Publications

Kolody, B. C., Smith, S. R., Zeigler Allen, L., McCrow, J. P., Moustafa, A., Shi, D., Hopkinson, B. M., Morel, F. M. M., Ward, B. B., & Allen, A. E. (2022). Nitrogen and Iron Availability Drive Metabolic Remodeling and Natural Selection of Diverse Phytoplankton during Experimental Upwelling. MSystems, e00729-22. https://doi.org/10.1128/msystems.00729-22

de Vargas, C., Le Bescot, N., Pollina, T., Henry, N., Romac, S., Colin, S., Haëntjens, N., Carmichael, M., Berger, C., Le Guen, D., Decelle, J., Mahé, F., Poulain, J., Malpot, E., Beaumont, C., Hardy, M., Guiffant, D., Probert, I., Gruber, D. F., … the Plankton Planet core team. (2022). Plankton Planet: A frugal, cooperative measure of aquatic life at the planetary scale. Frontiers in Marine Science, 9, 936972. https://doi.org/10.3389/fmars.2022.936972

James, C. C., Barton, A. D., Allen, L. Z., Lampe, R. H., Rabines, A., Schulberg, A., Zheng, H., Goericke, R., Goodwin, K. D., & Allen, A. E. (2022). Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region. Nature Communications, 13(1), 2448. https://doi.org/10.1038/s41467-022-30139-4

Kellogg, R. M., Moosburner, M. A., Cohen, N. R., Hawco, N. J., McIlvin, M. R., Moran, D. M., DiTullio, G. R., Subhas, A. V., Allen, A. E., & Saito, M. A. (2022). Adaptive responses of marine diatoms to zinc scarcity and ecological implications. Nature Communications, 13(1), 13. https://doi.org/10.1038/s41467-022-29603-y

Steele, T. S., Brunson, J. K., Maeno, Y., Terada, R., Allen, A. E., Yotsu-Yamashita, M., Chekan, J. R., & Moore, B. S. (2022). Domoic acid biosynthesis in the red alga Chondria armata suggests a complex evolutionary history for toxin production. Proceedings of the National Academy of Sciences of the United States of America, 119(6). https://doi.org/10.1073/pnas.2117407119

Kolody, B. C., Harke, M. J., Hook, S. E., & Allen, A. E. (2022). Chapter 13 - Transcriptomic and metatranscriptomic approaches in phytoplankton: insights and advances. In L. A. Clementson, R. S. Eriksen, & A. Willis (Eds.), Advances in Phytoplankton Ecology (pp. 435–485). Elsevier. https://doi.org/10.1016/B978-0-12-822861-6.00022-4

Valencia, B., Stukel, M. R., Allen, A. E., McCrow, J. P., Rabines, A., & Landry, M. R. (2022). Microbial communities associated with sinking particles across an environmental gradient from coastal upwelling to the oligotrophic ocean. Deep-Sea Research Part I-Oceanographic Research Papers, 179, 13. https://doi.org/10.1016/j.dsr.2021.103668

Petras, D., Phelan, V. V., Acharya, D., Allen, A. E., Aron, A. T., Bandeira, N., Bowen, B. P., Belle-Oudry, D., Boecker, S., Cummings, D. A., Deutsch, J. M., Fahy, E., Garg, N., Gregor, R., Handelsman, J., Navarro-Hoyos, M., Jarmusch, A. K., Jarmusch, S. A., Louie, K., … Wang, M. X. (2022). GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nature Methods, 3. https://doi.org/10.1038/s41592-021-01339-5

Hippmann, A. A., Schuback, N., Moon, K. M., McCrow, J. P., Allen, A. E., Foster, L. F., Green, B. R., & Maldonado, M. T. (2022). Proteomic analysis of metabolic pathways supports chloroplast-mitochondria cross-talk in a Cu-limited diatom. Plant Direct, 6(1), 16. https://doi.org/10.1002/pld3.376

