IV. Publications
Tintinnids
Bachy, C., Gomez, F., Lopez-Garcia, P., Dolan, J.R., Moreira, D. 2012. Molecular phylogeny of Tintinnid Ciliates (Tintinnida, Ciliophora). Protist, 6:873-887. PDF
Bachy, C., Dolan, J.R., López-García, P., Deschamps, P., Moreira, D. 2013. Accuracy of protist diversity assessments: morphology compared to cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study. ISME Journal 7:244-255 . PDF
Bachy, C., Morira, D., Dolan, J.R., Lopez-Garcia, P. 2014. Seasonal dynamics of free-living tintinnid ciliate communities revealezs by environmental sequences from the North-West Mediterranean Sea. FEMS Microbiology Ecology, 87:330-342. PDF
Dolan, J.R. 2010. Morphology and ecology in tintinnid ciliates of the marine plankton: correlates of lorica dimensions. Acta Protozoologica, 49: 235-244. PDF
Dolan, J.R. 2012. Tintinntinid Ciliates: an Introduction and Overview. in Biology and Ecology of Tintinnid Ciliates: Models for Marine Plankton, Dolan, J.R., Agatha, S., Coats, D.W., Montagnes, D.J.S., Stocker, D.K. (eds). Wiley-Blackwell, Oxford, pp 1-16 . PDF
Dolan, J.R., Pierce, RW. 2012. Diversity and Distributions of Tintinnid Ciliates. in Biology and Ecology of Tintinnid Ciliates: Models for Marine Plankton, Dolan, J.R., Agatha, S., Coats, D.W., Montagnes, D.J.S., Stocker, D.K. (eds). Wiley-Blackwell, Oxford, pp 214-243. PDF
Dolan, J.R., Pierce, RW. 2014. Tintinnid ciliates of the marine plankton. in Biogeographic Atlas of the Southern Ocean, De Broyer C. et al. (eds.). Scientific Committee on Antarctic Research, Cambridge, pp. 254-259. PDF
Dolan, J.R, Stoeck, T. 2011. Repeated sampling reveals differential variability in measures of species richness and community composition in planktonic protists. Environmental Microbiology Reports, 3:661-666. PDF
Dolan, J.R., Ritchie, M.E., Tunin-Ley, A., Pizay, M.-D. 2009. Dynamics of core and occasional species in the marine plankton: tintinnid ciliates of the N.W. Mediterranean Sea. Journal of Biogeography, 36:887-895. PDF
Dolan J.R., Pierce, R.W., Yang, E.J., Kim, S.Y. 2012. Southern Ocean biogeography of tintinnid ciliates of the marine plankton. Journal of Eukaryotic Microbiology, 59: 511-519. PDF
Dolan, J.R., Landry, M.R., Ritchie, M.E. 2013. The species-rich assemblages of tintinnids (marine planktonic protists) are structured by mouth size. ISME Journal, 7: 244-255. PDF
Dolan, J.R., Yang, E.J., Lee, S. H., Kim, S.Y. 2013. Tintinnid ciliates of the Amundsen Sea (Antarctica) Plankton Communities. Polar Research 32: 19784. PDF
Kim, S.Y., Choi, J.K., Dolan, J.R., Shin, H.C., Lee, S., Yang, E.J. 2013. Morphological and Ribosomal DNA-based Characterization of Six Antarctic Ciliate Morphopecies from the Amundsen Sea with Phylogenetic Analyses. Journal of Eukaryotic Microbiology, 60:497-513. PDF
Dolan, J.R., Yang, E.J., Kim, T.W., Kang, S.-H. 2014. Microzooplankton in a Warming Arctic: A comparison of tintinnids and radiolarians from summer 2011 and 2012 in the Chukchi Sea. Acta Protozoologica 53:101-113. PDF
Dolan, J.R., Pierce, R.W., Bachy, C. 2014. Cyttarocylis ampulla, a polymorphic ciliate of the marine plankton. Protist 165: 66-80. PDF
Ceratium
Gomez, F., Moreira, D., Lopez-Garcia, P. 2009. Neoceratium gen. nov., a new genus for all marine species currently assigned to Ceratium (Dinophyceae). Protist, 161:35-54. PDF
