%0 Journal Article %J Scientific Reports %D 2021 %T Annual phytoplankton dynamics in coastal waters from fildes bay, western antarctic peninsula %A Trefault, Nicole %A de la Iglesia, Rodrigo %A Moreno-Pino, Mario %A Lopes dos Santos, Adriana %A Gérikas Ribeiro, Catherine %A Parada-Pozo, Génesis %A Cristi, Antonia %A Marie, Dominique %A Vaulot, Daniel %K RCC2265 %K RCC2289 %K RCC4582 %K RCC4586 %K RCC5152 %X Year-round reports of phytoplankton dynamics in the West Antarctic Peninsula are rare and mainly limited to microscopy and/or pigment-based studies. We analyzed the phytoplankton community from coastal waters of Fildes Bay in the West Antarctic Peninsula between January 2014 and 2015 using metabarcoding of the nuclear and plastidial 18/16S rRNA gene from both size-fractionated and flow cytometry sorted samples. Overall 14 classes of photosynthetic eukaryotes were present in our samples with the following dominating: Bacillariophyta (diatoms), Pelagophyceae and Dictyochophyceae for division Ochrophyta, Mamiellophyceae and Pyramimonadophyceae for division Chlorophyta, Haptophyta and Cryptophyta. Each metabarcoding approach yielded a different image of the phytoplankton community with for example Prymnesiophyceae more prevalent in plastidial metabarcodes and Mamiellophyceae in nuclear ones. Diatoms were dominant in the larger size fractions and during summer, while Prymnesiophyceae and Cryptophyceae were dominant in colder seasons. Pelagophyceae were particularly abundant towards the end of autumn (May). In addition of Micromonas polaris and Micromonas sp. clade B3, both previously reported in Arctic waters, we detected a new Micromonas 18S rRNA sequence signature, close to, but clearly distinct from M. polaris , which potentially represents a new clade specific of the Antarctic. These results highlight the need for complementary strategies as well as the importance of year-round monitoring for a comprehensive description of phytoplankton communities in Antarctic coastal waters. %B Scientific Reports %V 11 %P 1368 %8 dec %G eng %U http://biorxiv.org/content/early/2020/10/27/2020.10.27.356600.abstract http://www.nature.com/articles/s41598-020-80568-8 %R 10.1038/s41598-020-80568-8 %0 Journal Article %J Protist %D 2021 %T Hemiselmis aquamarina sp . nov . (Cryptomonadales , Cryptophyceae), a cryptomonad with a novel phycobiliprotein type (Cr-PC 564) %A Magalhães, Karoline %A Lopes dos Santos, Adriana %A Vaulot, Daniel %A de Oliveira, Mariana Cabral %K RCC4102 %K RCC5634 %K to add %B Protist %V in press %G eng %U https://doi.org/10.1016/j.protis.2021.125832 %R 10.1016/j.protis.2021.125832 %0 Journal Article %J Journal of Phycology %D 2021 %T No evidence of Phago-mixotropy in Micromonas polaris (Mamiellophyceae), the Dominant Picophytoplankton Species in the Arctic %A Jimenez, Valeria %A Burns, John A. %A Le Gall, Florence %A Not, Fabrice %A Vaulot, Daniel %K Arctic %K Micromonas %K phago-mixotrophy %K phytoplankton %K rcc %K RCC21 %K RCC2288 %K RCC2306 %K RCC4298 %X In the Arctic Ocean, the small green alga Micromonas polaris dominates picophytoplankton during the summer months but is also present in winter. It has been previously hypothesized to be phago-mixotrophic (capable of bacteria ingestion) based on laboratory and field experiments. Prey uptake was analyzed in several M. polaris strains isolated from different regions and depths of the Arctic Ocean and in Ochromonas triangulata, a known phago-mixotroph used as a control. Measuring ingestion of either fluorescent beads or fluorescently labeled bacteria by flow cytometry, we found no evidence of phago-mixotrophy in any M. polaris strain while O. triangulata was ingesting both beads and bacteria. In addition, in silico predictions revealed that members of the genus Micromonas lack a genetic signature of phagocytotic capacity. %B Journal of Phycology %V 57 %P 435–446 %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13125 %R 10.1111/jpy.13125 %0 Journal Article %J Elementa: Science of the Anthropocene %D 2020 %T Culturable diversity of Arctic phytoplankton during pack ice melting %A Ribeiro, Catherine Gérikas %A dos Santos, Adriana Lopes %A Gourvil, Priscillia %A Le Gall, Florence %A Marie, Dominique %A Tragin, Margot %A Probert, Ian %A Vaulot, Daniel %K RCC5197 %K RCC5198 %K RCC5199 %K RCC5200 %K RCC5201 %K RCC5202 %K RCC5203 %K RCC5204 %K RCC5205 %K RCC5206 %K RCC5207 %K RCC5208 %K RCC5209 %K RCC5210 %K RCC5211 %K RCC5212 %K RCC5213 %K RCC5214 %K RCC5215 %K RCC5216 %K RCC5217 %K RCC5218 %K RCC5219 %K RCC5220 %K RCC5221 %K RCC5222 %K