Moosburner, M., Allen, A. E. (corresponding author), & Daboussi, F. (2022). Genetic Engineering in Marine Diatoms: Current Practices and Emerging Technologies. In A. Falciatore & T. Mock (Eds.), The Molecular Life of Diatoms (pp. 743–773). Springer International Publishing. https://doi.org/10.1007/978-3-030-92499-7_25

Smith, S. R., & Allen, A. E. (2022). Comparative and Functional Genomics of Macronutrient Utilization in Marine Diatoms. In A. Falciatore & T. Mock (Eds.), The Molecular Life of Diatoms (pp. 529–566). Springer International Publishing. https://doi.org/10.1007/978-3-030-92499-7_19

Kumar, M., Zuniga, C., Tibocha-Bonilla, J. D., Smith, S. R., Coker, J., Allen, A. E., & Zengler, K. (2022). Constraint-Based Modeling of Diatoms Metabolism and Quantitative Biology Approaches. In A. Falciatore & T. Mock (Eds.), The Molecular Life of Diatoms (pp. 775–808). Springer International Publishing. https://doi.org/10.1007/978-3-030-92499-7_26

Coale, T. H., Bertrand, E. M., Lampe, R. H., & Allen, A. E. (2022). Molecular Mechanisms Underlying Micronutrient Utilization in Marine Diatoms. In A. Falciatore & T. Mock (Eds.), The Molecular Life of Diatoms (pp. 567–604). Springer International Publishing. https://doi.org/10.1007/978-3-030-92499-7_20

Hao, X. H., Chen, W. C., Amato, A., Jouhet, J., Marechal, E., Moog, D., Hu, H. H., Jin, H., You, L. J., Huang, F. H., Moosburner, M., Allen, A. E., & Gong, Y. M. (2021). Multiplexed CRISPR/Cas9 editing of the long-chain acyl-CoA synthetase family in the diatom Phaeodactylum tricornutum reveals that mitochondrial ptACSL3 is involved in the synthesis of storage lipids. New Phytologist, 16. https://doi.org/10.1111/nph.17911

Schulte, N. O., Khan, A. L., Smith, E. W., Zoumplis, A., Kaul, D., Allen, A. E., Adams, B. J., & McKnight, D. M. (2021). Blowin’ in the wind: Dispersal, structure, and metacommunity dynamics of aeolian diatoms in the McMurdo Sound region, Antarctica. Journal of Phycology, 19. https://doi.org/10.1111/jpy.13223

Valencia, B., Stukel, M. R., Allen, A. E., McCrow, J. P., Rabines, A., Palenik, B., & Landry, M. R. (2021). Relating sinking and suspended microbial communities in the California Current Ecosystem: digestion resistance and the contributions of phytoplankton taxa to export. Environmental Microbiology, 15. https://doi.org/10.1111/1462-2920.15736

McCain, J. S. P., Allen, A. E., & Bertrand, E. M. (2021). Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom. Isme Journal, 11. https://doi.org/10.1038/s41396-021-01084-9

Oliver, A., Podell, S., Pinowska, A., Traller, J. C., Smith, S. R., McClure, R., Beliaev, A., Bohutskyi, P., Hill, E. A., Rabines, A., Zheng, H., Allen, L. Z., Kuo, A., Grigoriev, I. V., Allen, A. E., Hazlebeck, D., & Allen, E. E. (2021). Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom. Scientific Reports, 11(1), 14. https://doi.org/10.1038/s41598-021-95106-3

McCain, J. S. P., Tagliabue, A., Susko, E., Achterberg, E. P., Allen, A. E., & Bertrand, E. M. (2021). Cellular costs underpin micronutrient limitation in phytoplankton. Science Advances, 7(32), 17. https://doi.org/10.1126/sciadv.abg6501

