Zackary Johnson | Scholars@Duke

Zackary Johnson
Associate Professor of Biological Oceanography and Marine Bi

Our group broadly studies the abundance, diversity and activity of marine microbes. We are biological oceanographers , marine molecular ecologists , marine microbiologists and biogeochemists. Our research focuses on the marine cyanobacteria Prochlorococcus , the most abundant phytoplankton in the open oceans and an excellent model marine microbe, as well as the biotechnological applications of marine microalgae. We are at the Marine Laboratory as part of the Nicholas School of the Environment at Duke University .

Current Appointments & Affiliations

Associate Professor of Biological Oceanography and Marine Bi, Marine Science and Conservation, Nicholas School of the Environment 2017
Faculty Network Member of The Energy Initiative, Nicholas Institute-Energy Initiative, Initiatives 2012

Contact Information

135 Duke Marine Lab Rd., Duke Marine Laboratory, Beaufort, NC 28516
zackary.johnson@duke.edu (252) 504-7543
Johnson Lab Web Page

Background
Education, Training, & Certifications
- Ph.D., Duke University 2004
- B.S., Massachusetts Institute of Technology 1994
Previous Appointments & Affiliations
- Assistant Professor of Biological Oceanography and Marine Biotechnology, Marine Science and Conservation, Nicholas School of the Environment 2009 - 2017
- Arthur P. Kaupe Assistant Professor of Molecular Biology in Marine Science, Marine Science and Conservation, Nicholas School of the Environment 2012 - 2017
- Assistant Professor in the Department of Biology, Biology, Trinity College of Arts & Sciences 2014 - 2017
Recognition
In the News
- AUG 14, 2015
  
  New Duke-Led Consortium To Focus On Creating Food And Fuel From Algae
Expertise
Subject Headings
- Muser Mentor
Research
Selected Grants
- Development of high value bioproducts and enhancement of direct-air capture efficiency with a marine algae biofuel production system awarded by Department of Energy 2020 - 2024
- REU Site: Undergraduate Research in Estuarine and Coastal Marine Systems awarded by National Science Foundation 2021 - 2024
- Carbon utilization efficiency in marine algae biofuel production systems through loss minimization and carbonate chemistry modification awarded by Department of Energy 2018 - 2023
- Empowering US Poultry Farmer Sustainability through Innovative Genetic Selection, Environmentally Responsible Production, and Animal Wellbeing awarded by Cornell University 2019 - 2022
- Concentration and dewatering of micro-algal cultures with high throughput ceramic/metal membranes awarded by Molecule Works Inc. 2019 - 2021
- Marine Algae Industrialization Consortium (MAGIC): Combining biofuel and high-value bioproducts to meet the RFS awarded by Department of Energy 2015 - 2021
- Planning Grant: Engineering Research Center for Precision Microbiome Engineering (PreMiEr) awarded by National Science Foundation 2018 - 2021
- Collaborative Research: Ocean Acidification: microbes as sentinels of adaptive responses to multiple stressors awarded by National Science Foundation 2015 - 2019
- Large-Scale Production of Fuels and Feed from Marine Microalgae awarded by Cornell University 2011 - 2015
- Collaborative Research: Seasonal and Decadal Changes in Temperature Drive Prochlorococcus Ecotype Distribution Patterns awarded by National Science Foundation 2010 - 2015
- MRI-R-2: Acquisition of High-Speed Sorting Flow Cytometer for Multi-User Environmental Microbiology Research awarded by National Science Foundation 2010 - 2012
Fellowships, Supported Research, & Other Grants
- Seed Grant: Building Bridges in Beaufort: A Shoebox Lunch Series to Connect Faculty and BIPOC Community Leaders awarded by Duke Office for Faculty Advancement 2021
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Gronniger, Jessica L., Zhao Wang, Genevieve R. Brandt, Christopher S. Ward, Despina Tsementzi, Han Mu, Junyao Gu, Zackary I. Johnson, Konstantinos T. Konstantinidis, and Dana E. Hunt. “Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables.” Environmental Microbiology, June 2022. https://doi.org/10.1111/1462-2920.16086.
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  - Xie, Ningdong, Mohan Bai, Lu Liu, Jiaqian Li, Yaodong He, Jackie L. Collier, Dana E. Hunt, Zackary I. Johnson, Nianzhi Jiao, and Guangyi Wang. “Patchy Blooms and Multifarious Ecotypes of Labyrinthulomycetes Protists and Their Implication in Vertical Carbon Export in the Pelagic Eastern Indian Ocean.” Microbiology Spectrum 10, no. 3 (June 2022): e0014422. https://doi.org/10.1128/spectrum.00144-22.
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  - Lu, Z., C. M. Beal, and Z. I. Johnson. “Comparative performance and technoeconomic analyses of two microalgae harvesting systems evaluated at a commercially relevant scale.” Algal Research 64 (May 1, 2022). https://doi.org/10.1016/j.algal.2022.102667.