RCC5223 %K RCC5224 %K RCC5225 %K RCC5226 %K RCC5227 %K RCC5228 %K RCC5229 %K RCC5230 %K RCC5231 %K RCC5232 %K RCC5233 %K RCC5234 %K RCC5235 %K RCC5236 %K RCC5237 %K RCC5238 %K RCC5239 %K RCC5240 %K RCC5241 %K RCC5242 %K RCC5243 %K RCC5244 %K RCC5245 %K RCC5246 %K RCC5247 %K RCC5248 %K RCC5249 %K RCC5250 %K RCC5251 %K RCC5252 %K RCC5253 %K RCC5254 %K RCC5255 %K RCC5256 %K RCC5257 %K RCC5258 %K RCC5259 %K RCC5260 %K RCC5261 %K RCC5262 %K RCC5263 %K RCC5264 %K RCC5265 %K RCC5266 %K RCC5267 %K RCC5268 %K RCC5269 %K RCC5270 %K RCC5271 %K RCC5272 %K RCC5273 %K RCC5274 %K RCC5275 %K RCC5276 %K RCC5277 %K RCC5278 %K RCC5279 %K RCC5280 %K RCC5281 %K RCC5282 %K RCC5283 %K RCC5284 %K RCC5285 %K RCC5286 %K RCC5287 %K RCC5288 %K RCC5289 %K RCC5290 %K RCC5291 %K RCC5292 %K RCC5293 %K RCC5294 %K RCC5295 %K RCC5296 %K RCC5297 %K RCC5298 %K RCC5299 %K RCC5300 %K RCC5301 %K RCC5302 %K RCC5303 %K RCC5304 %K RCC5305 %K RCC5306 %K RCC5307 %K RCC5308 %K RCC5309 %K RCC5310 %K RCC5311 %K RCC5312 %K RCC5313 %K RCC5314 %K RCC5315 %K RCC5316 %K RCC5317 %K RCC5318 %K RCC5319 %K RCC5320 %K RCC5321 %K RCC5322 %K RCC5323 %K RCC5324 %K RCC5325 %K RCC5326 %K RCC5327 %K RCC5328 %K RCC5329 %K RCC5330 %K RCC5331 %K RCC5332 %K RCC5333 %K RCC5334 %K RCC5335 %K RCC5336 %K RCC5337 %K RCC5338 %K RCC5339 %K RCC5340 %K RCC5341 %K RCC5342 %K RCC5343 %K RCC5344 %K RCC5345 %K RCC5346 %K RCC5347 %K RCC5348 %K RCC5349 %K RCC5350 %K RCC5351 %K RCC5352 %K RCC5353 %K RCC5354 %K RCC5355 %K RCC5356 %K RCC5357 %K RCC5358 %K RCC5359 %K RCC5360 %K RCC5361 %K RCC5362 %K RCC5363 %K RCC5364 %K RCC5365 %K RCC5366 %K RCC5367 %K RCC5368 %K RCC5369 %K RCC5370 %K RCC5371 %K RCC5372 %K RCC5373 %K RCC5374 %K RCC5375 %K RCC5376 %K RCC5377 %K RCC5378 %K RCC5379 %K RCC5380 %K RCC5381 %K RCC5382 %K RCC5383 %K RCC5384 %K RCC5385 %K RCC5386 %K RCC5387 %K RCC5388 %K RCC5389 %K RCC5390 %K RCC5391 %K RCC5392 %K RCC5393 %K RCC5394 %K RCC5395 %K RCC5396 %K RCC5397 %K RCC5398 %K RCC5399 %K RCC5400 %K RCC5401 %K RCC5402 %K RCC5403 %K RCC5404 %K RCC5405 %K RCC5406 %K RCC5407 %K RCC5408 %K RCC5409 %K RCC5410 %K RCC5411 %K RCC5412 %K RCC5413 %K RCC5414 %K RCC5415 %K RCC5416 %K RCC5417 %K RCC5418 %K RCC5419 %K RCC5420 %K RCC5421 %K RCC5422 %K RCC5423 %K RCC5424 %K RCC5425 %K RCC5426 %K RCC5427 %K RCC5428 %K RCC5429 %K RCC5430 %K RCC5431 %K RCC5432 %K RCC5433 %K RCC5434 %K RCC5435 %K RCC5436 %K RCC5437 %K RCC5438 %K RCC5439 %K RCC5440 %K RCC5441 %K RCC5442 %K RCC5443 %K RCC5444 %K RCC5445 %K RCC5446 %K RCC5447 %K RCC5448 %K RCC5449 %K RCC5450 %K RCC5451 %K RCC5452 %K RCC5453 %K RCC5454 %K RCC5455 %K RCC5456 %K RCC5457 %K RCC5458 %K RCC5459 %K RCC5460 %K RCC5461 %K RCC5462 %K RCC5463 %K RCC5464 %K RCC5465 %K RCC5466 %K RCC5467 %K RCC5468 %K RCC5469 %K RCC5470 %K RCC5471 %K RCC5472 %K RCC5473 %K RCC5474 %K RCC5475 %K RCC5476 %K RCC5477 %K RCC5478 %K RCC5479 %K RCC5480 %K RCC5481 %K RCC5482 %K RCC5483 %K RCC5484 %K RCC5485 %K RCC5486 %K RCC5487 %K RCC5488 %K RCC5489 %K RCC5490 %K RCC5491 %K RCC5492 %K RCC5493 %K RCC5494 %K RCC5495 %K RCC5496 %K RCC5497 %K RCC5498 %K RCC5499 %K RCC5500 %K RCC5501 %K RCC5502 %K RCC5503 %K RCC5504 %K RCC5505 %K RCC5506 %K RCC5507 %K RCC5508 %K RCC5509 %K RCC5510 %K RCC5511 %K RCC5512 %K RCC5513 %K RCC5514 %K RCC5515 %K RCC5516 %K RCC5517 %K RCC5518 %K RCC5519 %K RCC5520 %K RCC5521 %K RCC5522 %K RCC5523 %K RCC5524 %K RCC5525 %K RCC5526 %K RCC5527 %K RCC5528 %K RCC5529 %K RCC5530 %K RCC5531 %K RCC5532 %K RCC5533 %K RCC5534 %K RCC5535 %K RCC5536 %K RCC5537 %K RCC5538 %K RCC5539 %K RCC5540 %K RCC5541 %K RCC5542 %K RCC5543 %K RCC5544 %K RCC5545 %K RCC5546 %K RCC5547 %K RCC5548 %K RCC5549 %K RCC5550 %K RCC5551 %K RCC5552 %K RCC5553 %K RCC5554 %K RCC5555 %K RCC5556 %K RCC5557 %K RCC5558 %K RCC5559 %K RCC5560 %K RCC5561 %K RCC5562 %K RCC5563 %K RCC5564 %K RCC5565 %K RCC5566 %K RCC5567 %K RCC5568 %K RCC5569 %K RCC5570 %K RCC5571 %K RCC5572 %K RCC5573 %K RCC5574 %K RCC5575 %K RCC5576 %K RCC5577 %K RCC5578 %K RCC5579 %K RCC5580 %K RCC5581 %K RCC5582 %K RCC5583 %K RCC5584 %K RCC5585 %K RCC5586 %K RCC5587 %K RCC5588 %K RCC5589 %K RCC5590 %K RCC5591 %K RCC5592 %K RCC5593 %K RCC5594 %K RCC5595 %K RCC5596 %K RCC5597 %K RCC5598 %K RCC5599 %K RCC5600 %K RCC5601 %K RCC5602 %K RCC5603 %K RCC5604 %K RCC5605 %K RCC5606 %K RCC5607 %K RCC5608 %K RCC5609 %K RCC5610 %K RCC5611 %K RCC5612 %X Massive phytoplankton blooms develop at the Arctic ice edge, sometimes extending far under the pack ice. An extensive culturing effort was conducted before and during a phytoplankton bloom in Baffin Bay between April and July 2016. Different isolation strategies were applied, including