Publications

Smith, J.C., A. Lie, E.L. Seubert, N. Crowley, G. Robertson and D.A. Caron.  2019.  Co-occurring dissolved algal toxins observed at multiple monitoring stations off southern California via Solid Phase Adsorption Toxin Tracking (SPATT).  Toxicon.  171: 62-65. pdf

Boeuf, D., B.R. Edwards, J.M. Eppley, S.K. Hu, K.E. Poff, A.E. Romano, D.A. Caron, D.M. Karl and E.F. DeLong.  Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the open ocean.  Submitted to Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1903080116 pdf

Liu, Z., L.Y. Mesrop, S.K. Hu and D.A. Caron.  2019.  Transcriptome of Thalassicolla nucleata holobiont reveals details of a radiolarian symbiotic relationship.  Frontiers in Marine Science.  DOI: 10.3389/fmars.2019.00284 pdf

Tatters, A.O., M.D.A. Howard, C. Nagoda, A.B. Fetscher, R.M. Kudela and D.A. Caron.  2019.  Heterogeneity of toxin-producing cyanobacteria and cyanotoxins in coastal watersheds of Southern California.  Estuaries and Coasts. DOI: 10.1007/s12237-019-00546-w. pdf

Pasulka, A., S.K. Hu, P.D. Countway, K.J. Coye, S.C. Cary, K.B. Heidelberg and D.A. Caron.  2019.  SSU-rRNA gene sequencing survey of benthic microbial eukaryotes from Guaymas Basin hydrothermal vent.  Journal of Eukaryotic Microbiology.  66: 637-653. pdf

Smith, J., P. Connell, R.H. Evans, A.G. Gellene, M.D.A. Howard, B.H. Jones, S. Kaveggia, L. Palmer, A. Schnetzer, B.N. Seegers, E.L. Seubert, A.O. Tatters and D.A. Caron.  2018.  A decade and a half of Pseudo-nitzschia spp. and domoic acid along the coast of southern California. Harmful Algae.  DOI: https://doi.org/10.1016/j.hal.2018.07.007 pdf

Caron D.A. and S.K. Hu. 2018. Are we overestimating protistan diversity in nature?  Trends in Microbiology. DOI:https://doi.org/10.1016/j.tim.2018.10.009 pdf

Hu, S.K. P.E. Connell, L.Y. Mesrop and D.A. Caron.  2018.  A hard day’s night: diel shifts in microbial eukaryotic activity in the north pacific subtropical gyre.  Frontiers in Marine Science. DOI: 10.3389/fmars.2018.00351 pdf

Connell, P.E., G. Meisterhans, C. Michel, K.R. Arrigo and D.A. Caron.  2018.  Phytoplankton and bacterial dynamics in the Chukchi Sea during the spring-summer transition.  Marine Ecology Progress Series.  602: 49-62. pdf

Bowers, H.A., J.P. Ryan, K. Hayashi, A.L. Woods, R. Marin III, G.J. Smith, K.A. Hubbard, G.J. Doucette, C.M. Mikulski, A.G. Gellene, R.M. Kudela, D.A. Caron, J.M. Birch, C.A. Scholin.  2018.  Diversity and toxicity of Pseudo-nitzschia species in Monterey Bay: perspectives from targeted and adaptive sampling.  Harmful Algae.  78: 129-141. pdf

Turk-Kubo, K.A., P. Connell, D.A. Caron, M.E. Hogan, H.M. Farnelid and Jonathan P. J.P. Zehr.  2018.  In situ diazotroph population dynamics under different resource ratios in the North Pacific Subtropical Gyre.  Frontiers in Microbiology.  DOI: 10.3389/fmicb.2018.01616. pdf

Medina, F.F., J. Bailey, F. Corsetti, M. Moldowan and D.A. Caron.  2018.  Assessing biomarker syngeneity: an in situ approach using monoclonal antibodies to detect squalene.  Organic Geochemistry.  DOI: https://doi.org/10.1016/j.orggeochem.2018.05.006. pdf

Hu, S.K., Z. Liu, H. Alexander, V. Campbell, P.E. Connell, S.T. Dyhrman, K.B. Heidelberg, and D.A. Caron.  2018.  Shifting metabolic priorities among key protistan taxa within and below the euphotic zone.  Environmental Microbiology. DOI: https://doi.org/10.1111/1462-2920.14259. pdf

Carpenter, K.J., M. Bose, L. Polerecky, A. Lie, K.B. Heidelberg, D.A. Caron.  2018.  Single-cell view of carbon and nitrogen acquisition in the mixotrophic alga Prymnesium parvum (Haptophyta) inferred from stable isotope tracers and NanoSIMS.  Frontiers in Marine Science (Marine Ecosystem Ecology).  5:157.  DOI: 10.3389/fmars.2018.00157. pdf

Lie A.A.Y., Z. Liu, R. Terrado, A.O. Tatters, K.B. Heidelberg and D.A. Caron DA.  2018.  A tale of two mixotrophic chrysophytes: insights into the metabolisms of two Ochromonas species (Chrysophyceae) through a comparison of gene expression.  PLoS ONE 13(2): e0192439. https://doi.org/10.1371/journal.pone.0192439. pdf

Smith, J., A.G. Gellene, K.A. Hubbard, H.A. Bowers, R.M. Kudela, K. Negrey and D.A. Caron. 2018.  Pseudo-nitzschia species composition varies concurrently with domoic acid concentrations during two different blooms events in the Southern California Bight.  Journal of Plankton Research.  40: 29-45. pdf

Tatters, A.O., A. Schnetzer, K. Xu, N. Walworth, F. Fu, J.L. Spackeen, R.E. Sipler, E.M. Bertrand, J.B. McQuaid, A.E. Allen, D.A. Bronk, K. Gao, J. Sun, D.A. Caron and D.A. Hutchins.  2018.  Interactive effects of temperature, CO2, and nitrogen source on a coastal California diatom assemblage.  Journal of Plankton Research.  40: 151-164. pdf

