@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 {dedman_shotgun_2023,
	title = {Shotgun proteomics reveals temperature-dependent regulation of major nutrient metabolism in coastal Synechococcus sp. WH5701},
	journal = {Algal Research},
	year = {2023},
	month = {oct},
	pages = {103279},
	abstract = {Marine cyanobacteria are major contributors to the oceanic carbon sink and are predicted to increase in numbers in the future warmed ocean. As a result, the influence of marine cyanobacteria on marine biogeochemical cycling will likely be enhanced. Associated with elevations in temperature the ocean will undergo increased stratification, reducing supply of essential nutrients to upper phototrophic layers. It is therefore critical that we resolve the manners by which cyanobacteria respond to variations in temperature, and consequences for major nutrient metabolism which may ultimately direct global biogeochemistry and trophic transfer. In this study we use the coastal Synechococcus sp. WH5701 to examine proteomic alterations in major nutrient (C, N and P) metabolic pathways following exposure to varying temperature. In response to temperature treatments, Synechococcus displayed higher rates of growth and photosynthetic efficiency when temperatures were raised from 17 {\textdegree}C to 23 {\textdegree}C and 28 {\textdegree}C, associated with a significant \textasciitilde30{\textendash}40 \% alteration in the cellular proteome. As temperatures increased, proteomic investment towards photosynthetic machinery appeared up-regulated, whilst abundance of RuBisCO was reduced, associated with an apparent alteration in CCM composition and carbon metabolism. N demand appeared to increase in-line with temperature, associated with alterations in the GS-GOGAT pathway, likely due to increased demand for and efficiency of protein synthesis. In contrast, P demand at the highest temperature appeared reduced as investment in the ribosome declines due to improved translation efficiency, whilst luxury P-storage appeared a feature of growth at low temperature. It appears likely that as seawater temperatures rise under ocean warming, the biochemical composition of cyanobacteria will be altered, increasing cellular C- and N- to P ratios, ultimately impacting upon their contribution to oceanic biogeochemical cycling.},
	keywords = {climate change, Ocean warming, phytoplankton, Proteomics: Marine biogeochemistry, rcc1084},
	issn = {2211-9264},
	doi = {10.1016/j.algal.2023.103279},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926423003120},
	author = {Dedman, Craig J. and Barton, Samuel and Fournier, Marjorie and Rickaby, Rosalind E. M.}
}
@article {Dore2020,
	title = {Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria},
	journal = {Frontiers in Microbiology},
	volume = {11},
	number = {September},
	year = {2020},
	note = {tex.mendeley-tags: RCC1084,RCC1085,RCC1086,RCC1087,RCC156,RCC158,RCC162,RCC2033,RCC2035,RCC2319,RCC2366,RCC2368,RCC2369,RCC2374,RCC2376,RCC2378,RCC2379,RCC2380,RCC2381,RCC2382,RCC2383,RCC2385,RCC2433,RCC2436,RCC2438,RCC2527,RCC2528,RCC2533,RCC2534,RCC2535,RCC2553,RCC2554,RCC2555,RCC2556,RCC2571,RCC2673,RCC278,RCC296,RCC307,RCC328,RCC3377,RCC407,RCC515,RCC539,RCC555,RCC556,RCC752,RCC753,RCC791},
	month = {sep},
	pages = {1{\textendash}23},