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  - Bai, Mohan, Ningdong Xie, Yaodong He, Jiaqian Li, Jackie L. Collier, Dana E. Hunt, Zackary I. Johnson, Nianzhi Jiao, and Guangyi Wang. “Vertical community patterns of Labyrinthulomycetes protists reveal their potential importance in the oceanic biological pump.” Environmental Microbiology 24, no. 4 (April 2022): 1703–13. https://doi.org/10.1111/1462-2920.15709.
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  - Neave, Erika F., Harvey Seim, Scott M. Gifford, Olivia Torano, Zackary I. Johnson, Diego Páez-Rosas, and Adrian Marchetti. “Protistan plankton communities in the Galápagos Archipelago respond to changes in deep water masses resulting from the 2015/16 El Niño.” Environmental Microbiology 24, no. 4 (April 2022): 1746–59. https://doi.org/10.1111/1462-2920.15863.
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  - Gray, P. C., A. E. Windle, J. Dale, I. B. Savelyev, Z. I. Johnson, G. M. Silsbe, G. D. Larsen, and D. W. Johnston. “Robust ocean color from drones: Viewing geometry, sky reflection removal, uncertainty analysis, and a survey of the Gulf Stream front.” Limnology and Oceanography: Methods, January 1, 2022. https://doi.org/10.1002/lom3.10511.
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  - Xie, Ningdong, Zhao Wang, Dana E. Hunt, Zackary I. Johnson, Yaodong He, and Guangyi Wang. “Niche Partitioning of Labyrinthulomycete Protists Across Sharp Coastal Gradients and Their Putative Relationships With Bacteria and Fungi.” Frontiers in Microbiology 13 (January 2022): 906864. https://doi.org/10.3389/fmicb.2022.906864.
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  - Duan, Yingbo, Ningdong Xie, Zhao Wang, Zackary I. Johnson, Dana E. Hunt, and Guangyi Wang. “Patchy Distributions and Distinct Niche Partitioning of Mycoplankton Populations across a Nearshore to Open Ocean Gradient.” Microbiology Spectrum 9, no. 3 (December 2021): e0147021. https://doi.org/10.1128/spectrum.01470-21.
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  - Sun, T., K. Wang, B. Wyman, H. Sudibyo, G. Liu, C. Beal, S. Manning, et al. “Supplemental dietary full-fatted and defatted Desmodesmus sp. exerted similar effects on growth performance, gut health, and excreta hydrothermal liquefaction of broiler chicks.” Algal Research 54 (April 1, 2021). https://doi.org/10.1016/j.algal.2021.102205.
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  - Marra, J. F., R. T. Barber, E. Barber, R. R. Bidigare, W. S. Chamberlin, R. Goericke, B. R. Hargreaves, et al. “A database of ocean primary productivity from the ¹⁴C method.” Limnology and Oceanography Letters 6, no. 2 (April 1, 2021): 107–11. https://doi.org/10.1002/lol2.10175.
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  - Wang, Zhao, Despina Tsementzi, Tiffany C. Williams, Doris L. Juarez, Sara K. Blinebry, Nathan S. Garcia, Brooke K. Sienkiewicz, Konstantinos T. Konstantinidis, Zackary I. Johnson, and Dana E. Hunt. “Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity.” The Isme Journal 15, no. 1 (January 2021): 19–28. https://doi.org/10.1038/s41396-020-00748-2.
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  - Xie, Ningdong, Dana E. Hunt, Zackary I. Johnson, Yaodong He, and Guangyi Wang. “Annual Partitioning Patterns of Labyrinthulomycetes Protists Reveal Their Multifaceted Role in Marine Microbial Food Webs.” Applied and Environmental Microbiology 87, no. 2 (January 2021): e01652–e01620. https://doi.org/10.1128/aem.01652-20.
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  - Doo, S. S., A. Kealoha, A. Andersson, A. L. Cohen, T. L. Hicks, Z. I. Johnson, M. H. Long, et al. “The challenges of detecting and attributing ocean acidification impacts on marine ecosystems.” Ices Journal of Marine Science 77, no. 7 (December 1, 2020): 2411–22. https://doi.org/10.1093/icesjms/fsaa094.
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  - Loftus, S. E., D. E. Hunt, and Z. I. Johnson. “Reused cultivation water from a self-inhibiting alga does not inhibit other algae but alters their microbiomes.” Algal Research 51 (October 1, 2020). https://doi.org/10.1016/j.algal.2020.102067.
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  - Lu, Z., S. Loftus, J. Sha, W. Wang, M. S. Park, X. Zhang, Z. I. Johnson, and Q. Hu. “Water reuse for sustainable microalgae cultivation: Current knowledge and future directions.” Resources, Conservation and Recycling 161 (October 1, 2020). https://doi.org/10.1016/j.resconrec.2020.104975.
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  - Hall, Emily R., Leslie Wickes, Louis E. Burnett, Geoffrey I. Scott, Debra Hernandez, Kimberly K. Yates, Leticia Barbero, et al. “Acidification in the U.S. Southeast: Causes, Potential Consequences and the Role of the Southeast Ocean and Coastal Acidification Network.” Frontiers in Marine Science 7 (July 2020): 1–548. https://doi.org/10.3389/fmars.2020.00548.