Jones, A.J. K.D. Hambright and D.A. Caron.  2018.  Ecological patterns among bacteria and microbial eukaryotes derived from network analyses in a low salinity lake.  Microbial Ecology.  DOI 10.1007/s00248-017-1087-7. pdf

Leles, S., A. Mitra, K. Flynn, D. Stoecker, P. Hansen, A. Calbet, G. McManus, R. Sanders, D. Caron, F. Not, G. Hallegraeff, P. Paraskevi, J. Raven, M. Johnson, P. Glibert and S. Våge.  2017.  Oceanic protists with different forms of acquired phototrophy display diverse biogeographies and abundance.  Proceedings of the Royal Society B.  284: 20170664.  DOI: 10.1098/rspb.2017.0664. pdf

Stauffer, B.A., A.G. Gellene, D. Rico, C. Sur and D.A. Caron. 2017. Grazing of the heterotrophic dinoflagellate Noctiluca scintillans on dinoflagellate and raphidophyte prey. Aquatic Microbial Ecology. 80: 193-207.  pdf

Wilson, S.T., F.O. Aylward, F. Ribalet, B. Barone, J.R. Casey, P.E. Connell, J.A. Eppley, S. Ferrón, A.E. Romano, K.A. Turk-Kubo, A. Visloval, E.V. Armburst, D.A. Caron, M.J. Church, J.P. Zehr, D.M. Karl and E.F. DeLong. 2017. Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera. Nature Microbiology. 2: 17118.  pdf

Howard, M.D.A., C. Nagoda, R.M. Kudela, K. Hayashi, A. Tatters, D.A. Caron., L. Busse, J. Brown, M.A. Sutula, E.D. Stein. 2017. Microcystin prevalence throughout lentic waterbodies in Coastal Southern California. Toxins. 9: 231. DOI: 10.3390/toxins907023.  pdf

Terrado, R., A.L. Pasulka, A.A.Y. Lie, V.J. Orphan, K.B. Heidelberg and D.A. Caron. 2017. Autotrophic and heterotrophic acquisition of carbon and nitrogen by a mixotrophic chrysophyte established through stable isotope analysis. The ISME Journal. DOI: 10.1038/ismej.2017.68. pdf

Berney, C., A. Ciuprina, S. Bender, J. Brodie, V. Edgcomb, E. Kim, J. Rajan, L. Wegener Parfrey, S. Adl, S. Audic, D. Bass, D.A. Caron, G. Cochrane, L. Czech, M. Dunthorn, S. Geisen, F. Oliver Glöckner, F. Mahé, C. Quast, J.Z. Kaye, A.G.B. Simpson, A. Stamatakis, J. del Campo, P. Yilmaz, C. de Vargas. 2017. UniEuk: time to speak a common language in protistology! Journal of Euakryotic Microbiology. 64: 407-411. pdf

Lie, A.A.Y., Z. Liu, R. Terrado, A.O. Tatters, K.B. Heidelberg and D.A. Caron. 2017. Effect of light and prey availability on gene expression of the mixotrophic chrysophyte, Ochromonas sp. BMC Genomics. 18: 163. DOI: 10.1186/s12864-017-3549-1. pdf

Seubert, E.L., A.G. Gellene, V. Campbell, J. Smith, G. Robertson and D.A. Caron. 2017. Incubation experiments to determine the response of a natural plankton community to treated sewage effluent. Estuarine, Coastal and Shelf Science. 186: 250-262. pdf

Seegers, B., E.N. Teel, R.M. Kudela, D.A. Caron and B.H. Jones. 2017. Glider and remote sensing observations of the upper layer response to an extended shallow coastal diversion of wastewater effluent. Estuarine, Coastal and Shelf Science. 186: 198-208. pdf

Connell, P.E., V. Campbell, A.G. Gellene, S.K. Hu and D.A. Caron. 2017. Planktonic food web structure at a coastal time-series site: II. Spatiotemporal variability of microbial trophic activities. Deep-Sea Research I. 121: 210-223. pdf

Caron, D.A., P.E. Connell, R.A. Schaffner, A. Schnetzer, J.A. Fuhrman, P.D. Countway and D.Y. Kim. 2017. Planktonic food web structure at a coastal time-series site: I. Partitioning of microbial abundances and carbon biomass. Deep-Sea Research I. 121: 14-29. pdf

Stoecker, D.K., P.J. Hansen, D.A. Caron and A. Mitra. 2017. Mixotrophy in the marine plankton. Annual Reviews of Marine Sciences. 9: 311-335. pdf

Tatters, A.O., M.D.A. Howard, C. Nagoda, L. Busse, A.G. Gellene, D.A. Caron. 2017. Multiple stressors at the land-sea interface: cyanotoxins at the land-sea interface in the Southern California Bight. Toxins. 9(30): 95. DOI: 10.3390/toxins9030095. pdf

Caron, D.A. 2017. Acknowledging and incorporating mixed nutrition into aquactic protistan ecology, finally. Environmental Microbiology Reports. 9: 41-43. pdf

Caron, D.A., A.G. Gellene, J. Smith, E.L. Seubert, V. Campbell, G.S. Sukhatme, B. Seegers, B.H. Jones, A.Y. Lie, M.D.A. Howard, R.M. Kudela, K. Hayashi, J. Ryan, J. Birch, E. Demir-Hilton, K. Yamahara, C. Scholin, M. Mengel and G. Robertson. 2017. Response of phytoplankton and bacterial biomass during a wastewater effluent diversion into nearshore coastal waters. Estuarine, Coastal and Shelf Science. 186: 223-236. pdf

Caron, D.A., R.J. Gast and M.È. Garneau. 2017. Sea ice as a habitat for micrograzers. In: Thomas, D.N. and G.S. Dieckmann (eds.), Sea Ice, Third Edition. John Wiley & Sons, West Sussex, Chapter 15. Pages: 370-393. pdf

Liu, Z., S.K. Hu, V. Campbell, A.O. Tatters, K.B. Heidelberg and D.A. Caron. 2017. Single-cell transcriptomics of small microbial eukaryotes: insights and limitations. The ISME Journal. DOI: 10.1038/ismej.2016.190. pdf

