@booklet {barton_novel_2023,
	title = {A novel fluoro-electrochemical technique for classifying diverse marine nanophytoplankton},
	year = {2023},
	month = {apr},
	publisher = {Life Sciences},
	type = {preprint},
	abstract = {<p>To broaden our understanding of pelagic ecosystem responses to environmental change, it is essential that we improve the spatio-temporal resolution of in situ monitoring of phytoplankton communities. A key challenge for existing methods is in classifying and quantifying cells within the nanophytoplankton size range (2-20{\textmu}m). This is particularly difficult when there are similarities in morphology, making visual differentiation difficult for both trained taxonomists and machine learning based approaches. Here we present a rapid fluoro-electrochemical technique for classifying nanophytoplankton, and using a library of 52 diverse strains of nanophytoplankton we assess the accuracy of this technique based on two measurements at the individual level: charge required to reduce per cell chlorophyll a fluorescence by 50\%, and cell radius. We demonstrate a high degree of accuracy overall (\&gt;90\%) in categorising cells belonging to widely recognised key functional groups, however this is reduced when we consider the broader diversity of {\textquotedblleft}nano-phytoflagellates{\textquotedblright}. Notably, we observe that some groups, for example calcifying Isochrysidales, have much greater resilience to electrochemically driven oxidative conditions relative to others of a similar size, making them more easily categorised by the technique. The findings of this study present a promising step forward in advancing our toolkit for monitoring phytoplankton communities. We highlight that, for improved categorisation accuracy, future iterations of the method can be enhanced by measuring additional predictor variables with minimal adjustments to the set-up. In doing so, we foresee this technique being highly applicable, and potentially invaluable, for in situ classification and enumeration of the nanophytoplankton size fraction.</p>
},
	keywords = {RCC1, rcc1084, RCC1130, RCC1150, RCC1178, RCC1185, RCC1198, RCC1216, rcc1217, RCC1242, RCC1314, RCC1346, RCC1489, RCC1511, RCC1546, RCC1557, RCC1614, rcc1731, RCC191, RCC2570, RCC3598, RCC3696, RCC3776, RCC3780, RCC4207, RCC4221, RCC4273, RCC4657, RCC4660, RCC6, RCC623, RCC6516, RCC656, RCC678, RCC69, RCC74, RCC76, RCC8, RCC80, RCC81, RCC88, RCC911, RCC950},
	doi = {10.1002/lom3.10572},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/10.1002/lom3.10572},
	author = {Barton, Samuel and Yang, Minjun and Chen, Haotian and Batchelor-McAuley, Christopher and Compton, Richard and Bouman, Heather and Rickaby, Rosalind}
}
@article {Bestion2020,
	title = {Abrupt declines in marine phytoplankton production driven by warming and biodiversity loss in a microcosm experiment},
	journal = {Ecology Letters},
	volume = {23},
	number = {3},
	year = {2020},
	note = {tex.mendeley-tags: RCC1303,RCC1512,RCC4221,RCC623,RCC626,RCC652,RCC80,RCC834},
	month = {mar},
	pages = {457{\textendash}466},
	abstract = {Rising sea surface temperatures are expected to lead to the loss of phytoplankton biodiversity. However, we currently understand very little about the interactions between warming, loss of phytoplankton diversity and its impact on the oceans{\textquoteright} primary production. We experimentally manipulated the species richness of marine phytoplankton communities under a range of warming scenarios, and found that ecosystem production declined more abruptly with species loss in communities exposed to higher temperatures. Species contributing positively to ecosystem production in the warmed treatments were those that had the highest optimal temperatures for photosynthesis, implying that the synergistic impacts of warming and biodiversity loss on ecosystem functioning were mediated by thermal trait variability. As species were lost from the communities, the probability of taxa remaining that could tolerate warming diminished, resulting in abrupt declines in ecosystem production. Our results highlight the potential for synergistic effects of warming and biodiversity loss on marine primary production.},
	keywords = {biodiversity, biodiversity loss, climate change, ecosystem functioning, phytoplankton, RCC1303, rcc1512, RCC4221, RCC623, RCC626, RCC652, RCC80, RCC834, thermal per-},