Lasternas, S., Tunin-Ley, A., Ibanez, F., Andersen, V., Pizay, M.-D., Lemée, R. 2011. Short-term dynamics of microphytoplankton abundance and diversity in NW Mediterranean Sea during late summer condition (DYNAPROC 2 Cruise; 2004). Biogeosciences 8:743-761. PDF
Pizay, M.-D., Lemeé, R., Simon, N., Cras, A.-L., Laugier, J.-P., Dolan, J.R. 2009. Night and day morphologies in a planktonic dinoflagellate. Protist, 160:565-575. PDF
-> Editors' Choice Science: 'Fingers or Toes?' (17 July 2009) 325: 247. PDF
Tunin-Ley, A., Ibanez, F., Labat, J.P., Zingone, A., Lemée R. 2009. Phytoplankton biodiversity and climate change in NW Mediterranean Sea: changes in dinoflagellate genus Ceratium over the last century. Marine Ecology Progress Series, 375:85-90. PDF
Tunin-Ley A., Lemée, R. The genus Neoceratium (planktonic dinoflagellates) as a potential indicator of ocean warming. Microorganisms 1: 58-78. PDF
Ceratium & Tintinnids
Andersen, V., Goutx, M,. Prieur, L., Dolan, J.R. 2009. Short-scale temporal variability of physical, biological and biogeochemical processes in the NW Mediterranean Sea: an introduction. Biogeosciences, 6:453-461. PDF
Raybaud, V., Tunin-Ley, A., Ritchie, M. E., Dolan, J.R. 2009. Similar patterns of community organization characterize distinct groups of different trophic levels in the plankton of the NW Mediterranean Sea. Biogeosciences, 6:431-438. PDF
Dolan, J.R. 2011. The legacy of the last cruise of the Carnegie: a lesson in the value of dusty old taxonomic monographs. Journal of Plankton Research, 33: 1317-1324. PDF
-> Editors' Choice Science: 'Carnegie blows up biodiversity' (8 July 2011) 333:137. PDF
Syndiniales & other parasites
Alves-de-Souza, C., Cornet, C., Nowaczyk, A., Gasparini, S., Skovgaard, A., Guillou, L. 2011. Blastodinium spp. infect copepods in the ultra-oligotrophic marine waters of the Mediterranean Sea. Biogeosciences 8: 2125-2136. PDF
Alves-de-Souza, C., Varela, D., Iriarte, J.L., Gonzalez, H.E., Guillou, L. 2012. Infection dynamics of Amoebophryidae parasitoids on harmful dinoflagellates in a southern Chiliean fjord dominated by diatoms. Aquatic Microbial Ecology, 66: 183-197. PDF
Bachvaroff, T.R., Kim, S., Guillou, L., Delwiche, C.F., Coats, D.W. 2012. Molecular Diversity of the syndinean genus Euduboscquella based on single-cell PCR analysis. Applied and Environmental Microbiology, in press. PDF
Chambouvet, A., Morin, P., Marie, D., Guillou, L. 2008. Control of toxic marine dinoflagellate blooms by serial parasitic killers. Science, 322: 1254-1257. PDF
Chambouvet A., Alves-de-Souza C., Cueff, V., Marie D., Karpov S., Guillou L. 2011. Interplay between the parasite Amoebophrya sp. (Alveolata) and the cyst formation of the red tide dinoflagellate Scrippsiella trochoidea. Protist. 162:637-649. PDF
Chambouvet, A., Laabir, M., Sengco, M., Vaquer, A., Guillou, L. 2011. Genetic diversity of Amoebophryidae (Syndiniales) during Alexandrium catenella/tamarense (Dinophyceae) blooms in the Thau lagoon (Mediterranean Sea, France). Research in Microbiology, 9: 959-968. PDF
Coats, D.W., Kim, S., Bachvaroff, T.R., Handy, S.M., Delwich, C.F. 2010. Tintinnophagus acutus n. g., n. sp. (Phylum Dinoflagellata), an ectoparasite of the ciliate Tintinnopsis cylindrica Daday 1887, and its relationship to Duboscquodinium collini Grassé 1952. Journal of Eukaryotic Microbiology, 57: 468-482. PDF
Gomez, F., Lopez-Garcia, P., Nowaczyk, A., Moreira, D. 2009. The crustacean parasites Ellobiopsis Caullery, 1910 and Thalassomyces Niezabitowski, 1913 form a monophyletic divergent clade within the Alveolata. Systematic Parasitology, 74:65-74. PDF
