@article {mertens_morpho-molecular_2023, title = {Morpho-molecular analysis of podolampadacean dinoflagellates (Dinophyceae), with the description of two new genera}, journal = {Phycologia}, year = {2023}, note = {Publisher: Taylor \& Francis _eprint: https://doi.org/10.1080/00318884.2022.2158281}, month = {feb}, pages = {1{\textendash}19}, abstract = {Sequences were obtained for 58 podolampadacean single cells from France, Reunion Island (French territories) and Japan (6 SSU rDNA only, 40 SSU+LSU and 12 LSU only). The sequenced taxa belong to five of the eight described genera: Podolampas, Blepharocysta, Lissodinium, Gaarderiella and Mysticella. Two new genera, Alatosphaera and Pseudalatosphaera, were erected to accommodate {\textquoteleft}Blepharocysta{\textquoteright} hermosillae and {\textquoteleft}Blepharocysta{\textquoteright} denticulata. Most genera are well supported by concatenated LSU{\textendash}SSU rDNA phylogenies, with the least support for Lissodinium. Metabarcoding of podolampadaceans using the V4 region of SSU rDNA showed a resolution too low to discriminate genera or species. Roscoffia and Cabra are here considered podolampadaceans, whilst Lessardia is considered to belong in a separate family. The relationship of Rhinodinium to the Podolampadaceae needs further study. Desmoschisis was recorded for the first time in Alatosphaera and Pseudalatosphaera. Several ribotypes need further study to attribute a species name to them.}, keywords = {Alatosphaera, Blepharocysta, desmoschisis, Gaarderiella, Lissodinium, LSU rDNA, Mysticella, Podolampas, Pseudalatosphaera, SSU rDNA}, issn = {0031-8884}, doi = {10.1080/00318884.2022.2158281}, url = {https://doi.org/10.1080/00318884.2022.2158281}, author = {Mertens, Kenneth Neil and Carbonell-Moore, M. Consuelo and Chom{\'e}rat, Nicolas and Bilien, Gwenael and Boulben, Sylviane and Guillou, Laure and Romac, Sarah and Probert, Ian and Ishikawa, Akira and N{\'e}zan, Elisabeth} } @article {schmitt_temperature_2022, title = {Temperature Affects the Biological Control of Dinoflagellates by the Generalist Parasitoid Parvilucifera rostrata}, journal = {Microorganisms}, volume = {10}, number = {2}, year = {2022}, note = {Number: 2 Publisher: Multidisciplinary Digital Publishing Institute}, pages = {385}, abstract = {The increase in emerging harmful algal blooms in the last decades has led to an extensive concern in understanding the mechanisms behind these events. In this paper, we assessed the growth of two blooming dinoflagellates (Alexandrium minutum and Heterocapsa triquetra) and their susceptibility to infection by the generalist parasitoid Parvilucifera rostrata under a temperature gradient. The growth of the two dinoflagellates differed across a range of temperatures representative of the Penz{\'e} Estuary (13 to 22 {\textdegree}C) in early summer. A. minutum growth increased across this range and was the highest at 19 and 22 {\textdegree}C, whereas H. triquetra growth was maximal at intermediate temperatures (15{\textendash}18 {\textdegree}C). Interestingly, the effect of temperature on the parasitoid infectivity changed depending on which host dinoflagellate was infected with the dinoflagellate responses to temperature following a positive trend in A. minutum (higher infections at 20{\textendash}22 {\textdegree}C) and a unimodal trend in H. triquetra (higher infections at 18 {\textdegree}C). Low temperatures negatively affected parasitoid infections in both hosts (i.e., {\textquotedblleft}thermal refuge{\textquotedblright}). These results demonstrate how temperature shifts may not only affect bloom development in microalgal species but also their control by parasitoids.