flow cytometry cell sorting, manual single cell pipetting and serial dilution. Although all three techniques yielded the most common organisms, each technique retrieved specific taxa, highlighting the importance of using several methods to maximize the number and diversity of isolated strains. More than 1,000 cultures were obtained, characterized by 18S rRNA sequencing and optical microscopy and de-replicated to a subset of 276 strains presented in this work. Strains grouped into 57 genotypes defined by 100% 18S rRNA sequence similarity. These genotypes spread across five divisions: Heterokontophyta, Chlorophyta, Cryptophyta, Haptophyta and Dinophyta. Diatoms were the most abundant group (193 strains), mostly represented by the genera Chaetoceros and Attheya. The genera Rhodomonas and Pyramimonas were the most abundant non-diatom nanoplankton strains, while Micromonas polaris dominated the picoplankton. Diversity at the class level was higher during the peak of the bloom. Potentially new species were isolated, in particular within the genera Navicula, Nitzschia, Coscinodiscus, Thalassiosira, Pyramimonas, Mantoniella and Isochrysis. %B Elementa: Science of the Anthropocene %V 8 %P 6 %8 feb %G eng %U https://www.biorxiv.org/content/10.1101/642264v1 https://www.elementascience.org/article/10.1525/elementa.401/ %R 10.1525/elementa.401 %0 Journal Article %J Phycologia %D 2020 %T Taxonomic reassignment of \textit{Pseudohaptolina birgeri comb. nov . (Haptophyta) %A Gérikas Ribeiro, Catherine %A Lopes dos Santos, Adriana %A Probert, Ian %A Vaulot, Daniel %A Edvardsen, Bente %K RCC5268 %K RCC5270 %B Phycologia %V in press %P 1–10 %8 oct %G eng %U https://www.biorxiv.org/content/10.1101/2020.05.06.081489v1 https://www.tandfonline.com/doi/full/10.1080/00318884.2020.1830255 %R 10.1080/00318884.2020.1830255 %0 Journal Article %J Frontiers in Marine Science %D 2018 %T Bolidophyceae, a sister picoplanktonic group of diatoms – a review %A Kuwata, Akira %A Yamada, Kazumasa %A Ichinomiya, Mutsuo %A Yoshikawa, Shinya %A Tragin, Margot %A Vaulot, Daniel %A Lopes dos Santos, Adriana %K RCC1657 %K RCC201 %K RCC205 %K RCC206 %K rcc212 %K RCC239 %B Frontiers in Marine Science %V 5 %P 370 %8 oct %G eng %U https://www.frontiersin.org/article/10.3389/fmars.2018.00370/full %R 10.3389/fmars.2018.00370 %0 Journal Article %J Scientific Reports %D 2018 %T A novel species of the marine cyanobacterium Acaryochloris with a unique pigment content and lifestyle %A Partensky, Frédéric %A Six, Christophe %A Ratin, Morgane %A Garczarek, Laurence %A Vaulot, Daniel %A Probert, Ian %A Calteau, Alexandra %A Gourvil, Priscillia %A Marie, Dominique %A Grébert, Théophile %A Bouchier, Christiane %A Le Panse, Sophie %A Gachenot, Martin %A Rodríguez, Francisco %A Garrido, José L. %K RCC1774 %B Scientific Reports %V 8 %P 9142 %8 dec %G eng %U http://www.nature.com/articles/s41598-018-27542-7 %R 10.1038/s41598-018-27542-7 %0 Journal Article %J Scientific Reports %D 2017 %T Chloropicophyceae, a new class of picophytoplanktonic prasinophytes %A Lopes dos Santos, Adriana %A Pollina, Thibaut %A Gourvil, Priscillia %A Corre, Erwan %A Marie, Dominique %A Garrido, José Luis %A Rodríguez, Francisco %A Noël, Mary-Hélène %A Vaulot, Daniel %A Eikrem, Wenche %K 2017 %K RCC1019 %K RCC1021 %K RCC1032 %K RCC1043 %K RCC1124 %K RCC138 %K RCC15 %K RCC1871 %K RCC19 %K RCC227 %K RCC2335 %K RCC2337 %K RCC2339 %K RCC287 %K RCC297 %K RCC3368 %K RCC3373 %K RCC3374 %K RCC3375 %K RCC3376 %K RCC3402 %K RCC4429 %K RCC4430 %K RCC4434 %K RCC4572 %K RCC4656 %K RCC696 %K RCC700 %K RCC701 %K RCC712 %K RCC713 %K RCC717 %K RCC719 %K RCC722 %K RCC726 %K RCC856 %K RCC857 %K RCC887 %K RCC917 %K RCC996 %K RCC997 %K RCC998 %K RCC999 %K sbr?hyto$_\textrmd$ipo %B Scientific Reports %V 7 %P 14019 %8 dec %G eng %U http://www.nature.com/articles/s41598-017-12412-5 %R 10.1038/s41598-017-12412-5 %0 Journal Article %J The ISME Journal %D 2017 %T Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters %A Lopes dos Santos, Adriana %A Gourvil, Priscillia %A Tragin, Margot %A Noël, Mary-Hélène %A Decelle, Johan %A Romac, Sarah %A Vaulot, Daniel %K 2016 %K MACUMBA %K MicroB3 %K RCC1019 %K RCC1021 %K RCC1032 %K RCC1043 %K RCC1124 %K RCC138 %K RCC15 %K RCC1871 %K RCC19 %K RCC227 %K RCC2335 %K RCC2337 %K RCC2339 %K RCC287 %K RCC297 %K RCC3368 %K RCC3373 %K RCC3374 %K RCC3375 %K RCC3376 %K RCC3402 %K RCC4429 %K RCC4430 %K RCC4434 %K RCC4656 %K RCC696 %K RCC700 %K RCC701 %K RCC712 %K RCC713 %K RCC717 %K RCC719 %K RCC722 %K RCC726 %K RCC856 %K RCC857 %K RCC917 %K RCC996 %K RCC997 %K RCC998 %K RCC999 %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?ppo %B The ISME Journal %V 11 %P 512–528 %8 feb %G eng %U http://www.nature.com/doifinder/10.1038/ismej.2016.120 %R 10.1038/ismej.2016.120 %0 Journal Article %J Journal of Phycology %D 2017 %T Improvement of phytoplankton culture isolation using single cell sorting by flow cytometry %A Marie, Dominique %A Le Gall, Florence %A Edern, Roseline %A Gourvil, Priscillia %A Vaulot, Daniel %E Valentin, K. %K 2016 %K RCC1008 %K RCC299 %K RCC350 %K RCC4108 %K RCC4548 %K RCC4549 %K RCC4550 %K RCC4551 %K RCC4552 %K RCC4553 %K RCC4554 %K RCC4555 %K RCC4556 %K RCC4557 %K RCC4558 %K RCC4559 %K RCC4560 %K RCC4561 %K RCC4562 %K RCC4563 %K RCC4564 %K RCC4565 %K RCC4566 %K RCC4567 %K RCC4568 %K RCC4569 %K RCC4570 %K RCC4571 %K RCC4572 %K RCC4573 %K RCC4574 %K RCC4575 %K RCC4576 %K RCC4577 %K RCC4578 %K RCC4579 %K RCC4657 %K RCC4658 %K RCC4659 %K RCC4660 %K RCC4661 %K RCC4662 %K RCC4663 %K RCC4664 %K RCC4665 %K RCC4666 %K RCC90 %B Journal of Phycology %V 53 %P 271–282 %8 apr %G eng %U http://doi.wiley.com/10.1111/jpy.12495 %R 10.1111/jpy.12495 %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 Protist %D 2017 %T Revision of the genus micromonas manton et parke (chlorophyta, mamiellophyceae), of the type species m. pusilla (butcher) manton & parke and of the species m. commoda van baren, bachy and worden and description of two new species based on the genetic %A Simon, Nathalie %A Foulon, Elodie %A Grulois, Daphne %A Six, Christophe %A Desdevises, Yves %A Latimier, Marie %A Le Gall, Florence %A Tragin, Margot %A Houdan, Aude %A Derelle, Evelyne %A Jouenne, Fabien %A Marie, Dominique %A Le Panse, Sophie %A Vaulot, Daniel %A Marin, Birger %K 2017 %K ASSEMBLE %K rcc %K RCC1109 %K RCC114 %K RCC2306 %K RCC2308 %K RCC299 %K RCC372 %K RCC373 %K RCC418 %K RCC434 %K RCC447 %K RCC448 %K RCC449 %K RCC450 %K RCC451 %K RCC461 %K RCC465 %K RCC472 %K RCC497 %K RCC498 %K RCC570 %K RCC629 %K RCC647 %K RCC658 %K RCC676 %K RCC692 %K RCC746 %K RCC803 %K RCC804 %K RCC805 %K RCC806 %K RCC807 %K RCC808 %K RCC828 %K RCC829 %K RCC830 %K RCC831 %K RCC833 %K RCC834 %K RCC835 %K RCC836 %K SBR$_\textrmP$hyto$_\textrmD$IPO %K SBR$_\textrmP$hyto$_\textrmP$PM %K sbr?hyto$_\textrmd$ipo %B Protist %V 168 %P 612–635 %8 nov %G eng %U http://linkinghub.elsevier.com/retrieve/pii/S1434461017300780 %R 10.1016/j.protis.2017.09.002 %0 Journal Article %J Perspectives in Phycology %D 2016 %T Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review %A Edvardsen, Bente %A Egge, Elianne Sirnaes %A Vaulot, Daniel %K 2016 %K rcc %K sbr?hyto$_\textrmd$ipo %B Perspectives in Phycology %V 3 %P 77–91 %8 apr %G eng %U https://dx.doi.org/10.6084/m9.figshare.2759983.v1 http://www.schweizerbart.de/papers/pip/detail/3/85671/Diversity_and_distribution_of_haptophytes_revealed?af=crossref %R 10.1127/pip/2016/0052 %0 Journal Article %J The ISME Journal %D 2016 %T Diversity and oceanic distribution of Parmales (Bolidophyceae), a picoplankton group closely related to diatoms %A Ichinomiya, Mutsuo %A Lopes dos Santos, A %A Gourvil, Priscillia %A Yoshikawa, Shinya %A Kamiya, Mitsunobu %A Ohki, Kaori %A Audic, S %A de Vargas, Colomban %A Vaulot, Daniel %A Kuwata, Akira %K 2016 %K MACUMBA %K MicroB3 %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?ppo %B The ISME Journal %V in press %G eng %R 10.1038/ismej.2016.38 %0 Journal Article %J Journal of Phycology %D 2016 %T Photosynthetic pigments of oceanic Chlorophyta belonging to prasinophytes clade VII %A Lopes dos Santos, Adriana %A Gourvil, Priscillia %A Rodriguez-Hernandez, Francisco %A Garrido, José Luis %A Vaulot, Daniel %K 2016 %K MACUMBA %K rcc %K RCC1124 %K RCC15 %K RCC1871 %K RCC2337 %K RCC2339 %K RCC287 %K RCC3374 %K RCC3376 %K RCC3402 %K RCC719 %K RCC856 %K RCC857 %K RCC996 %K RCC998 %K RCC?o?dd %K SBR$_\textrmP$hyto$_\textrmD$IPO %K sbr?hyto$_\textrmd$ipo %X The ecological importance and diversity of pico/ nanoplanktonic algae remains poorly studied in marine waters, in part because many are tiny and without distinctive morphological features. Amongst green algae, Mamiellophyceae such as Micromonas or Bathycoccus are dominant in coastal waters while prasinophytes clade VII, yet not formerly described, appear to be major players in open oceanic waters. The pigment composition of 14 strains representative of different subclades of clade VII was analyzed using a method that improves the separation of loroxanthin and neoxanthin. All the prasinophytes clade VII analyzed here showed a pigment composition similar to that previously reported for RCC287 