Graduate Program Director
- Stanford University
Phytoplankton physiological ecology, Biocomplexity and microbial diversity, Planktonic ecosystem processes in marine estuarine and freshwater systems
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 ( http://geoweb.princeton.edu/research/biocomplexity/index.html), 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.
Bai, M., Xie, N., He, Y., Li, J., Collier, J. L., Hunt, D. E., … & Wang, G. (2021). Vertical community patterns of Labyrinthulomycetes protists reveal their potential importance in the oceanic biological pump. Environmental microbiology.
Ishaq, S. L., Parada, F. J., Wolf, P. G., Bonilla, C. Y., Carney, M. A., Benezra, A., … Collier, J.L., … & Morar, N. (2021). Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice. Msystems, 6(4), e00471-21.
Rubino, C. V., Katz, B. G., Langlois, K., Wang, H. H., Carrion, J. A., Walker, S. G., Collier, J. L., Iacono, V. J. and Myneni, S. R., (2021). Evaluation of different materials used for sealing of implant abutment access channel and the peri‐implant sulcus microbiota: A 6‐month, randomized controlled trial. Clinical Oral Implants Research.
Rubino, C. V., Katz, B. G., Langlois, K., Wang, H. H., Carrion, J. A., Walker, S. G., … & Myneni, S. R. (2021). Evaluation of Different Materials Used for Sealing of Implant Abutment Access Channel and the Peri‐implant Sulcus Microbiota: A 6 Month, Randomized Controlled Trial. Clinical Oral Implants Research.
Kang, Y., Harke, M. J., Berry, D. L., Collier, J. L., Wilhelm, S. W., Dyhrman, S. T., & Gobler, C. J. (2021). Transcriptomic Responses of Four Pelagophytes to Nutrient (N, P) and Light Stress. Frontiers in Marine Science, 8, 223.
Geraci-Yee, S., Brianik, C. J., Rubin, E., Collier, J. L., & Allam, B. (2021). Erection of a New Genus and Species for the Pathogen of Hard Clams ‘Quahog Parasite Unknown’(QPX): Mucochytrium quahogii gen. nov., sp. nov. Protist, 125793.
Faktorová, D., Nisbet, R. E. R., Robledo, J. A. F., Casacuberta, E., Sudek, L., Allen, A. E., … & Beardslee, P. (2020). Genetic tool development in marine protists: Emerging model organisms for experimental cell biology. Nature methods, 1-14.
Langlois, K., Gobler, C. J., Walker, H. W., & Collier, J. L. (2020). Microbial communities in partially and fully treated effluent of three nitrogen-removing biofilters. Journal of Sustainable Water in the Built Environment, 6(2), 04020010.
Collier, J. L., & Rest, J. S. (2019). Swimming, gliding, and rolling toward the mainstream: cell biology of marine protists. Molecular biology of the cell, 30(11), 1245-1248.
Rius, M., Rest, J., & Collier, J. (2019). Why does a heterotrophic marine protist produce carotenoids? Genetic approaches to investigate the ecophysiology of the thraustochytrid Aurantiochytrium limacinum. Access Microbiology, 1(1A).
Gobler, C. J., Young, C. S., Goleski, J., Stevens, A., Thickman, J., Wallace, R. B., … & Hattenrath-Lehmann, T. K. (2019). Accidental ecosystem restoration? Assessing the estuary-wide impacts of a new ocean inlet created by Hurricane Sandy. Estuarine, Coastal and Shelf Science.
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. https://doi.org/10.1371/journal.pbio.2006333
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., SaÃ±udo-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: http://dx.doi.org/10.1016/j.hal.2014.01.003