Publications Multimedia Investigators
Simons Collaboration on Ocean Processes and Ecology
Home » Publications



  • Acker, M. S.L. Hogle, P.M. Berube, T. Hackl, A. Coe, R.M. Stepanauskas, S.W. Chisholm, D.J. Repeta. Phosphonate production by marine microbes: exploring new sources and potential function. Proceedings of the National Academy of Sciences 119 (11), e2113386119. doi: 10.1073/pnas.2113386119.

  • Allen J.G., Dugenne M., Letelier R.M., White A.E. (2022) Optical determinations of photophysiology along an ecological gradient in the North Pacific Ocean. Limnol Oceanogr. 67:713-725. doi: 10.1002/lno.12031.

  • Baran, N., M.C.G. Carlson, G. Sabehi, M. Peleg, K. Kondratyeva, I. Pekarski, D. Lindell. (2022) Widespread yet persistent low abundance of TIM5-like cyanophages in the oceans. Environmental Microbiology doi: 10.1111/1462-2920.16210.

  • Barone, B. M. Church, M. Dugenne, N. Hawco, O. Jahn, A.White, S. John, M. Follows, E. Delong, and D. Karl (2022) Biogeochemical dynamics in adjacent mesoscale eddies of opposite polarity, Global Biogeochemical Cycles. doi: 10.1029/2021GB007115.

  • Barone, B., R. M. Letelier, K. H. Rubin and D. M. Karl. (2022) Satellite detection of a massive phytoplankton bloom following the 2022 submarine eruption of the Hunga Tonga-Hunga Ha’apai volcano. Geophys Res Lett. 49:e2022GL099293. doi: 10.1029/2022GL099293.

  • Biller, S.J. A.Coe, A.Arellano, K.Dooley, J. S. Gong, E.A. Yeager, J.W. Becker, S.W. Chisholm (2022). Environmental and taxonomic drivers of bacterial extracellular vesicle production in marine ecosystems. bioRxiv. Jan. 20, 2022.

  • Biller, S.J., R.A. Lundeen, L.R. Hmelo, J.W. Becker, A. A Arellano, K. Dooley, K.R. Heal, L. T. Carlson, B. A. S. Van Mooy, A. E. Ingalls, and S. W. Chisholm. Prochlorococcus extracellular vesicles: Molecular composition and adsorption to diverse microbes. Environmental Microbiology 24 (1), 420-435. doi: 10.1111/1462-2920.15834.

  • Boysen, A.K., B.P. Durham, W. Kumler, R.S. Key, K.R. Heal, L.T. Carson, R.D. Groussman, E.V. Armbrust, and A.E. Ingalls. Glycine betaine uptake and metabolism in marine microbial communities. Environmental Microbiology 24:2380-2403. doi: 10.1111/1462-2920.16020.

  • Britten G.L., Padalino C., Forget G., Follows M.J. (2022) Seasonal photoacclimation in the North Pacific Transition Zone. Global Biogeochemical Cycles. 36:e2022GB007324. doi: 10.1029/2022GB007324.

  • Carlson, M.C.G., F. Ribalet, I. Maidanik, B.P. Durham, Y. Hulata, S. Ferrón, J. Weissenbach, N. Shamir, S. Goldin, N. Baran, B.B. Cael, D.M. Karl, A.E. White, E.V. Armbrust, and D. Lindell (2022). Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean. Nature Microbiology 7:570-580. doi: 10.1038/s41564-022-01088-x.

  • Durham B.P., Boysen A.K., Heal K.R., Carlson L.T., Boccamazzo R., Deodato C.R., Qin W., Cattolico R.A., Armbrust E.V., Ingalls A.E. (2022) Chemotaxonomic patterns in intracellular metabolites of marine microbial plankton. Front Mar Sci. 9:864796. doi: 10.3389/fmars.2022.864796.

  • Ebenezer V., Y. Hu, O. Carnicer, A.J. Irwin, M.J. Follows, Z.V. Finkel. (2022) Elemental and macromolecular composition of the marine Chloropicophyceae, a major group of oceanic photosynthetic picoeukaryotes. Limnology and Oceanography 67: 540-551. doi: 10.1002/lno.12013.

  • Eppley J.M., Biller S.J., Luo E., Burger A., DeLong E.F. (2022) Marine viral particles reveal an expansive repertoire of phage-parasitizing mobile elements. Proc Natl Acad Sci U S A. 2022 Oct 25;119(43):e2212722119. doi: 10.1073/pnas.2212722119.

  • Follett C.L., Dutkiewicz S., Ribalet F., Zakem E., Caron D., Armbrust E.V., Follows M.J. (2022) Trophic interactions with heterotrophic bacteria limit the range of Prochlorococcus. Proc Natl Acad Sci USA. 119:e2110993118. doi: 10.1073/pnas.2110993118.

  • Gupta, M., R. G. Williams, J. M. Lauderdale, and M. J. Follows. (2022) A nutrient relay sustains subtropical ocean productivity. Proc Natl Acad USA. 119:e2206504119. doi: 10.1073/pnas.2206504119.

  • Hogle, S.L., T. Hackl, R.M. Bundy, J. Park, B. Satinsky, T. Hiltunen, S. Biller, P.M. Berube, and S.W. Chisholm. Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean. The ISME Journal, 16:1636-1646. doi: 10.1038/s41396-022-01215-w.

  • Hu Y.-Y., A. J. Irwin, Z. V. Finkel. (2022) Improving quantification of particulate phosphorus. Limnology and Oceanography: Methods. 20: 729-740. doi: 10.1002/lom3.10517.