Subbaraya, S., A. Breitenmoser, A. Molchanov, J. Mueller, C. Oberg, D.A. Caron, G. Sukhatme. 2016. Design of Lagrangian drifters for ocean monitoring. IEEE Robotics & Automation Magazine. DOI: 10.1109/MRA.2016.2535154. pdf

Caron, D.A., H. Alexander, A.E., J. M. Archibald, E.V. Armbrust, C. Bachy, A. Bharti, C.J. Bell, S.T. Dyhrman, S. Guida, K.B. Heidelberg, J.Z. Kaye, J. Metzner, S.R. Smith and A.Z. Worden. 2016. Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nature Reviews Microbiology. DOI: 10.1038/nrmicro.2016.160.  pdf

Hu S.K., V. Campbell, P. Connell, A.G. Gellene, Z. Liu, R.Terrado and D.A. Caron. 2016. Protistan diversity and activity inferred from RNA and DNA at a coastal ocean site in the eastern North Pacific. FEMS Microbiol. Ecol. 92(4)  DOI: 10.1093/femsec/fiw050.  pdf

Mitra, A., K.J. Flynn, U. Tillmann, J. Raven, D. Caron, D. Stoecker, F. Not, P. Hansen, G. Hallegraeff,  R. Sanders, S. Wilken, G. McManus, M. Johnson, P. Pitta, S. Våge, R. Berje, A. Calbet, F. Thingstad, J.J. Jeong, J. Burkholder, P. Glibert, E. Granéli and V. Lundgren.  2016.  Defining planktonic protist functional groups on mechanisms for energy and nutrient acquisition; incorporation of diverse mixotrophic strategies. Protist.  167: 106-120.  pdf

Liu, Z., V. Campbell, K. Heidelberg and D.A. Caron.  2016.  Gene expression characterizes  different nutritional strategies among three mixotrophic protists.  FEMS Microbiology Ecology. 92: fiw106.  pdf

Martiny, A.C., A. Talarmin, C. Mouginot, J. Lee, J. Huang, A. Gellene and D.A. Caron.  2016.  Biogeochemical interactions control a temporal succession in the elemental composition of marine communities.  Limnology and Oceanography.  61: 531-542. pdf

Caron, D.A.  2016.  Mixotrophy stirs up our understanding of marine food webs.  Proceedings of the Academy of National Sciences of the U.S.  113 (11): 2806-2808.  pdf

Caron, D.A.  2016.  The rise of Rhizaria.  Nature News & Views.  DOI: 10.1038/nature17892.  pdf

Caron, D.A., M. Echt, J. Folsom, E.L. Seubert, A.O. Tatters and A.G. Gellene.  2016. Managing Algal Blooms at a Botanical Garden Lake: A Success Story.  North American Lake Management Society (NALMS) Lakeline, Spring. Pages: 17-21.  pdf

Liu, Z., A.C. Jones, V. Campbell, K.D. Hambright, K.B. Heidelberg and D.A. Caron, Gene expression in the mixotrophic prymnesiophyte, Prymnesium parvum, responds to prey availability. Frontiers in Microbiology 6 (2015).  DOI: 10.3389/fmicb.2015.00319.  pdf

Seegers, B.N., J.M. Birch, R. Marin III, C.A. Scholin, D.A. Caron, E.L. Seubert, M.D.A. Howard, G.L. Roberston and B.H. Jones.  2015.  Subsurface seeding of surface harmful algal blooms observed through the integration of autonomous gliders, moored Environmental Sample Processors, and satellite remote sensing in Southern California.  Limnology and Oceanography.  60: 754-764.  pdf

Hu, S., Z. Liu, A.A. Y. Lie, P.D. Countway, D.Y. Kim, A.C. Jones, R.J. Gast, S.C. Cary, E.B. Sherr, B.F. Sherr and D.A. Caron. 2015. Estimating protistan diversity using highthrough putsequencing. Journal of Eukaryotic Microbiology. 62: 688-693..  pdf

Das, J., F. Py, J. Harvey, J. Ryan, A. Gellene, R. Grahamk, D.A. Caron, K. Rajan and G,S. Sukhatme.  2015.  Data-driven robotic sampling for marine ecosystem monitoring.  International Journal of Robotics Research.  DOI: 10.1177/0278364915587723.  pdf

Liu, Z., A.E. Koid, R. Terrado, V. Campbell, D.A. Caron and K.B. Heidelberg.  2015.  Changes in gene expression of Prymnesium parvum due to nitrogen and phosphorus limitation.  Frontiers in Microbiology, Aquatic Microbiology. Vol. 6.  DOI: 10.3389/fmicb.2015.00631. pdf

Fuhrman, J.A. and D.A. Caron. (2015) Heterotrophic planktonic microbes: virus, bacteria, archaea, and protozoa, in Manual of Environmental Microbiology, Fourth Edition, Yates MV, et al., Editors. 2015, American Society of Microbiology. p. 4.2.2-1 - 4.2.2-34.  pdf

Howard, M.D.A.,  M. Sutula, D.A. Caron, Y. Chao, J.D. Farrara, H. Frenzel, B. Jones, G. Robertson, K. McLaughlin and A. Sengupta^.  2014.  Anthropogenic nutrient sources rival natural sources on small scales in the coastal waters of the Southern California Bight.  Limnology and Oceanography.  59: 285-297. pdf

Chow, C.-E., D.Y. Kim, R. Sachdeva, D.A. Caron and J.A. Fuhrman.  2014.  Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists.  The ISME Journal.  8: 816-829. pdf

Keeling, P.J. and 78 others.  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: e1001889.

