Select Page

Jackie L. Collier

Associate Professor

Ph.D., 1994, Stanford University

Phytoplankton physiological ecology; Biocomplexity and microbial diversity; Planktonic ecosystem processes in marine, estuarine, and freshwater systems

Collier Lab webpage

Google Scholar Profile

Research Interests

The long-term goal of my research program is to improve our understanding of phytoplankton physiological ecology, population dynamics, community structure, and ecosystem roles by taking an autecological approach to investigating the lives of these microorganisms. The tools we use to answer these questions include observational and experimental (e.g., dilution gradient and nutrient addition) field studies, which are analyzed by techniques such as flow cytometry; lab-based investigations of phytoplankton physiology using various isolates growing in culture; and a variety of molecular biological, molecular genetic, and biochemical techniques. For many reasons, the cyanobacteria are the predominant model system used in my lab.

One part of my lab is focused on investigating basic cyanobacterial molecular genetics and physiology. For example, with support from DOE we are investigating the function of a thioredoxin-like gene, TxlA, which is found only in cyanobacteria and photosynthetic eukaryotes. Also with support from DOE and in collaboration with Chip Lawrence and coworkers at Wadsworth, we are just embarking on a new project that will take advantage of the availability of several complete cyanobacterial genome sequences to define the transcription regulation networks in cyanobacteria.

Another major focus of work in my lab grew out of my interest in the utilization of urea as a nitrogen source by marine Synechococcus. As part of an NSF-funded Biocomplexity project (, we are investigating the biochemically-defined functional group of microorganisms that can degrade urea, which is one of many potentially important but poorly understood forms of organic nitrogen present in aquatic ecosystems. Since most organisms use the well-conserved enzyme urease to degrade urea, we have designed oligonucleotide primers that are expected to be universal; that is, they should enable us to amplify any urease gene. Application of these primers to samples from Chesapeake Bay has revealed a very high diversity of urease sequences. Our current efforts are focused on developing a similar approach to describe the diversity of phytoplankton, and to adapt both to high-throughput technologies, such as gene array hybridization.

A third part of my lab is focused on investigating the comparative ecology of the small (<2 mm) planktonic picocyanobacteria that are found in both marine and freshwater ecosystems. We have been using flow cytometry and molecular techniques to investigate the picocyanobacteria in Lake George, NY, which we have found to be numerically dominated by organisms very much like marine Synechococcus. A similar project, funded by the Hudson River Foundation, is underway in the Hudson River Estuary, where we are seeking to define the role of picophytoplankton in the estuarine food web.


Recent Publications

Ohnemus, D. C., Krause, J. W., Brzezinski, M. A., Collier, J. L., Baines, S. B., & Twining, B. S. (2018). The chemical form of silicon in marine Synechococcus. Marine Chemistry.

Waller R.F., Cleves P.A., Rubio-Brotons M., Woods A., Bender S.J., Edgcomb V., Gann, E.R., Jones, A.C., Teytelman, L., von Dassow, P., Wilhelm, S.W., and Collier, J.L. (2018) Strength in numbers: Collaborative science for new experimental model systems. PLoS Biol 16(7): e2006333.

Mao, X., Waugh, S., Langlois, K., Collier, J.L., Price, R., Garvey, J., Gobler, C. and Walker, H., 2017. Nitrogen transformations and microbial characterization in passive nitrogen removing biofilters (NRBs) for onsite wastewater treatment. Proceedings of the Water Environment Federation, 2017(15), pp.898-906.

Collier, J. L., Geraci-Yee, S., Lilje, O., & Gleason, F. H. (2017). Possible impacts of zoosporic parasites in diseases of commercially important marine mollusc species: part II. Labyrinthulomycota. Botanica Marina, 60(4), 409-417.

Gleason, F. H., Lilje, O., Dang, C., Geraci-Yee, S., & Collier, J. L. (2017). Possible impacts of zoosporic parasites in diseases of commercially important marine mollusc species: part I. Perkinsozoa. Botanica Marina, 60(4), 401-408.

