Below you will find a chronological list of lab publications with the most recent listed first. Please click on the “pdf” link after each individual reference to open the publication in a new tab in your browser window.

For a complete list of publications for an individual, please visit our People Page, click on that individual's name and open the CV.


Schnetzer A., Moorthi S., Gast R.J., Countway P.D., * Gilg I.C. and Caron D.A. (2011) Depth matters: Microbial eukaryote diversity and community structure in the eastern North Pacific as indicated by environmental gene libraries. Deep Sea Research I 58: 16-26
Gilg, I. C., L. A. Amaral-Zettler, et al. (In press). "Phylogenetic affiliations of mesopelagic acantharia and acantharian-like environmental 18S rRNA genes off the Southern California coast." Protist.
Pereira, A., H. Heidarsson, et al. (In press). A communication framework for cost-effective operation of AUVs in coastal regions. 7th International Conference on Field and Service Robotics, Cambridge, MA.
Smith, R. N., Y. Chao, et al. (In press). "Trajectory design for autonomous underwater vehicles based on ocean model predictions for feature tracking." Proceedings of the International Conference on Field and Service Robotics.
Smith, R. N., J. Das, et al. (In press). "The USC Center for Integrated Networked Aquatic PlatformS (CINAPS): observing and monitoring the Southern California Bight." IEEE Robotics and Automation.
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:

Caron, D. A., M.-E. Garneau, et al. (2009). "Harmful algae and their potential impacts on desalination operations off southern California." Water Research In press. pdf
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. pdf
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
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. pdf
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
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


  • Caron Laboratory
  • University of Southern California
  • 3616 Trousdale Parkway, AHF 301
  • Los Angeles, CA 90089-0371