Jabre, L. J., Allen, A. E., McCain, J. S. P., McCrow, J. P., Tenenbaum, N., Spackeen, J. L., Sipler, R. E., Green, B. R., Bronk, D. A., Hutchins, D. A., & Bertrand, E. M. (2021). Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a Southern Ocean. Proceedings of the National Academy of Sciences of the United States of America, 118(30), 9. https://doi.org/10.1073/pnas.2107238118

Turnšek, J., Brunson, J. K., Viedma, M. del P. M., Deerinck, T. J., Horák, A., Oborník, M., Bielinski, V. A., & Allen, A. E. (2021). Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. Elife, 10, e52770. https://doi.org/10.7554/eLife.52770

Cohen, N. R., McIlvin, M. R., Moran, D. M., Held, N. A., Saunders, J. K., Hawco, N. J., Brosnahan, M., DiTullio, G. R., Lamborg, C., McCrow, J. P., Dupont, C. L., Allen, A. E., & Saito, M. A. (2020). Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean. Nature Microbiology. https://doi.org/10.1038/s41564-020-00814-7

Breier, J. A., Jakuba, M. V., Saito, M. A., Dick, G. J., Grim, S. L., Chan, E. W., McIlvin, M. R., Moran, D. M., Alanis, B. A., Allen, A. E., Dupont, C. L., & Johnson, R. (2020). Revealing ocean-scale biochemical structure with a deep-diving vertical profiling autonomous vehicle. Science Robotics, 5(48). https://doi.org/10.1126/scirobotics.abc7104

Horak, A., Allen, A. E., & Obornik, M. (2020). Common origin of ornithine-urea cycle in opisthokonts and stramenopiles. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-73715-8

Jallet, D., Xing, D. H., Hughes, A., Moosburner, M., Simmons, M. P., Allen, A. E., & Peers, G. (2020). Mitochondrial fatty acid beta-oxidation is required for storage-lipid catabolism in a marine diatom. New Phytologist. https://doi.org/10.1111/nph.16744

Schulhof, M. A., Allen, A. E., Allen, E. E., Mladenov, N., McCrow, J. P., Jones, N. T., Blanton, J., Cavalheri, H. B., Kaul, D., Symons, C. C., & Shurin, J. B. (2020). Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location. Molecular Ecology. https://doi.org/10.1111/mec.15469

Tan, M. H., Smith, S. R., Hixson, K. K., Tan, J., McCarthy, J. K., Kustka, A. B., & Allen, A. E. (2020). The importance of protein phosphorylation for signaling and metabolism in response to diel light cycling and nutrient availability in a marine diatom. Biology, 9(7), 155. https://doi.org/10.3390/biology9070155

Faktorova, D., Nisbet, R. E. R., Robledo, J. A. F., Casacuberta, E., Sudek, L., Allen, A. E., Ares, M., Areste, C., Balestreri, C., Barbrook, A. C., Beardslee, P., Bender, S., Booth, D. S., Bouget, F. Y., Bowler, C., Breglia, S. A., Brownlee, C., Burger, G., Cerutti, H., … Lukes, J. (2020). Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods. https://doi.org/10.1038/s41592-020-0796-x

Wang, H., Guo, R. Y., Lim, W. A., Allen, A. E., & Ki, J. S. (2020). Comparative transcriptomics of toxin synthesis genes between the non-toxin producing dinoflagellate Cochlodinium polykrikoides and toxigenic Alexandrium pacificum. Harmful Algae, 93. https://doi.org/10.1016/j.hal.2020.101777

Krause, J. W., Brzezinski, M. A., Largier, J. L., McNair, H. M., Maniscalco, M., Bidle, K. D., Allen, A. E., & Thamatrakoln, K. (2020). The interaction of physical and biological factors drives phytoplankton spatial distribution in the northern California Current. Limnology and Oceanography. https://doi.org/10.1002/lno.11431

Moosburner, M. A., Gholami, P., McCarthy, J. K., Tan, M., Bielinski, V. A., & Allen, A. E. (2020). Multiplexed knockouts in the model diatom phaeodactylum by episomal delivery of a selectable Cas9. Frontiers in Microbiology, 11. https://doi.org/10.3389/fmicb.2020.00005