Brzezinski, M. A., Krause, J. W., Baines, S. B., Collier, J. L., & Ohnemus, D. C. (2017). Patterns and regulation of silicon accumulation in Synechococcus spp. Journal of Phycology.

Krause, J. W., Brzezinski, M. A., Baines, S. B., Collier, J. L., Twining, B. S., & Ohnemus, D. C. (2017). Picoplankton contribution to biogenic silica stocks and production rates in the Sargasso Sea. Global Biogeochemical Cycles.

Liu, Q., Collier, J. L., & Allam, B. (2017). Seasonality of QPX disease in the Raritan Bay (NY) wild hard clam (Mercenaria mercenaria) population. Aquaculture Research, 48(3), 1269-1278.

Ohnemus, D.C., Rauschenberg, S., Krause, J.W., Brzezinski, M.A., Collier, J.L., Geraci-Yee, S., Baines, S.B. and Twining, B.S., 2016. Silicon content of individual cells of Synechococcus from the North Atlantic Ocean. Marine Chemistry, 187, pp.16-24.

Chao Ye, Weihua Qiao, Xiaobin Yu, Xiaojun Ji, He Huang, J. L. Collier, Liming Liu. 2015. Reconstruction and analysis of the genome-scale metabolic model ofschizochytrium limacinum SR21 for docosahexaenoic acid production. BMC Genomics 16 :799 (11pp). DOI 10.1186/s12864-015-2042-y

P. J. Keeling, F. Burki, H. M. Wilcox, B. Allam, E. E. Allen, L. A. Amaral-Zettler, E. V. Armbrust, J. M. Archibald, A. K. Bharti, C. J. Bell, B. Beszteri, K. D. Bidle, C. T. Cameron, L. Campbell, D. A. Caron, R. A. Cattolico, J. L. Collier, K. Coyne, S. K. Davy, P. Deschamps, S. T. Dyhrman, B. Edvardsen, R. D. Gates, C. J. Gobler, S. J. Greenwood, S. M. Guida, J. L. Jacobi, K. S. Jakobsen, E. R. James, B. Jenkins, U. John, M. D. Johnson, A. R. Juhl, A. Kamp, L. A. Katz, R. Kiene, A. Kudryavtsev, B. S. Leander, S. Lin, C. Lovejoy, D. Lynn, A. Marchetti, G. McManus, A. M. Nedelcu, S. Menden-Deuer, C. Miceli, T. Mock, M. Montresor, M. A. Moran, S. Murray, G. Nadathur, S. Nagai, P. B. Ngam, B. Palenik, J. Pawlowski, G. Petroni, G. Piganeau, M. C. Posewitz, K. Rengefors, G. Romano, M. E. Rumpho, T. Rynearson, K. B. Schilling, D. C. Schroeder,A. G. B. Simpson, C. H. Slamovits, D. R. Smith, G. J. Smith, S. R. Smith, H. M. Sosik, P. Stief, E. Theriot, S. N. Twary, P. E. Umale, D. Vaulot, B. Wawrik, G. L. Wheeler, W. H. Wilson, Y. Xu, A. Zingone, A. Z. Worden. 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing. PLoS Biology 12(6):e1001889. DOI: 10.1371/journal.pbio.1001889

Collier, J.L., S.P. Fitzgerald, L.A. Hice, M.G. Frisk, and A.E. McElroy (2014) A New PCR-Based Method Shows That Blue Crabs (Callinectes sapidus (Rathbun)) Consume Winter Flounder (Pseudopleuronectes americanus (Walbaum)). Plos One 9.

Koch, F., Burson, A., Tang, Y. Z., Collier, J. L., Fisher, N. S., Sañudo-Wilhelmy, S., & Gobler, C. J. (2014). Alteration of plankton communities and biogeochemical cycles by harmful Cochlodinium polykrikoides (Dinophyceae) blooms. Harmful Algae, 33(0), 41-54. doi:

Selected Publications

Zani, S., M.T. Mellon, J.L. Collier, and J.P. Zehr. 2000. Expression of nifH genes in natural microbial assemblages in Lake George, NY detected with RT-PCR. Applied and Environmental Microbiology 66: 3119-3124.