Koid, A.E., A, Jones, Z. Liu, D.A. Caron and K.B. Heidelberg.  2014.  Comparative transcriptomics of four prymnesiophyte algae.  PLoS One.  9: e97801.  pdf

Seubert, E.L., M.D.A. Howard, R.M. Kudela, T.N. Stewart, R.W. Litaker, R. Evans and D.A. Caron.  2014.  Development, comparison and validation using ELISAs for the analysis of domoic acid in California sea lion body fluids.  Journal of AOAC International.  97: 345-355. pdf

Lie, A.A.Y., Z. Liu, S. Hu, A.C. Jones, D.Y. Kim, P.D. Countway, L.A. Amaral-Zettler, R.J. Gast, E.B. Sherr⁴, B.F. Sherr⁴, S.C. Cary and D.A. Caron.  2014.  Investigating microbial eukaryote diversity: Insights from a comparison of pyrotag and full-length sequences of 18S rDNA from a global survey.  Applied and Environmental Microbiology.  80: 4363-4373. pdf

Kim, D.Y., P.D. Countway, A.C. Jones, A. Schnetzer, W. Yamashita, C. Tung and D.A. Caron.  2014.  Monthly, seasonal and interannual variability of microbial eukaryote assemblages within and below the euphotic zone in the eastern North Pacific.  The ISME Journal.  8: 515-530.  pdf

Rose, J.M., E. Fitzpatrick, A. Wang, R.J. Gast and D.A. Caron.  2013.  Low temperature constrains growth rates but not instantaneous grazing rates of Antarctic microzooplankton.  Polar Biology.  36: 645–659

Caron, D.A. and D.A. Hutchins.  2013.  The effects of changing climate on microzooplankton grazing and community structure: drivers, predictions and knowledge gaps.  Journal of Plankton Research.  35: 235-252.  pdf

Tatters, A. O., A. Schnetzer, F. Fu, A. Y. A. Lie, D. A. Caron, and D. A. Hutchins. 2013. Short- versus long-term responses to changing CO₂ in a coastal dinoflagellate bloom: implications for interspecific competitive interactions and community structure. Evolution 67:1879-1891.  pdf

Tatters, A.O., M.Y. Roleda, A. Schnetzer, F. Fu, C. Hurd, P.W. Boyd, D.A. Caron, A.A.Y. Lie, L.J. Hoffmann and D.A. Hutchins.  2013.  Long-term conditioning of a temperate marine diatom community to acidification and warming. Philosophical Transactions of the Royal Society B.  368: 20120437.  pdf

Coyne, K. J., P. D. Countway, C. A. Pilditch, C. K. Lee, D. A. Caron, and S. C. Cary. 2013. Diversity and Distributional Patterns of Ciliates in Guaymas Basin Hydrothermal Vent Sediments. Journal of Eukaryotic Microbiology.  60: 433-44.  pdf

Caron, D.A.  2013.  Towards a molecular taxonomy for protists: benefits, risks and applications in plankton ecology.  Journal of Eukaryotic Microbiology. 60: 407-413.  pdf

Lie, A.A.Y., D.Y. Kim, A. Schnetzer and D.A. Caron.  2013.  Small-scale temporal and spatial variations in protistan community composition at the San Pedro Ocean Time-series station off the coast of southern California.  Aquatic Microbial Ecology. 70: 93–110. pdf

Schnetzer, A., B.H. Jones, R.A. Schaffner, I. Cetinic, E. Fitzpatrick, P.E. Miller and D.A. Caron.  2013.  Coastal upwelling linked to toxic Pseudo-nitzschia australis blooms in Los Angeles coastal waters, 2005 – 2007.  Journal of Plankton Research.  35: 1080-1092.  pdf

Jones, A.C., T.S. Vivian Liao, F.Z. Najar, B.A. Roe, K.D. Hambright and D.A. Caron.  2013.  Seasonality and disturbance: annual pattern and response of the bacterial and microbial eukaryotic assemblages in a freshwater ecosystem.  Environmental Microbiology. 15: 2557–2572.  pdf

Seubert, E.L., A.G. Gellene, M.D.A. Howard, P. Connell, M. Ragan, B.H. Jones, J. Runyan, D.A. Caron.  2013.  Seasonal and annual dynamics of harmful algae and algal toxins revealed through weekly monitoring at two coastal ocean sites off southern California, USA.  Environmental Sciences and Pollution Research.  20: 6878–6895.  pdf

Caron, D.A. P.D. Countway, A.C. Jones, D.Y. Kim, A. Schnetzer.  Marine Protistan Diversity. 2012. Marine Protistan Diversity. Annual Review of Marine Science 4:467-493.  pdf

Howard, M.D.A., A.C. Jones, A. Schnetzer, P.D. Countway, C.R. Tomas, R.M. Kudela, K. Hayashi, P. Chia and D.A. Caron.  2012.  Quantitative real-time PCR for Cochlodinium fulvescens (Dinophyceae), a potentially harmful dinoflagellate from California coastal waters.  Journal of Phycology.  48:  384-393.  pdf

Lewitus A.J., R.A. Horner, D.A. Caron, E. Garcia-Mendoza, B.M. Hickey, M. Hunter, D.D. Huppert, D. Kelly, R.M. Kudela, G.W. Langlois, J.L. Largier, E.J. Lessard, R. RaLonde, J.E. Rensell, P.G. Strutton, V.L. Trainer, J.F. Tweddle.  2012.  Harmful algal blooms in the North American west coast region:  history, trends, causes, and impacts.  Harmful Algae. 19: 133-159.  pdf

Stauffer, B.A., A.G. Gellene, A. Schnetzer, E.L. Seubert, C. Oberg, G.S. Sukhatme, D.A. Caron.  2012.  An oceanographic, meterological and biological ‘perfect storm’ yields a massive fish kill.  Marine Ecology Progress Series. 468: 231-243.  pdf

Stauffer, B.A., A. Schnetzer, A.G. Gellene, C. Oberg, G.S. Sukhatme, D.A. Caron.  2012.  Effects of an acute hypoxia event on microplankton community structure in a coastal harbor of Southern California.  Estuaries and Coasts.  36: 135-148.  pdf

Seubert, E.L., S. Trussell, J. Eagleton, A. Schnetzer, I. Cetinić, P. Lauri, B.H. Jones and D.A. Caron.  2012.  Algal toxins and reverse osmosis desalination operations: laboratory bench testing and field monitoring of domoic acid, saxitoxin, brevetoxin and okadaic acid.  Water Research.  46: 6563-6573.  pdf

