Dr. Kimberly Halsey, Associate Professor

Halsey photo

354 Nash Hall
352 Nash Hall
For more information
about the Halsey Lab:
Phone (office)
FAX 541-737-0496  


Education Ph.D. Oregon State University  

Research Interests: Environmental Microbiology, Phytoplankton Ecophysiology, Systems Biology, Volatile Organic Carbon

CoursesTaught:  MB 302 General Microbiology; MB 448/548 Microbe - Environment Interactions; MB 511 Scientific Skills



Also featured on National Public Radio's Science Friday:  A Peek Into the Sex Lives of Algae
New research shows a species of diatom, a single-celled algae, thought to be asexual does reproduce sexually, and scientists learned it's a common compound - ammonium - that puts the ubiquitous organism in the mood. The findings, published today in PLOS One, may be a key step toward greater understanding of the evolution of sexual behavior and also have important biotechnology implications.  “Our discoveries solve two persistent mysteries that have plagued diatom researchers,” said corresponding author Dr. Kimberly Halsey, a microbiologist at OSU. “Yes, they have sex, and yes, we can make them do it.” Read more at:


Our research goal is to understand the processes that control the flow of carbon and energy through the marine carbon cycle. Phytoplankton are the single celled microbes that use light energy to convert carbon dioxide to organic carbon in aquatic systems. Research in my lab focuses on understanding strategies used by phytoplankton to optimize their growth. We are interested in determining how these strategies vary with different environmental conditions (i.e., nutrients, light, CO2, pH) and between species. Understanding these growth strategies can then be used to improve global models of primary production and models of microbial phototrophic growth.

Photosynthetic Metabolism:  In aquatic systems, phytoplankton acclimate to dynamic ranges of external resource concentrations that influence rates of primary productivity. Underlying environmental acclimation are metabolic shifts that reallocate carbon and energetic currencies through a variety of pathways to balance resource availability and growth. We track the distribution of carbon and energy through the primary metabolic pathways leading to net carbon accumulation (net growth). This approach provides a complete accounting of photosynthetic electron flow and reveals growth rate-dependent shifts in photosynthetic product allocation. We recently showed that the basis for these cell behaviors is linked to photosynthetic properties of specific phases of the cell cycle. These behaviors were captured in a mathematical model describing carbon utilization and suggest the intriguing possibility that a single model framework may be used to broadly characterize steady-state phototrophic metabolism.

Systems Biology:  Systems biology aims to expand understanding of phototrophy from gene and reaction-centric views to the broader integration of genome sequences, metabolic processes, and physiological responses to environmental factors. This holistic perspective merges multiple layers of cell phenomics with computational modeling to achieve predictive capability. We are currently expanding our understanding of processes controlling phytoplankton growth by studying the molecular basis for carbon and energy flow through cells. These ‘-omics’ analyses will complement our physiological measurements and may reveal unexpected strategies for metabolic adaptation to growth conditions. Using this combination of approaches, we are constructing a model describing photosynthetic product allocation and cell growth. This modeling effort can be further applied to ecosystem models of primary production and to models aimed at developing high quality sources of food, vitamins, and bioenergy.

C1 Metabolism:  Genome analyses revealed the unexpected capacity of many marine bacterioplankton to metabolize low molecular weight C1 or methylated carbon compounds. Many of these compounds are also volatile (VOCs: volatile organic carbon) and thus impact atmospheric chemistry. Our work with pure cultures has demonstrated that these C1 compounds are primarily used for energy generation; however, some C1 specialists that require methanol for growth (e.g., HTCC2181) are very significant members of the microbial community, particularly in coastal ecosystems. These discoveries highlight the potential significance of C1 and methylated compounds as products of phytoplankton productivity and as substrates for rapid microbial oxidation in the marine surface layer. We are pursuing these investigations using both pure cultures in laboratory studies and natural plankton communities in field studies during research cruises.



SEM image HTCC 2181 filtered onto a 0.2 μm filter.


Web of Knowledge     PubMed

Polerecky, L., Eichner, M., Masuda, T., Zavrel, T., Rabouille, S.., Campbell, D. and Halsey, K.  2021.  Calculation and Interpretation of Substrate Assimilation Rates in Microbial Cells Based on Isotopic Composition Data Obtained by nanoSIMS  Front. in Microbiol. 12.

