@article {coleman_fine-tuning_2023,
	title = {Fine-tuning the flavor of Tetraselmis chuii by modifying nitrogen supply},
	journal = {Algal Research},
	year = {2023},
	pages = {103208},
	abstract = {Dried Tetraselmis chuii biomass has potential as flavoring agent for the development of plant-based seafood alternatives because of its seafood-like aroma and strong umami taste. Depending on the cultivation conditions, microalgae can adapt their metabolism, resulting in a change in biochemical composition. The aim of this study was to assess if the flavor of T. chuii could be modified by changing the nitrogen (N) supply in the cultivation medium in order to maximize the potential of T. chuii as flavoring agent. The sensory evaluation by a trained panel showed that the T. chuii biomass obtained from N starved cultivation conditions (N-deplete) is characterized by a significantly stronger odor intensity and earthy-like off-odor compared to T. chuii biomass obtained from N sufficient cultivation conditions (N-replete). The analysis of volatile organic compounds (VOCs) using SPME-GC{\textendash}MS showed that these odor features of N-deplete biomass are attributed to an increased formation of odor-active VOCs including 2,3-butanedione, 3-methylbutanal, 3-methylbutanol and sulfur-containing dimethyl sulfide and dimethyl disulfide. In contrast, the T. chuii N-replete biomass possessed a significantly stronger taste intensity, umami and salty taste compared to the T. chuii N-deplete biomass. The higher umami is attributed to the significantly higher free glutamic acid (Glu) and adenosine monophosphate (AMP) concentrations in N-replete biomass compared to N-deplete biomass. This study illustrates that flavor and palatability of microalgae biomass is strongly affected by cultivating conditions and modifying these conditions can be an important tool in the development of plant-based seafood alternatives.},
	keywords = {Microalgae, Nitrogen starvation, RCC128, Sensory evaluation, Umami, Volatile organic compounds},
	issn = {2211-9264},
	doi = {10.1016/j.algal.2023.103208},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926423002412},
	author = {Coleman, Bert and Van Poucke, Christof and Dewitte, Bavo and Casciaro, Valentina and Moerdijk-Poortvliet, Tanja and Muylaert, Koenraad and Robbens, Johan}
}
@article {pinto_features_2021,
	title = {Features of the Opportunistic Behaviour of the Marine Bacterium Marinobacter algicola in the Microalga Ostreococcus tauri Phycosphere},
	journal = {Microorganisms},
	volume = {9},
	year = {2021},
	pages = {1777},
	abstract = {Although interactions between microalgae and bacteria are observed in both natural environment and the laboratory, the modalities of coexistence of bacteria inside microalgae phyco-spheres in laboratory cultures are mostly unknown. Here, we focused on well-controlled cultures of the model green picoalga Ostreococcus tauri and the most abundant member of its phycosphere, Marinobacter algicola. The prevalence of M. algicola in O. tauri cultures raises questions about how this bacterium maintains itself under laboratory conditions in the microalga culture. The results showed that M. algicola did not promote O. tauri growth in the absence of vitamin B12 while M. algicola depended on O. tauri to grow in synthetic medium, most likely to obtain organic carbon sources provided by the microalgae. M. algicola grew on a range of lipids, including triacylglycerols that are known to be produced by O. tauri in culture during abiotic stress. Genomic screening revealed the absence of genes of two particular modes of quorum-sensing in Marinobacter genomes which refutes the idea that these bacterial communication systems operate in this genus. To date, the {\textquoteright}opportunistic{\textquoteright} behaviour of M. algicola in the laboratory is limited to several phytoplanktonic species including Chlorophyta such as O. tauri. This would indicate a preferential occurrence of M. algicola in association with these specific microalgae under optimum laboratory conditions.},
	keywords = {RCC4221},
	doi = {10.3390/microorganisms9081777},
	author = {Pinto, Jordan and Lami, Rapha{\"e}l and Krasovec, Marc and Grimaud, R{\'e}gis and Urios, Laurent and Lupette, Josselin and Escande, Marie-Line and Sanchez, Fr{\'e}d{\'e}ric and Intertaglia, Laurent and Grimsley, Nigel and Piganeau, Gwenael and Sanchez, Sophie}
}
@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 {Henry2020,
	title = {Formation and fate of oil-related aggregates (ORAs) in seawater at different temperatures},
	journal = {Marine Pollution Bulletin},
	volume = {159},
	number = {July},
	year = {2020},
	note = {Publisher: Elsevier tex.mendeley-tags: RCC4289},
	month = {oct},
	pages = {111483},
