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Publications
Beckett S.J., Weitz J.S. Disentangling niche competition from grazing mortality in phytoplankton dilution experiments. PLoS ONE. 12(5): e0177517. doi:10.1371/journal.pone.0177517.
Biller S.J., McDaniel L.D., Breitbart M., Rogers E., Paul J.H., Chisholm S.W. Membrane vesicles in sea water: Heterogeneous DNA content and implications for viral abundance estimates. ISME J. 11(2):394-404. doi:10.1038/ismej.2016.134.
Böttjer D., Dore J.E., Karl D.M., Letelier R.M., Mahaffey C., Wilson S.T., Zehr J., Church M.J. Temporal variability of nitrogen fixation and particulate nitrogen export at Station ALOHA. Limnol Oceanogr. 62:200-216. doi:10.1002/lno.10386.
Braakman R., Follows M.J., Chisholm S.W. Metabolic evolution and the self-organization of ecosystems. PNAS USA. 114(15):E3091–E3100. doi:10.1073/pnas.1619573114.
Caron D.A., Alexander H., Allen A.E., Archibald J.M., Armbrust E.V., Bachy C., Bharti A., Bell C.J., Dyrhman S.T., Guida S., Heidelberg K.B., Kaye J.Z., Metzner J., Smith S.R., Worden A.Z. Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nat Rev Microbiol. 15:6-20. doi:10.1038/nrmicro.2016.160.
Caron D.A. Acknowledging and incorporating mixed nutrition into aquatic protistan ecology, finally. Enviro Microbiol Rep. 9(1):41-43. doi:10.1111/1758-2229.12514.
Cermak N., Becker J.W., Knudsen S.M., Chisholm S.W., Manalis S.R., Polz M.F. Direct single cell biomass estimates for marine bacteria via Archimedes' principle. ISME J. 11(3):825-828. doi:10.1038/ismej.2016.161.
Cubillos-Ruiz A., Berta-Thompson J.W., Becker J.W., van der Donk W.A., Chisholm S.W. Evolutionary radiation of lanthipeptides in marine cyanobacteria. PNAS USA. 30 May. doi:10.1073/pnas.1700990114.
Cunningham B.R., John S.G The effect of iron limitation on cyanobacteria major nutrient and trace element stoichiometry. Limnol Oceanogr. 62(2):846-858. doi:10.1002/lno.10484.
Eichner M.J., Klawonn I., Wilson S.T., Littmann S., Whitehouse M., Church M.J., Kuypers M.M., Karl D.M., Ploug H. Chemical microenvironments and single-cell carbon and nitrogen uptake in field-collected colonies of Trichodesmium under different pCO2. ISME J. 11:1305-1317. doi:10.1038/ismej.2017.15.
Goldberg S.J., Nelson C.E., Viviani D.A., Shulse C.N., Church M.J. Cascading influence of inorganic nitrogen sources on DOM production, composition, lability and microbial community structure in the open ocean. Enviro Microbiol. 15 Jun* doi:10.1111/1462-2920.13825.
Gradoville M.R., Bombar D., Crump B., Letelier R.M., Zehr J.P. White, A.E. Diversity and activity of nitrogen-fixing communities across ocean basins. Limnol Oceanogr. 31 Mar. doi:10.1002/lno.10542.
Gradoville M.R., Crump B.C., Letelier R.M., Church M.J., White A.E. Microbiome of Trichodesmium colonies from the North Pacific Subtropical Gyre. Front Marine Microbiol. 8:1122. doi:10.3389/fmicb.2017.01122.
Heal K.R., Qin W., Ribalet F., Bertagnolli A.D., Coyote-Maestas W., Hmelo L.R., Moffett J.W., Devol A.H., Armbrust E.V., Stahl D.A., Ingalls A.E. Two distinct pools of B12 analogs reveal community interdependencies in the ocean. PNAS USA. 114(2):364-369. doi:10.1073/pnas.1608462114.
Inomura K., Bragg J., Follows M.J. A quantitative analysis of the direct and indirect costs of nitrogen fixation: a model based on Azotobacter vinelandii. ISME J. 11(1):166-175. doi:10.1038/ismej.2016.97.
Karl D.M., Church M.J. Ecosystem structure and dynamics in the North Pacific Subtropical Gyre: New views of an old ocean. Ecosystems 112:20th Anniversary. doi:10.1007/s10021-017-0117-0.
Karl D.M., Grabowski E. The importance of H in particulate matter stoichiometry, export and energy flow. Front. Microbiol. 8:826. doi:10.3389/fmicb.2017.00826.