corresponding to pigment group prasino-2A. However, we detected in addition astaxanthin for which it is the first report in prasinophytes. Among the strains analyzed, the pigment signature is qualitatively similar within subclades A and B. By contrast, RCC3402 from subclade C (Picocystis) lacks loroxanthin, astaxanthin, and antheraxanthin but contains alloxanthin, diatoxanthin, and monadoxanthin that are usually found in diatoms or cryptophytes. For subclades A and B, loroxanthin was lowest at highest light irradiance suggesting a light-harvesting role of this pigment in clade VII as in Tetraselmis. %B Journal of Phycology %V 52 %P 148–155 %G eng %R 10.1111/jpy.12376 %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 Scientific Reports %D 2016 %T Survey of the green picoalga Bathycoccus genomes in the global ocean %A Vannier, Thomas %A Leconte, Jade %A Seeleuthner, Yoann %A Mondy, Samuel %A Pelletier, Eric %A Aury, Jean-Marc %A de Vargas, Colomban %A Sieracki, Michael %A Iudicone, Daniele %A Vaulot, Daniel %A Wincker, Patrick %A Jaillon, Olivier %K 2016 %K RCC1105 %K RCC715 %K RCC716 %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?ppo %B Scientific Reports %V 6 %P 37900 %8 dec %G eng %U http://www.nature.com/articles/srep37900 %R 10.1038/srep37900 %0 Journal Article %J Molecular Ecology Resources %D 2015 %T PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy %A Decelle, Johan %A Romac, Sarah %A Stern, Rowena F. %A Bendif, El Mahdi %A Zingone, Adriana %A Audic, Stéphane %A Guiry, Michael D. %A Guillou, Laure %A Tessier, Désiré %A Le Gall, Florence %A Gourvil, Priscillia %A dos Santos, Adriana Lopes %A Probert, Ian %A Vaulot, Daniel %A de Vargas, Colomban %A Christen, Richard %K 2015 %K MACUMBA %K rcc %K RCC?o?dd %K SBR$_\textrmP$hyto$_\textrmD$IPO %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?ppo %X 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. %B Molecular Ecology Resources %V 15 %P 1435–1445 %G eng %U http://doi.wiley.com/10.1111/1755-0998.12401 %R 10.1111/1755-0998.12401 %0 Journal Article %J PLoS biology %D 2014 %T The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing %A Keeling, Patrick J %A Burki, Fabien %A Wilcox, Heather M %A Allam, Bassem %A Allen, Eric E %A Amaral-Zettler, Linda A %A Armbrust, E Virginia %A Archibald, John M %A Bharti, Arvind K %A Bell, Callum J %A Beszteri, Bank %A Bidle, Kay D %A Cameron, Connor T %A Campbell, Lisa %A Caron, David A %A Cattolico, Rose Ann %A Collier, Jackie L %A Coyne, Kathryn %A Davy, Simon K %A Deschamps, Phillipe %A Dyhrman, Sonya T %A Edvardsen, Bente %A Gates, Ruth D %A Gobler, Christopher J %A Greenwood, Spencer J %A Guida, Stephanie M %A Jacobi, Jennifer L %A Jakobsen, Kjetill S %A James, Erick R %A Jenkins, Bethany %A John, Uwe %A Johnson, Matthew D %A Juhl, Andrew R %A Kamp, Anja %A Katz, Laura A %A Kiene, Ronald %A Kudryavtsev, Alexander %A Leander, Brian S %A Lin, Senjie %A Lovejoy, Connie %A Lynn, Denis %A Marchetti, Adrian %A McManus, George %A Nedelcu, Aurora M %A Menden-Deuer, Susanne %A Miceli, Cristina %A Mock, Thomas %A Montresor, Marina %A Moran, Mary Ann %A Murray, Shauna %A Nadathur, Govind %A Nagai, Satoshi %A Ngam, Peter B %A Palenik, Brian %A Pawlowski, Jan %A Petroni, Giulio %A Piganeau, Gwenael %A Posewitz, Matthew C %A Rengefors, Karin %A Romano, Giovanna %A Rumpho, Mary E %A Rynearson, Tatiana %A Schilling, Kelly B %A Schroeder, Declan C %A Simpson, Alastair G B %A Slamovits, Claudio H %A Smith, David R %A Smith, G Jason %A Smith, Sarah R %A Sosik, Heidi M %A Stief, Peter %A Theriot, Edward %A Twary, Scott N %A Umale, Pooja E %A Vaulot, Daniel %A Wawrik, Boris %A Wheeler, Glen L %A Wilson, William H %A Xu, Yan %A Zingone, Adriana %A Worden, Alexandra Z %K 2014 %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto$_\textrmd$ipo %X Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans %B PLoS biology %V 12 %P e1001889 %G eng %U http://dx.doi.org/10.1371%252Fjournal.pbio.1001889 %R 10.1371/journal.pbio.1001889 %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 The ISME journal %D 2012 %T Composition of the summer photosynthetic pico and nanoplankton communities in the Beaufort Sea assessed by T-RFLP and sequences of the 18S rRNA gene from flow cytometry sorted samples %A Balzano, Sergio %A Marie, Dominique %A Gourvil, Priscillia %A Vaulot, Daniel %K 2012 %K ASSEMBLE %K Chaetoceros %K MALINA %K Pyramimonas %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto$_\textrmd$ipo %K Souchotheque %X The composition of photosynthetic pico and nanoeukaryotes was investigated in