  • Inomura, K., C. Deutsch, O. Jahn, S. Dutkiewicz, and M. J. Follows. (2022) Global patterns in marine organic matter stoichiometry driven by phytoplankton ecophysiology. Nat Geosci. doi: 10.1038/s41561-022-01066-2.

  • Karl D.M., Björkman K.M., Church M.J., Fujieki L.A., Grabowski E.M., Letelier R.M. (2022) Temporal dynamics of total microbial biomass and particulate detritus at Station ALOHA. Prog Oceanogr. 205:102803. doi: 10.1016/j.pocean.2022.102803.

  • Kearney S.M., A. Coe, K.G. Castro, S.W. Chisholm. Filter plating method for rendering Picocyanobacteria cultures free of Heterotrophic bacterial contaminants and clonal. Frontiers in Microbiology 13, 821803. doi: 10.3389/fmicb.2022.821803.

  • Kumler W., Ingalls A.E. (2022) Tidy data neatly resolves mass-spectrometry ragged arrays. R Journal, in press.

  • Kwon, E. Y., M. G. Sreeush, A. Timmermann, D. M. Karl, M. J. Church, S.-S. Lee and R. Yamaguchi. (2022) Nutrient update plasticity in phytoplankton sustains future ocean net primary production. Sci Adv., in press.

  • Lambert, B.S., Groussman, R.D., Schatz, M.J., Coesel, S.N., Durham, B.P., Alverson, A.J., White, A.E. and Armbrust, E.V. (2022). The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics. Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.2100916119.

  • Leu A.O., Eppley J.M., Burger A., DeLong E.F. (2022) Diverse genomic traits differentiate sinking-particle-associated versus free-living microbes throughout the oligotrophic open ocean water column. mBio.13:e0156922. doi: 10.1128/mbio.01569-22.

  • Linney M.D., Eppley J.M., Romano A.E., Luo E., DeLong E.F., Karl D.M. (2022) Microbial sources of exocellular DNA in the ocean. Applied and Environmental Microbiology. 88:02093-21. doi: 10.1128/aem.02093-21.

  • Luo E., Leu A.O., Eppley J.M., Karl D.M., DeLong E.F. (2022) Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean. ISME Journal. 16:1627-1635. doi: 10.1038/s41396-022-01202-1.

  • Maidanik, I., S. Kirzner, I. Pekarski, L. Arsenieff, R. Tahan, M.C.G. Carlson, D. Shitrit, N. Baran, S. Goldin, J. S. Weitz and D. Lindell. Cyanophages from a less virulent clade dominate over their sister clade in global oceans. The ISME journal. doi: 10.1038/s41396-022-01259-y

  • Martiny A.C., Hagstrom G.I., DeVries T., Letscher R.T., Britten G.L., Garcia C.A., Galbraith E., Karl D., Levin S.A., Lomas M.W., Moreno A.R., Talmy D., Wang W., Matsumoto K. (2022) Marine phytoplankton resilience may moderate oligotrophic ecosystem responses and biogeochemical feedbacks to climate change. Limnology and Oceanography. doi: 10.1002/lno.12029.

  • Meiler S., Britten G.L., Dutkiewicz S., Gradoville M.R., Moisander P.H., Jahn O., Follows M.J. (2022) Constraining uncertainties of diazotroph biogeography from nifH gene abundance. Limnology and Oceanography 67:816-829. doi: 10.1002/lno.12036.

  • Moran, M. A., E. B. Kujawinski, W. F. Schroer, S. A. Amin, N. R. Bates, E. M. Bertrand, R. Braakman, C. Titus Brown, M. W. Covert, S. C. Doney, S. T. Dyhrman, A. S. Edison, A. Murat Eren, N. M. Levine, L. Li, A. C. Ross, M. A. Saito, A. E. Santoro, D. Segrè, A. Shade, M. B. Sullivan, and A. Vardi. 2022. Microbial metabolites in the marine carbon cycle. Nat. Microbiol. doi: 10.1038/s41564-022-01090-3.

  • Muñoz-Marín, M. d. C., S. Duhamel, K. M. Björkman, J. D. Magasin, J. Díez, D. M. Karl, and J. M. García-Fernández. (2022) Differential timing for glucose assimilation in Prochlorococcus and coexistent microbial populations in the North Pacific Subtropical Gyre. Microbiol Spectrum. doi: 10.1128/spectrum.02466-22.

  • Muratore D., Boysen A.K., Harke M.J., Becker K.W., Casey J.R., Coesel S.N., Mende D.R., Wilson S.T., Aylward F.O., Eppley J.M., Vislova A., Peng S., Rodriguez-Gonzalez R.A., Beckett S.J., Armbrust E.V., DeLong E.F., Karl D.M., White A.E., Zehr J.P., Van Mooy B.A.S., Dyhrman S.T., Ingalls A.E., Weitz J.S. (2022) Complex marine microbial communities partition metabolism of scarce resources over the diel cycle. Nature Ecology and Evolution. doi: 10.1038/s41559-021-01606-w.

  • Rii Y., Peoples L., Karl D., Church M. (2022) Seasonality and episodic variation in picoeukaryote diversity and structure reveal community resilience to disturbances in the North Pacific Subtropical Gyre. Limnology and Oceanography. 67:S331-S351. doi: 10.1002/lno.11916.

  • Sacks J.S., Heal K.R., Boysen A.K., Carlson L.T., Ingalls A.E. (2022) Quantification of dissolved metabolites in environmental samples through cation-exchange solid-phase extraction paired with liquid chromatography-mass spectrometry. Limnol Oceanogr Meth. 20:683-700. doi: 10.1002/lom3.10513.

  • Schvarcz, C.R., S.T. Wilson, M. Caffin, R. Stancheva, Q. Li, K. A. Turk-Kubo, A. E. White, D. M. Karl, J. P. Zehr, and G. F. Steward (2022) Overlooked and widespread pennate diatom-diazotroph symbiosis in the sea. Nature Communications doi: 10.1038/s41467-022-28065-6.