	keywords = {amino-acid substitutions, comparative genomics, evolution, genomic islands, marine cyanobacteria, niche adaptation, Prochlorococcus, rcc1084, RCC1085, RCC1086, RCC1087, RCC156, RCC158, rcc162, RCC2033, RCC2035, RCC2319, RCC2366, RCC2368, RCC2369, RCC2374, RCC2376, RCC2378, RCC2379, rcc2380, RCC2381, rcc2382, RCC2383, RCC2385, RCC2433, RCC2436, RCC2438, RCC2527, RCC2528, RCC2533, RCC2534, RCC2535, RCC2553, RCC2554, RCC2555, RCC2556, RCC2571, RCC2673, RCC278, rcc296, RCC307, RCC328, RCC3377, RCC407, RCC515, rcc539, rcc555, RCC556, rcc752, RCC753, rcc791, Synechococcus},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2020.567431},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.567431/full},
	author = {Dor{\'e}, Hugo and Farrant, Gregory K. and Guyet, Ulysse and Haguait, Julie and Humily, Florian and Ratin, Morgane and Pitt, Frances D. and Ostrowski, Martin and Six, Christophe and Brillet-Gu{\'e}guen, Loraine and Hoebeke, Mark and Bisch, Antoine and Le Corguill{\'e}, Gildas and Corre, Erwan and Labadie, Karine and Aury, Jean-Marc and Wincker, Patrick and Choi, Dong Han and Noh, Jae Hoon and Eveillard, Damien and Scanlan, David J. and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence}
}
@article {Gaignard2019,
	title = {Screening of marine microalgae: Investigation of new exopolysaccharide producers},
	journal = {Algal Research},
	volume = {44},
	year = {2019},
	note = {tex.ids= Gaignard2019a tex.mendeley-tags: RCC1084,RCC1196,RCC1504,RCC1714,RCC1774,RCC1786,RCC1863,RCC1978,RCC1983,RCC2035,RCC232,RCC2350,RCC2352,RCC2368,RCC2380,RCC2381,RCC2383,RCC2436,RCC2558,RCC2598,RCC2608,RCC2614,RCC2624,RCC2638,RCC269,RCC2696,RCC2703,RCC2932,RCC3069,RCC3072,RCC3092,RCC3093,RCC3436,RCC3649,RCC377,RCC4094,RCC4438,RCC4555,RCC4621,RCC4631,RCC4657,RCC76,RCC775,RCC821,RCC97 publisher: Elsevier},
	month = {dec},
	pages = {101711},
	abstract = {Biopolymers, such as exopolysaccharides are widely exploited by industry as hydrocolloids (gelling, thickening agents) and biological agents (anti-inflammatory, anti-parasitic, antioxidant, etc.). In this study, 166 marine microalgae and cyanobacteria species have been screened in order to identify strains producing original exopolysaccharides. This screening allowed the highlighting of 45 positive strains. In a second time, the monosaccharide compositions from 20 EPS of them were determined by GC/MS and HPAEC-PAD. The results led to a discovery of 8 new genera of microalgae producing EPS, including polymers with a very original composition like richness in GlcA. Finally, a phylogenic tree has been contructed in order to assess the link between the phylogeny of microalgae and the global composition of their exopolymers, based on data obtained in this study and from the literature.},
	keywords = {rcc1084, RCC1196, RCC1504, RCC1714, RCC1774, RCC1786, RCC1863, RCC1978, RCC1983, RCC2035, RCC232, RCC2350, RCC2352, RCC2368, rcc2380, RCC2381, RCC2383, RCC2436, RCC2558, RCC2598, RCC2608, RCC2614, RCC2624, RCC2638, RCC269, RCC2696, RCC2703, RCC2932, RCC3069, RCC3072, RCC3092, RCC3093, RCC3436, RCC3649, RCC377, RCC4094, RCC4438, RCC4555, RCC4621, RCC4631, RCC4657, RCC76, RCC775, RCC821, RCC97},
	issn = {22119264},
	doi = {10.1016/j.algal.2019.101711},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926419303261 https://linkinghub.elsevier.com/retrieve/pii/S2211926419303261},
	author = {Gaignard, C. and Laroche, C. and Pierre, G. and Dubessay, P. and Delattre, C. and Gardarin, C. and Gourvil, P. and Probert, I. and Dubuffet, A. and Michaud, P.}
}
@article {Grebert2018,
	title = {Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {in press},
	year = {2018},