Kim, D.Y., P.D. Countway, W. Yamashita and D.A. Caron.  2012.  A combined sequence-based and fragment-based characterization of microbial eukaryote assemblages provides taxonomic context for the Terminal Restriction Fragment Length Polymorphism (T-RFLP) method.  Journal of Microbiological Methods.  91:527-536.  pdf

Schnetzer, A., S.D. Moorthi, P.D. Countway R.J. Gast, I.C. Gilg and D.A. Caron.  2011.  Depth matters: microbial eukaryote diversity and community structure in the eastern North Pacific revealed through environmental gene libraries.  Deep-Sea Research I.  58:16-26. pdf

Sun, J. D.A. Hutchins, Y. Feng, E.L. Seubert, D.A. Caron and F.-X. Fu.  2011.  Effects of changing pCO₂ and phosphate availability on domoic acid production and physiology of the marine harmful bloom diatom Pseudo-nitzschia multiseries.  Limnology and Oceanography  56: 829-840.  pdf

Golubchik, L., D.A. Caron, A. Das, A. Dhariwal, R. Govindan, D. Kempe, C. Oberg, A. Sharma, B. Stauffer, G. Sukhatme, and B. Zhang.  2011.  AMBROSia: An overview and recent results.  Journal of Algorithms and Computational Technology: 5:  583-599.  pdf

Kim, D.Y., P.D. Countway, R.J. Gast and D.A. Caron.  2011.  Rapid shifts in protistan community structure and composition during bottle incubations.  Microbial Ecology.  62: 383-398.  pdf

Steele, J.A., P.D. Countway, L. Xia, P.D.Vigil, J.M. Beman, D.Y. Kim, C.-E. T. Chow, R. Sachdeva, A.C. Jones, M.S. Schwalbach, J.M. Rose, I. Hewson, A. Patel, F. Sun, D.A. Caron, J.A. Fuhrman.  2011.  Marine bacterial, archaeal, and protistan assocation networks reveal ecological linkages.  The ISME Journal.  5: 1414-1425.  pdf

Garneau, M.-È., A. Schnetzer, P.D. Countway, A.C. Jones, E.L. Seubert and D.A. Caron.  2011.  Seasonal dynamics of the toxic dinoflagellate Alexandrium catenella at Redondo Beach, California, examined by quantitative PCR.  Applied and Environmental Microbiology.  77: 7669–7680.  pdf

Caron, D.A. and R.J. Gast.  2010.  Heterotrophic protists associated with sea ice.  In: Thomas, D.N. and G.S. Dieckmann (eds.).  Sea Ice.  Second Edition, Wiley-Blackwell, Oxford, pp. 327-356.

Caron, D.A. Garneau, M.-E., E. Seubert, M.D.A. Howard, D. Darjany, A. Schnetzer, I. Cetinic, G. Filteau, P. Lauri, B. Jones and S. Trussell.  2010.  Harmful algae and their potential impacts on desalination operations off southern California.  Water Research.  44: 385-416.  pdf

Gilg, I.C., L.A. Amaral-Zettler, P.D. Countway, S. Moorthi, A. Schnetzer and D.A. Caron.  2010.  Phylogenetic affiliations of mesopelagic acantharia and acantharian-like environmental 18S rRNA genes off the Southern California coast.  Protist. 161: 197–211. pdf

Countway, P.D., P. Vigil, A. Schnetzer, S. Moorthi and D.A. Caron.  2010.  Seasonal Analysis of Protistan Community Structure and Diversity at the USC Microbial Observatory (San Pedro Channel, Pacific Ocean).  Limnology and Oceanography.  55: 2381-2396.  pdf

Fitzpatrick, E., D.A. Caron and A. Schnetzer. 2010.  Development and environmental application of a genus-specific quantitative PCR approach for Pseudo-nitzschia species.  Marine Biology.  157: 1161-1169.  pdf

Smith, R.N., J. Das, H. Heidarsson, A.M. Pereira, F. Arrichiello, I. Cetinic, L. Darjany, M.-E. Garneau, M.D. Howard, C. Oberg, M. Ragan, E. Seubert, E.C. Smith, B.A. Stauffer, A. Schnetzer, G. Toro-Farmer, D.A. Caron B.H. Jones and G.S. Sukhatme.  2010.  USC CINAPS builds bridges: observing and monitoring the Southern California Bight.  IEEE Robotics and Automation Magazine.  17: 20-30.  pdf

Smith, R., A. de Menezes Pereira, Y. Chao, P. Li, D.A. Caron, B. Jones, and G. Sukhatme.  2010.  Autonomous underwater vehicle trajectory design coupled with predictive ocean models: a case study.  IEEE International Conference on Robotics and Automation 2010.  pp. 4770-4777.  pdf

Smith, R., Y. Chao, D.A. Caron, B. Jones, and G. Sukhatme.  2010.  Cooperative multi-AUV tracking of phytoplankton blooms based on ocean model predictions.  Oceans '10 - IEEE Sydney, Sydney, Australia.  Oceans '10 - IEEE Sydney.  Sydney, Australia.  May 2010.  pdf

Das, J., K. Rajan, S. Frolov, J. Ryan, F. Py, D.A. Caron, and G. Sukhatme.  2010.  Towards marine bloom trajectory prediction for AUV mission planning.  IEEE International Conference on Robotics and Automation, May 2010.  pdf

Smith, R., Y. Chao, P. Li, D.A. Caron, B. Jones, and G. Sukhatme.  2010.  Planning and implementing trajectories for autonomous underwater vehicles to track evolving ocean processes based on predictions from a regional ocean model.  International Journal of Robotics Research.  29: 1475-1497.  pdf

Caron, D. A. (2009). "New accomplishments and approaches for assessing protistan diversity and ecology in natural ecosystems." BioScience 59: 287-299. pdf

Caron, D. A. (2009). "Protistan biogeography: why all the fuss?" Journal of Eukaryotic Microbiology 56: 105-112. pdf

Caron, D. A. and P. D. Countway (2009). "Hypotheses on the role of the protistan rare biosphere in a changing world." Aquatic Microbial Ecology 57: 227-238. pdf

Caron, D. A., P. D. Countway, et al. (2009). "Defining DNA-based operational taxonomic units for microbial eukaryote ecology." Applied and Environmental Microbiology 75: 5797-5808. pdf     Download the Microbial Eukaryote Species Assignment (MESA) programs, example files & instructions here: MESA

Ishikawa, F.N,  B. Stauffer, D.A. Caron and C. Zhoua.  2009.  Rapid and label-free cell detection by metal-cluster-decorated carbon nanotube biosensors.  Biosensors and Bioelectronics  24: 2967–2972. 