  • Shitrit, D., T. Hackl, R. Laurenceau, N. Raho, M.G.C Carlson, G. Sabehi, D.A. Schwartz, S.W Chisholm, and D. Lindell. Genetic engineering of marine cyanophages reveals integration but not lysogeny in T7-like cyanophages. The ISME journal 16 (2), 488-499. doi: 10.1038/s41396-021-01085-8.

  • Tiedje J.M., Bruns M.A., Casadevall A., Criddle C.S., Eloe-Fadrosh E., Karl D.M., Nguyen N.K., Zhou J. (2022) Microbes and climate change: A research prospectus for the future. mBio. doi: 10.1128/mbio.00800-22.

  • White, A. E., J. Granger, and K. Turk-Kubo (2022) Questioning high nitrogen fixation rate measurements in the Southern Ocean. Nature Geoscience 15:29-30 doi: 10.1038/s41561-021-00873-3.

  • Wu, Z., D. Aharonovich, D. Roth-Rosenberg, O. Weissberg, T. Luzzatto-Knaan, A. Vogts, L. Zoccarato, F. Eigemann, H.-P. Grossart, M. Voss, M. J. Follows, and D. Sher. (2022) Single-cell measurements and modelling reveal substantial organic carbon acquisition by Prochlorococcus. Nat Microbiol. doi: 10.1038/s41564-022-01250-5.


  • Alber M., Blair J., Driscoll C.T., Ducklow H., Fahey T., Fraser W.R., Hobbie J.E., Karl D.M., Kingsland S.E., Knapp A., Rastetter E.B., Seastedt T., Shaver G.R., Waide R.B. (2021) Sustaining long-term ecological research: Perspectives from inside the LTER program. In: The Challenges of long term ecological research: A Historical analysis (Waide R.B. and Kingsland S.E., Eds.), pp. 81-116. Springer. doi: 10.1007/978-3-030-66933-1_4.

  • Becker K.W., Harke M.J., Mende D.R., Muratore D., Weitz J.S., DeLong E.F., Dyhrman S.T., Van Mooy B.A. (2021) Combined pigment and metatranscriptomic analysis reveals highly synchronized diel patterns of phenotypic light response across domains in the open oligotrophic ocean. The ISME Journal, 15 (2), 520-533. doi: 10.1038/s41396-020-00793-x.

  • Boeuf D., Eppley J.M., Mende D.R., Malmstrom R.R., Woyke T., DeLong E.F. (2021) Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage. Microbiome 9, 172. doi: 10.1186/s40168-021-01119-5.

  • Böttjer-Wilson* D., White* A.E., Björkman K.M., Church M.J., Poulos S., Shimabukuro E., Rii Y.M., Ludwig A., von Bröckel K., Riebesell U., Letelier R.M., Karl D.M. (2021) Effects of nutrient enrichments on oligotrophic phytoplankton communities: a mesocosm experiment near Hawai’i, USA. Aquat Microb Ecol., 87:167-183. doi: 10.3354/ame01977. * both authors contributed equally

  • Boysen A.K., Carlson L.T., Durham B.P., Groussman R.D., Aylward F.O., Ribalet F., Heal K.R., DeLong E.F., Armbrust E.V., Ingalls A.E. (2021) Particulate metabolites and transcripts reflect diel oscillations of microbial activity in the Surface Ocean. Msystems, 6(3). doi: 10.1128/mSystems.00896-20.

  • Cael B.B., Bisson K., Conte M., Duret M.T., Follett C.L., Henson S.A., Honda M.C., Iversen M.H., Karl D.M., Lampitt R.S., Mouw C.B., Muller-Karger F., Pebody C.A., Smith K.L. Jr., Talmy D. (2021) Open ocean particle flux variability from surface to seafloor. Geophys Res Lett. 48:e2021GL092895. doi: 10.1029/2021GL092895.

  • Cheung S., Zehr J.P., Xia X., Tsurumoto C., Endo H., Nakaoka S.-I., Mak W., Suzuki K., Liu H. (2021) Gamma4: a genetically versatile Gammaproteobacterial nifH phylotype that is widely distributed in the North Pacific Ocean. Environ Microbiol. 23:4246-4259. doi: 10.1111/1462-2920.15604.

  • Church M.J., Kyi E., Hall R.O., Karl D.M., Lindh M., Nelson A., and Wear E.K. (2021) Production and diversity of microorganisms associated with sinking particles in the subtropical North Pacific Ocean. Limnology and Oceanography 66: 3255-3270. doi: 10.1002/lno.11877.

  • Coe A., Biller S.J., Thomas E., Boulias K., Bliem C., Arellano A., Dooley K., Rasmussen A.N., LeGault K., O’Keefe T.J., Stover S., Greer E.L., Chisholm S.W. (2021) Coping with darkness: The adaptive response of marine picocyanobacteria to repeated light energy deprivation. Limnol Oceanogr. 66:3300-3312. doi: 10.1002/lno.11880.

  • Coesel S.N., Durham B.P., Groussman R.D., Hu S.K., Caron D.A., Morales R.L., Ribalet F. and Armbrust E.V. (2021) Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. Proceedings of the National Academy of Science of the United States of America. 118: e2011038118. doi: 10.1073/pnas.2011038118.

  • Cornejo-Castillo F.M., Zehr J.P. (2021) Intriguing size distribution of the uncultured and globally widespread marine non-cyanobacterial diazotroph Gamma-A. ISME J. 15:124-128. doi: 10.1038/s41396-020-00765-1.