	issn = {1461-023X},
	doi = {10.1111/ele.13444},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.13444},
	author = {Bestion, Elvire and Barton, Samuel and Garc{\'\i}a, Francisca C. and Warfield, Ruth and Yvon-Durocher, Gabriel},
	editor = {Hillebrand, Helmut}
}
@article {Connell2020,
	title = {Diel oscillations in the feeding activity of heterotrophic and mixotrophic nanoplankton in the North Pacific Subtropical Gyre},
	journal = {Aquatic Microbial Ecology},
	volume = {85},
	year = {2020},
	note = {Publisher: Inter-Research Science Center tex.mendeley-tags: RCC80},
	month = {dec},
	pages = {167{\textendash}181},
	abstract = {Daily oscillations in photosynthetically active radiation strongly influence the timing of metabolic processes in picocyanobacteria, but it is less clear how the light-dark cycle affects the activities of their consumers. We investigated the relationship between marine picocyanobacteria and nanoplanktonic consumers throughout the diel cycle to determine whether heterotrophic and mixotrophic protists (algae with phagotrophic ability) display significant periodicity in grazing pressure. Carbon biomass of Prochlorococcus and Synechococcus was estimated continuously from abundances and cell size measurements made by flow cytometry. Picocyanobacterial dynamics were then compared to nanoplankton abundances and ingestion of fluorescently labeled bacteria measured every 4 h during a 4 d survey in the North Pacific Subtropical Gyre. Grazing of the labeled bacteria by heterotrophic nanoplankton was significantly greater at night than during the day. The grazing activity of mixotrophic nanoplankton showed no diel periodicity, suggesting that they may feed continuously, albeit at lower rates than heterotrophic nanoplankton, to alleviate nutrient limitation in this oligotrophic environment. Diel changes in Prochlorococcus biomass indicated that they could support substantial growth of nanoplankton if those grazers are the main source of picocyanobacterial mortality, and that grazers may contribute to temporally stable abundances of picocyanobacteria.},
	keywords = {bacterivory, diel cycles, mixotrophy, nanoplankton grazing, picocyanobacteria, RCC80},
	issn = {0948-3055},
	doi = {10.3354/ame01950},
	url = {http://dx.doi.org/10.3354/ame01950 https://www.int-res.com/abstracts/ame/v85/p167-181/},
	author = {Connell, PE and Ribalet, F and Armbrust, EV and White, A and Caron, DA}
}
@article {Barton2020,
	title = {Evolutionary temperature compensation of carbon fixation in marine phytoplankton},
	journal = {Ecology Letters},
	year = {2020},
	note = {tex.mendeley-tags: RCC1303,RCC1512,RCC1773,RCC4221,RCC623,RCC626,RCC652,RCC80,RCC834},
	month = {feb},
	pages = {ele.13469},
	abstract = {The efficiency of carbon sequestration by the biological pump could decline in the coming decades because respiration tends to increase more with temperature than photosynthesis. Despite these differences in the short-term temperature sensitivities of photosynthesis and respiration, it remains unknown whether the long-term impacts of global warming on metabolic rates of phytoplankton can be modulated by evolutionary adaptation. We found that respiration was consistently more temperature dependent than photosynthesis across 18 diverse marine phytoplankton, resulting in universal declines in the rate of carbon fixation with short-term increases in temperature. Long-term experimental evolution under high temperature reversed the short-term stimulation of metabolic rates, resulting in increased rates of carbon fixation. Our findings suggest that thermal adaptation may therefore have an ameliorating impact on the efficiency of phytoplankton as primary mediators of the biological carbon pump.},
	keywords = {climate change, evolutionary ecology, metabolism, phytoplankton physiology, RCC1303, rcc1512, RCC1773, RCC4221, RCC623, RCC626, RCC652, RCC80, RCC834, thermal performance curves},
	issn = {1461-023X},
	doi = {10.1111/ele.13469},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.13469},
	author = {Barton, Samuel and Jenkins, James and Buckling, Angus and Schaum, C.-Elisa and Smirnoff, Nicholas and Raven, John A. and Yvon-Durocher, Gabriel},
	editor = {Ezenwa, Vanessa}
}
