Matt Harke, Ph.D.

Research Scientist II

Matt Harke comes to GMGI with broad interests in molecular and aquatic microbial ecology. Before joining GMGI, he was an Associate Research Scientist at Columbia University’s Lamont-Doherty Earth Observatory where he used metatranscriptomics to characterize the distribution, composition, and function of microorganisms in situ and in response to physical and chemical changes. He completed his MS and PhD at Stony Brook University investigating a range of topics including harmful algal bloom ecology (both fresh and marine), benthic-pelagic coupling, and microbial ecology.


1997 – BSc English, University of Wisconsin – Madison, Madison, WI, USA

2009 – MS Marine & Atmospheric Science, School of Marine and Atmospheric Sciences (SoMAS), Stony Brook University, Stony Brook, NY, USA, Advisor: Christopher J. Gobler

2015 – PhD Marine & Atmospheric Science, School of Marine and Atmospheric Sciences (SoMAS), Stony Brook University, Stony Brook, NY, USA, Advisor: Christopher J. Gobler

Research Interests

Microbes have played critical roles in shaping the biosphere since their evolution almost 3.5 billion years ago. The Earth harbors an estimated 1030 microbial cells, and we are still challenged with understanding the full extent of their diversity and function. Microbes are recognized to have fundamental roles in global biogeochemical cycles, are critical to host well-being, and are involved in the evolution of plants and animals. Anthropogenic changes to the biosphere have led to shifting dominance of microbes and in some cases have caused deleterious ecosystem effects such as harmful algal blooms. As such, understanding how microbes interact with the environment and how the environment shapes microbial structure has been an important research topic for decades. As an aquatic microbiologist, a central theme of my research is to understand the genetic underpinnings that drive the proliferation of microbes in response to changing conditions in both marine and freshwater ecosystems. My research crosses trophic boundaries, from nutrient poor oligotrophic waters to eutrophic coastal estuaries and freshwater lakes, investigating the causative drivers of microbial diversity, occurrence, function and toxicity.

Research Profile Links

Research Projects

Polinski, J.M., Rodrigue, M., Meyer, J.D., Harke, M.J. (2023) Drifting in the deep: Metatranscriptomics and metabarcoding reveal sustained metabolic activity and community composition in hydrothermal vent plume microbial communities. Frontiers in Marine Science. 10:1219784.

Major, S.R., Harke, M.J., Cruz-Flores, R., Dhar, A.K., Bodnar, A.G. and SA Wanamaker. (2023) Rapid detection of DNA and RNA shrimp viruses using CRISPR-based diagnostics. Applied and Environmental Microbiology. 0:e02151-02122.

Muratore, D., Boysen, A.K., Harke, M.J. et al. 2022. Complex marine microbial communities partition metabolism of scarce resources over the diel cycle. Nat Ecol Evol 6, 218–229.

Kramer, B.J., Jankowiak, J.G., Nanjappa, D. Harke, M.J., Gobler, C.J. 2022. Nitrogen and phosphorus significantly alter growth, nitrogen fixation, anatoxin-a content, and the transcriptome of the bloom-forming cyanobacterium, Dolicospermum. Frontiers in Microbiology. 13:955032. 10.3389/fmicb.2022.955032

Kolody, B. C., M. J. Harke, S. E. Hook, and A. E. Allen. 2022. “Transcriptomic and metatranscriptomic approaches in phytoplankton: insights and advances”. Pages 435-485 in L. A. Clementson, R. S. Eriksen, and A. Willis, editors. Advances in Phytoplankton Ecology. Elsevier.

Harke, M. J., K. R. Frischkorn, G. M. M. Hennon, S. T. Haley, D. M. Karl, S. T. Dyhrman. 2021. Microbial community transcriptional patterns vary in response to mesoscale forcing in the North Pacific Subtropical Gyre. Environmental Microbiology. 23(8): 4807-4822.

Kang, Y., M. J. Harke, D. L. Berry, J. L. Collier, S. W. Wilhelm, S. T. Dyhrman, C. J. Gobler. 2021. Transcriptomic responses of four pelagophytes to nutrient and light limitation. Frontiers in Mar Sci. 8:636699.

Becker, K.W., M. J. Harke, D.R. Mende, D. Muratore, J.W. Weitz, E.F. DeLong, S.T. Dyhrman, B.A.S.Van Mooy. 2021. 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.

Hernandez Limon, M. D., G. M. M. Hennon, M. J. Harke, K. R. Frischkorn, S. T. Haley, S. T. Dyhmran. 2019.  Transcriptional patterns of Emiliania huxleyi in the North Pacific Subtropical Gyre reveal the daily rhythms of its metabolic potential. Environmental Microbiology. 22(1):381- 396. doi: 10.1111/1462-2920.14855

Wilson, S. T., Hawco, N. J., Armbrust, E. V., Barone, B., Björkman, K., Boyson, A. K., Burgos, M., Burrel, T. J., Casey, J. R., DeLong, E. F., Dugenne, M. Dutkiewicz, S., Dyhrman, S. T., Ferrón, S., Follows, M. J., Foreman, R. K., Funky, C. P., Harke, M. J., Henke, B. A., Hill, C. N., Hynes, A. M., Ingalls, A. E., Jahn, O., Kelly, R. L., Knapp, A. N., Letelier, R. M., Ribalet, F., Shimabukuro, E. M., Tabata, R. K. S., Turk-Kubo, K. A., White, A. E., Zehr, J. P., John, S., Karl, D. M. 2019.  Kīlauea lava fuels phytoplankton bloom in the North Pacific Ocean. Science. 365(6457): 1040-1044. doi: 10.1126/science.aax4767

Griffith, A. W., M. J. Harke, E. DePasquale, D. L. Berry, C. J. Gobler. 2019.  The harmful algae, Cochlodinium polykrikoides and Aureococcus anophagefferens, elicit stronger transcriptomic and mortality responses in larval bivalves (Argopecten irradians) than climate change stressors. Ecology and Evolution. 00:1–18. doi: 10.1002/ece3.5100.