Caron, D. A. and R. J. Gast (2009). Heterotrophic protists associated with sea icea. Sea Ice. D. N. Thomas and G. S. Dieckmann. Oxford, Wiley-Blackwell: 327-356.

Caron, D. A., R. J. Gast, et al. (2009). "Microbial eukaryote diversity and biogeography." Microbe 4: 71-77. pdf

Caron, D. A., A. Z. Worden, et al. (2009). "Protists are microbes too: a perspective." The ISME Journal 3: 4-12. pdf

Gast, R. J., R. W. Sanders, et al. (2009). "Ecological strategies of protists and their symbiotic relationships with prokaryotic microbes." Trends in Microbiology 17: 563-569. pdf

Lonsdale, D. J., R. M. Cerrato, et al. (2009). "Influence of suspension-feeding bivalves on the pelagic food webs of shallow enclosed bays." Aquatic Biology 6: 263-279. pdf

Moorthi, S. D., D. A. Caron, et al. (2009). "Mixotrophy: a widespread and important ecological strategy for planktonic and sea-ice nanoflagellates in the Ross Sea, Antarctica" Aquatic Microbial Ecology 54: 269-277. pdf

Pereira, A., H. Heidarsson, H., C. Oberg, D.A. Caron, B. Jones and G.S. Sukhatme.  2009.  A communication framework for cost-effective operation of AUVs in coastal regions. The 7^th International Conference on Field and Service Robotics (FSR-2009), Cambridge, MA, July 2009.  pdf

Rose, J. M., N. M. Vora, et al. (2009). "Effects of temperature on growth rate and gross growth efficiency of an Antarctic bacterivorous protist." The ISME Journal 3: 252-260. pdf

Sekula-Wood, E., A. Schnetzer, et al. (2009). "Rapid downward transport of the neurotoxin domoic acid in coastal waters." Nature Geoscience 2: 272-275. pdf

Smith, R. N., Stauffer, B, et al. (2009). "Design and Implementation of Sensor Networks for the Observation and Research of Harmful Algal Blooms in Southern California Coastal Waters." In Proceedings of the Conference on Coastal Environmental Sensing Networks, Boston, MA, Jul 2009. pdf

Smith, R. N., Y. Chao, et al. (2009). "Trajectory Design for Autonomous Underwater Vehicles based on Ocean Model Predictions for Feature Tracking." In the Proceedings of the International Conference on Field and Service Robotics, Jul 2009. pdf

Smith, R. N., J. Das, et al (2009). "Implementation of an Embedded Sensor Network for the Coordination of Slocum Gliders for Coastal Monitoring and Observation." In the Proceedings of the ACM International Workshop on UnderWater Networks, Berkeley, CA, Nov 2009. pdf

Vigil, P., P. D. Countway, et al. (2009). "Rapid shifts in dominant taxa among microbial eukaryotes in estuarine ecosystems." Aquatic Microbial Ecology 54: 83-100. pdf

Caron, D. A. and R. J. Gast (2008). The diversity of free-living protists: seen and unseen, cultured and uncultured. Accessing uncultivated microorganisms: From the environment to organisms and genomes and back. K. Zengler. Washington, DC, ASM Press: 67-93.

Caron, D. A. and J. M. Rose (2008). "The metabolic theory of ecology and algal bloom formation (Reply to comment by López-Urrutia)." Limnology and Oceanography 53: 2048-2049. pdf

Caron, D. A., B. A. Stauffer, et al. (2008). "Macro- to fine-scale spatial and temporal distributions and dynamics of phytoplankton and their environmental driving forces in a small subalpine lake in southern California, USA." Limnology and Oceanography 58: 2333-2349. pdf

Rose, J. M., N. M. Vora, et al. (2008). "Effect of temperature and prey type on nutrient regeneration by an Antarctic bacterivorous protist." Microbial Ecology 56: 101-111. pdf

Smith, J. K., D. J. Lonsdale, et al. (2008). "Feeding behavior and development of Acartia tonsa nauplii on the brown tide alga Aureococcus anophagefferens." Journal of Plankton Research 30: 937-950. pdf

Stauffer, B. A., R. A. Schaffner, et al. (2008). "Immunofluorescenceflow cytometry technique for enumeration of the brown-tide alga, Aureococcus anophagefferens." Applied and Environmental Microbiology 74: 6931-6940. pdf

Caron, D. A. and A. Schnetzer (2007). Protistan community structure. Manual of environmental microbiology. C. J. Hurst, R. L. Crawford, J. L. Garlandet al. Washington, ASM Press: 454-468. pdf

Caron, D.A., A. Das, A. Dhariwal, L. Golubchik, R. Govindan, D. Kempe, C. Oberg, A. Sharma, B. Stauffer, G. Sukhatme, and B. Zhang.  2007.  AMBROSia: An Autonomous Model-Based Reactive Observing System.  ICCS 2007; Lecture Notes in Computer Science, 4487: 995-1001. 

