@article {merritt_variability_2024,
	title = {Variability in spectral absorption within cryptophyte phycobiliprotein types},
	journal = {Journal of Phycology},
	volume = {n/a},
	number = {n/a},
	year = {2024},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jpy.13439},
	abstract = {Cryptophytes are known to vary widely in coloration among species. These differences in color arise primarily from the presence of phycobiliprotein accessory pigments. There are nine defined cryptophyte phycobiliprotein (Cr-PBP) types, named for their wavelength of maximal absorbance. Because Cr-PBP type has traditionally been regarded as a categorical trait, there is a paucity of information about how spectral absorption characteristics of Cr-PBPs vary among species. We investigated variability in primary and secondary peak absorbance wavelengths and full width at half max (FWHM) values of spectra of Cr-PBPs extracted from 75 cryptophyte strains (55 species) grown under full spectrum irradiance. We show that there may be substantial differences in spectral shapes within Cr-PBP types, with Cr-Phycoerythrin (Cr-PE) 545 showing the greatest variability with two, possibly three, subtypes, while Cr-PE 566 spectra were the least variable, with only {\textpm}1 nm of variance around the mean absorbance maximum of 565 nm. We provide additional criteria for classification in cases where the wavelength of maximum absorbance alone is not definitive. Variations in spectral characteristics among strains containing the same presumed Cr-PBP type may indicate differing chromophore composition and/or the presence of more than one Cr-PBP in a single cryptophyte species.},
	keywords = {absorbance, Absorption, chromophore, cryptomonad, cryptophyte, phycobilin, phycobiliprotein, RCC1505, RCC2614, RCC3072, RCC350, RCC3575, RCC4102, RCC4116, RCC439, RCC4444, RCC4474, RCC4787, RCC4843, RCC4857},
	issn = {1529-8817},
	doi = {10.1111/jpy.13439},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13439},
	author = {Merritt, Kristia{\"a}n A. and Richardson, Tammi L.}
}
@article {walde_viral_2023,
	title = {Viral infection impacts the 3D subcellular structure of the abundant marine diatom Guinardia delicatula},
	journal = {Frontiers in Marine Science},
	volume = {9},
	year = {2023},
	abstract = {Viruses are key players in marine ecosystems where they infect abundant marine microbes. RNA viruses are emerging as key members of the marine virosphere. They have recently been identified as a potential source of mortality in diatoms, a group of microalgae that accounts for roughly 40\% of the primary production in the ocean. Despite their likely importance, their impacts on host populations and ecosystems remain difficult to assess. In this study, we introduce an innovative approach that combines automated 3D confocal microscopy with quantitative image analysis and physiological measurements to expand our understanding of viral infection. We followed different stages of infection of the bloom-forming diatom Guinardia delicatula by the RNA virus GdelRNAV-04 until the complete lysis of the host. From 20h after infection, we observed quantifiable changes in subcellular host morphology and biomass. Our microscopy monitoring also showed that viral infection of G. delicatula induced the formation of auxospores as a probable defense strategy against viruses. Our method enables the detection of discriminative morphological features on the subcellular scale and at high throughput for comparing populations, making it a promising approach for the quantification of viral infections in the field in the future.},
	keywords = {RCC3083, RCC5812},
	issn = {2296-7745},
	doi = {10.3389/fmars.2022.1034235},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2022.1034235},
	author = {Walde, Marie and Camplong, Cyprien and de Vargas, Colomban and Baudoux, Anne-claire and Simon, Nathalie}
}
@article {yee_v-type_2023,
	title = {The V-type ATPase enhances photosynthesis in marine phytoplankton and further links phagocytosis to symbiogenesis},
	journal = {Current Biology},
	year = {2023},
	month = {may},
	pages = {S0960982223006152},
