%0 Journal Article %J Scientific Reports %D 2021 %T Bacteria enhance the production of extracellular polymeric substances by the green dinoflagellate Lepidodinium chlorophorum %A Roux, Pauline %A Siano, Raffaele %A Collin, Karine %A Bilien, Gwenael %A Sinquin, Corinne %A Marchand, Laetitia %A Zykwinska, Agata %A Delbarre-Ladrat, Christine %A Schapira, Mathilde %K RCC1489 %X High biomasses of the marine dinoflagellate Lepidodinium chlorophorum cause green seawater discolorations along Southern Brittany (NE Atlantic, France). The viscosity associated to these phenomena has been related to problems in oyster cultivation. The harmful effect of L. chlorophorum might originate from the secretion of Extracellular Polymeric Substances (EPS). To understand whether the EPS are produced by L. chlorophorum or its associated bacteria, or if they are a product of their interaction, batch cultures were performed under non-axenic and pseudo-axenic conditions for three strains. Maximum dinoflagellate cell abundances were observed in pseudo-axenic cultures. The non-sinking fraction of polymers (Soluble Extracellular Polymers, SEP), mainly composed of proteins and the exopolysaccharide sulphated galactan, slightly increased in pseudo-axenic cultures. The amount of Transparent Exopolymer Particles (TEP) per cell increased under non-axenic conditions. Despite the high concentrations of Particulate Organic Carbon (POC) measured, viscosity did not vary. These results suggest that the L. chlorophorum-bacteria interaction could have a detrimental consequence on the dinoflagellate, translating in a negative effect on L. chlorophorum growth, as well as EPS overproduction by the dinoflagellate, at concentrations that should not affect seawater viscosity. %B Scientific Reports %V 11 %P 1–15 %G eng %U http://www.nature.com/articles/s41598-021-84253-2 %R 10.1038/s41598-021-84253-2 %0 Journal Article %D 2021 %T Les Efflorescences de Lepidodinium chlorophorum au large de la Loire et de la Vilaine : Déterminisme et conséquences sur la qualité des masses d’eau côtières %A Schapira, Mathilde %A Roux, Pauline %A Andre, Coralie %A Mertens, Kenneth %A Bilien, Gwenael %A Terre Terrillon, Aouregan %A Le Gac-Abernot, Chantal %A Siano, Raffaele %A Quéré, Julien %A Bizzozero, Lucie %A Bonneau, Francoise %A Bouget, Jean-Francois %A Cochennec-Laureau, Nathalie %A Collin, Karine %A Fortune, Mireille %A Gabellec, Raoul %A Le Merrer, Yoann %A Manach, Soazig %A Pierre-Duplessix, Olivier %A Retho, Michael %A Schmitt, Anne %A Souchu, Philippe %A Stachowski-Haberkorn, Sabine %K ? No DOI found %K rcc %K RCC1489 %X Ce projet, organisé en trois actions, avait pour objectif de mieux évaluer les risques d’eaux colorées vertes se produisant sur le secteur côtier situé au large de la Loire et de la Vilaine, en termes (i) de fréquence de ces épisodes, (ii) d’abondance et (iii) de localisation des zones à risque. Action 1 : Amélioration du recensement des eaux vertes à L. chlorophorum Action 2 : Optimisation de l’estimation des abondances de L. chlorophorum Action 3 : Identification des zones à risque au large de la Loire et de la Vilaine. %G eng %U https://archimer.ifremer.fr/doc/00724/83598/ %0 Journal Article %J Scientific Reports %D 2020 %T Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach %A Cai, Ruibo %A Kayal, Ehsan %A Alves-de-Souza, Catharina %A Bigeard, Estelle %A Corre, Erwan %A Jeanthon, Christian %A Marie, Dominique %A Porcel, Betina M %A Siano, Raffaele %A Szymczak, Jeremy %A Wolf, Matthias %A Guillou, Laure %K RCC1627 %K RCC1720 %K RCC3018 %K RCC3043 %K RCC3044 %K RCC3047 %K RCC3048 %K RCC3049 %K RCC3145 %K RCC3278 %K RCC3596 %K RCC4381 %K RCC4382 %K RCC4383 %K RCC4384 %K RCC4385 %K RCC4386 %K RCC4387 %K RCC4388 %K RCC4389 %K RCC4390 %K RCC4391 %K RCC4392 %K RCC4393 %K RCC4394 %K RCC4395 %K RCC4396 %K RCC4397 %K RCC4398 %K RCC4399 %K RCC4400 %K RCC4401 %K RCC4402 %K RCC4403 %K RCC4404 %K RCC4405 %K RCC4406 %K