the North East Pacific and the Arctic Ocean with special emphasis on the Beaufort Sea during the MALINA cruise in summer 2009. Photosynthetic populations were sorted using flow cytometry based on their size and pigment fluorescence. Diversity of the sorted photosynthetic eukaryotes was determined using terminal-restriction fragment length polymorphism analysis and cloning/sequencing of the 18S ribosomal RNA gene. Picoplankton was dominated by Mamiellophyceae, a class of small green algae previously included in the prasinophytes: in the North East Pacific, the contribution of an Arctic Micromonas ecotype increased steadily northward becoming the only taxon occurring at most stations throughout the Beaufort Sea. In contrast, nanoplankton was more diverse: North Pacific stations were dominated by Pseudo-nitzschia sp. whereas those in the Beaufort Sea were dominated by two distinct Chaetoceros species as well as by Chrysophyceae, Pelagophyceae and Chrysochromulina spp.. This study confirms the importance of Arctic Micromonas within picoplankton throughout the Beaufort Sea and demonstrates that the photosynthetic picoeukaryote community in the Arctic is much less diverse than at lower latitudes. Moreover, in contrast to what occurs in warmer waters, most of the key pico- and nanoplankton species found in the Beaufort Sea could be successfully established in culture. %B The ISME journal %V 6 %P 1480–1498 %G eng %R 10.1038/ismej.2011.213 %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 %0 Journal Article %J PLoS ONE %D 2012 %T Evaluating the ribosomal internal transcribed spacer (ITS) as a candidate dinoflagellate barcode marker %A Stern, Rowena F %A Andersen, Robert A %A Jameson, Ian %A Küpper, Frithjof C %A Coffroth, Mary-Alice %A Vaulot, Daniel %A Gall, Florence Le %A Veron, Benoit %A Brand, Jerry J %A Skelton, Hayley %A Kasai, Fumai %A Lilly, Emily L %A Keeling, Patrick J %K 2012 %K ASSEMBLE %K Barcoding %K ITS %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto$_\textrmd$ipo %B PLoS ONE %V 7 %P e42780 %G eng %U http://www.plosone.org/article/info%253Adoi%252F10.1371%252Fjournal.pone.0042780 %R 10.1371/journal.pone.0042780 %0 Journal Article %J Protist %D 2012 %T Lotharella reticulosa sp. nov.: A highly reticulated network forming chlorarachniophyte from the mediterranean sea %A Ota, Shuhei %A Vaulot, Daniel %K Chlorarachniophytes %K Lotharella %K Mediterranean Sea %K RCC375 %K RCC376 %K Taxonomy. %X A new chlorarachniophyte Lotharella reticulosa sp. nov. is described from a culture isolated from the Mediterranean Sea. This strain is maintained as strain RCC375 at the Roscoff Culture Collection, France. This species presents a multiphasic life cycle: vegetative cells of this species were observed to be coccoid, but amoeboid cells with filopodia and globular suspended cells were also present in the life cycle, both of which were not dominant phases. Flagellate cells were also observed but remained very rare in culture. The vegetative cells were 9-16 ??m in diameter and highly vacuolated, containing several green chloroplasts with a projecting pyrenoid, mitochondria, and a nucleus. The chloroplast was surrounded by four membranes possessing a nucleomorph in the periplastidial compartment near the pyrenoid base. According to ultrastructural observations of the pyrenoid and nucleomorph, the present species belongs to the genus Lotharella in the phylum Chlorarachniophyta. This taxonomic placement is consistent with the molecular phylogenetic trees of the 18S rRNA gene and ITS sequences. This species showed a unique colonization pattern. Clusters of cells extended cytoplasmic strands radially. Then, amoeboid cells being born proximately moved distally along the cytoplasmic strand like on a "railway track" Subsequently the amoeboid cell became coccoid near the strand. In this way, daughter cells were dispersed evenly on the substratum. We also observed that the present species regularly formed a structure of filopodial nodes in mid-stage and later-stage cultures, which is a novel phenotype in chlorarachniophytes. The unique colonization pattern and other unique features demonstrate that RCC375 is a new chlorarachniophyte belonging to genus Lotharella, which we describe as Lotharella reticulosa sp. nov. ?? 