  • Correa A.M.S., Howard-Varona C., Coy S.R., Buchan A., Sullivan M.B., Weitz J.S. (2021) Revisiting the rules of life for viruses of microorganisms. Nat Rev Microbiol. 19:501-513. doi: 10.1038/s41579-021-00530-x.

  • DeLong E.F. (2021) Exploring marine planktonic Archaea: then and now. Front. Microbiol. 11:3257. doi: 10.3389/fmicb.2020.616086.

  • DeLong E.F. (2021) Genome-enabled exploration of microbial ecology and evolution in the sea: A rising tide lifts all boats. Environmental Microbiology. 23: 1301-1321. doi: 10.1111/1462-2920.15403.

  • Demory D., Weitz J.S., Baudoux A.-C., Touzeau S., Simon N., Rabouille S., Sciandra A., Bernard O. (2021) A thermal trade-off between viral production and degradation drives virus-phytoplankton population dynamics. Ecol Lett. 24:1133-1144. doi: 10.1111/ele.13722.

  • Dextro R.B., Delbaje E., Cotta S.R., Zehr J.P., Fiore M.F. (2021) Trends in free-access genomic data accelerate advances in Cyanobacteria taxonomy. J Phycol. 57: 1392-1402. doi: 10.1111/jpy.13200.

  • Farnelid H., Turk-Kubo K., Zehr J.P. (2021) Cell sorting reveals few novel prokaryote and photosynthetic picoeukaryote associations in the oligotrophic ocean. Environ Microbiol. 23:1469-1480. doi: 10.1111/1462-2920.15351.

  • Ferrón S., Barone B., Church M.J., White A.E., & Karl D.M. (2021) Euphotic zone metabolism in the North Pacific Subtropical Gyre based on oxygen dynamics. Global Biogeochemical Cycles, 35, e2020GB006744. doi: 10.1029/2020GB006744.

  • Follett C.L., Dutkiewicz S., Forget G., Cael B.B., Follows M.J. (2021) Moving ecological and biogeochemical transitions across the North Pacific. Limnol Oceanogr. 66:2442-2454. doi: 10.1002/lno.11763.

  • Foreman R.K., Björkman K.M., Funkey C.P., Hawco N.J., Wilson S.T., Rohrer T., White A.E., John S.G. and Karl D.M. (2021) Phosphate scavenging during lava‐seawater interaction offshore of Kīlauea volcano, Hawaii. Geochemistry, Geophysics, Geosystems, doi: 10.1029/2021GC009754.

  • Foster R.A., Tienken D., Littman S., Whitehouse M., Kuypers M., and White A.W. (2021) The rate and fate of N2 and C fixation by diatom-diazotroph symbioses. The ISME Journal. doi: 10.1038/s41396-021-01086-7.

  • Gauglitz J., Boiteau R., McLean C., Babcock-Adams L., McIlvin M., Moran D., Repeta D.J., and Saito M. (2021) Dynamic proteome response of a marine Vibrio to a gradient of iron and ferrioxamine bioavailability. Marine Chemistry. doi: 10.1016/j.marchem.2020.103913.

  • Gradoville M.R., Cabello A.M., Wilson S.T., Turk-Kubo K.A., Karl D.M., Zehr J.P. (2021) Light and depth dependency of nitrogen fixation by the non-photosynthetic, symbiotic cyanobacterium UCYN-A. Environ Microbiol. 23:4518-4531. doi: 10.1111/1462-2920.15645.

  • Granzow B.N., Sosa O.A., Gonnelli M., Santinelli C., Karl D.M. and Repeta D.J. (2021) A sensitive fluorescent assay for measuring carbon-phosphorus lyase activity in aquatic systems. Limnol. Oceanogr. doi: 10.1002/lom3.10418.

  • Groussman R.D., Coesel S.N., Durham B.P., Armbrust E.V. (2021) Diel-regulated transcriptional cascades of microbial eukaryotes in the North Pacific Subtropical Gyre. Frontiers in Microbiology, doi: 10.3389/fmicb.2021.682651.

  • Harke M.J., Frischkorn K.R., Hennon G.M.M., Haley S.T., Barone B., Karl D.M., Dyhrman S.T. (2021) Microbial community transcriptional patterns vary in response to mesoscale forcing in the North Pacific Subtropical Gyre. Environ. Microbiol. 23:4807-4822. doi: 10.1111/1462-2920.15677.

  • Hawco N.J., Barone B., Church M.J., Babcock-Adams L., Repeta D.J., Wear E.K., Foreman R.K., Björkman K.M., Bent S., Van Mooy B.A.S., Sheyn U., DeLong E.F., Acker M., Kelly R.L., Nelson A., Ranieri J., Clemente T.M., Karl D.M., John S.G. (2021) Iron depletion in the deep chlorophyll maximum: Mesoscale eddies as natural iron fertilization experiments. Glob Biogeochem Cy 35:e2021GB007112. doi: 10.1029/2021GB007112.

  • Hawco N.J., Fu F., Yang N., Hutchins D.A., John S.G. (2021) Independent iron and light limitation in a low-light-adapted Prochlorococcus from the deep chlorophyll maximum. ISME J. 15:359-362. doi: 10.1038/s41396-020-00776-y.

  • Heal K.R., Durham B.P., Boysen A.K., Carlson L.T., Qin W., Ribalet F., White A.E., Bundy R.M., Armbrust E.V., Ingalls A.E. (2021) Marine community metabolomes carry fingerprints of phytoplankton community composition. mSystems. doi: 10.1128/mSystems.01334-20.

  • Heal K.R., Maloney A.E., Ingalls A.E., Bundy R. (2021) Diverse arsenic-containing lipids in the surface ocean. Limnology & Oceanography Letters. 7:43-51. doi: 10.1002/lol2.10216.