	abstract = {In this study, the formation and fate of oil-related aggregates (ORAs) from chemically dispersed oil in seawater (SW) were investigated at different temperatures (5 {\textdegree}C, 13 {\textdegree}C, 20 {\textdegree}C). Experiments in natural SW alone, and in SW amended with typical marine snow constituents (phytoplankton and mineral particles), showed that the presence of algae stimulated the formation of large ORAs, while high SW temperature resulted in faster aggregate formation. The ORAs formed at 5 {\textdegree}C and 13 {\textdegree}C required mineral particles for sinking, while the aggregates also sank in the absence of mineral particles at 20{\textdegree}. Early in the experimental periods, oil compound accumulation in ORAs was faster than biodegradation, particularly in aggregates with algae, followed by rapid biodegradation. High abundances of bacteria associated with hydrocarbon biodegradation were determined in the ORAs, together with algae-associated bacteria, while clustering analyses showed separation between bacterial communities in experiments with oil alone and oil with algae/mineral particles.},
	keywords = {Aggregation, biodegradation, Dispersed oil, Marine snow, Microbial communities, RCC4289, Sinking},
	issn = {0025326X},
	doi = {10.1016/j.marpolbul.2020.111483},
	url = {https://doi.org/10.1016/j.marpolbul.2020.111483 https://linkinghub.elsevier.com/retrieve/pii/S0025326X20306019},
	author = {Henry, Ingrid A. and Netzer, Roman and Davies, Emlyn J. and Brakstad, Odd Gunnar}
}
@article {Hackl2019,
	title = {Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis},
	journal = {Scientific Data},
	volume = {7},
	number = {1},
	year = {2020},
	note = {tex.mendeley-tags: RCC4623,RCC4624,RCC4625,RCC970},
	month = {dec},
	pages = {29},
	keywords = {RCC4623, RCC4624, RCC4625, RCC970},
	issn = {2052-4463},
	doi = {10.1038/s41597-020-0363-4},
	url = {http://www.nature.com/articles/s41597-020-0363-4},
	author = {Hackl, Thomas and Martin, Roman and Barenhoff, Karina and Duponchel, Sarah and Heider, Dominik and Fischer, Matthias G.}
}
@article {Krasovec2019,
	title = {First estimation of the spontaneous mutation rate in Diatoms},
	journal = {Genome Biology and Evolution},
	volume = {1},
	year = {2019},
	note = {tex.mendeley-tags: RCC2967},
	pages = {1{\textendash}23},
	keywords = {diatoms, Mutation accumulation, mutation rate in phaeodactylum, mutation spectrum, phaeodactylum, RCC2967, running title, spontaneous mutation rate, tricornutum},
	issn = {1759-6653},
	doi = {10.1093/gbe/evz130},
	url = {https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evz130/5520952},
	author = {Krasovec, Marc and Sanchez-Brosseau, Sophie and Piganeau, Gwenael},
	editor = {Baer, Charles}
}
@article {Arsenieff2019,
	title = {First viruses infecting the marine diatom guinardia delicatula},
	journal = {Frontiers in Microbiology},
	volume = {9},
	number = {January},
	year = {2019},
	note = {tex.mendeley-tags: RCC1000,RCC2023,RCC3046,RCC3083,RCC3093,RCC3101,RCC4657,RCC4659,RCC4660,RCC4667,RCC4834,RCC5154,RCC5777,RCC5778,RCC5779,RCC5780,RCC5781,RCC5782,RCC5783,RCC5784,RCC5785,RCC5787,RCC5788,RCC5789,RCC5790,RCC5792,RCC5793,RCC5794,RCC80},
	month = {jan},
	keywords = {diatoms, genomics, host-virus dynamics, RCC1000, RCC2023, RCC3046, RCC3083, RCC3093, RCC3101, RCC4657, RCC4659, RCC4660, RCC4667, RCC4834, RCC5154, RCC5777, RCC5778, RCC5779, RCC5780, RCC5781, RCC5782, RCC5783, RCC5784, RCC5785, RCC5787, RCC5788, RCC5789, RCC5790, RCC5792, RCC5793, RCC5794, RCC80, single-stranded RNA viruses, Western English Channel},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2018.03235},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.03235/full},
	author = {Arsenieff, Laure and Simon, Nathalie and Rigaut-jalabert, Fabienne and Le Gall, Florence and Chaffron, Samuel and Corre, Erwan and Com, Emmanuelle and Bigeard, Estelle and Baudoux, Anne-claire}
}
@article {Kuhlisch2017,
	title = {A fast and direct liquid chromatography-mass spectrometry method to detect and quantify polyunsaturated aldehydes and polar oxylipins in diatoms},
	journal = {Limnology and Oceanography: Methods},
	volume = {15},
	number = {1},
	year = {2017},
	note = {Publisher: John Wiley \& Sons, Ltd tex.mendeley-tags: RCC75,RCC776},
	month = {jan},
	pages = {70{\textendash}79},