RCC4407 %K RCC4408 %K RCC4409 %K RCC4410 %K RCC4411 %K RCC4412 %K RCC4413 %K RCC4414 %K RCC4415 %K RCC4416 %K RCC4711 %K RCC4712 %K RCC4713 %K RCC4715 %K RCC4716 %K RCC4722 %K RCC4723 %K RCC4726 %K RCC4728 %K RCC4729 %K RCC4732 %K RCC4733 %K RCC4734 %K RCC5984 %K RCC5985 %K RCC5986 %K RCC5987 %K RCC5988 %K RCC5989 %K RCC5990 %K RCC5991 %K RCC5992 %K RCC5993 %K RCC5994 %K RCC5995 %K RCC5997 %K RCC5998 %K RCC5999 %K RCC6000 %K RCC6001 %K RCC6002 %K RCC6003 %K RCC6004 %K RCC6005 %K RCC6006 %K RCC6007 %K RCC6008 %K RCC6009 %K RCC6010 %K RCC6079 %K RCC6080 %K RCC6081 %K RCC6082 %K RCC6083 %K RCC6084 %K RCC6085 %K RCC6087 %K RCC6088 %K RCC6094 %K RCC6096 %K RCC6100 %K RCC6101 %K RCC6102 %K RCC6103 %K RCC6104 %K RCC6105 %K RCC6106 %K RCC6107 %K RCC6108 %K RCC6109 %K RCC6110 %K RCC6111 %K RCC6112 %K RCC6113 %K RCC6115 %K RCC6116 %K RCC6117 %K RCC6118 %K RCC6119 %K RCC6120 %K RCC6121 %B Scientific Reports %V 10 %P 2531 %8 dec %G eng %U http://dx.doi.org/10.1038/s41598-020-59524-z http://www.nature.com/articles/s41598-020-59524-z %R 10.1038/s41598-020-59524-z %0 Journal Article %J Molecular Ecology %D 2018 %T Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network %A Meng, Arnaud %A Corre, Erwan %A Probert, Ian %A Gutierrez-Rodriguez, Andres %A Siano, Raffaele %A Annamale, Anita %A Alberti, Adriana %A Da Silva, Corinne %A Wincker, Patrick %A Le Crom, Stéphane %A Not, Fabrice %A Bittner, Lucie %K Genomics/Proteomics %K Microbial Biology %K Molecular Evolution %K Protists %K rcc1491 %K RCC1516 %K RCC3387 %K rcc3468 %K rcc3507 %K transcriptomics %X Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated to functional traits. With respect to toxicity, sequences homologous to those of proteins found in species with toxicity potential (e.g. sxtA4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of respectively the toxic and symbiotic species represented in our analyses. Of these, 56% and 57% respectively (i.e. 25,393 and 52,193 pCDs) completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization. This article is protected by copyright. All rights reserved. %B Molecular Ecology %P 0–2 %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/29624751%0Ahttp://doi.wiley.com/10.1111/mec.14579 %R 10.1111/mec.14579 %0 Journal Article %J Phycologia %D 2017 %T Adenoides sinensis , a new sand-dwelling dinoflagellate species from China and reexamination of A. eludens from an Atlantic strain %A Gu, Haifeng %A Li, Xintian %A Chomérat, Nicolas %A Luo, Zhaohe %A Sarno, Diana %A Gourvil, Priscillia %A Balzano, Sergio %A Siano, Raffaele %K 2017 %K rcc %K RCC1982 %K sbr?hyto$_\textrmd$ipo %X The sand-dwelling?1dinoflagellate generaAdenoidesandPseudadenoidesare morphologically very close butdistinct in their molecular phylogeny. We established three cultures by isolating single cells from sand samples collected inintertidal zones of Qingdao (Yellow Sea), Dongshan (South China Sea) and Brittany (English Channel, North Atlantic,France). Strain morphology was examined with light and scanning electron microscopy, and both large subunitribosomal DNA (LSU rDNA) and small subunit ribosomal DNA (SSU rDNA) sequences were amplified. Molecularphylogeny, corroborated by morphological examination showing the existence of a ventral pore, confirmed theidentification of the French strain (RCC1982) asAdenoides eludens. The Chinese strains differed fromAdenoides eludensin two additional posterior intercalary plates and differed fromPseudadenoidesin one additional apical plate having theplate formula of Po, Cp, X, 50,600, 4S, 5000, 5p, 10000or alternatively Po, Cp, X, 50,600, 5S, 5000, 3p, 20000. Maximumlikelihood and Bayesian inference carried out with concatenated LSU and SSU sequences demonstrated that the Chinesestrains were closely related but different fromA. eludensand, in corroboration with morphological evidence, supportedtheir classification as a distinct species,Adenoides sinensis sp. nov. Morphological and