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus. PLoS Genetics 3:25152528

Kolber, Z. 2007. Energy cycle in the ocean: Powering the microbial world. Oceanography 20:79-88

Lindell, D., J.D. Jaffe, M.l. Coleman, I.M. Axmann, T. Rector, G. Kettler, M.B. Sullivan, R. Steen, W.R. Hess, G.M. Church, and S. W. Chisholm. 2007. Genome-wide expression dynamics of a marine virus and host reveal features of coevolution. Nature 449:83-86

Martinez, A., Bradley, A., Waldbauer, J., Summons, R., DeLong, E.F. 2007. Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proceedings of the National Academy of Sciences USA 104:5590-5595

McAndrew, P.M., Bjorkman, K.M., Church, M.J., Morris, P.J., Jachowski, N., Williams, P.J. le B., Karl, D.M. 2007. Metabolic response of oligotrophic plankton communities to deep water nutrient enrichment. Marine Ecology Progress Series 332:63-75

McCarren, J., DeLong, E.F. 2007. Proteorhodopsin photosystem gene clusters exhibit co–evolutionary trends and shared ancestry among diverse marine microbial phyla. Environmental Microbiology 9:846-858

Mincer T.J., Church, M.J., Taylor, L.T., Preston, C.M., Karl, D.M., DeLong, E.F. 2007. Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environmental Microbiology 9:1162-1175

Moisander, P.H., Morrison, A.E., Ward, B.B., Jenkins, B.D., Zehr, J.P. 2007. Spatial-temporal variability in diazotroph assemblages in Chesapeake Bay using an oligonucleotide nifH microarray. Environmental Microbiology 9:1823-1835

Moore, L.R., Coe, A., Zinser, E.R., Saito, M.A., Sullivan, M.B., Lindell, D., Frois–Moniz, K., Waterbury, J., Chisholm, S.W. 2007. Culturing the marine cyanobacterium Prochlorococcus. Limnology and Oceanography Methods 5:353-362

Needoba, J.A., Foster, R.A., Sakamoto, C., Zehr, J.P., Johnson, K.S. 2007. Nitrogen fixation by unicellular diazotrophic cyanobacteria in the temperate, oligotrophic North Pacific Ocean. Limnology and Oceanography 52:1317-1327

Rabouille, S., Edwards, C.A., Zehr, J.P. 2007. Modelling the vertical distribution of Prochlorococcus and Synechococcus in the North Pacific Subtropical Ocean. Environ. Microbiol. 9:2588-2602

Roman, B., C. Scholin, S. Jensen, E. Massion, R, Marin III, C. Preston, D. Greenfield, W. Jones, Wheeler, K. 2007. Controlling a robotic marine water sampler with the Ruby scripting language. Journal of American Laboratory Automation 12:56-61

Rusch, D. B., A. L. Halpern, G. Sutton, K. B. Heidelberg, S. Williamson, S. Yooseph, D. Wu, J. A. Eisen, J. M. Hoffman, K. Rrmington, K. Beeson, B. Tran, H. Smith, H. Baden–Tillson, C. Stewart, J. Thorpe, J. Freeman, C. Andrews–Pfannkoch, J. E. Venter, K. Li, S. Kravitz, J. F. Heidelberg, T. Utterback, Y.–H. Rogers, L. I. Falcon, V. Souza, G. Bonilla–Rosso, L. E. Eguiarte, D. M. Karl, S. Sathyendranath, T. Platt, E. Bermingham, V. Gal–lardo, G. Tamayo–Castillo, M. R. Ferrari, R. L. Strausberg, K. Nealson, R. Friedman, M. Frazier and J. C. Venter 2007. The Sorcerer II global ocean sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. Public Library of Science (PLOS), Biology 5:0398–0431

Steward, G.F., Rappé, M.S. 2007. What’s the ‘meta’ with metagenomics? The ISME Journal, 1:100-102

Vergin, K.L., Tripp, H.J., Wilhelm, L.J., Denver, D.R., Rappé, M.S., Giovannoni, S.J. 2007. High intraspecific recombination rate in a native population of Candidatus Pelagibacter ubique (SAR11). Environmental Microbiology 9:2430-2440

Ward, B.B., Capone, D.G., Zehr, J.P. 2007. What's new in the nitrogen cycle? Oceanography 20:101-109.