Kujawinski E.B., Longnecker K., Alexander H., Dyhrman S.T., Fiore C.L., Haley S.T., Johnson W.M. Phosphorus availability regulates intracellular nucleotides in marine eukaryotic phytoplankton. Limnol Oceanogr Lett. 5 Jun. doi:10.1002/lol2.10043.
Letelier R.M., White A.E., Bidigare R.R., Barone B., Church M.J., Karl D.M. Light absorption by phytoplankton in the North Pacific subtropical gyre. Limnol Oceanogr. 24 Mar. doi:10.1002/lno.10515.
Schwartz D.A., Lindell D. Genetic hurdles limit the arms race between Prochlorococcus and the T7-like podoviruses infecting them. ISME J. 25 Apr. doi:10.1038/ismej.2017.47.
Stoecker D.K., Hanse P.J., Caron D.A., Mitra A. Mixotrophy in the marine plankton. Ann Rev Mar Sci. 9:311-335. doi:10.1146/annurev-marine-010816-060617.
Turk-Kubo K.A., Farnelid H.M., Shilova I.N., Henke B., Zehr J.P. Distinct ecological niches of marine symbiotic N2-fixing cyanobacterium Candidatus Atelocyanobacterium thalassa sublineages. J Phycol. 53(2):451-461. doi:10.1111/jpy.12505.
Viviani D.A., Church M.J. Decoupling between bacterial production and primary production over multiple time scales in the North Pacific Subtropical Gyre. Deep Sea Research I. 121:1332-142. doi:10.1016/j.dsr.2017.01.006.
White A.E., Barone B., Letelier R.M., Karl D.M. Productivity diagnosed from the diurnal cycle of particulate carbon in the North Pacific Subtropical Gyre. Geophys Res Lett. 44(8):3752-3760. doi:10.1002/2016GL071607.
Zigah P.K., McNichol A.P., Xu L., Johnson C., Santinelli C., Karl D.M., Repeta D.J. Allochthonous sources and dynamic cycling of ocean dissolved organic carbon revealed by carbon isotopes. Geophys Res Lett. 44(5):2407-2415. doi:10.1002/2016GL071348.
Ashkezari M.D., Hill C.N., Follett C.N., Forget G., Follows M.J. Oceanic eddy detection and lifetime forecast using machine learning methods. Geophys Res Lett. 43(23)12234-12241. doi:10.1002/2016GL071269.
Berube P.M., Coe A., Roggensack S.E., Chisholm S.W. Temporal dynamics of Prochlorococcus cells with the potential for nitrate assimilation in the subtropical Atlantic and Pacific oceans. Limnol Oceanogr. 61(2):482-495. doi:10.1002/lno.10226.
Biller S.J., Coe A., Chisholm S.W. Torn apart and reunited: Impact of a heterotroph on the transcriptome of Prochlorococcus. ISME J. 10:2831-2843. doi:10.1038/ismej.2016.82.
Boiteau R.M., Mende D.R., Hawco N.J., McIlvin M.R., Fitzsimmons J.N., Saito M.A., Sedwick P.N., DeLong E.F., Repeta D.J. Siderophore-based microbial adaptations to iron scarcity across the eastern Pacific Ocean. PNAS USA. 113(50):14237-14242. doi:10.1073/pnas.1608594113.
Boiteau R.M., Till C.P., Ruacho A., Bundy R.M., Hawco N.J., McKenna A.M., Barbeau K.A., Bruland K.W., Saito M.A., Repeta D.K. Structural characterization of natural nickel and copper binding ligands along the US GEOTRACES Eastern Pacific Zonal transect. Front Mar Sci. 3:243. doi:10.3389/frmars.2016.00243.
Bryant J.A., Aylward F.O., Eppley J.M., Karl D.M., Church M.J., DeLong E.F. Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre. ISME J. 10:1308-1322. doi:10.1038/ismej.2015.221.
Bryant J.A., Clemente T.M, Viviani D.A., Fong A.A., Thomas K.A, Kemp P., Karl D.M., White, A., DeLong E.F. Diversity and activity of communities inhabiting plastic debris in the North Pacific Gyre. mSystems. 1(3):e00024-16. doi:10.1128/mSystems.00024-16.
Cael B.B., Follows M.J. On the temperature dependence of oceanic export efficiency. Geophys Res Lett. 43. doi:10.1002/2016GL068877.
Caron D.A. Ocean science: The rise of Rhizaria. Nat News & Views. 532:444-445. doi:10.1038/nature17892.