}, keywords = {dinoflagellate blooms, functional response, parasitic control, RCC2800, RCC2823, RCC2982, RCC3018, RCC4398, temperature effect}, issn = {2076-2607}, doi = {10.3390/microorganisms10020385}, url = {https://www.mdpi.com/2076-2607/10/2/385}, author = {Schmitt, Matthew and Telusma, Aaron and Bigeard, Estelle and Guillou, Laure and Alves-de-Souza, Catharina} } @article {long_dinophyceae_2021, title = {Dinophyceae can use exudates as weapons against the parasite Amoebophrya sp. (Syndiniales)}, journal = {ISME Communications}, volume = {1}, number = {1}, year = {2021}, note = {Bandiera_abtest: a Cg_type: Nature Research Journals Number: 1 Primary_atype: Research Publisher: Nature Publishing Group Subject_term: Microbial ecology;Plant ecology;Water microbiology Subject_term_id: microbial-ecology;plant-ecology;water-microbiology}, pages = {1{\textendash}10}, abstract = {Parasites in the genus Amoebophrya sp. infest dinoflagellate hosts in marine ecosystems and can be determining factors in the demise of blooms, including toxic red tides. These parasitic protists, however, rarely cause the total collapse of Dinophyceae blooms. Experimental addition of parasite-resistant Dinophyceae (Alexandrium minutum or Scrippsiella donghaienis) or exudates into a well-established host-parasite coculture (Scrippsiella acuminata-Amoebophrya sp.) mitigated parasite success and increased the survival of the sensitive host. This effect was mediated by waterborne molecules without the need for a physical contact. The strength of the parasite defenses varied between dinoflagellate species, and strains of A. minutum and was enhanced with increasing resistant host cell concentrations. The addition of resistant strains or exudates never prevented the parasite transmission entirely. Survival time of Amoebophrya sp. free-living stages (dinospores) decreased in presence of A. minutum but not of S. donghaienis. Parasite progeny drastically decreased with both species. Integrity of the dinospore membrane was altered by A. minutum, providing a first indication on the mode of action of anti-parasitic molecules. These results demonstrate that extracellular defenses can be an effective strategy against parasites that protects not only the resistant cells producing them, but also the surrounding community.}, keywords = {microbial ecology, Plant ecology, rcc, RCC1627, RCC4383, RCC4714, RCC749, Water microbiology}, issn = {2730-6151}, doi = {10.1038/s43705-021-00035-x}, url = {http://www.nature.com/articles/s43705-021-00035-x}, author = {Long, Marc and Marie, Dominique and Szymczak, Jeremy and Toullec, Jordan and Bigeard, Estelle and Sourisseau, Marc and Le Gac, Micka{\"e}l and Guillou, Laure and Jauzein, C{\'e}cile} } @article {geffroy_sxta4_2021, title = {From the sxtA4 Gene to Saxitoxin Production: What Controls the Variability Among Alexandrium minutum and Alexandrium pacificum Strains?}, journal = {Frontiers in Microbiology}, volume = {12}, year = {2021}, pages = {613199}, abstract = {Paralytic shellfish poisoning (PSP) is a human foodborne syndrome caused by the consumption of shellfish that accumulate paralytic shellfish toxins (PSTs, saxitoxin group). In PST-producing dinoflagellates such as Alexandrium spp., toxin synthesis is encoded in the nuclear genome via a gene cluster (sxt). Toxin production is supposedly associated with the presence of a 4th domain in the sxtA gene (sxtA4), one of the core genes of the PST gene cluster. It is postulated that gene expression in dinoflagellates is partially constitutive, with both transcriptional and post-transcriptional processes potentially co-occurring. Therefore, gene structure and expression mode are two important features to explore in order to fully understand toxin production processes in dinoflagellates. In this study, we determined the intracellular toxin contents of twenty European Alexandrium minutum and Alexandrium pacificum strains that we compared with their genome size and sxtA4 gene copy numbers. We observed a significant correlation between the sxtA4 gene copy number and toxin content, as well as a moderate positive correlation between the sxtA4 gene copy number and genome size. The 18 toxic strains had several sxtA4 gene copies (9{\textendash}187), whereas only one copy was found in the two observed non-toxin producing strains. Exploration of allelic frequencies and expression of sxtA4 mRNA in 11 A. minutum strains showed both a differential expression and specific allelic forms in the non-toxic strains compared with the toxic ones. Also, the toxic strains exhibited a polymorphic sxtA4 mRNA sequence between strains and between gene copies within strains. Finally, our study supported the hypothesis of a genetic determinism of toxin synthesis (i.e., the existence of several genetic isoforms of the sxtA4 gene and their copy numbers), and was also consistent with the hypothesis that constitutive gene expression and moderation by transcriptional and post-transcriptional regulation mechanisms are the cause of the observed variability in the production of toxins by A. minutum.