Countway, P. D., R. J. Gast, et al. (2007). "Distinct protistan assemblages characterize the euphotic zone and deep sea (2500 m) of the western N. Atlantic (Sargasso Sea and Gulf Stream)." Environmental Microbiology 9: 1219-1232. pdf

Gast, R. J., D. M. Moran, et al. (2007). "Kleptoplasty in an Antarctic dinoflagellate: caught in evolutionary transition?" Environmental Microbiology 9: 39-45. pdf

Lonsdale, D. J., R. M. Cerrato, et al. (2007). "Zooplankton changes associated with grazing pressure of northern quahogs (Mercenaria mercenaria L.) in experimental mesocosms." Estuarine and Coastal Shelf Science 73: 101-110. pdf

Moran, D. M., O. R. Anderson, et al. (2007). "A description of seven Antarctic marine Gymnamoebae including a new species and a new genus: Platyamoeba contorta n. sp. and Vermistella antarctica n. gen. n. sp." Journal of Eukaryotic Microbiology 54: 169-183. pdf

Rose, J. M. and D. A. Caron (2007). "Does low temperature constrain the growth rates of heterotrophic protists? Evidence and implications for algal blooms in cold water." Limnology and Oceanography 52: 886-895. pdf

Schnetzer, A., P. E. Miller, et al. (2007). "Blooms of Pseudo-nitzschia and domoic acid in the San Pedro Channel and Los Angeles harbor areas of the Southern California Bight, 2003-2004." Harmful Algae 6: 372-387. pdf

Sherr, B. F., E. B. Sherr, et al. (2007). "A sea of microbes: oceanic protists." Oceanography 20: 102-106. pdf

Singh, A., M. Batalin, et al. (2007). "Human assisted robotic team campaigns for aquatic monitoring." Journal of Field Robotics 24: 969-989. pdf

Sukhatme, G., A. Dhariwal, et al. (2007). "The design and development of a wireless robotic networked aquatic microbial observing system." Environmental Engineering Science 24: 205-215. pdf

Countway, P. D. and D. A. Caron (2006). "Abundance and distribution of Ostreococcus sp. in the San Pedro Channel, California (USA) revealed by qPCR." Applied and Environmental Microbiology 72: 2496-2506. pdf

Deonarine, S. N., C. J. Gobler, et al. (2006). "Role of zooplankton in the onset and demise of harmful brown tide blooms (Aureococcus anophagefferens) in US mid-Atlantic estuares." Aquatic Microbial Ecology 44: 181-195. pdf

Gast, R. J., D. M. Moran, et al. (2006). "Abundance of a novel dinoflagellate phylotype in the Ross Sea, Antarctica." Journal Of Phycology 42: 233-242. pdf

Lee, A. S., M. Mahapatro, et al. (2006). "Whole-cell sensing for a harmful bloom-forming microscopic alga by measuring antibody-antigen forces." IEEE Transactions on Bioscience 5: 149-156. pdf

Moorthi, S. D., P. D. Countway, et al. (2006). "Use of quantitative real-time PCR to investigate the dynamics of the red tide dinoflagellate Lingulodinium polyedrum." Microbial Ecology 52: 136-150. pdf

Caron, D. A. (2005). "Marine microbial ecology in a molecular world: what does the future hold?" Scientia Marina 69(S): 97-110. pdf

Countway, P. D., R. J. Gast, et al. (2005). "Protistan diversity estimates based on 18S rDNA from seawater incubations in the western North Atlantic." Journal of Eukaryotic Microbiology 52(2): 95-106. pdf

Dolan, J. R., F. Rassoulzadegan, et al. (2005). "The first decade of ‘Aquatic Microbial Ecology’ (1995-2005): evidence for gradualism or punctuated equilibrium?" Aquatic Microbial Ecology 39: 3-6. pdf

Schnetzer, A. and D. A. Caron (2005). "Assessing the impact of copepod grazing on the trophic structure of the microbial assemblage in the San Pedro Channel, California." Journal of Plankton Research 27: 959-971. pdf

Caron, D. A., P. D. Countway, et al. (2004). "The growing contributions of molecular biology and immunology to protistan ecology: Molecular signatures as ecological tools." Journal of Eukaryotic Microbiology 51(1): 38-48. pdf

Caron, D. A., C. J. Gobler, et al. (2004). "Microbial herbivory on the brown tide alga, Aureococcus anophagefferens: results from natural ecosystems, mesocosms and laboratory experiments." Harmful Algae 3(4): 439-457. pdf

Cerrato, R. M., D. A. Caron, et al. (2004). "Effect of the northern quahog Mercenaria mercenaria on the development of blooms of the brown tide alga Aureococcus anophagefferens." Marine Ecology Progress Series 281: 93-108. pdf

Gast, R. J., M. R. Dennett, et al. (2004). "Characterization of protistan assemblages in the Ross Sea, Antarctica by denaturing gradient gel electrophoresis." Applied and Environmental Microbiology 70: 2028-2037. pdf

Gastrich, M. D., R. Lathrop, et al. (2004). "Assessment of brown tide blooms, caused by Aureococcus anophagefferens, and contributing factors in New Jersey coastal bays: 2000-2002." Harmful Algae 3: 305-320. pdf

Gobler, C. J., G. E. Boneillo, et al. (2004). "Nutrient limitation, organic matter cycling, and plankton dynamics during an Aureococcus anophagefferens bloom." Aquatic Microbial Ecology 35: 31-43. pdf

Rose, J. M., D. A. Caron, et al. (2004). "Counting heterotrophic nanoplanktonic protists in cultures and in aquatic communities by flow cytometry." Aquatic Microbial Ecology 34: 263-277. pdf

Caron, D. A., M. R. Dennett, et al. (2003). "Development and application of a monoclonal-antibody technique for counting Aureococcus anophagefferens, an alga causing recurrent brown tides in the Mid-Atlantic United States." Applied and Environmental Microbiology 69(9): 5492-5502. pdf

Gast, R. J., D. J. Beaudoin, et al. (2003). "Isolation of symbiotically expressed genes from the dinoflagellate symbiont of the solitary radiolarian Thalassicolla nucleata " Biological Bulletin 204: 210-214. pdf

Smith, W. O., Jr., M. R. Dennett, et al. (2003). "The temporal dynamics of the flagellated and colonial stages of Phaeocystis antarctica in the Ross Sea." Deep-Sea Research 50: 605-617. pdf