molecular results confirmed theclose relationship between the two generaAdenoidesandPseudadenoides. %B Phycologia %V 57 %P 1–13 %G eng %R 10.2216/17-76.1 %0 Journal Article %J Journal of Phycology %D 2017 %T Morphological and genetic diversity of Beaufort Sea diatoms with high contributions from the Chaetoceros neogracilis species complex %A Balzano, Sergio %A Percopo, Isabella %A Siano, Raffaele %A Gourvil, Priscillia %A Chanoine, Mélanie %A Marie, Dominique %A Vaulot, Daniel %A Sarno, Diana %E Wood, M. %K RCC1984 %K RCC1985 %K RCC1986 %K RCC1988 %K RCC1989 %K RCC1990 %K RCC1991 %K RCC1992 %K RCC1993 %K RCC1995 %K RCC1997 %K RCC1999 %K RCC2000 %K RCC2002 %K RCC2003 %K RCC2004 %K RCC2005 %K RCC2006 %K RCC2008 %K RCC2010 %K RCC2011 %K RCC2012 %K RCC2014 %K RCC2016 %K RCC2017 %K RCC2021 %K RCC2037 %K RCC2038 %K RCC2039 %K RCC2042 %K RCC2043 %K RCC2261 %K RCC2262 %K RCC2263 %K RCC2264 %K RCC2265 %K RCC2266 %K RCC2267 %K RCC2268 %K RCC2269 %K RCC2270 %K RCC2272 %K RCC2273 %K RCC2274 %K RCC2275 %K RCC2276 %K RCC2277 %K RCC2278 %K RCC2279 %K RCC2280 %K RCC2281 %K RCC2282 %K RCC2318 %K RCC2506 %K RCC2517 %K RCC2520 %K RCC2521 %K RCC2522 %X Seventy-five diatom strains isolated from the Beaufort Sea (Canadian Arctic) in the summer of 2009 were characterized by light and electron microscopy (SEM and TEM), as well as 18S and 28S rRNA gene sequencing. These strains group into 20 genotypes and 17 morphotypes and are affiliated with the genera Arcocellulus, Attheya, Chaetoceros, Cylindrotheca, Eucampia, Nitzschia, Porosira, Pseudo-nitzschia, Shionodiscus, Thalassiosira, and Synedropsis. Most of the species have a distribution confined to the northern/polar area. Chaetoceros neogracilis and Chaetoceros gelidus were the most represented taxa. Strains of C. neogracilis were morphologically similar and shared identical 18S rRNA gene sequences, but belonged to four distinct genetic clades based on 28S rRNA, ITS-1 and ITS-2 phylogenies. Secondary structure prediction revealed that these four clades differ in hemi-compensatory base changes (HCBCs) in paired positions of the ITS-2, suggesting their inability to interbreed. Reproductively isolated C. neogracilis genotypes can thus co-occur in summer phytoplankton communities in the Beaufort Sea. C. neogracilis generally occurred as single cells but also formed short colonies. It is phylogenetically distinct from an Antarctic species, erroneously identified in some previous studies as C. neogracilis, but named here as Chaetoceros sp. This work provides taxonomically validated sequences for 20 Arctic diatom taxa, which will facilitate future metabarcoding studies on phytoplankton in this region. %B Journal of Phycology %V 53 %P 161–187 %8 feb %G eng %U http://doi.wiley.com/10.1111/jpy.12489 %R 10.1111/jpy.12489 %0 Journal Article %J FEMS Microbiology Ecology %D 2016 %T Historical records from dated sediment cores reveal the multidecadal dynamic of the toxic dinoflagellate Alexandrium minutum in the Bay of Brest (France) %A Klouch, Khadidja Z %A Schmidt, Sabine %A Andrieux-Loyer, Françoise %A Le Gac, Mickaël %A Hervio-Heath, Dominique %A Qui-Minet, Zujaila N %A Quéré, Julien %A Bigeard, Estelle %A Guillou, Laure %A Siano, Raffaele %E Laanbroek, Riks %K 2016 %K rcc %K sbr?hyto$_\textrmd$ipo %X 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 ± 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. %B FEMS Microbiology Ecology %V 92 %P fiw101 %8 jul %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/27162179 https://academic.oup.com/femsec/article-lookup/doi/10.1093/femsec/fiw101 %R 10.1093/femsec/fiw101 %0 Journal Article %J Journal of Phycology %D 2016 %T Pseudo-nitzschia arctica sp. nov., a new cold-water cryptic Pseudo-nitzschia species within the P. pseudodelicatissima complex %A Percopo, Isabella %A Ruggiero, Maria Valeria %A Balzano, Sergio %A Gourvil, Priscillia %A Lundholm, Nina %A Siano, Raffaele %A Tammilehto, Anna %A Vaulot, Daniel %A Sarno, Diana %E Mock, T. %K RCC2002 %K RCC2004 %K RCC2005 %K RCC2517 %X A new nontoxic Pseudo-nitzschia species belonging to the P. pseudodelicatissima complex, P. arctica, was isolated from different areas of the Arctic. The erection of P. arctica is mainly supported by molecular data, since the species shares identical ultrastructure with another species in the complex, P. fryxelliana, and represents a new case of crypticity within the genus. Despite their morphological similarity, the two species are not closely related in phylogenies based on LSU, ITS and rbcL. Interestingly, P. arctica is phylogenetically most closely related to P. granii and P. subcurvata, from which the species is, however, morphologically different. P. granii and P. subcurvata lack the central larger interspace which is one of the defining features of the P. pseudodelicatissima complex. The close genetic relationship between P. arctica and the two species P. granii and P. subcurvata is demonstrated by analysis of the secondary structure of ITS2 which revealed no compensatory base changes, two hemi-compensatory base changes, and two deletions in P. arctica with respect to the other two species. These findings emphasize that rates of morphological differentiation, molecular evolution and speciation are often incongruent for Pseudo-nitzschia species, resulting in a restricted phylogenetic value for taxonomic characters used to discriminate species. The description of a new cryptic species, widely distributed in the Arctic and potentially representing an endemic component of the Arctic diatom flora, reinforces the idea of the existence of noncosmopolitan Pseudo-nitzschia species and highlights the need for combined morphological and molecular analyses to assess the distributional patterns of phytoplankton species. %B Journal of Phycology %V 52 %P 184–199 %8 apr %G eng %U http://doi.wiley.com/10.1111/jpy.12395 %R 10.1111/jpy.12395 %0 Journal Article %J Journal of Phycology %D 2014 %T Brandtodinium gen. nov. and B. nutricula comb. Nov. (Dinophyceae), a dinoflagellate commonly found in symbiosis with polycystine radiolarians %A Probert, Ian %A Siano, Raffaele %A Poirier, Camille %A Decelle, Johan %A Biard, Tristan %A Tuji, Akihiro %A Suzuki, Noritoshi %A Not, Fabrice %K Dinoflagellate %K MACUMBA %K Peridiniales %K polycystines %K Radiolaria %K rcc %K RCC3378 %K RCC3379 %K RCC3380 %K RCC3381 %K RCC3382 %K RCC3383 %K RCC3384 %K RCC3385 %K RCC3386 %K RCC3387 %K RCC3388 %K SBR$_\textrmP$hyto$_\textrmD$PO %K Scrippsiella %K symbiosis %K taxonomy %K Zooxanthella %X Symbiotic interactions between pelagic hosts and microalgae have received little attention, although they are widespread in the photic layer of the world ocean, where they play a fundamental role in the ecology of the planktonic ecosystem. Polycystine radiolarians (including the orders Spumellaria, Collodaria and Nassellaria) are planktonic heterotrophic protists that are widely distributed and often abundant in the ocean. Many polycystines host symbiotic microalgae within their cytoplasm, mostly thought to be the dinoflagellate Scrippsiella nutricula, a species originally described by Karl Brandt in the late nineteenth century as Zooxanthella nutricula. The free-living stage of this dinoflagellate has never been characterized in terms of morphology and thecal plate tabulation. We examined morphological characters and sequenced conservative ribosomal markers of clonal cultures of the free-living stage of symbiotic dinoflagellates isolated from radiolarian hosts from the three polycystine orders. In addition, we sequenced symbiont genes directly from several polycystine-symbiont holobiont specimens from different oceanic regions. Thecal plate arrangement of the free-living stage does not match that of Scrippsiella or related genera, and LSU and SSU rDNA-based molecular phylogenies place these symbionts in a distinct clade within the Peridiniales. Both