	abstract = {Diatoms, dinoflagellates, and coccolithophores are dominant groups of marine eukaryotic phytoplankton that are collectively responsible for the majority of primary production in the ocean.1 These phytoplankton contain additional intracellular membranes around their chloroplasts, which are derived from ancestral engulfment of red microalgae by unicellular heterotrophic eukaryotes that led to secondary and tertiary endosymbiosis.2 However, the selectable evolutionary advantage of these membranes and the physiological significance for extant phytoplankton remain poorly understood. Since intracellular digestive vacuoles are ubiquitously acidified by V-type H+-ATPase (VHA),3 proton pumps were proposed to acidify the microenvironment around secondary chloroplasts to promote the dehydration of dissolved inorganic carbon (DIC) into CO2, thus enhancing photosynthesis.4,5 We report that VHA is localized around the chloroplasts of centric diatoms and that VHA significantly contributes to their photosynthesis across a wide range of oceanic irradiances. Similar results in a pennate diatom, dinoflagellate, and coccolithophore, but not green or red microalgae, imply the co-option of phagocytic VHA activity into a carbon-concentrating mechanism (CCM) is common to secondary endosymbiotic phytoplankton. Furthermore, analogous mechanisms in extant photosymbiotic marine invertebrates6{\textendash}8 provide functional evidence for an adaptive advantage throughout the transition from endosymbiosis to symbiogenesis. Based on the contribution of diatoms to ocean biogeochemical cycles, VHA-mediated enhancement of photosynthesis contributes at least 3.5 Gtons of fixed carbon per year (or 7\% of primary production in the ocean), providing an example of a symbiosis-derived evolutionary innovation with global environmental implications.},
	keywords = {RCC3387},
	issn = {09609822},
	doi = {10.1016/j.cub.2023.05.020},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982223006152},
	author = {Yee, Daniel P. and Samo, Ty J. and Abbriano, Raffaela M. and Shimasaki, Bethany and Vernet, Maria and Mayali, Xavier and Weber, Peter K. and Mitchell, B. Greg and Hildebrand, Mark and Decelle, Johan and Tresguerres, Martin}
}
@article {eyal_variability_2022,
	title = {The variability in the structural and functional properties of coccolith base plates},
	journal = {Acta Biomaterialia},
	volume = {148},
	year = {2022},
	pages = {336{\textendash}344},
	abstract = {Biomineralization processes exert varying levels of control over crystallization, ranging from poorly ordered polycrystalline arrays to intricately shaped single crystals. Coccoliths, calcified scales formed by unicellular algae, are a model for a highly controlled crystallization process. The coccolith crystals nucleate next to an organic oval structure that was termed the base plate, leading to the assumption that it is responsible for the oriented nucleation of the crystals via stereochemical interactions. In recent years, several works focusing on a well-characterized model species demonstrated a fundamental role for indirect interactions that facilitate coccolith crystallization. Here, we developed the tools to extract the base plates from five different species, giving the opportunity to systematically explore the relations between base plate and coccolith properties. We used multiple imaging techniques to evaluate the structural and chemical features of the base plates under native hydrated conditions. The results show a wide range of properties, overlaid on a common rudimentary scaffold that lacks any detectable structural or chemical motifs that can explain direct nucleation control. This work emphasizes that it is the combination between the base plate and the chemical environment inside the cell that cooperatively facilitate the exquisite control over the crystallization process. Statement of significance Biological organic scaffolds can serve as functional surfaces that guide the formation of inorganic materials. However, in many cases the specific interactions that facilitate such tight regulation are complex and not fully understood. In this work, we elucidate the architecture of such amodel biological template, an organic scale that directs the assembly of exquisite crystalline arrays of marine microalgae. By using cryo electron microscopy, we reveal the native state organization of these scales from several species. The observed similarities and differences allow us to propose that the chemical microenvironment, rather than stereochemical matching, is the pivotal regulator of the process.},