Caron D.A. Mixotrophy stirs up our understanding of marine food webs. (commentary on Ward & Follows). PNAS USA. 113(11):2806-2808. doi:10.1073/pnas.1600718113.
Casey J.R., Mardinoglu A., Nielsen J., Karl D.M. Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus. mSystems. 15 Nov. doi:10.1128/mSystems.00065-16.
Coe A., Ghizzoni J., LeGault K., Biller S., Roggensack S.E., Chisholm S.W. Survival of Prochlorococcus in extended darkness. Limnol Oceanogr. 61(4):1375-1388. doi:10.1002/lno.10302.
Collins J.R., Edwards B.R., Fredricks H.F., Van Mooy B.A.S. LOBSTAHS: An adduct-based lipidomics strategy for discovery and identification of oxidative stress biomarkers. Anal Chem. 88:7154-7162. doi:10.1021/acs.analchem.6b01260.
Cornejo-Castillo F.M., Cabello A.M., Salazar G., Sánchez-Baracaldo 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.M., Massana R., Acinas S.G. Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton. Nat Comms. 7:11071. doi:10.1038/ncomms11071.
Diaz J.M., Haley S.T., Longo A.F., Ingall E.D., Björkman K.M., Karl D.M., Dyhrman S.T. Polyphosphate content and dynamics at Station ALOHA, North Pacific Subtropical Gyre. Limnol Oceanogr. 61(1):227-239. doi:10.1002/lno.10206.
Farnelid H.M., Turk-Kubo K.A., Muñoz-Marín M., Zehr J.P. New insights into the distribution and ecology of the nitrogen-fixing symbiont (UCYN-A). Aquat Microbiol Ecol. 77:125-138. doi:10.3354/ame01794.
Farnelid H.M., Turk-Kubo K.A., Zehr J.P. Identification of associations between bacterioplankton and photosynthetic picoeukaryotes in coastal waters. Front Microbiol. 7:339. doi:10.3389/fmicb.2016.00339.
Ferrón S., del Valle D.A., Björkman K.M., Quay P.D., Church M.J., Karl D.M. Application of membrane inlet mass spectrometry to measure aquatic gross primary production by the 18O in vitro method. Limnol Oceanogr. 28 June. doi:10.1002/lom3.10116.
Foreman R., Segura-Noguera M., Karl D.M. Validation of Ti (III) as a reducing agent in the chemiluminescent determination of nitrate and nitrite in seawater. Mar Chem. 186:83-89. doi:10.1016/j.marchem.2016.08.003.
Gifford S.M., Becker J.W., Sosa O.A., Repeta D.J., DeLong E.F. Quantitative transcriptomics reveals the growth- and nutrient-dependent response of a streamlined marine methylotroph to methanol and naturally occurring dissolved organic matter. mBio.7:e01279-16. doi:10.1128/mBio.01279-16.
Hyrkas J., Clayton S., Ribalet F., Halperin D., Armbrust A.V., Howe B. Scalable clustering algorithms for continuous environmental flow cytometry. Bioinfo. 32(3):417-423. doi:10.1093/bioinformatics/btv594.
Laws E.A., Bidigare R.R., Karl D.M. Enigmatic relationship between chlorophyll a concentrations and photosynthetic rates at Station ALOHA. Heliyon 2:e00156. doi:101016/j.heliyon.2016.e-00156.
Ingalls, A.E. Signal from the subsurface. Nat Geosci. 9:572-573. doi:10.1038/ngeo2765.
Mende D.R., Aylward F.O., Eppley J.M, Nielsen T.N., DeLong E.F. Improved environmental genomes via integration of metagenomic and single-cell assemblies. Front Microbiol. 7:143 doi:10.3389/fmicb.2016.00143.
Mitra A., Flynn K.J., Tillmann, U., Raven J., Caron D., Stoecker D., Not F., Hansen P., Hallegraeff G., Sanders R., Wilken S., McManus G., Johnson M., Pitta P., Våge S., Berje R., Calbet A., Thingstad F., Jeong J.J., Burkholder J., Glibert P., Granéli E., Lundgren V. Defining planktonic protist functional groups on mechanisms for energy and nutrient acquisition; incorporation of diverse mixotrophic strategies. Protist. 167:160-120 doi:10.1016/j.protis.2016.01.003.
Pinhassi J., DeLong E.F., Béjà O., González J.M., Pedrós-Alió C. Marine bacterial and archaeal rhodopsins: Genetic diversity, physiology and ecology. Micro Mol Bio Rev. 80(4):929-954. doi:10.1128/MMBR.00003-16.