phylogenetic analyses and the comparison of morphological features of culture strains with those reported for other closely related species support the erection of a new genus that we name Brandtodinium gen. nov. and the recombination of S. nutricula as B. nutricula comb. nov. %B Journal of Phycology %V 50 %P 388–399 %G eng %U http://dx.doi.org/10.1111/jpy.12174 %R 10.1111/jpy.12174 %0 Journal Article %J Harmful Algae %D 2014 %T Genetic diversity of the harmful family Kareniaceae (Gymnodiniales, Dinophyceae) in France, with the description of ¡i¿Karlodinium gentienii¡/i¿ sp. nov.: A new potentially toxic dinoflagellate %A Nézan, Elisabeth %A Siano, Raffaele %A Boulben, Sylviane %A Six, Christophe %A Bilien, Gwenael %A Chèze, Karine %A Duval, Audrey %A Le Panse, Sophie %A Quéré, Julien %A Chomérat, Nicolas %K 2014 %K rcc %K sbr?hyto?app %X A B S T R A C T The family Kareniaceae is mostly known in France for recurrent blooms of Karenia mikimotoi in the Atlantic, English Channel, and Mediterranean Sea and for the unusual green discoloration in the saltwater lagoon of Diana (Corsica) caused by Karlodinium corsicum in April 1994. In terms of diversity, this taxonomic group was long overlooked owing to the difficult identification of these small unarmored dinoflagellates. In this study, thanks to the molecular characterization performed on single cells from field samples and cultures, twelve taxonomic units were assigned to the known genera Karenia, Karlodinium and Takayama, whereas one could not be affiliated to any described genus. The molecular phylogeny inferred from the D1–D2 region of the LSU rDNA showed that five of them formed a sister taxon of a known species, and could not be identified at species-level, on the basis of molecular analysis only. Among these latter taxa, one Karlodinium which was successfully cultured was investigated by studying the external morphological features (using two procedures for cells fixation), ultrastructure, pigment composition, and haemolytic activity. The results of our analyses corroborate the genetic results in favour of the erection of Karlodinium gentienii sp. nov., which possesses an internal complex system of trichocysts connected to external micro-processes particularly abundant in the epicone, and a peculiar pigment composition. In addition, preliminary assays showed a haemolytic activity. %B Harmful Algae %V 40 %P 75–91 %G eng %U http://linkinghub.elsevier.com/retrieve/pii/S1568988314001863 %R 10.1016/j.hal.2014.10.006 %0 Journal Article %J Nucleic Acids Research %D 2013 %T The protist ribosomal reference database (PR2): a catalog of unicellular eukaryote small SubUnit rRNA sequences with curated taxonomy %A Guillou, Laure %A Bachar, Dipankar %A Audic, Stéphane %A Bass, David %A Berney, Cedric %A Bittner, Lucie %A Boutte, Christophe %A Burgaud, Gaetan %A de Vargas, Colomban %A Decelle, Johan %A del Campo, Javier %A Dolan, John %A Dunthorn, Micah %A Bente, Edvardsen %A Holzmann, Maria %A Kooistra, Wiebe H C F %A Lara, Enrique %A Lebescot, Noan %A Logares, Ramiro %A Mahé, Frédéric %A Massana, Ramon %A Montresor, Marina %A Morard, Raphael %A Not, Fabrice %A Pawlowski, Jan %A Probert, Ian %A Sauvadet, Anne-Laure %A Siano, Raffaele %A Stoeck, Thorsten %A Vaulot, Daniel %A Zimmermann, Pascal %A Christen, Richard %K 2013 %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?ppo %B Nucleic Acids Research %V 41 %P D597–D604 %G eng %R 10.1093/nar/gks1160 %0 Journal Article %J Biogeosciences %D 2012 %T Diversity of cultured photosynthetic flagellates in the North East Pacific and Arctic Oceans in summer %A Balzano, Sergio %A Gourvil, Priscillia %A Siano, Raffaele %A Chanoine, Mélanie %A Marie, Dominique %A Lessard, Sylvie %A Sarno, Diana %A Vaulot, Daniel %K 2012 %K ASSEMBLE %K MACUMBA %K MALINA %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto$_\textrmd$ipo %B Biogeosciences %V 9 %P 4553–4571 %G eng %R 10.5194/bg-9-4553-2012