Caron, D. A., P. D. Countway, et al. (2002). Protozoa in marine/estuarine waters. Encyclopedia of environmental microbiology. G. Bitton. New York, John Wiley & Sons, Inc.: 2613-2626. pdf

Dennett, M. R., D. A. Caron, et al. (2002). "Video plankton recorder reveals high abundances of colonial Radiolaria in surface waters of the central North Pacific." Journal of Plankton Research 24(8): 797-805. pdf

Boissonneault-Cellineri, K. R., M. Mehta, et al. (2001). "Microbial food web interactions in two Long Island embayments." Aquatic Microbial Ecology 26(2): 139-155. pdf

Carlsson, P. and D. A. Caron (2001). "Seasonal variation of phosphorus limitation of bacterial growth in a small lake." Limnology and Oceanography 46(1): 108-120. pdf

Caron, D. A. (2001). Protistan community structure. Manual of Environmental Microbiology. C. J. Hurst, G. R. Knudsen, M. J. McInerney, L. D. Stetzenbach and M. V. Walter. Washington, DC, ASM Press: 378-389. pdf

Dennett, M. R., S. Mathot, et al. (2001). "Abundance and distribution of phototrophic and heterotrophic nano- and microplankton in the southern Ross Sea." Deep-Sea Research Part II-Topical Studies in Oceanography 48(19-20): 4019-4037. pdf

Gast, R. J. and D. A. Caron (2001). "Photosymbiotic associations in planktonic foraminifera and radiolaria." Hydrobiologia 461: 1-7. pdf

Lim, E. L., M. R. Dennett, et al. (2001). "Identification of heterotrophic nanoflagellates by restriction fragment length polymorphism analysis of small subunit ribosomal DNA." Journal of Eukaryotic Microbiology 48(3): 247-257. pdf

Sanders, R. W., D. A. Caron, et al. (2001). "Nutrient acquisition and population growth of a mixotrophic alga in axenic and bacterized cultures." Microbial Ecology 42(4): 513-523. pdf

Amaral Zettler, L. A. and D. A. Caron (2000). "New insights into the phylogeny of the Acantharea based on SSU rRNA gene sequencing." European Journal Of Protistology 36(1): 34-39. pdf

Caron, D. A., M. R. Dennett, et al. (2000). "Microzooplankton herbivory in the Ross Sea, Antarctica." Deep-Sea Research 47: 15-16. pdf

Caron, D. A. (2000). Protistan herbivory and bacterivory. Marine Microbiology: Methods in Microbiology. J. Paul. San Diego, ACADEMIC PRESS INC. 30: 289-315. pdf

Caron, D. A. (2000). Symbiosis and mixotrophy among pelagic microorganisms. Microbial Ecology of the Oceans. D. L. Kirchman. New York, Wiley-Liss, Inc.: 495-523. pdf

Caron, D. A., E. L. Lim, et al. (2000). "Responses of bacterioplankton and phytoplankton to organic carbon and inorganic nutrient additions in contrasting oceanic ecosystems." Aquatic Microbial Ecology 22(2): 175-184. pdf

Garrison, D. L., M. M. Gowing, et al. (2000). "Microbial food web structure in the Arabian Sea: a US JGOFS study." Deep-Sea Research Part Ii-Topical Studies in Oceanography 47(7-8): 1387-1422. pdf

Lonsdale, D. J., D. A. Caron, et al. (2000). "Predation by Oithona spp. on protozooplankton in the Ross Sea, Antarctica." Deep-Sea Research II 47(15-16): 3273-3283. pdf

Nigam, R. and D. A. Caron (2000). "Does temperature affect dimorphic reproduction in benthic foraminifera? A culture experiment on Rosalina leei." Current Science 79(8): 1105-1106. pdf

Sanders, R. W., U.-G. Berninger, et al. (2000). "Heterotrophic and mixotrophic nanoplankton predation on picoplankton in the Sargasso Sea and on Georges Bank." Marine Ecology Progress Series 192: 103-118. pdf

Amaral Zettler, L. A., O. R. Anderson, et al. (1999). "Towards a molecular phylogeny of colonial spumellarian radiolaria." Marine Micropaleontology 36: 67-79. pdf

Caron, D. A. and M. R. Dennett (1999). "Phytoplankton growth and mortality during the 1995 Northeast Monsoon and Spring Intermonsoon in the Arabian Sea." Deep-Sea Research 46: 1665-1690. pdf

Caron, D. A., E. L. Lim, et al. (1999). "Molecular phylogenetic analysis of the heterotrophic chrysophyte genus Paraphysomonas (chrysophyceae), and the design of rRNA-targeted oligonucleotide probes for two species." Journal of Phycology 35: 824-837. pdf

Caron, D. A., R. J. Gast, et al. (1999). "Protistan community structure: molecular approaches for answering ecological questions." Hydrobiologia 401: 215-227. pdf

Caron, D. A., E. R. Peele, et al. (1999). "Picoplankton and nanoplankton and their trophic coupling in surface waters of the Sargasso Sea south of Bermuda." Limnology and Oceanography 44(2): 259-272. pdf

Dennett, M. R., D. A. Caron, et al. (1999). "Abundance and biomass of nano- and microplankton during the 1995 Northeast Monsoon and Spring Intermonsoon in the Arabian Sea." Deep-Sea Research 46: 1691-1717. pdf

Gast, R. J., T. A. McDonnell, et al. (1999). "srDNA-based taxonomic affinities of algal symbionts from a planktonic foraminifer and a solitary radiolarian." Journal Of Phycology 36: 172-177. pdf

Gifford, D. J. and D. A. Caron (1999). Sampling, preservation, enumeration and biomass of marine protozooplankton. ICES zooplankton methodology manual. London, Academic Press: 193-221. pdf

Lim, E. L., D. A. Caron, et al. (1999). "The ecology of Paraphysomonas imperforata based on studies employing oligonucleotide probe identification in coastal water samples and enrichment culture." Limnology and Oceanography 44: 37-51. pdf