@mastersthesis {VanTol2019,
	title = {Computational and experimental models of diatom-bacteria interaction},
	year = {2019},
	note = {ISBN: 9781085779104 Pages: 161 Publication title: ProQuest dissertations and theses tex.mendeley-tags: RCC80},
	type = {phd},
	abstract = {Microbial interactions structure ecosystems and fuel biogeochemical cycling. The metabolic activities operating in the ocean are critical to the entire planet. In this work, I focused on interactions between diatoms and heterotrophic bacteria. Diatoms are a group of unicellular brown algae with frustules composed of silica. They form the base of coastal and polar marine food webs and contribute one fifth of global primary productivity. The inorganic nutrients fixed by oxygenic photosynthesis fuel secondary productivity by marine bacteria. Marine bacteria and diatoms have a range of different interaction strategies; many are still being elucidated.In Chapter 1, I studied the antagonistic effects of a flavobacterium on diatom cell division. Croceibacter atlanticus inhibits cytokinesis in many species, causing the cells to elongate, become mutlinucleated, and filled with plastids.In Chapter 2, I created a metabolic model of the diatom Thalassiosira pseudonana using the genome and physiological data from the literature. Simulations of diatom growth using Flux Balance Analysis revealed a role for nitrate and sulfate assimilation in dissipating reductants from the plastid. Changing redox and nutrient conditions causes the cell to secrete metabolites including organic carbon, nitrogen, and sulfur.In Chapter 3, I created a metabolic model of the B12-producing alphaproteobacterium Ruegeria pomeroyi. Previous work has demonstrated that R. pomeroyi will provide cobalamin to T. pseudonana in B12-starvation conditions in exchange for organic sulfur and nitrogen. I constrained the metabolic models with transcriptomic data of T. pseudonana and R. pomeroyi in co-culture and simulated their interaction.The distinct character of metabolites produced by diatoms likely fuels interactions with bacteria capable of utilizing those molecules. Bacteria influence diatom metabolism by interfering with the cell cycle, through nutrient-limitation, by altering redox conditions, and providing the cofactors required for growth. In this work, I have contributed to the literature exploring the complexity of diatom-bacteria interactions, where chemical or peptide cues, signals, and antagonists underlie the dynamics of microbial interactions. I have also created a framework for exploring more general metabolic exchanges between diatoms and bacteria. Genome-scale metabolic modeling of interactions between distinct marine microbial communities may be key to accurately predicting the character of dissolve organic matter in the ocean.},
	keywords = {Croceibacter atlanticus, diatoms, Genome-scale met, RCC80},
	url = {https://remotexs.ntu.edu.sg/user/login?url=https://search.proquest.com/docview/2305846221?accountid=12665},
	author = {van Tol, Helena M}
}
@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 {Parks2017,
	title = {Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)},
	journal = {American Journal of Botany},
	volume = {105},
	number = {3},
	year = {2017},
	note = {tex.mendeley-tags: RCC205,RCC80},
	pages = {1{\textendash}18},
	keywords = {and, b, c, citation, diatoms, e, gene tree, genome duplication, j, n, nakov, paleopolyploidy, parks m, polyploidy, RCC205, RCC80, ruck, synonymous divergence, t, these authors contributed equally, to this work, wickett},
	doi = {10.1101/181115},
	author = {Parks, Matthew and Nakov, Teofil and Ruck, Elizabeth and Wickett, Norman J and Alverson, Andrew J and Rice, Ada L and Conservation, Plant and Botanic, Chicago and Glencoe, Garden}
}
@article {VanTol2016,
	title = {Ubiquitous marine bacterium inhibits diatom cell division},
	journal = {The ISME Journal},
	volume = {11},
	number = {1},
	year = {2017},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: 2016,RCC80},
	month = {jan},
	pages = {31{\textendash}42},
	keywords = {2016, RCC80},
	issn = {1751-7362},
	doi = {10.1038/ismej.2016.112},
	url = {http://dx.doi.org/10.1038/ismej.2016.112 http://www.nature.com/doifinder/10.1038/ismej.2016.112},
	author = {van Tol, Helena M and Amin, Shady A and Armbrust, E Virginia}
}