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  - Sagues, William J., Camilla A. Assis, Phillip Hah, Daniel L. Sanchez, Zackary Johnson, Madhav Acharya, Hasan Jameel, and Sunkyu Park. “Decarbonizing agriculture through the conversion of animal manure to dietary protein and ammonia fertilizer.” Bioresource Technology 297 (February 2020): 122493. https://doi.org/10.1016/j.biortech.2019.122493.
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  - Wang, Zhao, Doris L. Juarez, Jin-Fen Pan, Sara K. Blinebry, Jessica Gronniger, James S. Clark, Zackary I. Johnson, and Dana E. Hunt. “Microbial communities across nearshore to offshore coastal transects are primarily shaped by distance and temperature.” Environmental Microbiology 21, no. 10 (October 2019): 3862–72. https://doi.org/10.1111/1462-2920.14734.
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  - Gong, Y., T. Bandara, M. Huntley, Z. I. Johnson, J. Dias, D. Dahle, M. Sørensen, and V. Kiron. “Microalgae Scenedesmus sp. as a potential ingredient in low fishmeal diets for Atlantic salmon (Salmo salar L.).” Aquaculture 501 (February 25, 2019): 455–64. https://doi.org/10.1016/j.aquaculture.2018.11.049.
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  - Loftus, S. E., and Z. I. Johnson. “Reused cultivation water accumulates dissolved organic carbon and uniquely influences different marine microalgae.” Frontiers in Bioengineering and Biotechnology 7, no. MAY (January 1, 2019). https://doi.org/10.3389/fbioe.2019.101.
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  - Loftus, Sarah E., and Zackary I. Johnson. “Reused Cultivation Water Accumulates Dissolved Organic Carbon and Uniquely Influences Different Marine Microalgae.” Frontiers in Bioengineering and Biotechnology 7 (January 2019): 101. https://doi.org/10.3389/fbioe.2019.00101.
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  - Hogle, Shane L., Christopher L. Dupont, Brian M. Hopkinson, Andrew L. King, Kristen N. Buck, Kelly L. Roe, Rhona K. Stuart, et al. “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, no. 52 (December 2018): 13300–305. https://doi.org/10.1073/pnas.1813192115.
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  - Duan, Yingbo, Ningdong Xie, Zhiquan Song, Christopher S. Ward, Cheuk-Man Yung, Dana E. Hunt, Zackary I. Johnson, and Guangyi Wang. “A High-Resolution Time Series Reveals Distinct Seasonal Patterns of Planktonic Fungi at a Temperate Coastal Ocean Site (Beaufort, North Carolina, USA).” Applied and Environmental Microbiology 84, no. 21 (November 2018): e00967–e00918. https://doi.org/10.1128/aem.00967-18.
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  - Xie, Ningdong, Biswarup Sen, Zhiquan Song, Yue Zhao, Zixi Chen, Weijie Shi, Yongfeng Zhang, Jianle Zhang, Zackary I. Johnson, and Guangyi Wang. “High phylogenetic diversity and abundance pattern of Labyrinthulomycete protists in the coastal waters of the Bohai Sea.” Environmental Microbiology 20, no. 8 (August 2018): 3042–56. https://doi.org/10.1111/1462-2920.14341.
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  - Beal, C. M., I. Archibald, M. E. Huntley, C. H. Greene, and Z. I. Johnson. “Integrating Algae with Bioenergy Carbon Capture and Storage (ABECCS) Increases Sustainability.” Earth’S Future 6, no. 3 (March 1, 2018): 524–42. https://doi.org/10.1002/2017EF000704.
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  - Prairie, J. C., K. Ziervogel, R. Camassa, R. M. McLaughlin, B. L. White, Z. I. Johnson, and C. Arnosti. “Ephemeral aggregate layers in the water column leave lasting footprints in the carbon cycle.” Limnology and Oceanography Letters 2, no. 6 (December 1, 2017): 202–9. https://doi.org/10.1002/lol2.10053.
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  - He, Yaodong, Biswarup Sen, Junyang Shang, Yike He, Ningdong Xie, Yongfeng Zhang, Jianle Zhang, Zackary I. Johnson, and Guangyi Wang. “Seasonal influence of scallop culture on nutrient flux, bacterial pathogens and bacterioplankton diversity across estuaries off the Bohai Sea Coast of Northern China.” Marine Pollution Bulletin 124, no. 1 (November 2017): 411–20. https://doi.org/10.1016/j.marpolbul.2017.07.062.
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  - Ma, Lanying, Benjamin C. Calfee, J Jeffrey Morris, Zackary I. Johnson, and Erik R. Zinser. “Degradation of hydrogen peroxide at the ocean's surface: the influence of the microbial community on the realized thermal niche of Prochlorococcus.” The Isme Journal, October 2017. https://doi.org/10.1038/ismej.2017.182.