}, keywords = {RCC2644, RCC2645, RCC3327, RCC4871, RCC4872, RCC4890, RCC7037, RCC7038, RCC7039}, issn = {1664-302X}, doi = {10.3389/fmicb.2021.613199}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2021.613199/full}, author = {Geffroy, Sol{\`e}ne and Lechat, Marc-Marie and Le Gac, Micka{\"e}l and Rovillon, Georges-Augustin and Marie, Dominique and Bigeard, Estelle and Malo, Florent and Amzil, Zouher and Guillou, Laure and Caruana, Amandine M. N.} } @article {Farhat2021, title = {Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp.}, journal = {BMC Biology}, year = {2021}, note = {Publisher: BMC Biology tex.mendeley-tags: RCC4383,RCC4398}, pages = {1{\textendash}21}, keywords = {Dinoflagellate, genome, Introner elements, Non-canonical introns, parasite, RCC4383, RCC4398}, doi = {10.1186/s12915-020-00927-9}, author = {Farhat, Sarah and Le, Phuong and Kayal, Ehsan and Noel, Benjamin and Bigeard, Estelle and Corre, Erwan and Maumus, Florian and Florent, Isabelle and Alberti, Adriana and Aury, Jean-Marc and Barbeyron, Tristan and Cai, Ruibo and Silva, Corinne Da and Istace, Benjamin and Labadie, Karine and Marie, Dominique and Mercier, Jonathan and Rukwavu, Tsinda and Szymczak, Jeremy and Tonon, Thierry and Alves-de-Souza, Catharina and Rouze, Pierre and de Peer, Yves Van and Wincker, Patrick and Rombauts, Stephane and Porcel, Betina M and Guillou, Laure} } @article {Cai2020, title = {Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach}, journal = {Scientific Reports}, volume = {10}, number = {1}, year = {2020}, note = {Publisher: Springer US tex.mendeley-tags: RCC1627,RCC1720,RCC3018,RCC3043,RCC3044,RCC3047,RCC3048,RCC3049,RCC3145,RCC3278,RCC3596,RCC4381,RCC4382,RCC4383,RCC4384,RCC4385,RCC4386,RCC4387,RCC4388,RCC4389,RCC4390,RCC4391,RCC4392,RCC4393,RCC4394,RCC4395,RCC4396,RCC4397,RCC4398,RCC4399,RCC4400,RCC4401,RCC4402,RCC4403,RCC4404,RCC4405,RCC4406,RCC4407,RCC4408,RCC4409,RCC4410,RCC4411,RCC4412,RCC4413,RCC4414,RCC4415,RCC4416,RCC4711,RCC4712,RCC4713,RCC4715,RCC4716,RCC4722,RCC4723,RCC4726,RCC4728,RCC4729,RCC4732,RCC4733,RCC4734,RCC5984,RCC5985,RCC5986,RCC5987,RCC5988,RCC5989,RCC5990,RCC5991,RCC5992,RCC5993,RCC5994,RCC5995,RCC5997,RCC5998,RCC5999,RCC6000,RCC6001,RCC6002,RCC6003,RCC6004,RCC6005,RCC6006,RCC6007,RCC6008,RCC6009,RCC6010,RCC6079,RCC6080,RCC6081,RCC6082,RCC6083,RCC6084,RCC6085,RCC6087,RCC6088,RCC6094,RCC6096,RCC6100,RCC6101,RCC6102,RCC6103,RCC6104,RCC6105,RCC6106,RCC6107,RCC6108,RCC6109,RCC6110,RCC6111,RCC6112,RCC6113,RCC6115,RCC6116,RCC6117,RCC6118,RCC6119,RCC6120,RCC6121}, month = {dec}, pages = {2531}, keywords = {RCC1627, RCC1720, RCC3018, RCC3043, RCC3044, RCC3047, RCC3048, RCC3049, RCC3145, RCC3278, RCC3596, RCC4381, RCC4382, RCC4383, RCC4384, RCC4385, RCC4386, RCC4387, RCC4388, RCC4389, RCC4390, RCC4391, RCC4392, RCC4393, RCC4394, RCC4395, RCC4396, RCC4397, RCC4398, RCC4399, RCC4400, RCC4401, RCC4402, RCC4403, RCC4404, RCC4405, RCC4406, RCC4407, RCC4408, RCC4409, RCC4410, RCC4411, RCC4412, RCC4413, RCC4414, RCC4415, RCC4416, RCC4711, RCC4712, RCC4713, RCC4715, RCC4716, RCC4722, RCC4723, RCC4726, RCC4728, RCC4729, RCC4732, RCC4733, RCC4734, RCC5984, RCC5985, RCC5986, RCC5987, RCC5988, RCC5989, RCC5990, RCC5991, RCC5992, RCC5993, RCC5994, RCC5995, RCC5997, RCC5998, RCC5999, RCC6000, RCC6001, RCC6002, RCC6003, RCC6004, RCC6005, RCC6006, RCC6007, RCC6008, RCC6009, RCC6010, RCC6079, RCC6080, RCC6081, RCC6082, RCC6083, RCC6084, RCC6085, RCC6087, RCC6088, RCC6094, RCC6096, RCC6100, RCC6101, RCC6102, RCC6103, RCC6104, RCC6105, RCC6106, RCC6107, RCC6108, RCC6109, RCC6110, RCC6111, RCC6112, RCC6113, RCC6115, RCC6116, RCC6117, RCC6118, RCC6119, RCC6120, RCC6121}, issn = {2045-2322}, doi = {10.1038/s41598-020-59524-z}, url = {http://dx.doi.org/10.1038/s41598-020-59524-z http://www.nature.com/articles/s41598-020-59524-z}, author = {Cai, Ruibo and Kayal, Ehsan and Alves-de-Souza, Catharina and Bigeard, Estelle and Corre, Erwan and Jeanthon, Christian and Marie, Dominique and Porcel, Betina M and Siano, Raffaele and Szymczak, Jeremy and Wolf, Matthias and Guillou, Laure} } @article {Kayal2020, title = {Dinoflagellate host chloroplasts and mitochondria remain functional during amoebophrya infection}, journal = {Frontiers in Microbiology}, volume = {11}, number = {December}, year = {2020}, note = {tex.mendeley-tags: RCC1627,RCC4398}, month = {dec}, pages = {1{\textendash}11}, abstract = {Dinoflagellates are major components of phytoplankton that play critical roles in many microbial food webs, many of them being hosts of countless intracellular parasites. The phototrophic dinoflagellate Scrippsiella acuminata (Dinophyceae) can be infected by the microeukaryotic parasitoids Amoebophrya spp. (Syndiniales), some of which primarily target and digest the host nucleus. Early digestion of the nucleus at the beginning of the infection is expected to greatly impact the host metabolism, inducing the knockout of the organellar machineries that highly depend upon nuclear gene expression, such as the mitochondrial OXPHOS pathway and the plastid photosynthetic carbon fixation. However, previous studies have reported that chloroplasts remain functional in swimming host cells infected by Amoebophrya . We report here a multi-approach monitoring study of S. acuminata organelles over a complete infection cycle by nucleus-targeting Amoebophrya sp. strain A120. Our results show sustained and efficient photosystem II activity as a hallmark of functional chloroplast throughout the infection period despite the complete digestion of the host nucleus. We also report the importance played by light on parasite production, i.e., the amount of host biomass converted to parasite infective propagules. Using a differential gene expression analysis, we observed an apparent increase of all 3 mitochondrial and 9 out of the 11 plastidial genes involved in the electron transport chains (ETC) of the respiration pathways during the first stages of the infection. The longer resilience of organellar genes compared to those encoded by the nucleus suggests that both mitochondria and chloroplasts remain functional throughout most of the infection. This extended organelle functionality, along with higher parasite production under light conditions, suggests that host bioenergetic organelles likely benefit the parasite Amoebophrya sp. A120 and improve its fitness during the intracellular infective stage.}, keywords = {amoebophrya, chloroplast, Dinoflagellate, frontiers in microbiology, frontiersin, kleptoplast, marine plankton, org, organelles, parasitism, RCC1627, RCC4398, www}, issn = {1664-302X}, doi = {10.3389/fmicb.2020.600823}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.600823/full}, author = {Kayal, Ehsan and Alves-de-Souza, Catharina and Farhat, Sarah and Velo-Suarez, Lourdes and Monjol, Joanne and Szymczak, Jeremy and Bigeard, Estelle and Marie, Dominique and Noel, Benjamin and Porcel, Betina M and Corre, Erwan and Six, Christophe and Guillou, Laure} } @article {Baumeister2020, title = {Identification to species level of live single microalgal cells from plankton samples with matrix-free laser/desorption ionization mass spectrometry}, journal = {Metabolomics}, volume = {16}, number = {3}, year = {2020}, note = {ISBN: 0123456789 Publisher: Springer US tex.mendeley-tags: RCC 4667,RCC1717,RCC2561,RCC2562,RCC3008,RCC5791,RCC6807,RCC6808,RCC6809,RCC6810,RCC6811,RCC6812,RCC6813,RCC6814,RCC6815,RCC6816,RCC6817,RCC6818,RCC6819,RCC6820,RCC6821}, month = {mar}, pages = {28}, keywords = {ionization high-, Live single-cell mass spectrometry, matrix-free laser desorption, Matrix-free