2011 Elsevier GmbH. %B Protist %V 163 %P 91–104 %G eng %0 Journal Article %J Science %D 2012 %T Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga %A Thompson, Anne W %A Foster, Rachel A %A Krupke, Andreas %A Carter, Brandon J %A Musat, Niculina %A Vaulot, Daniel %A Kuypers, Marcel M M %A Zehr, Jonathan P %K 2012 %K MicroB3 %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto$_\textrmd$ipo %X Symbioses between nitrogen (N)2–fixing prokaryotes and photosynthetic eukaryotes are important for nitrogen acquisition in N-limited environments. Recently, a widely distributed planktonic uncultured nitrogen-fixing cyanobacterium (UCYN-A) was found to have unprecedented genome reduction, including the lack of oxygen-evolving photosystem II and the tricarboxylic acid cycle, which suggested partnership in a symbiosis. We showed that UCYN-A has a symbiotic association with a unicellular prymnesiophyte, closely related to calcifying taxa present in the fossil record. The partnership is mutualistic, because the prymnesiophyte receives fixed N in exchange for transferring fixed carbon to UCYN-A. This unusual partnership between a cyanobacterium and a unicellular alga is a model for symbiosis and is analogous to plastid and organismal evolution, and if calcifying, may have important implications for past and present oceanic N2 fixation. %B Science %V 337 %P 1546–1550 %G eng %U http://www.sciencemag.org/content/337/6101/1546.abstract %R 10.1126/science.1222700 %0 Journal Article %D 2008 %T The diversity of small eukaryotic phytoplankton (¡3 µm) in marine ecosystems %A Vaulot, Daniel %A Eikrem, Wenche %A Viprey, Manon %A Moreau, Hervé %K 2008 %K diversity %K genomics %K Marine ecosystems %K Micro-algae %K picoplankton %K rcc %K sbr?hyto$_\textrmd$ipo %K taxonomy %X Small cells dominate photosynthetic biomass and primary production in many marine ecosystems. Traditionally, picoplankton refers to cells ¡ or =2 microm. Here we extend the size range of the organisms considered to 3 microm, a threshold often used operationally in field studies. While the prokaryotic component of picophytoplankton is dominated by two genera, Prochlorococcus and Synechococcus, the eukaryotic fraction is much more diverse. Since the discovery of the ubiquitous Micromonas pusilla in the early 1950s, just over 70 species that can be ¡3 microm have been described. In fact, most algal classes contain such species. Less than a decade ago, culture-independent approaches (in particular, cloning and sequencing, denaturing gradient gel electrophoresis, FISH) have demonstrated that the diversity of eukaryotic picoplankton is much more extensive than could be assumed from described taxa alone. These approaches revealed the importance of certain classes such as the Prasinophyceae but also unearthed novel divisions such as the recently described picobiliphytes. In the last couple of years, the first genomes of photosynthetic picoplankton have become available, providing key information on their physiological capabilities. In this paper, we discuss the range of methods that can be used to assess small phytoplankton diversity, present the species described to date, review the existing molecular data obtained on field populations, and end up by looking at the promises offered by genomics. %V 32 %P 795–820 %G eng %0 Journal Article %J Environmental Microbiology %D 2008 %T Wide genetic diversity of picoplanktonic green algae (Chloroplastida) in the Mediterranean Sea uncovered by a phylum-biased PCR approach %A Viprey, Manon %A Guillou, Laure %A Ferréol, Martial %A Vaulot, Daniel %K 2008 %K rcc %K sbr?hyto$_\textrmd$ipo %X 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. %B Environmental Microbiology %V 10 %P 1804–1822 %G eng %0 Journal Article %J Aquatic Microbial Ecology %D 2006 %T Analysis of photosynthetic picoeukaryote diversity at open ocean sites in the Arabian Sea using a PCR biased towards marine algal plastids %A Fuller, Nicholas J %A Campbell, Colin %A Allen, David J %A Pitt, Frances D %A Le Gall, F %A Vaulot, Daniel %A Scanlan, David J %K 2006 %K PICOCEAN %K PICODIV %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto$_\textrmd$ipo %B Aquatic Microbial Ecology %V 43 %P 79–93 %G eng %R 10.3354/ame043079 %0 Journal Article %J FEMS Microbiology Ecology %D 2005 %T Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene %A Zhu, Fei %A Massana, Ramon %A Not, Fabrice %A Marie, Dominique %A Vaulot, Daniel %K Coastal ecosystems %K Ecology %K Fluorescent in situ hybridization %K Micromonas %K picoplankton %K prasinophytes %K Quantitative PCR %K rcc %X A quantitative PCR (QPCR) assay based on the use of SYBR Green I was developed to assess the abundance of specific groups of picoeukaryotes in marine waters. Six primer sets were designed targeting four different taxonomic levels: domain (Eukaryota), division (Chlorophyta), order (Mamiellales) and genus (Bathycoccus, Micromonas, and Ostreococcus). Reaction conditions were optimized for each primer set which was validated in silico, on agarose gels, and by QPCR against a variety of target and non-target cultures. The approach was tested by estimating gene copy numbers for Micromonas, Bathycoccus, and Ostreococcus in seawater samples to which cultured cells were added in various concentrations. QPCR was then used to determine that rRNA gene (rDNA) copy number varied from one to more than 12,000 in 18 strains of phytoplankton. Finally, QPCR was applied to environmental samples from a Mediterranean Sea coastal site and the results were compared to those obtained by Fluorescent in situ hybridization (FISH). The data obtained demonstrate that Chlorophyta and more specifically Mamiellales were important in these waters, especially during the winter picoplankton bloom. The timing of major abundance peaks of the targeted species was similar by QPCR and FISH. When used in conjunction with other techniques such as FISH or gene clone libraries, QPCR appears as very promising to quickly obtain data on the ecological distribution of important phytoplankton groups. Data interpretation must take into account primer specificity and the varying rRNA gene copy number among eukaryotes. ?? 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved. %B FEMS Microbiology Ecology %V 52 %P 79–92 %G eng %0 Journal Article %D 2004 %T Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences %A Romari, Khadidja %A Vaulot, Daniel %K Micromonas %K rcc %X Abstract We analyzed picoeukaryote assemblages at a French coastal site of the English Channel by sequencing cloned eukaryotic 18S rRNA genes in eight genetic libraries constructed from environmental samples (seven coastal , one estuarine) collected at different periods of the ... %V 49 %P 784–798 %G eng %R 10.4319/lo.2004.49.3.0784 %0 Journal Article %J Applied and Environmental Microbiology %D 2003 %T Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea %A Fuller, Nicholas J %A Marie, Dominique %A Partensky, Frédéric %A Vaulot, Daniel %A Post, Anton F %A Scanlan, David J %K 2003 %K PICODIV %K rcc %K SBR$_\textrmP$hyto %K sbr?hyto %X Phylogenetic relationships among members of the marine Synechococcus genus were determined following sequencing of the 16S ribosomal DNA (rDNA) from 31 novel cultured isolates from the Red Sea and several other oceanic environments. This revealed a large genetic diversity within the marine Synechococcus cluster consistent with earlier work but also identified three novel clades not previously recognized. Phylogenetic analyses showed one clade, containing halotolerant isolates lacking phycoerythrin (PE) and including strains capable, or not, of utilizing nitrate as the sole N source, which clustered within the MC-A (Synechococcus subcluster 5.1) lineage. Two copies of the 16S rRNA gene are present in marine Synechococcus genomes, and cloning and sequencing of these copies from Synechococcus sp. strain WH 7803 and genomic information from Synechococcus sp. strain WH 8102 reveal these to be identical. Based on the 16S rDNA sequence information, clade-specific oligonucleotides for the marine Synechococcus genus were designed and their specificity was optimized. Using dot blot hybridization technology, these probes were used to determine the in situ community structure of marine Synechococcus populations in the Red Sea at the time of a Synechococcus maximum during April 1999. A predominance of genotypes representative of a single clade was found, and these genotypes were common among strains isolated into culture. Conversely, strains lacking PE, which were also relatively easily isolated into culture, represented only a minor component of the Synechococcus population. Genotypes corresponding to well-studied laboratory strains also appeared to be poorly represented in this stratified water column in the Red Sea. %B Applied and Environmental Microbiology %V 69 %P 2430–2443 %G eng %U http://aem.asm.org/cgi/content/abstract/69/5/2430 %R 10.1128/AEM.69.5.2430-2443.2003 %0 Journal Article %J Journal of Marine Research %D 1993 %T Prochlorococcus and Synechococcus: a comparative study of their size, pigmentation and related optical properties %A Morel, A %A Ahn, Y.-W. %A Partensky, F %A Vaulot, Daniel %A Claustre, H %K 1993 %K hplc %K OPTICS %K Pigment %K rcc %K SBR$_\textrmP$hyto %K sbr?hyto %K Synechococcus %K \#PROCHLOROPHYTE %B Journal of Marine Research %V 51 %P 617–649 %G eng %R 10.1357/0022240933223963