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  - Cohen, N. R., K. A. Ellis, W. G. Burns, R. H. Lampe, N. Schuback, Z. Johnson, S. Sañudo-Wilhelmy, and A. Marchetti. “Iron and vitamin interactions in marine diatom isolates and natural assemblages of the Northeast Pacific Ocean.” Limnology and Oceanography 62, no. 5 (September 1, 2017): 2076–96. https://doi.org/10.1002/lno.10552.
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  - Liu, Ying, Purnima Singh, Yuanmei Liang, Jingjing Li, Ningdong Xie, Zhiquan Song, Maurycy Daroch, Keming Leng, Zackary I. Johnson, and Guangyi Wang. “Abundance and molecular diversity of thraustochytrids in coastal waters of southern China.” Fems Microbiology Ecology 93, no. 6 (June 2017). https://doi.org/10.1093/femsec/fix070.
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  - Loftus, S. E., and Z. I. Johnson. “Cross-study analysis of factors affecting algae cultivation in recycled medium for biofuel production.” Algal Research 24 (June 1, 2017): 154–66. https://doi.org/10.1016/j.algal.2017.03.007.
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  - Ward, Christopher S., Cheuk-Man Yung, Katherine M. Davis, Sara K. Blinebry, Tiffany C. Williams, Zackary I. Johnson, and Dana E. Hunt. “Annual community patterns are driven by seasonal switching between closely related marine bacteria.” The Isme Journal 11, no. 6 (June 2017): 1412–22. https://doi.org/10.1038/ismej.2017.4.
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  - Gainer, P Jackson, Helena L. Pound, Alyse A. Larkin, Gary R. LeCleir, Jennifer M. DeBruyn, Erik R. Zinser, Zackary I. Johnson, and Steven W. Wilhelm. “Contrasting seasonal drivers of virus abundance and production in the North Pacific Ocean.” Plos One 12, no. 9 (January 2017): e0184371. https://doi.org/10.1371/journal.pone.0184371.
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  - Greene, C. H., M. E. Huntley, I. Archibald, L. N. Gerber, D. L. Sills, J. Granados, J. W. Tester, et al. “Marine microalgae: Climate, energy, and food security from the sea.” Oceanography 29, no. 4 (December 1, 2016): 10–15. https://doi.org/10.5670/oceanog.2016.91.
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  - Walsh, M. J., L. Gerber Van Doren, D. L. Sills, I. Archibald, C. M. Beal, X. G. Lei, M. E. Huntley, Z. Johnson, and C. H. Greene. “Algal food and fuel coproduction can mitigate greenhouse gas emissions while improving land and water-use efficiency.” Environmental Research Letters 11, no. 11 (October 28, 2016). https://doi.org/10.1088/1748-9326/11/11/114006.
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  - Morris, J. J., Z. I. Johnson, S. W. Wilhelm, and E. R. Zinser. “Diel regulation of hydrogen peroxide defenses by open ocean microbial communities.” Journal of Plankton Research 38, no. 4 (August 1, 2016): 1103–14. https://doi.org/10.1093/plankt/fbw016.
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  - Larkin, Alyse A., Sara K. Blinebry, Caroline Howes, Yajuan Lin, Sarah E. Loftus, Carrie A. Schmaus, Erik R. Zinser, and Zackary I. Johnson. “Niche partitioning and biogeography of high light adapted Prochlorococcus across taxonomic ranks in the North Pacific.” The Isme Journal 10, no. 7 (July 2016): 1555–67. https://doi.org/10.1038/ismej.2015.244.
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  - McMurray, S. E., Z. I. Johnson, D. E. Hunt, J. R. Pawlik, and C. M. Finelli. “Selective feeding by the giant barrel sponge enhances foraging efficiency.” Limnology and Oceanography 61, no. 4 (July 1, 2016): 1271–86. https://doi.org/10.1002/lno.10287.
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  - Yung, Cheuk-Man, Christopher S. Ward, Katherine M. Davis, Zackary I. Johnson, and Dana E. Hunt. “Insensitivity of Diverse and Temporally Variable Particle-Associated Microbial Communities to Bulk Seawater Environmental Parameters.” Applied and Environmental Microbiology 82, no. 11 (June 2016): 3431–37. https://doi.org/10.1128/aem.00395-16.
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  - Chandler, Jeremy W., Yajuan Lin, P Jackson Gainer, Anton F. Post, Zackary I. Johnson, and Erik R. Zinser. “Variable but persistent coexistence of Prochlorococcus ecotypes along temperature gradients in the ocean's surface mixed layer.” Environmental Microbiology Reports 8, no. 2 (April 2016): 272–84. https://doi.org/10.1111/1758-2229.12378.
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  - Huntley, M. E., Z. I. Johnson, S. L. Brown, D. L. Sills, L. Gerber, I. Archibald, S. C. Machesky, J. Granados, C. Beal, and C. H. Greene. “Corrigendum to "Demonstrated large-scale production of marine microalgae for fuels and feed" [Algal Res. 10 (July 2015) 249-265] DOI: 10.1016/j.algal.2015.04.016.” Algal Research 11 (September 1, 2015): 379–80. https://doi.org/10.1016/j.algal.2015.06.012.