Stephens, B. M., Wankel, S. D., Beman, J. M., Rabines, A. J., Allen, A. E., & Aluwihare, L. I. (2019). Euphotic zone nitrification in the California Current Ecosystem. Limnology and Oceanography. https://doi.org/10.1002/lno.11348

Coale, T. H., Moosburner, M., Horak, A., Obornik, M., Barbeau, K. A., & Allen, A. E. (2019). Reduction-dependent siderophore assimilation in a model pennate diatom. Proceedings of the National Academy of Sciences of the United States of America, 116(47), 23609–23617. https://doi.org/10.1073/pnas.1907234116

Smith, S. R., Dupont, C. L., McCarthy, J. K., Broddrick, J. T., Oborník, M., Horák, A., Füssy, Z., Cihlář, J., Kleessen, S., Zheng, H., McCrow, J. P., Hixson, K. K., Araújo, W. L., Nunes-Nesi, A., Fernie, A., Nikoloski, Z., Palsson, B. O., & Allen, A. E. (2019). Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom. Nature Communications, 10(1), 4552. https://doi.org/10.1038/s41467-019-12407-y

Wu, M., McCain, J. S. P., Rowland, E., Middag, R., Sandgren, M., Allen, A. E., & Bertrand, E. M. (2019). Manganese and iron deficiency in Southern Ocean Phaeocystis antarctica populations revealed through taxon-specific protein indicators. Nature Communications, 10(1), 3582. https://doi.org/10.1038/s41467-019-11426-z

Kolody, B. C., McCrow, J. P., Allen, L. Z., Aylward, F. O., Fontanez, K. M., Moustafa, A., Moniruzzaman, M., Chavez, F. P., Scholin, C. A., Allen, E. E., Worden, A. Z., Delong, E. F., & Allen, A. E. (2019). Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. The ISME Journal. https://doi.org/10.1038/s41396-019-0472-2

Kranzler, C. F., Krause, J. W., Brzezinski, M. A., Edwards, B. R., Biggs, W. P., Maniscalco, M., McCrow, J. P., Van Mooy, B. A. S., Bidle, K. D., Allen, A. E., & Thamatrakoln, K. (2019). Silicon limitation facilitates virus infection and mortality of marine diatoms. Nature Microbiology. https://doi.org/10.1038/s41564-019-0502-x

Murik, O., Tirichine, L., Prihoda, J., Thomas, Y., Araujo, W. L., Allen, A. E., Fernie, A. R., & Bowler, C. (2019). Downregulation of mitochondrial alternative oxidase affects chloroplast function, redox status and stress response in a marine diatom. New Phytologist, 221(3), 1303–1316. https://doi.org/10.1111/nph.15479

Goodwin, K. D., Muller-Karger, F. E., Djurhuus, A., Zeigler Allen, L., Allen, A. E., McCrow, J. P., & Canonico Hyde, G. (2019). Chapter 32 - Molecular Approaches for an Operational Marine Biodiversity Observation Network. In C. Sheppard (Ed.), World Seas: an Environmental Evaluation (Second Edition) (pp. 613–631). Academic Press. https://doi.org/10.1016/B978-0-12-805052-1.00032-2

Broddrick, J. T., Du, N., Smith, S. R., Tsuji, Y., Jallet, D., Ware, M. A., Peers, G., Matsuda, Y., Dupont, C. L., Mitchell, B. G., Palsson, B. O., & Allen, A. E. (2019). Cross-compartment metaoblic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum. New Phytol. https://doi.org/10.1111/nph.15685

Hogle, S. L., Dupont, C. L., Hopkinson, B. M., King, A. L., Buck, K. N., Roe, K. L., Stuart, R. K., Allen, A. E., Mann, E. L., Johnson, Z. I., & Barbeau, K. A. (2018). Pervasive iron limitation at subsurface chlorophyll maxima of the California Current. Proceedings of the National Academy of Sciences of the United States of America, 115(52), 13300–13305. https://doi.org/10.1073/pnas.1813192115