	keywords = {biomineralization, Calcite, Coccoliths, Cryo electron tomography, Crystallization, RCC1130, RCC1181, RCC190, RCC3777},
	issn = {1742-7061},
	doi = {10.1016/j.actbio.2022.06.027},
	url = {https://www.sciencedirect.com/science/article/pii/S174270612200366X},
	author = {Eyal, Zohar and Krounbi, Leilah and Ben Joseph, Oz and Avrahami, Emanuel M. and Pinkas, Iddo and Peled-Zehavi, Hadas and Gal, Assaf}
}
@article {bachy_viruses_2021,
	title = {Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts},
	journal = {The ISME Journal},
	year = {2021},
	note = {Publisher: Nature Publishing Group},
	month = {may},
	pages = {1{\textendash}19},
	abstract = {The marine picoeukaryote Bathycoccus prasinos has been considered a cosmopolitan alga, although recent studies indicate two ecotypes exist, Clade BI (B. prasinos) and Clade BII. Viruses that infect Bathycoccus Clade BI are known (BpVs), but not that infect BII. We isolated three dsDNA prasinoviruses from the Sargasso Sea against Clade BII isolate RCC716. The BII-Vs do not infect BI, and two (BII-V2 and BII-V3) have larger genomes (\textasciitilde210 kb) than BI-Viruses and BII-V1. BII-Vs share \textasciitilde90\% of their proteins, and between 65\% to 83\% of their proteins with sequenced BpVs. Phylogenomic reconstructions and PolB analyses establish close-relatedness of BII-V2 and BII-V3, yet BII-V2 has 10-fold higher infectivity and induces greater mortality on host isolate RCC716. BII-V1 is more distant, has a shorter latent period, and infects both available BII isolates, RCC716 and RCC715, while BII-V2 and BII-V3 do not exhibit productive infection of the latter in our experiments. Global metagenome analyses show Clade BI and BII algal relative abundances correlate positively with their respective viruses. The distributions delineate BI/BpVs as occupying lower temperature mesotrophic and coastal systems, whereas BII/BII-Vs occupy warmer temperature, higher salinity ecosystems. Accordingly, with molecular diagnostic support, we name Clade BII Bathycoccus calidus sp. nov. and propose that molecular diversity within this new species likely connects to the differentiated host-virus dynamics observed in our time course experiments. Overall, the tightly linked biogeography of Bathycoccus host and virus clades observed herein supports species-level host specificity, with strain-level variations in infection parameters.},
	keywords = {RCC715, RCC716},
	issn = {1751-7370},
	doi = {10.1038/s41396-021-00989-9},
	url = {https://www.nature.com/articles/s41396-021-00989-9},
	author = {Bachy, Charles and Yung, Charmaine C. M. and Needham, David M. and Gazit{\'u}a, Maria Consuelo and Roux, Simon and Limardo, Alexander J. and Choi, Chang Jae and Jorgens, Danielle M. and Sullivan, Matthew B. and Worden, Alexandra Z.}
}
@article {Yau2020,
	title = {Virus-host coexistence in phytoplankton through the genomic lens},
	journal = {Science Advances},
	volume = {6},
	number = {14},
	year = {2020},
	note = {tex.mendeley-tags: RCC2590,RCC2596},
	month = {apr},
	pages = {eaay2587},
	abstract = {Virus-microbe interactions in the ocean are commonly described by {\textquotedblleft}boom and bust{\textquotedblright} dynamics, whereby a numerically dominant microorganism is lysed and replaced by a virus-resistant one. Here, we isolated a microalga strain and its infective dsDNA virus whose dynamics are characterized instead by parallel growth of both the microalga and the virus. Experimental evolution of clonal lines revealed that this viral production originates from the lysis of a minority of virus-susceptible cells, which are regenerated from resistant cells. Whole-genome sequencing demonstrated that this resistant-susceptible switch involved a large deletion on one chromosome. Mathematical modeling explained how the switch maintains stable microalga-virus population dynamics consistent with their observed growth pattern. Comparative genomics confirmed an ancient origin of this {\textquotedblleft}accordion{\textquotedblright} chromosome despite a lack of sequence conservation. Together, our results show how dynamic genomic rearrangements may account for a previously overlooked coexistence mechanism in microalgae-virus interactions.},