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  - Huntley, M. E., Z. I. Johnson, S. L. Brown, D. L. Sills, L. Gerber, I. Archibald, S. C. Machesky, J. Granados, C. Beal, and C. H. Greene. “Demonstrated large-scale production of marine microalgae for fuels and feed.” Algal Research 10 (July 1, 2015): 249–65. https://doi.org/10.1016/j.algal.2015.04.016.
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  - Yung, Cheuk-Man, Marissa K. Vereen, Amy Herbert, Katherine M. Davis, Jiayu Yang, Agata Kantorowska, Christopher S. Ward, Jennifer J. Wernegreen, Zackary I. Johnson, and Dana E. Hunt. “Thermally adaptive tradeoffs in closely related marine bacterial strains.” Environ Microbiol 17, no. 7 (July 2015): 2421–29. https://doi.org/10.1111/1462-2920.12714.
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  - Ribalet, Francois, Jarred Swalwell, Sophie Clayton, Valeria Jiménez, Sebastian Sudek, Yajuan Lin, Zackary I. Johnson, Alexandra Z. Worden, and E Virginia Armbrust. “Light-driven synchrony of Prochlorococcus growth and mortality in the subtropical Pacific gyre.” Proceedings of the National Academy of Sciences of the United States of America 112, no. 26 (June 2015): 8008–12. https://doi.org/10.1073/pnas.1424279112.
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  - Yates, K. K., C. Turley, B. M. Hopkinson, A. E. Todgham, J. N. Cross, H. Greening, P. Williamson, R. Van Hooidonk, D. D. Deheyn, and Z. Johnson. “Transdisciplinary science a path to understanding the interactions among ocean acidification, ecosystems, and society.” Oceanography 28, no. 2 (June 1, 2015): 212–25. https://doi.org/10.5670/oceanog.2015.43.
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  - Dupont, Chris L., John P. McCrow, Ruben Valas, Ahmed Moustafa, Nathan Walworth, Ursula Goodenough, Robyn Roth, et al. “Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities.” The Isme Journal 9, no. 5 (May 2015): 1076–92. https://doi.org/10.1038/ismej.2014.198.
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  - Johnson, Zackary I., and Adam C. Martiny. “Techniques for quantifying phytoplankton biodiversity.” Annual Review of Marine Science 7 (January 2015): 299–324. https://doi.org/10.1146/annurev-marine-010814-015902.
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  - Kopf, Anna, Mesude Bicak, Renzo Kottmann, Julia Schnetzer, Ivaylo Kostadinov, Katja Lehmann, Antonio Fernandez-Guerra, et al. “The ocean sampling day consortium.” Gigascience 4 (January 2015): 27. https://doi.org/10.1186/s13742-015-0066-5.
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  - Jiao, N., T. Luo, R. Zhang, W. Yan, Y. Lin, Z. I. Johnson, J. Tian, et al. “Presence of Prochlorococcus in the aphotic waters of the western Pacific Ocean.” Biogeosciences 11, no. 8 (April 29, 2014): 2391–2400. https://doi.org/10.5194/bg-11-2391-2014.
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  - Wang, Xin, Purnima Singh, Zheng Gao, Xiaobo Zhang, Zackary I. Johnson, and Guangyi Wang. “Distribution and diversity of planktonic fungi in the West Pacific Warm Pool.” Plos One 9, no. 7 (January 2014): e101523. https://doi.org/10.1371/journal.pone.0101523.
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  - Johnson, Z. I., and D. W. Johnston. “Smartphones: Powerful tools for geoscience education.” Eos 94, no. 47 (November 19, 2013): 433–34. https://doi.org/10.1002/2013EO470001.
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  - Lin, Yajuan, Katrina Gazsi, Veronica P. Lance, Alyse A. Larkin, Jeremy W. Chandler, Erik R. Zinser, and Zackary I. Johnson. “In situ activity of a dominant Prochlorococcus ecotype (eHL-II) from rRNA content and cell size.” Environmental Microbiology 15, no. 10 (October 2013): 2736–47. https://doi.org/10.1111/1462-2920.12135.
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  - Bittar, Thais B., Yajuan Lin, Lara R. Sassano, Benjamin J. Wheeler, Susan L. Brown, William P. Cochlan, and Zackary I. Johnson. “Carbon allocation under light and nitrogen resource gradients in two model marine phytoplankton(1).” Journal of Phycology 49, no. 3 (June 2013): 523–35. https://doi.org/10.1111/jpy.12060.
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  - Hunt, Dana E., Yajuan Lin, Matthew J. Church, David M. Karl, Susannah G. Tringe, Lisa K. Izzo, and Zackary I. Johnson. “Relationship between abundance and specific activity of bacterioplankton in open ocean surface waters.” Applied and Environmental Microbiology 79, no. 1 (January 2013): 177–84. https://doi.org/10.1128/aem.02155-12.