Guillou, L., Viprey, M., Chambouvet, A., Welsh, R.M., Kirkham, A.R., Massana, R., Scanlan, D.J., Worden, A.Z. 2008. Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environmental Microbiology, 10: 3349-3365. PDF
Guillou L., Alves-de-Souza C., Siano R., Gonzalez H. 2010. The ecological significance of small eukaryotic parasites in marine systems. Microbiology Today. May, 2010: 93-95. PDF
Jacquet, S., Domaizon, I., Masquelier, S., Lepère, C., Guillou, L., Chambouvet, A., Debroas, D., Sime-Ngando, T. 2011. Virus, bactéries et protistes pathogènes Le rôle insoupçonné des parasites dans le fonctionnement des écosystèmes aquatiques. Courrier de l'Environnement de l'INRA n°60: 33-46. PDF
Montagnes, D.J.S., Chambouvet, A., Guillou, L., Fenton, A. 2008. Responsibility of microzooplankton and parasite pressure for demise of toxic dinoflagellate blooms. Aquatic Microbial Ecology, 53: 211-225. PDF
Siano, R., Alves-de-Souza, C., Foulon, E., Bendif, El M., Simon, N., Guillou, L., Not, F. Distribution and host diversity of Amoebophryidae parasites across oligotrophic waters of the Mediterranean Sea. 2011. Biogeosciences, 8:267-278. PDF
Micromonas
Foulon, E., Not, F., Jalabert, F., Caroiu, T., Massana, R., Simon, N. 2008. Ecological niche partitioning in the picoplanktonic green algae Micromonas pusilla: evidence from environmental surveys using phylogenetic probes. Environmental Microbiology, 10: 2433-2443 .PDF
Bio-Informatics
Stoeck, T., Behnke, A., Christen, R., Amaral-Zettler, L., Rodriquez-Mora, M.J., Chistoserdov, A., Orsi, W., Edgcomb,V.P. 2009. Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities. BMC Biology, 7:72. PDF
Chevenet, F., Croce, O., Hebrard, M., Christen, R. 2010. ScripTree: scripting phylogentic graphics. Bioinformatics, 26:1125-1126. PDF
Edgcomb, V., Orsi, W., Bunge, J., Jeon, S., Christen, R., Leslin, C., Holder, M., Taylor, G.T., Suarez, P. Varela, R., Epstein, S. 2011. Protistan microbial observatory in the Cariaco Basin, Caribbean. 1. Pyrosequencing vs Sanger insights into species richness. ISME, 5: 1344-1356. PDF
Pawlowski, J., Christen, R., Lecroq, B., Bachar, D., Shahbazkia, H.R., Amaral-Ettler, L., Guillou, L. 2011. Eukaryotic richness in the abyss: insights from pyrotag sequencing. PLoS ONE 6: e18169. doi:10.1371/journal.pone.0018169. PDF
Lecroq, B., Lejzerowicz, F., Bachar, D., Christe, R., Esling, P., Baerlocher, L., Østeras, M., Farinelli, L., Pawlowski, J. 2011. Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments. Proceedings of the National Academy of Sciences, 108:13177-13182. PDF
Chemidlin Prévost-Bouré, N., Christen R., Dequiedt S., Mougel C., Lelièvre M., Jolivet, C., Shahbazkia, H.R., Guillou, L. Arrouays, D. 2011. Validation and Application of a PCR Primer Set to Quantify Fungal Communities in the Soil Environment by Real-Time Quantitative PCR. PLoS ONE 6: e24166. doi:10.1371/journal.pone.0024166 PDF
Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C., Burgaud, G., de Vargas, C., Decelle, J., del Campo, J., Dolan, J.R., Dunthorn, M., Edvardsen, B., Holzman, M., Kooistra, W. H. C. F., Lara, E., Le Bescot, N., Logares, R., Mahé, F., Massana, R., Montresor, M., Morad, R., Not, F., Pawlowski, J., Probert, I., Sauvadet, A.-L., Siano, R., Stoeck, T., Vaulot, D., Zimmermann, P., Christen, R. 2012. The Protist Ribosomal Reference database (PR2 : a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Research, in press. doi: 10.1093/nar/gks1160