  • Henderikx-Freitas F., Björkman K., Karl D., and White A.E. (2021) Constraining growth rates and the ratio of living to non-living particulate carbon using beam attenuation and adenosine-5’-triphosphate at Station ALOHA. Limnology and Oceanography Letters, doi: 10.1002/lol2.10199.

  • Karl D.M., Letelier R.M., Bidigare R.R., Björkman K.M., Church M.J., Dore J.E., White A.E. (2021) Seasonal-to-decadal scale variability in primary production and particulate matter export at Station ALOHA. Progress in Oceanography 195: 102563. doi: 10.1016/j.pocean.2021.102563.

  • Kearney S.M., Thomas E., Coe A., and Chisholm S.W. (2021) Microbial diversity of co-occurring heterotrophs in cultures of marine picocyanobacterial. Environ. Microbiome. 16:1. doi: 10.1186/s40793-020-00370-x.

  • Kelly R.L., Bian X., Feakins S.J., Fornace K.L., Gunderson T., Hawco N.J., Liang H., Niggemann J., Paulson S.E., Pinedo‐Gonzalez P., West A.J., Yang S.-C., John S.G. (2021) Delivery of metals and dissolved black carbon to the Southern California coastal ocean via aerosols and floodwaters following the 2017 Thomas fire. J Geophys Res Biogeosci. 126:e2020JG006117. doi: 10.1029/2020JG006117.

  • Landa M., Turk-Kubo K.A., Cornejo-Castillo F.M., Henke B.A., Zehr J.P. (2021) Critical role of light in the growth and activity of the marine N2-fixing UCYN-A symbiosis. Front Microbiol. 12:666739. doi: 10.3389/fmicb.2021.666739.

  • Lauderdale J.M., Cael B.B. (2021) Impact of remineralization profile shape on the air-sea carbon balance. Geophys Res Lett. 48:e2020GL091746. doi: 10.1029/2020GL091746.

  • Li F., Leu A., Poff K., Carlson L.T., Ingalls A.E., DeLong E.F. (2021) Planktonic archaeal ether lipid origins in surface waters of the North Pacific Subtropical Gyre. Frontiers in Microbiology. doi: 10.3389/fmicb.2021.610675.

  • Li J., Boiteau R.M., Babcock-Adams L., Acker M., Song S., McILvin M., and Repeta D.J. (2021) Element-selective targeting of nutrient metabolites in environmental samples by inductively coupled plasma mass spectrometry and electrospray ionization mass spectrometry. Frontiers Mar. Sci. doi: 10.3389/fmars.2021.630494.

  • Li Z., Li W., Zhang Y., Hu Y., Sheward R., Irwin A.J., Finkel Z.V. (2021) Dynamic photophysiological stress response of a model diatom to ten environmental stresses. J Phycol.57:484-495. doi: 10.1111/jpy.13072.

  • Linney M.D., Schvarcz C.R., Steward G.F., DeLong E.F. and Karl D.M. (2021) A method for characterizing dissolved DNA and its application to the North Pacific Subtropical Gyre, Limnol. Oceanogr. Methods   doi: 10.1002/lom3.10415.

  • McGinty N., A. Barton, D.G. Johns, Z.V. Finkel, A.J. Irwin. 2021. Niche conservation in copepods between ocean basins. Ecography 44: 1653-1664. doi: 10.1111/ecog.05690.

  • McGinty N., A.D. Barton, N.R. Record, Z.V. Finkel, D.G. Johns, C.A. Stock, A.J. Irwin. 2021. Anthropogenic climate change impacts on copepod trait biogeography. Global Change Biology 27: 1431-1442. doi: 10.1111/gcb.15499.

  • Mruwat N., Carlson M.C.G., Goldin S., Ribalet F., Kirzner S., Hulata Y., Beckett S.J., Shitrit D., Weitz J.S., Armbrust E.V., Lindell D. (2021) A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances. The ISME Journal. doi: 10.1038/s41396-020-00752-6.

  • Muratore, D., A.K. Boysen, M.J. Harke, K.W. Becker, J.R. Casey, S.N. Coesel, D. R. Mende, S.T. Wilson, F.O. Aylward, J.M. Eppley, A. Vislova, , S. Peng, R.A. Rodriguez-Gonzalez, S.J. Beckett, E.V. Armbrust, E.F. Delong, D.M. Karl, A.E. White, J.P. Zehr, B.A.S. Van Mooy, S.T. Dyhrman, A.E. Ingalls, and J.S. Weitz. (2021) Complex marine microbial communities partition metabolism of scarce resources over the diel cycle. Nature Ecology and Evolution, doi: 10.1038/s41559-021-01606-w.

  • Muratore D., Weitz J.S. (2021) Infect while the iron is scarce: nutrient-explicit phage-bacteria games. Theor Ecol. doi: 10.1007/s12080-021-00508-8.

  • Ollison G.A., Hu S.K., Mesrop L.Y., DeLong E.F. and Caron D.A. (2021) Come rain or shine: Depth not season shapes the active protistan community at station ALOHA in the North Pacific Subtropical Gyre. Deep-Sea Res I 170: 103494. doi: doi: 10.1016/j.dsr.2021.103494.

  • Poff K.E., Leu A.O., Eppley J.M., Karl D.M., DeLong E.F. (2021) Microbial dynamics of elevated carbon flux in the open ocean's abyss. Proc Natl Acad Sci U S A. 118(4):e2018269118. doi: 10.1073/pnas.2018269118.

  • Pollara S.B., Becker J.W., Nunn B.L., Boiteau R.M., Repeta D.J., Mudge M.C., Downing G., Chase D., Harvey E., and Whalen K.E. (2021) Bacterial quorum sensing signal arrests phytoplankton cell division and impacts viral induced mortality. mSphere. doi: 10.1128/mSphere.00009-21.