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  - Johnson, Zackary I., Benjamin J. Wheeler, Sara K. Blinebry, Christina M. Carlson, Christopher S. Ward, and Dana E. Hunt. “Dramatic variability of the carbonate system at a temperate coastal ocean site (Beaufort, North Carolina, USA) is regulated by physical and biogeochemical processes on multiple timescales.” Plos One 8, no. 12 (January 2013): e85117. https://doi.org/10.1371/journal.pone.0085117.
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  - Ringuet, S., L. Sassano, and Z. I. Johnson. “Erratum: A suite of microplate reader-based colorimetric methods to quantify ammonium, nitrate, orthophosphate and silicate concentrations for aquatic nutrient monitoring (Journal of Environmental Monitoring (2011) 13 (370-376) DOI: 10.1039/c0em00290a).” Journal of Environmental Monitoring 14, no. 12 (December 1, 2012): 3305. https://doi.org/10.1039/c2em90060b.
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  - Ferrón, Sara, David T. Ho, Zackary I. Johnson, and Mark E. Huntley. “Air-water fluxes of N₂O and CH₄ during microalgae (Staurosira sp.) cultivation in an open raceway pond.” Environmental Science & Technology 46, no. 19 (October 2012): 10842–48. https://doi.org/10.1021/es302396j.
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  - Ritchie, Anna E., and Zackary I. Johnson. “Abundance and genetic diversity of aerobic anoxygenic phototrophic bacteria of coastal regions of the pacific ocean.” Applied and Environmental Microbiology 78, no. 8 (April 2012): 2858–66. https://doi.org/10.1128/aem.06268-11.
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  - Rowe, Janet M., Jennifer M. DeBruyn, Leo Poorvin, Gary R. LeCleir, Zackary I. Johnson, Erik R. Zinser, and Steven W. Wilhelm. “Viral and bacterial abundance and production in the Western Pacific Ocean and the relation to other oceanic realms.” Fems Microbiology Ecology 79, no. 2 (February 2012): 359–70. https://doi.org/10.1111/j.1574-6941.2011.01223.x.
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  - Morris, J. J., M. J. Szul, Z. Johnson, M. Keller, and E. R. Zinser. “EVOLUTION TOWARDS DEPENDENCY FOR A FREE-LIVING ORGANISM: HETEROTROPHIC "HELPERS" INCREASE RESISTANCE OF PROCHLOROCOCCUS TO ECOLOGICALLY RELEVANT CONCENTRATIONS OF HYDROGEN PEROXIDE.” Journal of Phycology 47 (February 1, 2011): 5–5.
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  - Ringuet, Stephanie, Lara Sassano, and Zackary I. Johnson. “A suite of microplate reader-based colorimetric methods to quantify ammonium, nitrate, orthophosphate and silicate concentrations for aquatic nutrient monitoring.” Journal of Environmental Monitoring : Jem 13, no. 2 (February 2011): 370–76. https://doi.org/10.1039/c0em00290a.
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  - Morris, J Jeffrey, Zackary I. Johnson, Martin J. Szul, Martin Keller, and Erik R. Zinser. “Dependence of the cyanobacterium Prochlorococcus on hydrogen peroxide scavenging microbes for growth at the ocean's surface.” Plos One 6, no. 2 (February 2011): e16805. https://doi.org/10.1371/journal.pone.0016805.
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  - Morris, J. J., Z. I. Johnson, M. J. Szul, M. Keller, and E. R. Zinser. “Dependence of the cyanobacterium Prochlorococcus on hydrogen peroxide scavenging microbes for growth at the ocean's surface.” Plos One 6, no. 2 (2011). https://doi.org/10.1371/journal.pone.0016805.
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  - Wang, G., and Z. I. Johnson. “Impact of parasitic fungi on the diversity and functional ecology of marine phytoplankton,” January 1, 2011, 205–22.
  - O’Kelly, C., Susan Brown, Robert Bidigare, Zackary Johnson, Andrea Messer, Henry Trapido-Rosenthal, and Jay Wheeler. “CORRELATED MORPHOLOGICAL AND MOLECULAR DATA ESTABLISH THE POLYPHYLY OF NANODIATOMS PREVIOUSLY ASSIGNED TO NANOFRUSTULUM SHILOI.” Journal of Phycology 47 (2011): S88–S88.
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  - Johnson, Z. I., R. Shyam, A. E. Ritchie, C. Mioni, V. P. Lance, J. W. Murray, and E. R. Zinser. “The effect of iron-and light-limitation on phytoplankton communities of deep chlorophyll maxima of the western Pacific Ocean.” Journal of Marine Research 68, no. 2 (March 1, 2010): 283–308. https://doi.org/10.1357/002224010793721433.
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  - Gao, Zheng, Zackary I. Johnson, and Guangyi Wang. “Molecular characterization of the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters.” The Isme Journal 4, no. 1 (January 2010): 111–20. https://doi.org/10.1038/ismej.2009.87.
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  - Marchetti, A., D. E. Varela, V. P. Lance, Z. Johnson, M. Palmucci, M. Giordano, and E. Virginia Armbruste. “Iron and silicic acid effects on phytoplankton productivity, diversity, and chemical composition in the central equatorial Pacific Ocean.” Limnology and Oceanography 55, no. 1 (January 1, 2010): 11–29. https://doi.org/10.4319/lo.2010.55.1.0011.