laser desorption/ionization high-resol, Metabolic fingerprinting, Microalgal identification, RCC1717, RCC2561, RCC2562, RCC3008, RCC4667, RCC5791, RCC6807, RCC6808, RCC6809, RCC6810, RCC6811, RCC6812, RCC6813, RCC6814, RCC6815, RCC6816, RCC6817, RCC6818, RCC6819, RCC6820, RCC6821, resolution mass spectrometry, Spectral pattern matching, Spectrum similarity}, issn = {1573-3882}, doi = {10.1007/s11306-020-1646-7}, url = {https://doi.org/10.1007/s11306-020-1646-7 http://link.springer.com/10.1007/s11306-020-1646-7}, author = {Baumeister, Tim U H and Vallet, Marine and Kaftan, Filip and Guillou, Laure and Svato{\v s}, Ale{\v s} and Pohnert, Georg} } @article {Farhat2018, title = {Comparative time-scale gene expression analysis highlights the infection processes of two amoebophrya strains}, journal = {Frontiers in Microbiology}, volume = {9}, number = {October}, year = {2018}, note = {tex.mendeley-tags: RCC1627,RCC3596,RCC4383,RCC4398}, month = {oct}, pages = {1{\textendash}19}, keywords = {amoebophrya, Dinoflagellates, Gene Expression, infection, oxidative stress response, parasite, plankton, RCC1627, RCC3596, RCC4383, RCC4398, syndiniales}, issn = {1664-302X}, doi = {10.3389/fmicb.2018.02251}, url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.02251/full}, author = {Farhat, Sarah and Florent, Isabelle and Noel, Benjamin and Kayal, Ehsan and Da Silva, Corinne and Bigeard, Estelle and Alberti, Adriana and Labadie, Karine and Corre, Erwan and Aury, Jean-Marc and Rombauts, Stephane and Wincker, Patrick and Guillou, Laure and Porcel, Betina M.} } @article {Klouch2016, title = {Historical records from dated sediment cores reveal the multidecadal dynamic of the toxic dinoflagellate Alexandrium minutum in the Bay of Brest (France)}, journal = {FEMS Microbiology Ecology}, volume = {92}, number = {7}, year = {2016}, note = {tex.mendeley-tags: 2016,rcc,sbr?hyto$_\textrmd$ipo}, month = {jul}, pages = {fiw101}, abstract = {The multiannual dynamic of the cyst-forming and toxic marine dinoflagellate Alexandrium minutum was studied over a time scale of about 150 years by a paleoecological approach based on ancient DNA (aDNA) quantification and cyst revivification data obtained from two dated sediment cores of the Bay of Brest (Brittany, France). The first genetic traces of the species presence in the study area dated back to 1873 {\textpm} 6. Specific aDNA could be quantified by a newly-developed real-time PCR assay in the upper core layers, in which the germination of the species (in up to 17-19 year-old sediments) was also obtained. In both cores studied, our quantitative paleogenetic data showed a statistically significant increasing trend in the abundance of A. minutum ITS1 rDNA copies over time, corroborating three decades of local plankton data that have documented an increasing trend in the species cell abundance. By comparison, paleogenetic data of the dinoflagellate Scrippsiella donghaienis did not show a coherent trend between the cores studied, supporting the hypothesis of the existence of a species-specific dynamic of A. minutum in the study area. This work contributes to the development of paleoecological research, further showing its potential for biogeographical, ecological and evolutionary studies on marine microbes.}, keywords = {2016, rcc, sbr?hyto$_\textrmd$ipo}, issn = {1574-6941}, doi = {10.1093/femsec/fiw101}, url = {http://www.ncbi.nlm.nih.gov/pubmed/27162179 https://academic.oup.com/femsec/article-lookup/doi/10.1093/femsec/fiw101}, author = {Klouch, Khadidja Z and Schmidt, Sabine and Andrieux-Loyer, Fran{\c c}oise and Le Gac, Micka{\"e}l and Hervio-Heath, Dominique and Qui-Minet, Zujaila N and Qu{\'e}r{\'e}, Julien and Bigeard, Estelle and Guillou, Laure and Siano, Raffaele}, editor = {Laanbroek, Riks} } @article {Lu2016, title = {Transcriptomic profiling of Alexandrium fundyense during physical interaction with or exposure to chemical signals from the parasite Amoebophrya.