  • Ponsero A.J., Bomhoff M., Blumberg K., Youens-Clark K., Herz N.M., Wood-Charlson E.M., DeLong E.F. and Hurwitz B.L. (2021) Planet Microbe: a platform for marine microbiology to discover and analyze interconnected ‘omics and environmental data. Nuc. Acid Res. 49(D1):D792-D802. doi: 10.1093/nar/gkaa637.

  • Repeta D.J. (2021) Unifying chemical and biological perspectives on carbon accumulation in the environment. (commentary) Proc Natl Acad Sci USA. doi: 10.1073/pnas.2100935118.

  • Rii Y.M., Peoples L.M., Karl D.M. and Church M.J. (2021) Seasonality and episodic variation in picoeukaryote diversity and structure reveals community resilience to disturbances in the North Pacific Subtropical Gyre. Limnology and Oceanography. doi: 10.1002/lno.11916.

  • Sarkar D., Landa M., Bandyopadhyay A., Pakrasi H.B., Zehr J.P., Maranas C.D. (2021) Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling. PLoS Comput Biol. 17:e1008983. doi: 10.1371/journal.pcbi.1008983.

  • Turk-Kubo K.A., Mills M.M., Arrigo K.R., van Dijken G., Henke B.A., Stewart B., Wilson S.T., Zehr J.P. (2021) UCYN-A/haptopphyte symbioses dominate N2 fixation in the Southern California Current System. ISME Comm. 1:42. doi: 10.1038/s43705-021-00039-7.

  • Wilson S.T., Caffin M., White A.E. and Karl D.M. (2021) Evaluation of argon induced hydrogen production as a method to measure nitrogen fixation by cyanobacteria. Journal of Phycology. doi: 10.1111/jpy.13129.

  • Wu Z., Dutkiewicz S., Jahn O., Sher D., White A.E. and Follows M.J. (2021) Modeling photosynthesis and exudation of DOM in Subtropical Oceans. Global Biogeochemical Cycles, doi: 10.1029/2021GB006941.

  • Zakem E.J., Lauderdale J.M., Schlitzer R. and Follows M.J. (2021) A flux-based threshold for anaerobic activity in the ocean. Geophys Res Lett. 48:e2020GL090423. doi: 10.1029/2020GL090423.

  • Zehr J.P. and Capone D.G. (2021) Marine Nitrogen Fixation. Springer Nature.

  • Zehr J.P. and Caron D.A. (2021) Symbiosis in the ocean microbiome. In: Stahl, L.J., The marine microbiome, 2nd Edition, Springer Nature. In press.

  • Zhang Y., Z.-K. Li, K.G. Schulz, Y. Hu, A.J. Irwin, Z.V. Finkel. 2021. Growth-dependent changes in elemental stoichiometry and macromolecular allocation in the coccolithophore Emiliania huxleyi under different environmental conditions. Limnology and Oceanography 66: 2999-3009. doi: 10.1002/lno.11854.

  • Zhang Y., Ryan J.P., Hobson B.W., Kieft B., Romano A.E., Barone B., Preston C.M., Roman B., Raanan B.Y., Pargett D., Dugenne M., White A.E., Freitas F.H., Poulos S., Wilson S.T., DeLong E.F., Karl D.M., Birch J.M., Bellingham J.G., Scholin C.A. (2021) A system of coordinated autonomous robots for Lagrangian studies of microbes in the oceanic deep chlorophyll maximum. Sci Robot. 6(50) . doi: 10.1126/scirobotics.abb9138. PMID: 34043577.


  • Alexander H., Rouco M., Haley S.T., Dyhrman S.T. (2020) Transcriptional response of Emiliania huxleyi under changing nutrient environments in the North Pacific Subtropical Gyre. Environ. Microbiol. 22:1847-1860.

  • Beaulaurier J., Luo E., Eppley J.M., Uyl P.D., Dai X., Burger A., Turner D.J., Pendelton M., Juul S., Harrington E., DeLong E.F. (2020) Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities. Genome Res. 30:437-446. doi: 10.1101/gr.251686.119.

  • Becker K.W., Harke M.J., Mende D.R., Muratore D., Weitz J.S., DeLong E.F., Dyhrman S.T., Van Mooy B.A.S. (2020) Combined pigment and metatranscriptomic analysis reveals highly synchronized diel patterns of phenotypic light response across domains in the open oligotrophic ocean. ISME J. 15:520-533. doi: 10.1038/s41396-020-00793-x.

  • Cabello A.M., Turk-Kubo K.A., Hayashi K., Jacobs L., Kudela R.M., Zehr J.P. (2020) Unexpected presence of the nitrogen-fixing symbiotic cyanobacterium UCYN-A in Monterey Bay, California. J Phycol. 56:1521-1533. doi: 10.1111/jpy.13045-20-043.

  • Cael B.B. and White A.E. (2020). Sinking versus suspended particle size distributions in the North Pacific Subtropical Gyre. Geophysical Research Letters, 47(15), p.e2020GL087825.

  • Coenen A.R., Hu S.K., Luo E., Muratore D. and Weitz J.S. (2020) A Primer for microbiome Time-series analysis.

  • Connell P.E., Ribalet F., Armbrust E.V., White A.E. and Caron D.A. (2020) Diel oscillations in the feeding activity of heterotrophic and mixotrophic nanoplankton in the North Pacific Subtropical Gyre. Aquatic Microbial Ecology, 85, pp.167-181.

  • DeLong E.F. (2020) Exploring marine planktonic Archaea: then and now. Front Microbiol. 11:616086. doi: 10.3389/fmicb.2020.616086.