Moore, E.R., Weaver, A.J., Davis, E.W., Giovannoni, S.J., and Halsey, K.H.  2021.  Metabolism of key atmospheric volatile organic compounds by the marine heterotrophic bacterium Pelagibacter HTCC1062 (SAR11)  Environ. Microbiol. doi: 10.1111/1462-2920.15837. Online ahead of print.

Behrenfeld, M.J., Halsey, K.H., Boss, E., Karp-Boss, L., Milligan, A.J. and Peers, G.  2021.  Thoughts on the evolution and ecological niche of diatoms  Ecol. Monogr.. 13, e01457

Penta, W.B., Fox, J. and Halsey, K.H.  2021.  Rapid photoacclimation during episodic deep mixing augments the biological carbon pump  Limnol. and Oceanogr. 66 (5), 1850-1866

Baetge, N., Behrenfeld, M.J., Fox, J., Halsey, K.H., Mojica, K., Novoa, A., Stephens, B.M., and Carlson, C.A.  2021.  The seasonal flux and fate of dissolved organic carbon through bacterioplankton in the Western North Atlantic.  Front. Microbiol. 12:669883.

Schuback, N., Tortell, P., Berman, Frank, I., Campbell, D., Ciotti, A., Courtecuisse, E., Erickson, Z., Fujiki, T., Halsey, K., Hickman, A., Huot, Y., Gorbunov, M., Hughes, D., Kolber, Z., Moore, C., Oxborough, K., Prasil, O., Robinson, C., Ryan-Keogh, T., Silsbe, G., Simis, S., Suggett, D., Thomalla, S., and Varkey, D.  2021.  Single-turnover variable chlorophyll fluorescence as a tool for assessing phytoplankton photosynthesis and primary productivity: Opportunities, caveats and recommendations  Front.  in Mar. Sci. 895 pages.

Behrenfeld, M.J., Boss, E.S., and Halsey, K.H.  2021.  Phytoplankton community structuring and succession in a competition-neutral resource landscape.  2021.  ISME Commun.  1(1):1-8.

Rabouille, S., Campbell, D., Masuda, T., Zavrel, T., Bernát, G., Polerecky, L., Halsey, K., Eichner, M., Kotabova, E., Stephan, S., Lukes, M., Claquin, P., Bonomi-Barufi, J., Lombardi, A., Cerveny, J., Suggett, D., Giordano, M., Kromkamp, J. and Prasil, O.  2021.  Electron and biomass dynamics of Cyanothece under interacting nitrogen and carbon limitations.  Frontiers in Microbiol. 12:260.

Fox, J., Behrenfeld, M.J., Haentjens, N., Chase, A., Kramer, S., Boss, E., Karp-Boss, L., Fisher, N., Penta, W.B., Westberry, T.K., and Halsey, K.H.  2021.  Corrigendum:  Phytoplankton growth and productivity in the Western North Atlantic:  Observations of regiona variability from the NAAMES field campaigns.  Frontiers in Mar. Sci. 8:130.

Polerecky, L., Masuda, T., Eichner, M., Rabouille, S., Vancova, M., Kienhuis, M., Bernat, G., Bonomi-Barufi, J., Campell, D.A., Claquin, P., Cerveny, J., Giordanao, M., Kotabova, E., Kromkamp, J., Lombardi, A.T., Lukes, M., Prasil, O., Stephan, S., Suggett, D., Zavrel, T. and Halsey, K.H.  2021.  Temporal patterns and intra- and inter-cellular variability in carbon and nitrogen assimilation by the unicellular cyanobacterium Cyanothese sp. ATCC 51142.  Frontiers in Microbiol. 12:89.

Yang, B., Fox, J., Behrenfeld, M.J., Boss, E.S., Haëntjens, N., Halsey, K.H., Emerson, S.R. and Doney, S.C.   2021.  In situ estimates of net primary production in the western North Atlantic with Argo profiling floats.  J. of Geophys. Res. Biogeosci. 126(2).

Behrenfeld, M.J., Halsey, K.H., Boss, E., Karp-Boss, L., Milligan, A.J., and Peers, G.  2021.  Thoughts on the evolution and ecological niche of diatoms.  Ecol. Monogr.  00(00):e01457. 10.1002/ecm.1457.

Fisher, N.L., Campbell, D.A., Hughes, D.J., Kuzhiumparambil, U., Halsey, K.H., Ralph, P.J. and Suggett, D.  2021.  Divergence of photosynthetic strategies amongst marine diatoms.  PloS One 15(12):e0244252.