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  - Marchetti, A., D. Varela, V. P. Lance, Z. I. Johnson, and E. V. Armbrust. “Iron and silic acid controls on phytoplankton composition and productivity assessed by Si, C, and N utilization in the central equatorial Pacific Ocean.” Limnology and Oceanography 55 (2010): 11–29.
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  - Johnson, Zackary I., and Yajuan Lin. “Prochlorococcus: approved for export.” Proceedings of the National Academy of Sciences of the United States of America 106, no. 26 (June 2009): 10400–401. https://doi.org/10.1073/pnas.0905187106.
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  - Zinser, Erik R., Debbie Lindell, Zackary I. Johnson, Matthias E. Futschik, Claudia Steglich, Maureen L. Coleman, Matthew A. Wright, et al. “Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, prochlorococcus.” Plos One 4, no. 4 (January 2009): e5135. https://doi.org/10.1371/journal.pone.0005135.
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  - Morris, J Jeffrey, Robin Kirkegaard, Martin J. Szul, Zackary I. Johnson, and Erik R. Zinser. “Facilitation of robust growth of Prochlorococcus colonies and dilute liquid cultures by "helper" heterotrophic bacteria.” Applied and Environmental Microbiology 74, no. 14 (July 2008): 4530–34. https://doi.org/10.1128/aem.02479-07.
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  - Hiscock, M., V. Lance, A. Apprill, R. R. Bidigare, B. G. Mitchell, W. O. Smith, Z. I. Johnson, and R. T. Barber. “Photosynthetic maximum quantum yield increases are an essential component of the Southern Ocean phytoplankton response to iron.” Pnas 105, no. 12 (2008): 4775–80.
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  - Johnson, Z. I., and T. L. Sheldon. “A high-throughput method to measure photosynthesis-irradiance curves of phytoplankton.” Limnology and Oceanography: Methods 5, no. 11 (November 1, 2007): 417–24. https://doi.org/10.4319/lom.2007.5.417.
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  - Johnson, Z. I., and T. L. Sheldon. “A high-throughput method to measure photosynthesis-irradiance curves of phytoplankton.” Limnology and Oceanography: Methods 5, no. NOV (2007): 417–24.
  - Zinser, E. R., Z. I. Johnson, A. Coe, E. Karaca, D. Veneziano, and S. W. Chisholm. “Influence of light and temperature on Prochlorococcus ecotype distributions in the Atlantic Ocean.” Limnology and Oceanography 52, no. 5 (January 1, 2007): 2205–20. https://doi.org/10.4319/lo.2007.52.5.2205.
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  - Johnson, Zackary I., Erik R. Zinser, Allison Coe, Nathan P. McNulty, E Malcolm S. Woodward, and Sallie W. Chisholm. “Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients.” Science (New York, N.Y.) 311, no. 5768 (March 2006): 1737–40. https://doi.org/10.1126/science.1118052.
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  - Tolonen, Andrew C., John Aach, Debbie Lindell, Zackary I. Johnson, Trent Rector, Robert Steen, George M. Church, and Sallie W. Chisholm. “Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability.” Molecular Systems Biology 2 (January 2006): 53. https://doi.org/10.1038/msb4100087.
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  - Zinser, Erik R., Allison Coe, Zackary I. Johnson, Adam C. Martiny, Nicholas J. Fuller, David J. Scanlan, and Sallie W. Chisholm. “Prochlorococcus ecotype abundances in the North Atlantic Ocean as revealed by an improved quantitative PCR method.” Applied and Environmental Microbiology 72, no. 1 (January 2006): 723–32. https://doi.org/10.1128/aem.72.1.723-732.2006.
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  - Lindell, Debbie, Jacob D. Jaffe, Zackary I. Johnson, George M. Church, and Sallie W. Chisholm. “Photosynthesis genes in marine viruses yield proteins during host infection.” Nature 438, no. 7064 (November 2005): 86–89. https://doi.org/10.1038/nature04111.
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  - Gopalakrishna, V. V., Z. Johnson, G. Salgaonkar, K. Nisha, C. K. Rajan, and R. R. Rao. “Observed variability of sea surface salinity and thermal inversions in the Lakshadweep Sea during contrast monsoons.” Geophysical Research Letters 32, no. 18 (September 28, 2005): 1–4. https://doi.org/10.1029/2005GL023280.
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  - Johnson, Z. I. “Description and application of the background irradiance gradient-single turnover fluorometer (BIG-STf).” Marine Ecology Progress Series 283 (November 30, 2004): 73–80. https://doi.org/10.3354/meps283073.
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  - Johnson, Zackary I., and Sallie W. Chisholm. “Properties of overlapping genes are conserved across microbial genomes.” Genome Research 14, no. 11 (November 2004): 2268–72. https://doi.org/10.1101/gr.2433104.