White, A.E., Prahl, F.G., Letelier, R.M., Popp, B.N. 2007. Summer surface waters in the Gulf of California: prime habitat for biological N2 fixation. Global Biogeochemical Cycles 21: GB2017 doi:10.1029/2006GBC002779

White, A.E., Spitz, Y.H., Letelier, R.M. 2007. What factors are driving summer phytoplankton blooms in the North Pacific subtropical gyre? J. Geophysical Research 112:C12006–doi:10.1029/2007JC004129

Woebken D., Teeling H., Wecker P., Dumitriu A., Kostadinov I., DeLong E.F., Amann R., Glockner, F.O. 2007. Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes. The ISME Journal 5:419-435

Zehr, J. P., Bench, S.R., Mondragon, E.A., McCarren, J., DeLong, E.F. 2007. Low genomic diversity in tropical oceanic N2-fixing cyanobacteria. Proceedings of the National Academy of Sciences USA 104:17807-17812.

Zehr, J.P., Montoya, J.P., Jenkins, B.D., Hewson, I., Mondragon, E., Short, C. M., Church, M.J., Hansen, A., Karl, D.M. 2007. Experiments linking nitrogenase gene expression to nitrogen fixation in the North Pacific subtropical gyre. Limnology and Oceanography 52:169-183

Zinser, E.R., Johnson, Z.I., Coe, A., Karaca, E., Veneziano, D., Chisholm, S.W. 2007. Influence of light and temperature on Prochlorococcus ecotype distributions in the Atlantic Ocean. Limnology and Oceanography 52:2205-2220


Brix, H., Gruber, N., Karl, D.M., Bates, N.R. 2006. On the relationship between primary, net community, and export production in subtropical gyres. Deep Sea Research II 53:698-717

DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.–U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R., Chisholm, S.W., Karl, D.M. 2006. Community genomics among stratified microbial assemblages in the ocean‘s interior. Science 311: 496-503

Greenfield, D.I., Marin III, R., Jensen, S., Massion, E., Roman, B., Feldman, J., Scholin, C. 2006. Application of the Environmental Sample Processor (ESP) methodology for quantifying Pseudonitzschia australis using ribosomal RNA–targeted probes in sandwich and fluorescent in situ hybridization. Limnology and Oceanography: Methods 4:426-435

Huisman, J., Thi, N.N.P., Karl, D.M., Sommeijer, B. 2006. Reduced mixing generates oscillations and chaos in the deep chlorophyll maximum. Nature 439:322-325

Martiny, A.C., Coleman, M.L., Chisholm, S.W. 2006. Phosphate acquisition genes in Prochlorococcus ecotypes: Evidence for genome-wide adaptation. Proceedings of the National Academy of Sciences USA 103:12552-12557

Rothstein, L.M., J.J. Cullen, M. Abbott, E. Chassignet, K. Denman, S. Doney, H. Ducklow, K. Fennel, M. Follows, D. Haidvogel, E. Hofmann, D. Karl, J. Kindle, I. Lima, M. Maltrud, C. McClain, D. McGillicuddy, J. Olascoaga, Y. Spitz, J. Wiggert and J. Yoder. 2006. Modeling ocean ecosystems: The PARADIGM program. Oceanography 19: 17-45

Saito, M.A., Schneider, D.L. 2006. Examination of the precipitation chemistry and improvements in precision using the Mg(OH)2 preconcentration ICP–MS method for high–throughput analysis of open-ocean Fe and Mn in seawater. Analytica Chimica Acta 565:222-233

Steglich, C. Futschik, M., Rector, T., Chisholm, S.W. 2006. Genome-wide analysis of light sensing in Prochlorococcus. J. Bacteriology 188: 7796-7806

Sullivan, M.B., Lindell, D., Lee, J.A., Thompson, L.R., Bielawski, J.P., Chisholm, S.W. 2006. Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLOS Biology 4:1345-1357.

Tolonen, A.C. Aach, J. Lindell, D., Johnson, Z.I., Rector, T. Steen, R., Church, G. M., Chisholm, S.W. 2006. Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability. Molecular Systems Biology 2: doi:10.1038/msb4100087.

White, A., Spitz, Y., Karl, D.M., Letelier, R.M. 2006. Flexible elemental stoichiometry in Trichodesmium spp. and its ecological implications. Limnology and Oceanography 51:1777-1790

[ Top of Page ]