Davie-Martin, C.L., Giovannoni, S.J., Behrenfeld, M.J., Penta, W.B., and Halsey, K.H.  2020.  Seasonal and spatial variability in the biogenic production and consumption of volatile organic compounds (VOCs) by marine plankton in the North Atlantic Ocean Frontiers in Mar. Sci.

Knowles, B., Bonachela, J.A., Behrenfeld, M.J., Bondoc, K.G., Cael, B.B., Carlson, C.A.  Cieslik, N., Diaz, B., Fuchs, H.L., Graff, J.R., Grasis, J.A., Halsey, K.H., Haramaty, L.,  Johns, C.T., Natale, F., Nissimov, J.I., Schieler, B., Thamatrakoln, K., Thingstad, T.F., Vage, S., Watkins, C., Westberry, T.K. and Bidle, K.D.  2020.  Temperate infection in a virus-host system previously known for virulent dynamics.  Nat. Commun. 11(1):1-13.

Fox, J., Behrenfeld, M.J., Haëntjens, N., Chase, A., Kramer, S.J., Boss, E., Karp-Boss, L., Fisher, N.L., Penta, W.B., Westberry, T.K. and Halsey, K.H.  2020.  Phytoplankton growth and productivity in the western North Atlantic:  Observations of regional variability from the NAAMES field campaigns.  Front. of Mar. Sci. 7:24; doi:  10.3389/fmars.2020.00024.

Moore, E.R., Davie-Martin, C.L., Giovannoni, S.J., and Halsey, K.H.  2020.   Pelagibacter metabolism of diatom-derived volatile organic compounds imposes an energetic tax on photosynthetic carbon fixation.  Environ Microbiol. 22(5):1720-1733; doi: 10.1111/1462-2920.14861.

Behrenfeld, M.J., Moore, R.H., Hostetler, C.A., Graff, J., Gaube, P., Russell, L.M., Chen, G., Doney, S.C., Giovannoni, S., Liu, Hongyu, Proctor, C., Bolanos, L.M., Baetge, N., Davie-Martin-C., Westberry, T.K., Bates, T.S., Bell, T.G., Bidle, K.D., Boss, E.S., Brooks, S.D., Cairns, B., Carlson, C., Halsey, K., et al.  2019.  The North Atlantic Aerosol and Marine Ecosystem Study (NAAMES):  Science Motive and Mission Overview.  Front. in Mar. Sci. 6.

Giovannoni, S.G., Halsey, K.H., Saw, J., Muslin, O., Suffridge, C.P., Sun, J., Lee, C., Moore, E.R., Temperton, B., and Noell, S.E.  2019.  A parasitic cycle that shuttles energy from phytoplankton to heterotrophic bacterioplankton.  mBio 10(2):e00246-19.

Dreher, T.W., Collart, L.P., Mueller, R.S., Halsey, K.H., Bildfell, R.J., Schreder, P., Sobhakumari, A., and Ferry, R.  2019.  Anabaena/Dolichospermum as the source of lethal microcystin levels responsible for a large cattle toxicosis event.  Elsevier/Toxicon: X, Vol 1(100003).  doi.org/10.1016/j.toxcs.2018.100003.

McBeain, K.A. and Halsey, K.H.  2018.  Altering phytoplankton growth rates changes their value as food for microzooplankton grazers. Aquatic Microb Ecol 82(1):19-29.

Jones, B.M., Halsey, K.H., and Behrenfeld, M.J.  2017. Novel incubation-free approaches to determine phytoplankton net primary productivity, growth, and biomass based on flow cytometry and quantification of ATP and NAD(H).  Limnol. and Oceanogr.-Methods 15(11):928-938.

Felcmanová, K., Lukes, M., Kotabová, E., Lawrenz, E., Halsey, K.H., and Prásil, O.  2017.  Carbon use efficiencies and allocation strategies in Prochlorococcus marinus strain PCC9511 during nitrogen-limited growth.  Photosynthesis Res.  https://doi.org/10.1007/s11120-017-0418-3.

Halsey, K.H., Giovannoni, S., Graus, M., Zhao, Y., Landry, Z., Thrash, J.C., and de Gouw, J.  2017.  Biological cycling of volatile organic carbon by phytoplankton and bacterioplankton.  Limnol. and Oceangr. doi:10.1002/Ino.10596.