}, journal = {Molecular ecology}, volume = {25}, number = {6}, year = {2016}, note = {tex.mendeley-tags: 2016,RCC3037}, pages = {1294{\textendash}307}, abstract = {Toxic microalgae have their own pathogens, and understanding the way in which these microalgae respond to antagonistic attacks may provide information about their capacity to persist during harmful algal bloom events. Here, we compared the effects of the physical presence of the parasite Amoebophrya sp. and exposure to waterborne cues from cultures infected with this parasite, on gene expression by the toxic dinoflagellates, Alexandrium fundyense. Compared with control samples, a total of 14,882 Alexandrium genes were differentially expressed over the whole-parasite infection cycle at three different time points (0, 6 and 96 h). RNA sequencing analyses indicated that exposure to the parasite and parasitic waterborne cues produced significant changes in the expression levels of Alexandrium genes associated with specific metabolic pathways. The observed upregulation of genes associated with glycolysis, the tricarboxylic acid cycle, fatty acid β-oxidation, oxidative phosphorylation and photosynthesis suggests that parasite infection increases the energy demand of the host. The observed upregulation of genes correlated with signal transduction indicates that Alexandrium could be sensitized by parasite attacks. This response might prime the defence of the host, as indicated by the increased expression of several genes associated with defence and stress. Our findings provide a molecular overview of the response of a dinoflagellate to parasite infection.}, keywords = {2016, Animals, Dinoflagellida, Dinoflagellida: genetics, Dinoflagellida: parasitology, Gene Expression Profiling, Harmful Algal Bloom, Host-Parasite Interactions, Metabolic Networks and Pathways, Microalgae, Microalgae: genetics, Microalgae: parasitology, Parasites, Parasites: chemistry, RCC3037, RNA, Sequence Analysis, Signal Transduction, Transcriptome}, issn = {1365-294X}, doi = {10.1111/mec.13566}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26841307}, author = {Lu, Yameng and Wohlrab, Sylke and Groth, Marco and Gl{\"o}ckner, Gernot and Guillou, Laure and John, Uwe} } @article {Stuken2015, title = {Paralytic shellfish toxin content is related to genomic sxtA4 copy number in Alexandrium minutum strains}, journal = {Frontiers in Microbiology}, volume = {6}, number = {May}, year = {2015}, note = {tex.mendeley-tags: 2015,rcc,sbr?hyto$_\textrmd$ipo}, pages = {1{\textendash}10}, abstract = {Dinoflagellates are microscopic aquatic eukaryotes with huge genomes and an unusual cell regulation. For example, most genes are present in numerous copies and all copies seem to be obligatorily transcribed. The consequence of the gene copy number (CPN) for final protein synthesis is, however, not clear. One such gene is sxtA, the starting gene of paralytic shellfish toxin (PST) synthesis. PSTs are small neurotoxic compounds that can accumulate in the food chain and cause serious poisoning incidences when ingested. They are produced by dinoflagellates of the genera Alexandrium, Gymnodium, and Pyrodinium. Here we investigated if the genomic CPN of sxtA4 is related to PST content in Alexandrium minutum cells. SxtA4 is the 4th domain of the sxtA gene and its presence is essential for PST synthesis in dinoflagellates. We used PST and genome size measurements as well as quantitative PCR to analyze sxtA4 CPN and toxin content in 15 A. minutum strains. Our results show a strong positive correlation between the sxtA4 CPN and the total amount of PST produced in actively growing A. minutum cells. This correlation was independent of the toxin profile produced, as long as the strain contained the genomic domains sxtA1 and sxtA4.}, keywords = {2015, Alexandrium, copy, copy number variation, Dinoflagellate, gene dosage, genome size, number variation, paralytic shellfish toxin, paralytic shellfish toxin (PST), pst, rcc, RCC?o?dd, saxitoxin, saxitoxin (STX), sbr?hyto$_\textrmd$ipo, stx, sxtA}, issn = {1664-302X}, doi = {10.3389/fmicb.2015.00404}, url = {http://journal.frontiersin.org/article/10.3389/fmicb.2015.00404}, author = {St{\"u}ken, Anke and Riob{\'o}, Pilar and Franco, Jos{\'e} and Jakobsen, Kjetill S. and Guillou, Laure and Figueroa, Rosa I.