Harke, M. J., K. R. Frischkorn, S. T. Haley, F. O. Aylward, J. P. Zehr, S. T. Dyhrman. 2018.  Periodic and coordinated gene expression between a diazotroph and its diatom host. ISME J. 13(1): 118- 131. doi: 10.1038/s41396-018-0262-2.

Harke, M. J., A. R. Juhl, S. T. Haley, H. Alexander, S. T. Dyhrman. 2017.  Conserved transcriptional responses to nutrient stress in bloom-forming algae. Frontiers in Microbiology. 8:1279. doi: 10.3389/fmicb.2017.01279.

Saraf, S. R., A. Frenkel, M. J. Harke, J. G. Jankowiak, C. J. Gobler, A. E. McElroy. 2017.  Effects of Microcystis on development of early life stage Japanese medaka (Oryzias latipes): Comparative toxicity of natural blooms, cultured Microcystis and microcystin-LR. Aquatic Toxicology. 194:18- 26. doi: 10.1016/j.aquatox.2017.10.026.

Harke, M. J., J. G. Jankowiak, B. K. Morrell, C. J. Gobler. 2017.  Transcriptomic responses in the bloom-forming cyanobacterium Microcystis induced during exposure to zooplankton. Applied and Environmental Microbiology 83(5) e02832-16. doi: 10.1128/AEM.02832-16

Harke, M. J., M. M. Steffen, C. J. Gobler, T. G. Otten, S. W. Wilhelm, S. A. Wood, and H. W. Paerl. 2016.  A review of the global ecology, genomics, and biogeography of the toxic cyanobacterium, Microcystis. Harmful Algae. 54:4-20. doi: 10.1016/j.hal.2015.12.007.

Gobler, C. J., J. M. Burkholder, T. W. Davis, M. J. Harke, T. Johengen, C. A. Stow, D. B. Van de Waal. 2016.  The dual role of nitrogen supply in controlling the growth and toxicity of cyanobacterial blooms. Harmful Algae. 54:87-97. doi: 10.1016/j.hal.2016.01.010.

Harke, M. J., T. W. Davis, S. B. Watson, and C. J. Gobler. 2015.  Nutrient-controlled niche differentiation of western Lake Erie cyanobacterial populations revealed via metatranscriptomic surveys. Environmental Science and Technology. 50(2): 604–615. doi: 10.1021/acs.est.5b03931.

Harke, M. J., C.J. Gobler. 2015.  Daily transcriptome changes reveal the role of nitrogen in controlling microcystin synthesis and nutrient transport in the toxic cyanobacterium, Microcystis aeruginosa. BMC Genomics. 16:1068. doi: 10.1186/s12864-015-2275-9.

Frischkorn, K. R., M. J. Harke, C. J. Gobler, S. T. Dyhrman. 2014.  De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms. Frontiers in Microbiology 5:375. doi: 10.3389/fmicb.2014.00375.

Harke, M. J., C. J. Gobler. 2013.  Global transcriptional responses of the toxic cyanobacterium, Microcystis aeruginosa, to nitrogen stress, phosphorus stress, and growth on organic matter. PLoS ONE 8(7): e69834. doi: 10.137/journal/pone.0069834.

Tang, Y. Z., M. J. Harke, C. J. Gobler. 2013.  Morphology, phylogeny, dynamics, and ichthyotoxicity of Pheopolykrikos hartmannii (Dinophyceae) isolates and blooms from NY, USA. Journal of Phycology 49(6): 1084-1094. doi: 10.1111/jpy.12114.

Harke, M. J., D. L. Berry, J. W. Ammerman, C. J. Gobler. 2012.  Molecular Response of the Bloom- Forming Cyanobacterium, Microcystis aeruginosa, to Phosphorus Limitation. Microbial Ecology 63:188-198. doi: 10.1007/s00248-011-9894-8

Harke, M. J., C. J. Gobler, S. E. Shumway. 2011.  Suspension feeding by the Atlantic slipper limpet (Crepidula fornicata) and the northern quahog (Mercenaria mercenaria) in the presence of cultured and wild populations of the harmful brown tide alga, Aureococcus anophagefferens. Harmful Algae 10(5):503-511. doi: 10.1016/j.hal.2011.03.005.

Davis, T. W., M. J. Harke, M. A. Marcoval, J. Goleski, C. Orano-Dawson, D. L. Berry, and C. J. Gobler. 2010.  Effects of nitrogenous compounds and phosphorus on the growth of toxic and non-toxic strains of Microcystis during cyanobacterial blooms. Aquatic Microbial Ecology 61(2):149-162. doi: 10.3354/ame01445.