Moore, E.R., Bullington, B.S., Weisberg, A.J., Jiang, Y., Chang, J.H., and Halsey, K.H.  2017.  Morphological and transcriptomic evidence for ammonium induction of sexual reproduction in Thalassiosira pseudonana and other centric diatoms.  PLoS One. doi.org/10.1101/144667.

Silsbe, G.M., Behrenfeld, M.J., Halsey, K.H.,  Milligan, A.J. and Westberry, T.K.  2016.  The CAFE model:  A net production model for global ocean phytoplankton.  Global BioGeochemical Cycles; 30(12):1756-1777.

Sun, J, Todd, J.D., Thrash, J.C., Qian, Y., Qian, M.C., Temperton, B., Guo, J., Fowler, E.K., Aldrich, J.T., Nicora, C.D., Lipton, M.S., Smith, R.D, De Leenheer, P, Payne, S.H., Johnston, A.W., Davie-Martin, C.L., Halsey, K.H. and Giovannoni, S.J.  2016.  Corrigendum: The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol.  Nat Microbiol. 1(11):16210.

Fisher, N.L. and Halsey, K.H.  2016.  Mechanisms that increase the growth efficiency of diatoms in low light.  Photosynthesis Res.  129:183-197.  DOI 10.1007/s11120-016-0282-6.

Sun, J., Todd, J.D., Thrash, C., Qian, Y., Temmperton, B., Guo, J., Fowler, E.K., Aldrich, J.T., Nicoira, C.D., Lipton, M.S., Smith, R.D., Leenheer, P., Payne, S.H., Johnston, A..W.B., Davie-Martin, C., Halsey, K.H. and Giovannoni, S.J.  2016.  The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol.  Nature Microbiol.  1:16065; doi:10.1038/nmicrobiol.2016.65.

Milligan, A.J., Halsey, K.H. and Behrenfeld, M.J.  2015.  Advancing interpretations of 14C-uptake measurements in the context of phytoplankton physiology and ecology.  J. of Plankton Res. 37:692-698.

Behrenfeld, M.J., O'Malley, R.T., Boss, E.S., Westberry, T.K., Graff, J.R., Halsey, K.H., Milligan, A.J., Siegel, D.A. and Brown, M.B.  2015.  Revaluating ocean warming impacts on global phytoplankton.  Nature Climate Change doi:10.1038/nclimate2838.

Halsey, K.H. and Jones, B.M.  2015.  Phytoplankton strategies for photosynthetic energy allocation.  Ann. Rev. of Mar. Sci.  7:265-297. 

O'Malley, R.T., Behrenfeld, M.J., Westberry, T.K., Milligan, A.J., Reese, D.C., and Halsey, K.H.  2014.  Improbability mapping:  A metric for satellite-detection of submarine volcanic eruptions.  Remote Sensing of Environ. 140:596-603.

Halsey, KH, Milligan, AJ, Behrenfeld, MJ.  2014. Contrasting strategies of photosynthetic energy utilization drive lifestyle strategies in ecologically important PicoeukaryotesMetabolites 4(2): 260-280.

Halsey KH, O’Malley, RT, Graff, JR, Milligan AJ, Behrenfeld MJ. 2013. A common partitioning strategy for photosynthetic products in evolutionarily distinct phytoplankton species. New Phytologist,  doi 10.1111/nph, 12209.

Halsey KH, Carter AE, Giovannoni SJ. 2012. Synergistic metabolism of a broad range of C1 compounds in the marine methylotrophic bacterium HTCC2181. Environ. Microbiol. 14(3): 630-640.

Halsey KH, Milligan AJ, Behrenfeld MJ. 2011. Linking time-dependent carbon-fixation efficiencies in Dunaliella tertiolecta (Chlorophyceae) to underlying metabolic pathways. J. of Phycol. 47(1): 66-76.

Sun J, Steindler L, Thrash JC,Halsey KH, Smith DP, Carter A, Landry Z, Giovannoni SJ. 2011. One carbon metabolism in SAR11 pelagic marine bacteria. PLOS One 6(8): e23973. doi:23910.21371/journal.pone.0023973.

Halsey KH, Milligan AJ, Behrenfeld MJ. 2010. Physiological optimization underlies growth rate-independent chlorophyll-specific gross and net primary production. Photosynthesis Res. 103(2): 125-137.