Pernice, M.C., Logares, R., Guillou, L., Masssana, R. 2013. General patterns of diversity in major marine microeukaryotic lineages. PLoS ONE 8: e57170. doi:10.1371/journal.pone.0057170. PDF
Prévost-Bouré, N.C., Christen, R., Dequiedt, S., Mougel, C., Lelièvre, M., Jolivet, C., Shahbazkia, H.R., Guillou, L., Arrouays, D., Ranjard, L. 2011. Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR. PLoS ONE 6: e24166. PDF
Bachar, D., Guillou, L. Christen, R. 2013. Detection of introns in eukaryotic small subunit ribosomal RNA gene sequences. Dataset Papers in Biology, Volume 2013, Article ID 854869. PDF
General Plankton Biodiversity
Bachy, C., Lopez-Garcia, P., Vereshchaka, A., Moreira, D. 2011. Diversity and vertical distribution of microbial eukaryotes in the snow, sea ice and seawater near the North Pole at the end of the polar night. Frontiers in Microbiology 2: Article 106. PDF
Cohu, S., Thibault, T., Mangialo, L., Labat, J.-P., Passafiume, O., Blanfuné, A., Simon, N., Cottalorda, J.-M., Lemée, R. 2011. Occurrence of the toxic dinoflagellate Ostreopsis cf. ovata in relation with environmental factors in Monaco (NW Mediterranean). Marine Pollution Bulletin, 62:2681-2691. PDF
Dolan, J.R., Coats, D.W. 2008. Physiological diversity in widely distributed microzooplankton: Digestion in the ciliate Euplotes vannus. in 'Microbial Ecology Research Trends ', T. Van Dijk (ed), Nova Biomedical, pp 207-220. PDF
Dolan, J.R., Mostajir, B., Sime-Ngando, T. 2009. Rassoulzadegan in Villefranche-sur-Mer and the 'evolution' of marine microbial ecology over three decades. Aquatic Microbial Ecology, 57:221-225. PDF
Simon, N., Cras, A.-L., Foulon, E., Lemée, R. 2009. Diversity and evolution of marine phytoplankton. Comptes Rendus Biologies, 332:159-170. PDF
Gómez, F. 2010.Changes in the Mediteranean phytoplankton community related to climate warming. in "Phytoplankton responses to Mediterranean environmental changes", N° 40, CIESM Workshop Monographs, (F. Briend, Ed.), CIEMS, Monaco, pp. 37-42. PDF
Gómez, F. 2010. Diversity and distribution of Noctilucoid dinoflagellates (Noctilucales, Dinophyceae) in the open Mediterranean Sea. Acta Protozoologica 49:365-372. PDF
Gómez, F., Lopez-Garcia, P., Moreira, D. 2009. Molecular phylogeny of the ocelloid-bearing dinoflagellates Erythropsidinium and Warnowia (Warnowiaceae, Dinophyceae). Journal of Eukaryotic Microbiology, 56:440-445. PDF
Gómez, F., Lopez-Garcia, P., Moreira, D. 2009. Life cycle and molecular phylogeny of the dinoflagellates Chytriodinium and Dissodinium, ecto parasites of copepod eggs. European Journal of Protistology, 45:260-270. PDF
Gómez, F., Moreira D. & López-García P. 2010. Molecular phylogeny of the dinoflagellates Podolampas and Blepharocysta (Peridiniales, Dinophyceae). Phycologia, 49: 212-220. PDF
Gómez, F., Moreira D. & López-García P. 2010. Molecular Phylogeny of Noctilucid Dinoflagellates (Noctilucales, Dinophyceae). Protist, 161: 466-478. PDF
Gomez, F., Moreira, D., Benzerara, Lopez-Garcia, P. 2011.Solenicola setigera is the first characterized member of the abundant and cosmopolitan uncultured marine stramenopile group MAST-3. Environmental Microbiology, 13: 193-202. PDF
Gómez, F., Moreira D. & López-García P. 2011.Molecular phylogeny of dinophysoid dinoflagellates: the systematic position of Oxyphysis oxytoxoides and the Dinophysis hastata group (Dinophysiales, Dinophyceae). Journal of Phycology,47: 393-406.