Repeta D.J., Ferrón S., Sosa O.A., Johnson C.G., Repeta L.D., Acker M., DeLong E.F., Karl D.M. Marine methane paradox explained by bacterial degradation of dissolved organic matter. Nat. Geosci. 9:884-887. doi:10.1038/ngeo2837.
Rii Y.M., Duhamel S., Bidigare R.R., Karl D.K., Repeta D.J., Church M.J. Diversity and productivity of photosynthetic picoeukaryotes in biogeochemically distinct regions of the South East Pacific Ocean. Limnol Oceanogr. 61(3):806-824. doi:10.1002/lno.10255.
Rii Y.M, Karl D.M., Church M.J. Temporal and vertical variability in picoplankton primary productivity in the North Pacific Subtropical Gyre. MEPS. 563:1-18. doi:10.3354/meps11954.
Rouco M., Haley S.T., Alexander H., Dyhrman S.T. Diversity of the Trichodesmium holobiont. Environ Microbiol. 18:5151-5160. doi:10.1111/1462-2920.13513.
Rouco M., Haley S.T., Alexander H., Wilson S.T., Karl D.M., Dyhrman S.T. Variable distribution of Trichodesmium clades in the North Pacific Ocean. Environ Microbiol Rep. 8:1058â1066. doi:10.1111/1758-2229.12488.
Shilova I.N., Robidart J.C., DeLong E.F., Zehr J.P. Genetic diversity affects the daily transcriptional oscillations of marine microbial populations. PLoS ONE. 11(1):e0146706. 11 Jan. doi:10.1371/journal.pone.0146706.
Talarmin A., Lomas M.W., Bozec Y., Savoye N., Frigstad H., Karl D.M., Martiny A.C. Seasonal and long-term changes in elemental concentrations and ratios of marine particulate organic matter. Global Biogeochem Cycles. 30(11):1699-1711. doi:10.1002/2016GB005409.
Ward B.A., Follows M.J. Marine mixotrophy increases trophic transfer efficiency, mean organism size, and vertical carbon flux. PNAS USA. 113(11):2958-2963. doi:10.1073/pnas.1517118113.
Wigington C.H., Sonderegger D., Brussard C.P.D., Buchan A., Finke J.F., Fuhrman J.A., Lennon J.T., Middelboe M., Suttle C.A., Stock C., Wilson W.H., Wommack K.E., Wilhelm S.W., Weitz J.S. Re-examination of the relationship between marine virus and microbial cell abundances. Nat Microbiol. 1:15024. 25 Jan. doi:10.1038/nmicrobiol.2015.24. Supplementary Information. Interactive data portal.
Yelton A.P., Acinas S.G., Sunagawa S., Bork P., Pedros-Alio C., Chisholm S.W. Global genetic capacity for mixotrophy in marine picocyanobacteria. ISME J. 3 May. doi:10.1038/ismej.2016.64.
Zakem E.J., Follows M.J. A theoretical basis for a nanomolar critical oxygen concentration. Limnol Oceanogr. 25 Nov. doi:10.1002/lno.10461.
Zehr J.P., Shilova I.N., Farnelid H.M., del Carmen Muñoz-Marín M., Turk-Kubo K.A. Unusual marine unicellular symbiosis with the nitrogen-fixing cyanobacterium UCYN-A. Nat Microbiol. 2:16214. doi:10.1038/nmicrobiol.2016.214.
Alexander H., Rouco M., Haley S.T., Wilson S.T., Karl D.M., Dyhrman S.T. Functional group specific traits drive shift in ecosystem state in the oligotrophic ocean. PNAS USA. 112(44):E5972-5979. doi:10.1073/pnas.1518165112.
Aylward F.O., Eppley J.M., Smith J.M., Chavez F.P., Scholin C.A., DeLong E.F. Microbial community transcriptional networks are conserved in three domains at ocean basin scales. PNAS USA. 112:5443-5448. doi:10.1073/pnas.1502883112.
Barone B., Bidigare R.R., Church M.J., Karl D.M., Letelier R.M., White A.E. Particle distributions and dynamics in the euphotic zone of the North Pacific Subtropical Gyre. J Geophys Res Oceans. 120:3229-3247. doi:10.1002/2015JC010774.
Biller S.J., Berube P., Lindell D., Chisholm S.W. Prochlorococcus. The structure and function of collective diversity. Nat Rev Microbiol. 13:13-27. doi:10.1038/nrmicro3378.