  • Demory D., Liu R., Chen Y., Zhao F., Coenen A.R., Zeng , Weitz J.S. (2020) Linking light-dependent life history traits with population dynamics for Prochlorococcus and cyanophage. mSystems 5:e00586-19. doi: 10.1128/mSystems.00586-19.

  • Dugenne M., Henderikx Freitas F., Wilson S.T., Karl D.M. and White A.E. (2020). Life and death of Crocosphaera sp. in the Pacific Ocean: fine scale predator–prey dynamics. Limnology and Oceanography, 65(11), pp.2603-2617.

  • Farnelid H., Turk-Kubo K., Zehr J.P. (2020) Cell sorting reveals few novel prokaryote and photosynthetic picoeukaryote associations in the oligotrophic ocean. Environ Microbiol.23:1469-1480. doi: 10.1111/1462-2920.15351.

  • Garcia-Pichel F., Zehr J.P., Bhattacharya D., Pakrasi H.B. (2020) What’s in a name? The case of Cyanobacteria. J Phycol. 56:1-5. doi: 10.1111/jpy.12934.

  • Goldin S., Hulata Y., Baran N., Lindell D. (2020) Quantification of T4-Like and T7-Like cyanophages using the polony method show they are significant members of the virioplankton in the North Pacific Subtropical Gyre. Frontiers in Microbiology 11:1210. doi: 10.3389/fmicb.2020.01210.

  • Gradoville M.R., Farnelid H., White A.E., Turk‐Kubo K.A., Stewart B., Ribalet F., Ferrón S., Pinedo‐Gonzalez P., Armbrust E.V., Karl D.M., John S. and Zehr J.P. (2020) Latitudinal constraints on the abundance and activity of the cyanobacterium UCYN‐A and other marine diazotrophs in the North Pacific. Limnology and Oceanography, 65(8), pp. 1858-1875. doi: 10.1002/lno.11423.

  • Hawco N.J., Yang S.C., Foreman R.K., Funkey C.P., Dugenne M., White A.E., Wilson S.T., Kelly R.L., Bian X., Huang K.F. and Karl D.M. (2020) Metal isotope signatures from lava-seawater interaction during the 2018 eruption of Kīlauea. Geochimica et Cosmochimica Acta, 282, pp.340-356.

  • Hayes C.T., Fitzsimmons J.N., Jensen L.T., Lanning N.T., Hatta M., McGee D. and Boyle E.A. (2020) A Lagrangian view of trace elements and isotopes in the North Pacific. Journal of Geophysical Research: Oceans, p.e2019JC015862.

  • Henderikx Freitas F., Dugenne M., Ribalet F., Hynes A., Barone B., Karl D.M. and White A.E. (2020) Diel variability of bulk optical properties associated with the growth and division of small phytoplankton in the North Pacific Subtropical Gyre. Applied Optics, 59(22), pp.6702-6716.

  • Henderikx Freitas F., White A.E. and Quay P.D. (2020) Diel measurements of oxygen‐and carbon‐based ocean metabolism across a trophic gradient in the North Pacific. Global Biogeochemical Cycles, 34(11), p.e2019GB006518.

  • Hernández Limón M., Hennon G.M.M., Harke M.J., Frischkorn K.R., Haley S.T., Dyhrman S.T. (2020) Transcriptional patterns of Emiliania huxleyi in the North Pacific Subtropical Gyre reveal the daily rhythms of its metabolic potential. Environ. Microbiol. 22:381-396.

  • Inomura K., Deutsch C. Masuda T., Prášil O., Follows M.J. (2020) Quantitative models of nitrogen-fixing organisms. Comp Structural Biotech J 18:3905-3924. doi: 10.1016/j.csbj.2020.11.022.

  • Inomura K., Omta A.W., Talmy D., Bragg J., Deutsch C., Follows M.J. (2020) A mechanistic model of macromolecular allocation, elemental stoichiometry, and growth rate in phytoplankton. Front Microbiol. 11:86. doi: 10.3389/fmicb.2020.00086.

  • Janssen D.J., Rikli J., Quay P.D., White A.E., Nasemann P., Jaccard S.L. (2020) Biological control of chromium redox and stable isotope composition in the surface ocean. Global Biogeochem Cy. 34:e2019GB006397. doi: 10.1029/2019GB006397.

  • John S.G., Liang H., Weber T., DeVries T., Primeau F., Moore K., Holzer M., Mahowald N., Gardner W., Mishonov A., Richardson M.J., Faugere Y., Taburet G. (2020) AWESOME OCIM: A simple, flexible, and powerful tool for modeling elemental cycling in the oceans. Chem Geol. 533:119403. doi: 10.1016/j.chemgeo.2019.119403.

  • Juranek* L.W., White* A.E., Dugenne M., Henderikx Freitas F., Dutkiewicz S., Ribalet F., Ferrón S., Armbrust E.V. and Karl D.M. (2020) The Importance of the phytoplankton "middle class" to ocean net community production. Global Biogeochemical Cycles, 34(12), p.e2020GB006702. *both authors contributed equally

  • Karl D.M. (2020) Oceans 2020. In: P. Tortell, Ed., Earth 2020: An Insider’s guide to a rapidly changing planet, pp. 203-211, Cambridge, UK: Open Book Publishers.

  • Klawonn I., Eichner M.J., Wilson S.T., Moradi N., Thamdrup B., Kümmel S., Gehre M., Khalili A., Grossart H.P., Karl D.M. and Ploug H. (2020) Distinct nitrogen cycling and steep chemical gradients in Trichodesmium colonies. ISME J. 14: 399-412.