Gómez, F., Moreira D. & López-García P. 2011. Molecular phylogeny of the sand-dwelling dinoflagellates Amphidiniopsis hirsuta and A. swedmarkii (Peridiniales, Dinophyceae). Acta Protozoologica 50: 255-262.
Gómez, F., Moreira, D., Lopez-Garcia, P. 2011. Avances en el estudio de los dinoflagelados (dinophyceae) con la filogenia molecular. Hidrobiologica 21: 343-364. PDF
Gómez, F., Moreira D. & López-García P. 2012. Sinophysis and Pseudophalacroma are distantly related to typical dinophysoid dinoflagellates (Dinophysales, Dinophyceae). Journal of Eukaryotic Microbiology, 58:188-190. PDF
Gómez, F., Lopez-Garcia, P., Dolan, J.R., Moreira, D. 2012. Molecular phylogeny of the marine dinoflagellate genus Heterodinium (Dinophyceae). European Journal of Phycology, 47:95-104. PDF
Lombard, F., D. Eloire, A. Gobet, L. Legendre, L. Stemmann, J. R. Dolan, A. Sciandra, Gorsky, G. 2010. Experimental and modeling evidence of appendicularian-ciliate interactions. Limnology and Oceanography, 55:77-90. PDF
Misc.
Dolan, J.R. 2013. Doing a Protist Book. Protist, 164:154-159. PDF
Dolan, J.R. 2014. The history of biological exploration of the Bay of Villefranche. Protist 165: 636-644. PDF
V. Presentations
Genetic Variability and molecular phylogeny of the genus Ceratium (phytoplanktonic dinoflagellates) from Ligurian Sea inferred from single-cell analysis of ITS rDNA sequences. Cras, A.-L., Gordon Research Conference Marine Microbes, Lucca, Italy, July 2008. Poster - Abstract PDF
Assessement of short-term temporal variability in the community structure of tintinnids, planktonic ciliates of the microzooplankton. Dolan, J.R., Tunin-Ley, A., Pizay, M.-D., Ritchie, M.E. 2008. Ocean Sciences Meeting, Orlando Fl, March 2008. Abstract - Abstract PDF
Regime shifts and species lists: Changes in the Black Sea reflected in species records of the microzooplankton. Dolan, J.R. World Conference on Marine Biodiversity, Valencia, Spain, November 2008. Abstract - Abstract PDF
Mesopelagic microbial loop: its diversity and function. Tanka, T., Rassoulzadegan, F.IMBER-IMBiZO, Integrating Biogeochemistry and Ecosystems in a Changing Ocean. Miami, FL, November 2008. Abstract - Abstract PDF
Amoebophryidae (Syndiniales), an important parasitoid group for dinoflagellates. Chambouvet, A., Guillou, L. ASLO Aquatic Sciences Meeting, Nice, France January 2009. Abstract PDF
Genetic variability and molecular phylogeny of the genus Ceratium (planktonic dinoflagellates) inferred from single-cell analysis of its rDNA sequences. Cras, A.-L., Bailly, X., Simon, N., Lemée, R. ASLO Aquatic Sciences Meeting, Nice, France January 2009. Abstract - Abstract Abstract PDF
Similar patterns of community organization characterize groups of different trophic levels in the plankton of the NW Mediterranean Sea. Dolan, J.R., Ritchie, M.E., Raybaud, V., Tunin -Ley, A. ASLO Aquatic Sciences Meeting, Nice, France January 2009. Abstract - Abstract PDF
Comparing ciliate community structure in the East and West (A vs. C). Dolan, J.R. BOUM Post-cruise Meeting, Marseille, France, June 2009.