} } @article {Decelle2015, title = {PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy}, journal = {Molecular Ecology Resources}, volume = {15}, number = {6}, year = {2015}, note = {tex.mendeley-tags: 2015,macumba,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo}, pages = {1435{\textendash}1445}, abstract = {Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongo- ing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF data- base that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classifica- tion were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.}, keywords = {2015, MACUMBA, rcc, RCC?o?dd, SBR$_\textrmP$hyto$_\textrmD$IPO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo}, issn = {1755098X}, doi = {10.1111/1755-0998.12401}, url = {http://doi.wiley.com/10.1111/1755-0998.12401}, author = {Decelle, Johan and Romac, Sarah and Stern, Rowena F. and Bendif, El Mahdi and Zingone, Adriana and Audic, St{\'e}phane and Guiry, Michael D. and Guillou, Laure and Tessier, D{\'e}sir{\'e} and Le Gall, Florence and Gourvil, Priscillia and dos Santos, Adriana Lopes and Probert, Ian and Vaulot, Daniel and de Vargas, Colomban and Christen, Richard} } @article {Lepelletier2014a, title = {Dinomyces arenysensis gen. et sp. nov. (rhizophydiales, dinomycetaceae fam. nov.), a chytrid infecting marine dinoflagellates}, journal = {Protist}, volume = {165}, number = {2}, year = {2014}, note = {tex.mendeley-tags: 2014,macumba,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app}, pages = {230{\textendash}244}, abstract = {Environmental 18S rRNA gene surveys of microbial eukaryotes have recently revealed the diversity of major parasitic agents in pelagic freshwater systems, consisting primarily of chytrid fungi. To date, only a few studies have reported the presence of chydrids in the marine environment and a limited number of marine chytrids have been properly identified and characterized. Here, we report the isolation and cultivation of a marine chytrid from samples taken during a bloom of the toxic dinoflagellate Alexandrium minutum in the Arenys de Mar harbour (Mediterranean Sea, Spain). Cross-infections using cultures and natural phytoplankton communities revealed that this chytrid is only able to infect certain species of dinoflagellates, with a rather wide host range but with a relative preference for Alexandrium species. Phylogenetic analyses showed that it belongs to the order Rhizophydiales, but cannot be included in any of the existing families within this order. Several ultrastructural characters confirmed the placement of this taxon within the Rhizophydiales as well its novelty notably in terms of zoospore structure. This marine chytridial parasitoid is described as a new genus and species, Dinomyces arenysensis, within the Dinomycetaceae fam. nov.}, keywords = {2014, chytrid, Dinoflagellates, Dinomyces arenysensis, Fungi, MACUMBA, microbial parasitoids, rcc, RCC?o?dd, Rhizophydiales., SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?app}, doi = {10.1016/j.protis.2014.02.004}, url = {http://www.sciencedirect.com/science/article/pii/S1434461014000170}, author = {Lepelletier, Fr{\'e}d{\'e}ric and Karpov, Sergey A and Alacid, Elisabet and Le Panse, Sophie and Bigeard, Estelle and Garc{\'e}s, Esther and Jeanthon, Christian and Guillou, Laure} } @article {Guillou2013, title = {The protist ribosomal reference database (PR2): a catalog of unicellular eukaryote small SubUnit rRNA sequences with curated taxonomy}, journal = {Nucleic Acids Research}, volume = {41}, year = {2013}, note = {tex.mendeley-tags: 2013,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo}, pages = {D597{\textendash}D604}, keywords = {2013, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo}, doi = {10.1093/nar/gks1160}, author = {Guillou, Laure and Bachar, Dipankar and Audic, St{\'e}phane and Bass, David and Berney, Cedric and Bittner, Lucie and Boutte, Christophe and Burgaud, Gaetan and de Vargas, Colomban and Decelle, Johan and del