  • Lauderdale J.M., Braakman R., Forget G., Dutkiewicz S., Follows M. (2020) Microbial feedbacks optimize ocean iron availability. Proc Natl Acad Sci USA. 117:4842-4849. doi: 10.1073/pnas.1917277117.

  • Laurenceau R., Bliem C., Osburne M.S., Becker J.W., Biller S.J., Cubillos-Ruiz A. and Chisholm S.W. (2020) Toward a genetic system in the marine cyanobacterium Prochlorococcus. Access Microbiology, p.acmi000107.

  • Laurenceau R., Raho N., Forget M., Arellano A., and Chisholm S.W. (2020). Frequency of mispackaging of Prochlorococcus DNA by cyanophage. ISME Journal.

  • Li G., Cortez M.H., Dushoff J., Weitz J.S. (2020) When to be temperate: on the fitness benefits of lysis vs. lysogeny. Virus Evol. 6:veaa042. doi: 10.1093/ve/veaa042.

  • Luo E., Eppley J.M., Romano A.E., Mende D.R., DeLong E.F. (2020) Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column. ISME J. doi: 10.1038/s41396-020-0604-8.

  • Martinez-Hernandez F., Luo E., Tominaga K., Ogata H., Yoshida T., DeLong E.F., Martinez-Garcia M. (2020) Diel cycling of the cosmopolitan abundant Pelagibacter virus 37-F6: one of the most abundant viruses on earth. Environ Microbiol Rep. 12:214-219. doi: 10.1111/1758-2229.12825.

  • Mills M.M., Turk-Kubo K.A., van Dijken G.L., Henke B.A., Harding K., Wilson S.T., Arrigo K.R., Zehr J.P. (2020) Unusual marine cyanobacteria/haptophyte symbiosis relies on N2 fixation even in N-rich environments. ISME J. 14:2395-2406. doi: 10.1038/s41396-020-0691-6.

  • Omta A.W., Talmy D., Inomura K., Irwin A.J., Finkel Z.V., Sher D., Liefer J.D., Follows M.J. (2020) Quantifying nutrient throughput and DOM production by algae in continuous culture. J Theor Biol. 494:11214. doi: 10.1016/j.jtbi.2020.110214.

  • Pinedo-González P., Hawco N.J., Bundy R.M., Armbrust E.V., Follows M.J., Cael B.B., White A.E., Ferrón S., Karl D.M. and John S.G. (2020) Anthropogenic Asian aerosols provide Fe to the North Pacific Ocean. Proceedings of the National Academy of Sciences USA, 117(45), pp.27862-27868.

  • Ponsero A.J., Bomhoff M., Blumberg K., Youens-Clark K., Herz N.M., Wood-Charlson E.M., DeLong E.F., Hurwitz B.L. (2020) Planet Microbe: a platform for marine microbiology to discover and analyze interconnected ‘omics and environmental data. Nuc Acid Res. Jul 31:gkaa637. doi: 10.1093/nar/gkaa637.

  • Qin W., Zheng Y., Bollmann A., Wang B., Zhang C., Mende D., Stahl D., Delong E.F., Armbrust E.V., Liu H., Urakawa H., Nielsen J.L., Zhou J., de la Torre J.R., Mori K., Li M., Lee P., Takahashi R., Amin S., Nakagawa T., Zhang T., Martens-Habbena W., Huang X., Zhang X., Zhang Y., Wang Y. and Ingalls A.E. (2020) Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea. ISME J.

  • Shilova I.N., Magasin J.D., Mills M.M., Robidart J.C., Turk-Kubo K.A., Zehr J.P. (2020) Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California current system. PLoS ONE 15:e0231771. doi: 10.1371/journal/pone.0231771.

  • Sosa O.A., Burrell T.J., Wilson S.T., Foreman R.K., Karl D.M., Repeta D.J. (2020) Phosphonate cycling supports methane and ethylene supersaturation in the phosphate-depleted western North Atlantic Ocean. Limnol Oceanogr. 65:2443-2459. doi: 10.1002/lno.11463.

  • Wear E.K., Carlson C.A., Church M.J. (2020) Bacterioplankton use of phytoplankton lysates across a cyclone-anticyclone eddy dipole impacts the turnover and production of semi-labile organic matter in the photic zone. Limnology and Oceanography 65: 1608-1622.

  • White A.E., Granger J., Selden C., Gradoville M.R., Potts L., Bourbonnais A., Fulweiler R.W., Knapp A.N., Mohr W., Moisander P., Tobias C.R., Caffin M., Wilson S.T., Benavides M., Bonnet S., Mulholland M., and Chang B.X. (2020) A critical review of the 15N2 tracer method to measure diazotrophic production in pelagic ecosystems. Limnology and Oceanography Methods. doi: 10.1002/lom3.10353.

  • Yang S.-C., Hawco N.J., Pinedo-González P., Bian X., Huang K.-F., Zhang R., John S.G. (2020) A new purification method for Ni and Cu stable isotopes in seawater provides evidence for widespread Ni isotope fractionation by phytoplankton in the North Pacific. Chem Geol. 547:119662. doi: 10.1016/j.chemgeo.2020.119662.

  • Zakem E.J., Pola M.F., Follows M.J. (2020) Redox-informed models of global biogeochemical cycles. Nature Commun. 11:5680. doi: 10.1038/s41467-020-19454-w.

  • Zehr J.P., Capone D.G. (2020) Changing perspectives in marine nitrogen fixation. Science 368:eaay9514. doi: 10.1126/science.aay9514.

  • Zimmerman A.E., Howard-Varona C., Needham D.M., John S.G., Worden A.Z., Sullivan M.B., Waldbauer J.R., Coleman M.L. (2020) Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nature Rev Microbiol. 18:21-33. doi: 10.1038/s41579-019-0270-x.