Infection of copepods by the parasitic photosynthetic dinoflagellate Blastodinium during the BOUM cruise. Guillou, L. BOUM Post-cruise Meeting, Marseille, France, June 2009.
Diversity and vertical distribution of microbial eukaryotes in the snow, sea ice and marine waters from North Pole. Bachy, C., Lopez-Garcia, P. Moreira, D., Vereshchaka, A. 11th Symposium on Aquatic Microbial Ecology, 30 August - 4 September 2009, Piran, Solvenia. Abstract PDF
Coherent species packing of planktonic protists: Tintinnid ciliates of the oligotrophic Mediterranean Sea. Dolan, J.R., Ritchie, M. 2010 AGU-ASLO-TOC Ocean Sciences Meeting, Portland OR, USA, Febuary 2010. Abstract PDF
Interplay between the marine parasite Amoebophrya (Syndiniales) survival and the sexuality of its host (Scrippsiella trochoidea, Dinoflagellate). Guillou, L., Chambouvet, A. 2010 AGU-ASLO-TOC Ocean Sciences Meeting, Portland OR, USA, Febuary 2010.
Stars, co-stars and understudies in planktonic protist communities: an analysis of niche separation among species in the tintinnid ciliate community of the Bay Villefranche (NW Mediterranean Sea). Dolan, J.R. International Society of Protistologists - British Society for Protist Biology Joint Meeting, Canterbury, UK, July 2010. Abstract PDF
Merging molecular phylogeny and classical taxonomy of tintinnid ciliates. Bachy, C., Gomez, F., Dolan, J., Moreira, D., Lopez-Garcia, P. International Society of Protistologists - British Society for Protist Biology Joint Meeting, Canterbury, UK, July 2010. Abstract PDF
The challenge of understanding ecological roles and diversity in heterotrophic protists of the plankton. Dolan, J.R. ANR/ARP meeting- Combining high throughput genomics, quantitative imaging, in situ oceanographic and satellite data and modeling to better understand plankton ecosystems at the planetary level. Villefranche-sur-Mer, January 2011. PowerPoint file
Niche separation and the role of dominants among tintinnid ciliates, grazers of the microzooplankton. Dolan, J.R. ASLO 2011 Aquatic Sciences Meeting, San Juan, PR, Feb. 2011. Abstract PDF
Similarity in widely separated communities of planktonic protists (tintinnid ciliates). Dolan, J.R. VI European Congress of Protistology, Berlin, July 2011. Abstract PDF
Morphological versus molecular-based diversity surveys of planktonic microbial eukaryotes: the case of tintinnid ciliates. Bachy, C., Lopez-Garcia, P., Dolan, J. Moreira, D. The 12th Symposium on Aquatic Microbial Ecology, Rostock, August 2011. Abstract PDF
Using Old Data to Examine Current Questions: The Last Voyage of the Carnegie. Dolan, J.R. 1st Asian Congress of Protistology (ACOP 2011), Jeju, Korea, October 2011. Abstract PDF
VI. Workshops
Resolving Species in Marine Protists. December 4-5, Observatoire Océanologique de Villefranche-sur-Mer. Program - PDF
Parasites and Symbionts in the Rade de Villefranche. August 31 - Sept 11 2009.
VII. Posters
Planktonic Protist Biodiversity - High Resolution PowerPoint File
Biodiversité des Protistes planctoniques - fichier PowerPoint haut resolution
VIII. Final Project Report PDF
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