Campo, Javier and Dolan, John and Dunthorn, Micah and Bente, Edvardsen and Holzmann, Maria and Kooistra, Wiebe H C F and Lara, Enrique and Lebescot, Noan and Logares, Ramiro and Mah{\'e}, Fr{\'e}d{\'e}ric and Massana, Ramon and Montresor, Marina and Morard, Raphael and Not, Fabrice and Pawlowski, Jan and Probert, Ian and Sauvadet, Anne-Laure and Siano, Raffaele and Stoeck, Thorsten and Vaulot, Daniel and Zimmermann, Pascal and Christen, Richard} } @article {Viprey2008, title = {Wide genetic diversity of picoplanktonic green algae (Chloroplastida) in the Mediterranean Sea uncovered by a phylum-biased PCR approach}, journal = {Environmental Microbiology}, volume = {10}, number = {7}, year = {2008}, note = {tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo}, pages = {1804{\textendash}1822}, abstract = {The genetic diversity of picoplanktonic (i.e. cells that can pass through a 3 mum pore-size filter) green algae was investigated in the Mediterranean Sea in late summer by a culture-independent approach. Genetic libraries of the 18S rRNA gene were constructed using two different primer sets. The first set is commonly used to amplify the majority of eukaryotic lineages, while the second was composed of a general eukaryotic forward primer and a reverse primer biased towards the phylum Chloroplastida. A total of 3980 partial environmental sequences were obtained: 1668 using the general eukaryotic primer set and 2312 using the Chloroplastida-biased primer set. Of these sequences, 65 (4\%) and 594 (26\%) belonged to the Chloroplastida respectively. A 99.5\% sequence similarity cut-off value allowed classification of these 659 Chloroplastida sequences into 74 different operational taxonomic units. A majority of the Chloroplastida sequences (99\%) belonged to the prasinophytes. In addition to the seven independent prasinophyte lineages previously described, we discovered two new clades (clades VIII and IX), as well as a significant genetic diversity at the species and subspecies levels, notably among the genera Crustomastix, Dolichomastix and Mamiella (Mamiellales), but also within Pyramimonas and Halosphaera (Pyramimonadales). Such diversity within prasinophytes has not previously been observed by cloning approaches, illustrating the power of using targeted primers for clone library construction. Prasinophyte assemblages differed especially in relation to nutrient levels. Micromonas and Ostreococcus were mainly recovered from mesotrophic areas, whereas Mamiella, Crustomastix and Dolichomastix were mostly detected in oligotrophic surface waters. Within genera such as Ostreococcus or Crustomastix for which several clades were observed, depth seemed to be the main factor controlling differential distribution of genotypes.}, keywords = {2008, rcc, sbr?hyto$_\textrmd$ipo}, author = {Viprey, Manon and Guillou, Laure and Ferr{\'e}ol, Martial and Vaulot, Daniel} } @article {Guillou2004, title = {Diversity of picoplanktonic prasinophytes assessed by direct nuclear SSU rDNA sequencing of environmental samples and novel isolates retrieved from oceanic and coastal marine ecosystems}, journal = {Protist}, volume = {155}, year = {2004}, note = {tex.mendeley-tags: 2004,rcc,sbr?hyto}, pages = {193{\textendash}214}, keywords = {2004, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto, SOMLIT}, doi = {10.1078/143446104774199592}, author = {Guillou, Laure and Eikrem, W and Chr{\'e}tiennot-Dinet, M.-J. and Le Gall, F and Massana, R and Romari, K and Pedr{\'o}s-Ali{\'o}, C and Vaulot, D} } @article {Latasa2004, title = {Pigment suites and taxonomic groups in Prasinophyceae}, journal = {Journal of Phycology}, volume = {40}, number = {6}, year = {2004}, note = {tex.mendeley-tags: 2004,rcc,sbr?hyto}, month = {dec}, pages = {1149{\textendash}1155}, keywords = {2004, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto}, issn = {00223646}, doi = {10.1111/j.1529-8817.2004.03136.x}, url = {http://doi.wiley.com/10.1111/j.1529-8817.2004.03136.x}, author = {Latasa, Mikel and Scharek, Renate and Gall, Florence Le and Guillou, Laure and Le Gall, F} }