Biller S.J., Coe A., Martin-Cuadrado A., Chisholm S.W. Draft genome sequence of Alteromonas macleodii Strain MIT1002, isolated from an enrichment culture of the marine cyanobacterium Prochlorococcus. Genome Announc. 3(4):e00967-15. doi:10.1128/genomeA.00967-15.
Björkman K.M., Church M.J., Doggett J.K., Karl D.M. Differential assimilation of inorganic carbon and leucine by Prochlorococcus in the oligotrophic North Pacific subtropical gyre. Front Microbiol. 6:1401. doi:10.3389/fmicb.2015.01401.
Casey J.R., Falkowski P.G., Karl D.M. Substrate selection for heterotrophic bacterial growth in the sea. Mar Chem. 177:349-356. doi:10.1016/j.marchem.2015.06.032.
Dutkiewicz S., Hickman A.E., Jahn O., Gregg W.W., Mouw C.B., Follows M.J. Capturing optically important constituents and properties in a marine biogeochemical and ecosystem model. Biogeosci. 12:4447-4481. doi:10.5194/bg-12-4447-2015.
Ferrón S., Wilson S.T., Martínez-García S., Quay P.D., Karl D.M. Metabolic balance in the mixed layer of the oligotrophic North Pacific Ocean from diel changes in O2/Ar saturation ratios. Geophys Res Lett. 42:3421-3430. doi:10.1002/2015GL063555.
Fontanez K.M., Eppley J.M., Samo T.J., Karl D.M., DeLong E.F. Microbial community structure and function on sinking particles in the North Pacific subtropical gyre. Front Aquat Microbiol. 6:469. doi:10.3389/fmicb.2015.00469.
Hyrkas J., Clayton S., Ribalet F., Halperin D., Armbrust E.V., Howe B. Scalable clustering algorithms for continuous environmental flow cytometry. Bioinformatics. 32(3):417-423. doi:10.1093/bioinformatics/btv594.
Lea-Smith D.J., Biller S.J., Davey M.P., Cotton C.A.R., Perez Sepulveda B.M., Turchyn A.B., Scanlan D.J., Smith A.G., Chisholm S.W., Howe C.J. Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle. PNAS USA. 112(44):13591-13596. doi:10.1073/pnas.1507274112.
Nicholson D.P., Wilson S.T., Doney S.C., Karl D.M. Quantifying subtropical North Pacific gyre primary productivity from Seaglider observations of diel oxygen cycles. Geophys Res Lett. 42:4032-4039. doi:10.1002/2015GL063065.
Sosa O., Gifford S.M., Repeta D., DeLong, E.F. High molecular weight dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures. ISME J. 9:2725-2739. doi:10.1038/ismej.2015.68.
Van Mooy B.A., Krupke A., Dyhrman S.T., Fredricks H.F., Frischkorn K.R., Ossolinski J.E., Repeta D.J., Rouco M., Seewald J.D., Sylva S. P. Major role of planktonic phosphate reduction in the marine phosphorus redox cycle. Science. 348:783-785. doi:10.1126/science.aaa8181.
Viviani D.A., Karl D.M., Church M.J. Variability in photosynthetic production of dissolved and particulate organic carbon in the North Pacific Subtropical Gyre. Front Mar Sci. 2:73. doi:10.3389/fmars.2015.00073.
White A.E., Letelier R.M., Whitmire A.L., Barone B., Bidigare R.R., Church M.J., Karl D.M. Phenology of particle size distributions and primary productivity in the North Pacific subtropical gyre (Station ALOHA). J Geophs Res Oceans. 120:7381-7399. doi:10.1002/2015JC010897.
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-García S., Nicholson D.P., Richards K.J., Rii Y.M., Rouco M., Viviani D.A., White A.E., Zehr J.P., Karl D.M. Short-term variability in euphotic zone biogeochemistry and primary productivity at Station ALOHA: A case study of summer 2012. Global Biogeochem Cycles. 29:1145-1164. doi:10.1002/2015GB005141.
Zehr J.P. How single cells work together. Science. 349:1163-1164. doi:10.1126/science.aac9752.
Chisholm S.W. Margalef's mandala, Prochlorococcus, and geoengineering. Contr to Science 10:7-17. doi:10.2436/20.7010.01.183
Karl D.M., Church M.J. Microbial oceanography and the Hawaii Ocean Time-series programme. Nat Rev Microbiol. 10:699-713. doi:10.1038/nrmicro3333.