	abstract = {Abstract Polyunsaturated aldehydes (PUAs) are a group of microalgal metabolites that have attracted a lot of attention due to their biological activity. Determination of PUAs has become an important routine procedure in plankton and biofilm investigations, especially those that deal with chemically mediated interactions. Here we introduce a fast and direct derivatization free method that allows quantifying PUAs in the nanomolar range, sufficient to undertake the analysis from cultures and field samples. The sample preparation requires one simple filtration step and the initiation of PUA formation by cell disruption. After centrifugation the samples are ready for measurement without any further handling. Within one chromatographic run this method additionally allows us to monitor the formation of the polar oxylipins arising from the cleavage of precursor fatty acids. The robust method is based on analyte separation and detection using ultra high performance liquid chromatography-atmospheric pressure chemical ionization mass spectrometry (UHPLC-APCI MS) and enables high throughput investigations by employing an analysis time of only 5 min. Our protocol thus provides an alternative and extension to existing PUA determinations based on gas chromatography-mass spectrometry (GC-MS) with shorter run times and without any chemical derivatization. It also enables researchers with widely available LC-MS analytical platforms to monitor PUAs. Additionally, non-volatile oxylipins such as ?-oxo-acids and related compounds can be elucidated and monitored.},
	keywords = {RCC75, RCC776},
	issn = {1541-5856},
	doi = {10.1002/lom3.10143},
	url = {https://doi.org/10.1002/lom3.10143},
	author = {Kuhlisch, Constanze and Deicke, Michael and Ueberschaar, Nico and Wichard, Thomas and Pohnert, Georg}
}
@article {Dupuy2000,
	title = {Feeding rate of the oyster Crassostrea gigas in a natural planktonic community of the Mediterranean Thau Lagoon},
	journal = {Marine Ecology - Progress Series},
	volume = {205},
	year = {2000},
	note = {ISBN: 0171-8630 Publisher: Inter-Research tex.address: Nordbunte 23, D-21385 Oldendorf Luhe, Germany tex.mendeley-tags: RCC,rcc},
	pages = {171{\textendash}184},
	abstract = {The Mediterranean Thau Lagoon is an important oyster farming area in Europe. Oyster growth rates are among the highest in France, although chlorophyll a concentration is low. Previous studies have demonstrated that picophytoplankton, nano-microphytoplankton, dinoflagellates and loricate ciliates such as tintinnids are abundant. However, heterotrophic flagellates and aloricate ciliates have not been investigated. The aim of this study was to assess picophytoplankton, protist and zooplankton abundances in the Lagoon and to investigate the particular structure of the microbial food web, which may explain such paradoxical oyster growth. In oligotrophic waters in the Thau Lagoon, the picoeukaryote Ostreococcus tauri is the dominant autotrophic picoplankter, with an abundance maximum in summer. On 17 August 1998, following a rainfall event, pico- and nanophytoplankton abundances were not as high as expected and we observed a high abundance of large diatoms. At this time, the available carbon resources were produced by microphytoplankton (84.5\%), and picoplank-tonic cells represented only 1.27 \% in terms of carbon. Heterotrophic cells were low in abundance and constituted {\textexclamdown}14\% of carbon resources. In order to evaluate the importance of the {\textquoteright}protozoan trophic link{\textquoteright} for energy transfer from the microbial food web to large benthic suspension feeders, the oyster Crassostrea gigas was offered a planktonic community as potential prey. In the grazing experiment, all {\textquestiondown}5 mum flagellates, microphytoplankton, dinoflagellates, ciliates and large zooplankton were retained by the oyster gills. Only flagellates {\textexclamdown}5 pm and O. Tauri were not very well retained (45 and 2\% respectively). The high clearance rates of C. Gigas found in this experiment can be explained by a low concentration of suspended particulate matter (0.65 mg l(-1)). The oysters adapted their retention mechanism when they Lived in oligotrophic waters. These results indicate that, under the given experimental conditions, picophytoplankton did not represent a valuable trophic resource for farmed oysters because (1) C. Gigas cannot retain picoparticles and (2) the picoplankton represented a poor carbon resource capable of being transferred via a weak heterotrophic protist community. In the oyster pens of the Thau Lagoon during this study, microphytoplanktonic primary producers, in particular diatoms, were the main food sources for bivalve suspension feeders.},
	keywords = {ABUNDANCE, bivalve, carbon, COASTAL WATERS, EPIFLUORESCENCE MICROSCOPY, FILTRATION-RATE, food source, FOOD-CHAINS, GEUKENSIA-DEMISSA, heterotrophic protist, microbial food web, MYTILUS-EDULIS, oyster, PARTICLE SELECTION, picophytoplankton, rcc, RETENTION, Thau Lagoon, trophic link},
	doi = {10.3354/meps205171},
	author = {Dupuy, C and Vaquer, A and LamHoai, T and Rougier, C and Mazouni, N and Lautier, J and Collos, Y and LeGall, S}
}