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  - Lindell, Debbie, Matthew B. Sullivan, Zackary I. Johnson, Andrew C. Tolonen, Forest Rohwer, and Sallie W. Chisholm. “Transfer of photosynthesis genes to and from Prochlorococcus viruses.” Proceedings of the National Academy of Sciences of the United States of America 101, no. 30 (July 2004): 11013–18. https://doi.org/10.1073/pnas.0401526101.
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  - Coale, K. H., K. S. Johnson, F. P. Chavez, K. O. Buesseler, R. T. Barber, M. A. Brzezinski, W. P. Cochlan, et al. “Southern Ocean Iron Enrichment Experiment: Carbon Cycling in High- and Low-Si Waters.” Science 304, no. 5669 (2004): 408–14. https://doi.org/10.1126/science.1089778.
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  - Johnson, Z. I., and S. W. Chisholm. “Properties of overlapping genes are conserved across microbial genomes.” Genome Research 14, no. 11 (2004): 2268–72. https://doi.org/10.1101/gr.2925604.
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  - Johnson, Z. I. “Development and application of the Background Irradiance Gradient - Single Turnover Fluorometer (BIG-STf).” Marine Ecology Progress Series 283 (2004): 73–80.
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  - Rocap, Gabrielle, Frank W. Larimer, Jane Lamerdin, Stephanie Malfatti, Patrick Chain, Nathan A. Ahlgren, Andrae Arellano, et al. “Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation.” Nature 424, no. 6952 (August 2003): 1042–47. https://doi.org/10.1038/nature01947.
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  - Johnson, Zackary, and Richard T. Barber. “The low-light reduction in the quantum yield of photosynthesis: potential errors and biases when calculating the maximum quantum yield.” Photosynthesis Research 75, no. 1 (January 2003): 85–95. https://doi.org/10.1023/a:1022440305765.
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  - Johnson, Z., R. R. Bidigare, R. Goericke, J. Marra, C. Trees, and R. T. Barber. “Photosynthetic physiology and physicochemical forcing in the Arabian Sea, 1995.” Deep Sea Research I 49, no. 3 (2002): 415–36. https://doi.org/10.1016/S0967-0637(01)00068-1.
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  - Barber, R. T., J. Marra, R. R. Bidigare, L. A. Codispoti, D. Halpern, Z. Johnson, M. Latasa, R. Goericke, and S. Smith. “Primary productivity and its regulation in the Arabian Sea during 1995.” Deep Sea Research Ii 48, no. 6–7 (2001): 1127–72. https://doi.org/10.1016/S0967-0645(00)00134-X.
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  - Johnson, Z., and P. Howd. “Marine photosynthetic performance forcing and periodicity for the Bermuda Atlantic Time Series, 1989-1995.” Deep Sea Research Part I: Oceanographic Research Papers 47, no. 8 (August 1, 2000): 1485–1512. https://doi.org/10.1016/S0967-0637(99)00111-9.
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  - Johnson, Z., M. L. Landry, R. R. Bidigare, S. L. Brown, L. Campbell, J. Gunderson, J. Marra, and C. Trees. “Energetics and growth kinetics of a deep Prochlorococcus spp. population in the Arabian Sea.” Deep Sea Research Part Ii: Topical Studies in Oceanography 46, no. 8–9 (August 1, 1999): 1719–43. https://doi.org/10.1016/S0967-0645(99)00041-7.
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  - Barber, R. T., L. Borden, Z. Johnson, J. Marra, C. Knudson, and C. C. Trees. “Ground truthing modeled kPAR and on-deck primary productivity incubations with in-situ observations.” Proceedings of Spie the International Society for Optical Engineering 2963 (December 1, 1997): 834–39. https://doi.org/10.1117/12.266409.
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  - Johnson, Z. “Modeled inherent scattering properties of small light-limited phytoplankton: Implications for deep phytoplankton size class distributions.” Proceedings of Spie the International Society for Optical Engineering 2963 (December 1, 1997): 862–67. https://doi.org/10.1117/12.266416.
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  - Bidigare, R. R., M. Latasa, Z. Johnson, R. T. Barber, C. C. Trees, and W. M. Balch. “Observations of a Synechococcus-dominated cyclonic eddy in open-oceanic waters of the Arabian Sea.” Proceedings Spie Ocean Optics. Xiii 2963 (1997): 260–65.
  - Marra, J., R. T. Barber, C. Trees, Z. Johnson, and C. Kinkade. “Primary production and irradiance during an intermonsoon cruise to the Arabian Sea (November, 1995).” Spie Ocean Optics Xii 2963 (1997): 302–7.
- Book Sections
  - Wang, G., and Z. I. Johnson. “Impact of parasitic fungi on the diversity and functional ecology of marine phytoplankton.” In Marine Phytoplankton, 205–21, 2009.
- Preprints
  - Neave, Erika F., Harvey Seim, Scott Gifford, Olivia Torano, Zackary I. Johnson, Diego Páez-Rosas, and Adrian Marchetti. “Protistan plankton communities in the Galápagos Archipelago respond to changes in deep water masses resulting from the 2015/16 El Niño.” Cold Spring Harbor Laboratory, May 7, 2021. https://doi.org/10.1101/2021.05.06.441682.
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