Collier, J.L. 2000. Flow cytometry and the single cell in phycology. Journal of Phycology 36: 628-644.

Collier, J.L. and L. Campbell. 1999. Flow cytometry in molecular aquatic ecology. In: Molecular Ecology of Aquatic Ecosystems. J.P. Zehr, ed. Kluwer Academic Publishers. Dordrecht, The Netherlands. Hydrobiologia 401:33-53.

Collier, J.L., B. Brahamsha, and B. Palenik. 1999. The marine cyanobacterium Synechococcus sp.WH7805 requires urease (urea amidohydrolase, EC to utilize urea as a nitrogen source: molecular genetic and biochemical analysis of the enzyme. Microbiology UK 145:447-459.

Collier, J.L., and A.R. Grossman. 1995. Disruption of a novel thioredoxin-like protein alters the cyanobacterial photosynthetic apparatus. Journal of Bacteriology 177:3269-3276.

Apt, K.E., J.L. Collier, and A.R. Grossman. 1995. The evolution of the phycobiliproteins. Journal of Molecular Biology 248:79-96.

Collier, J.L., S.K. Herbert, D.C. Fork, and A.R. Grossman. 1994. Changes in the cyanobacterial photosynthetic apparatus during acclimation to macronutrient deprivation. Photosynthesis Research 42:173-183.

Bhalerao, R.P., J.L. Collier, P. Gustaffson, and A.R. Grossman. 1994. The structure of phycobilisomes in mutants of Synechococcus sp. Strain PCC 7942 devoid of specific linker polypeptides. Photochemistry and Photobiology 61:298-302.

Collier, J.L. and A.R. Grossman. 1994. A small polypeptide triggers complete degradation of light-harvesting phycobiliproteins in nutrient-deprived cyanobacteria. EMBO (The European Molecular Biology Organization Journal) 13:1039-1047.

Collier, J.L. and A.R. Grossman. 1992. Chlorosis induced by nutrient deprivation in Synechococcus sp. strain PCC 7942: Not all bleaching is the same. Journal of Bacteriology 174:4718-4726.

Postdoctoral Associate – 1803048

Photo above: Carotenoid production mutants in various colors Applications for a Postdoctoral Associate are invited to work in the lab of Dr. Jackie Collier at the School of Marine and Atmospheric Sciences at Stony Brook University. Required Qualifications: Doctoral...

Summer Presentations by SoMAS Students

SoMAS students and faculty have spent some of their summer preparing for conferences, giving talks and training future scholars.  Here are a few updates: Nicholas Leonardo, Ph.D. candidate in Prof. Brian Colle's group, was awarded Best Student Oral...

Scientists Explore New Experimental Model Systems to Advance Biology

Photo above: Marine protists known as thraustochytrids produce carotenoids, which are responsible for giving them a yellow to orange color. Carotenoids are essential nutrients for animals, and of biotechnological interest for several applications. EMS scientists are...

SoMAS Alumni Reunite at 2016 Ocean Sciences Meeting in New Orleans

SoMAS faculty and alumni attending the 2016 Ocean Sciences Meeting in New Orleans gathered for an alumni reunion. Professors Gordon Taylor and Mary Scranton organized the event and invited SoMAS alumni present at the conference to reunite.  Other SoMAS faculty in...

“Souper Bowl I” Raises Funds for Teaching Award

Thanks to everyone who turned out for SoMAS Souper Bowl I!  We had a great time and raised $373 for the Protopopescu Teaching Award.  A dozen of the best cooks at SoMAS fired burners, simmered stock, and selected ingredients.  Entries included: Black Bean, Red Pepper,...

Print Friendly, PDF & Email
Skip to toolbar