	keywords = {RCC2590, RCC2596},
	issn = {2375-2548},
	doi = {10.1126/sciadv.aay2587},
	url = {https://advances.sciencemag.org/lookup/doi/10.1126/sciadv.aay2587},
	author = {Yau, Sheree and Krasovec, Marc and Benites, L. Felipe and Rombauts, Stephane and Groussin, Mathieu and Vancaester, Emmelien and Aury, Jean-Marc and Derelle, Evelyne and Desdevises, Yves and Escande, Marie-Line and Grimsley, Nigel and Guy, Julie and Moreau, Herv{\'e} and Sanchez-Brosseau, Sophie and Van de Peer, Yves and Vandepoele, Klaas and Gourbi{\`e}re, S{\'e}bastien and Piganeau, Gwenael}
}
@article {Castillo2020,
	title = {Visualization of viral infection dynamics in a unicellular eukaryote and quantification of viral production using virus fluorescence in situ hybridization},
	journal = {Frontiers in Microbiology},
	volume = {11},
	year = {2020},
	note = {Publisher: Frontiers Media S.A. tex.mendeley-tags: RCC4221},
	month = {jul},
	pages = {1559},
	abstract = {One of the major challenges in viral ecology is to assess the impact of viruses in controlling the abundance of specific hosts in the environment. To this end, techniques that enable the detection and quantification of virus-host interactions at the single-cell level are essential. With this goal in mind, we implemented virus fluorescence in situ hybridization (VirusFISH) using as a model the marine picoeukaryote Ostreococcus tauri and its virus Ostreococcus tauri virus 5 (OtV5). VirusFISH allowed the visualization and quantification of the proportion of infected cells during an infection cycle in experimental conditions. We were also able to quantify the abundance of free viruses released during cell lysis, discriminating OtV5 from other mid-level fluorescence phages in our non-axenic infected culture that were not easily distinguishable with flow cytometry. Our results showed that although the major lysis of the culture occurred between 24 and 48 h after OtV5 inoculation, some new viruses were already produced between 8 and 24 h. With this work, we demonstrate that VirusFISH is a promising technique to study specific virus-host interactions in non-axenic cultures and establish a framework for its application in complex natural communities.},
	keywords = {culture system, marine picoeukaryote, Ostreococcus tauri, Ostreococcus tauri virus 5, RCC4221, virus fluorescence in situ hybridization, virus-host interactions},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2020.01559},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.01559/full},
	author = {Castillo, Yaiza M. and Sebasti{\'a}n, Marta and Forn, Irene and Grimsley, Nigel and Yau, Sheree and Moraru, Cristina and Vaqu{\'e}, Dolors}
}
@article {Yau2016,
	title = {A viral immunity chromosome in the marine picoeukaryote, ostreococcus tauri},
	journal = {PLOS Pathogens},
	volume = {12},
	number = {10},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC299,RCC4221,RCC809},
	month = {oct},
	pages = {e1005965},
	keywords = {2016, RCC299, RCC4221, RCC809},
	issn = {1553-7374},
	doi = {10.1371/journal.ppat.1005965},
	url = {http://dx.plos.org/10.1371/journal.ppat.1005965},
	author = {Yau, Sheree and Hemon, Claire and Derelle, Evelyne and Moreau, Herv{\'e} and Piganeau, Gwenael and Grimsley, Nigel},
	editor = {Ding, Shou-Wei}
}
@article {Shimada1996,
	title = {Vertical distributions and photosynthetic action spectra of two oceanic picophytoplankers, Prochlorococcus marinus and Synechococcus sp},
	journal = {Marine Biology},
	volume = {127},
	year = {1996},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {15{\textendash}23},
	keywords = {OPTICAL-PROPERTIES, Photosynthesis, rcc, \#PROCHLOROCOCCUS},
	doi = {10.1007/BF00993639},
	author = {Shimada, A and Maruyama, T and Miyachi, S}
}