Spackeen, J. L., Sipler, R. E., Bertrand, E. M., Xu, K., McQuaid, J. B., Walworth, N. G., Hutchins, D. A., Allen, A. E., & Bronk, D. A. (2018). Impact of temperature, CO2, and iron on nutrient uptake by a late-season microbial community from the Ross Sea, Antarctica. Aquatic Microbial Ecology, 82(2), 145–159. https://doi.org/10.3354/ame01886

Brunson, J. K., McKinnie, S. M. K., Chekan, J. R., McCrow, J. P., Miles, Z. D., Bertrand, E. M., Bielinski, V. A., Luhavaya, H., Obornik, M., Smith, G. J., Hutchins, D. A., Allen, A. E., & Moore, B. S. (2018). Biosynthesis of the neurotoxin domoic acid in a bloom-forming diatom. Science, 361(6409), 1356-+. https://doi.org/10.1126/science.aau0382

Bender, S. J., Moran, D. M., McIlvin, M. R., Zheng, H., McCrow, J. P., Badger, J., DiTullio, G. R., Allen, A. E., & Saito, M. A. (2018). Colony formation in Phaeocystis antarctica: connecting molecular mechanisms with iron biogeochemistry. Biogeosciences, 15(16), 4923–4942. https://doi.org/10.5194/bg-15-4923-2018

Spackeen, J. L., Bronk, D. A., Sipler, R. E., Bertrand, E. M., Hutchins, D. A., & Allen, A. E. (2018). Stoichiometric N:P Ratios, Temperature, and Iron Impact Carbon and Nitrogen Uptake by Ross Sea Microbial Communities. Journal of Geophysical Research: Biogeosciences, 0(0). https://doi.org/10.1029/2017JG004316

Du, N., Gholami, P., Kline, D. I., DuPont, C. L., Dickson, A. G., Mendola, D., Martz, T., Allen, A. E., & Mitchell, B. G. (2018). Simultaneous quantum yield measurements of carbon uptake and oxygen evolution in microalgal cultures. PLOS ONE, 13(6). https://doi.org/10.1371/journal.pone.0199125

McQuaid, J. B., Kustka, A. B., Oborník, M., Horák, A., McCrow, J. P., Karas, B. J., Zheng, H., Kindeberg, T., Andersson, A. J., Barbeau, K. A., & Allen, A. E. (2018). Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms. Nature, 555, 534. https://doi.org/10.1038/nature25982

Rastogi, A., Maheswari, U., Dorrell, R. G., Vieira, F. R. J., Maumus, F., Kustka, A., McCarthy, J., Allen, A. E., Kersey, P., Bowler, C., & Tirichine, L. (2018). Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms. Scientific Reports, 8(1), 4834. https://doi.org/10.1038/s41598-018-23106-x

Berg, C., Dupont, C. L., Asplund-Samuelsson, J., Celepli, N. A., Eiler, A., Allen, A. E., Ekman, M., Bergman, B., & Ininbergs, K. (2018). Dissection of microbial community functions during a cyanobacterial bloom in the Baltic Sea via metatranscriptomics. Frontiers in Marine Science, 5(55). https://doi.org/10.3389/fmars.2018.00055

Tatters, A. O., Schnetzer, A., Xu, K., Walworth, N. G., Fu, F., Spackeen, J. L., Sipler, R. E., Bertrand, E. M., McQuaid, J. B., Allen, A. E., Bronk, D. A., Gao, K., Sun, J., Caron, D. A., & Hutchins, D. A. (2018). Interactive effects of temperature, CO2 and nitrogen source on a coastal California diatom assemblage. Journal of Plankton Research, 40(2), 151–164. https://doi.org/10.1093/plankt/fbx074