	note = {tex.mendeley-tags: 2018,RCC1016,RCC1017,RCC1018,RCC1020,RCC1023,RCC1027,RCC1030,RCC1031,RCC1084,RCC1085,RCC1086,RCC1087,RCC1096,RCC1097,RCC1649,RCC1661,RCC1688,RCC2032,RCC2033,RCC2035,RCC2319,RCC2366,RCC2368,RCC2369,RCC2370,RCC2372,RCC2373,RCC2374,RCC2375,RCC2376,RCC2378,RCC2379,RCC2380,RCC2381,RCC2382,RCC2383,RCC2384,RCC2385,RCC2415,RCC2432,RCC2433,RCC2434,RCC2435,RCC2436,RCC2437,RCC2438,RCC2457,RCC2525,RCC2526,RCC2527,RCC2528,RCC2529,RCC2530,RCC2532,RCC2533,RCC2534,RCC2536,RCC2553,RCC2554,RCC2555,RCC2556,RCC2567,RCC2568,RCC2569,RCC2570,RCC2571,RCC2673,RCC30,RCC3010,RCC3012,RCC3014,RCC307,RCC316,RCC318,RCC325,RCC326,RCC328,RCC37,RCC44,RCC46,RCC47,RCC515,RCC539,RCC542,RCC543,RCC550,RCC552,RCC553,RCC555,RCC556,RCC557,RCC558,RCC559,RCC62,RCC650,RCC66,RCC752,RCC753,RCC790,RCC791,RCC792,RCC793,RCC794,sbr?hyto?app},
	month = {feb},
	pages = {201717069},
	abstract = {Marine Synechococcus cyanobacteria are major contributors to global oceanic primary production and exhibit a unique diversity of photosynthetic pigments, allowing them to exploit a wide range of light niches. However, the relationship between pigment content and niche partitioning has remained largely undetermined so far due to the lack of a single-genetic marker resolving all pigment types (PT). Here, we developed a novel and robust method based on three distinct marker genes to estimate the relative abundance of all Synechococcus PTs from metagenomes. Analysis of the Tara Oceans dataset allowed us to unveil for the first time the global distribution of Synechococcus PTs and to decipher their realized environmental niches. Green-light specialists (PT 3a) dominated in warm, green equatorial waters, whereas blue-light specialists (PT 3c) were particularly abundant in oligotrophic areas. Type IV chromatic acclimaters (CA4-A/B), which are able to dynamically modify their light absorption properties to maximally absorb green or blue light, were unexpectedly the most abundant PT in our dataset and predominated at depth and high latitudes. We also identified local populations in which CA4 might be inactive due to the lack of specific CA4 genes, notably in warm high nutrient low chlorophyll areas. Major ecotypes within clades I-IV and CRD1 were preferentially associated with a particular PT, while others exhibited a wide range of PTs. Altogether, this study brings unprecedented insights into the ecology of Synechococcus PTs and highlights the complex interactions between vertical phylogeny, pigmentation and environmental parameters that shape Synechococcus populations and evolution.},
	keywords = {2018, RCC1016, RCC1017, RCC1018, RCC1020, RCC1023, RCC1027, RCC1030, RCC1031, rcc1084, RCC1085, RCC1086, RCC1087, RCC1096, RCC1097, RCC1649, RCC1661, RCC1688, RCC2032, RCC2033, RCC2035, RCC2319, RCC2366, RCC2368, RCC2369, RCC2370, RCC2372, RCC2373, RCC2374, RCC2375, RCC2376, RCC2378, RCC2379, rcc2380, RCC2381, rcc2382, RCC2383, RCC2384, RCC2385, RCC2415, RCC2432, RCC2433, RCC2434, RCC2435, RCC2436, RCC2437, RCC2438, RCC2457, RCC2525, RCC2526, RCC2527, RCC2528, RCC2529, RCC2530, RCC2532, RCC2533, RCC2534, RCC2536, RCC2553, RCC2554, RCC2555, RCC2556, RCC2567, RCC2568, RCC2569, RCC2570, RCC2571, RCC2673, rcc30, RCC3010, RCC3012, RCC3014, RCC307, RCC316, RCC318, RCC325, RCC326, RCC328, RCC37, RCC44, RCC46, RCC47, RCC515, rcc539, RCC542, RCC543, RCC550, RCC552, RCC553, rcc555, RCC556, RCC557, RCC558, RCC559, RCC62, RCC650, RCC66, rcc752, RCC753, RCC790, rcc791, RCC792, RCC793, RCC794, sbr?hyto?app},
	issn = {0027-8424},
	doi = {10.1073/pnas.1717069115},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1717069115},
	author = {Gr{\'e}bert, Th{\'e}ophile and Dor{\'e}, Hugo and Partensky, Fr{\'e}d{\'e}ric and Farrant, Gregory K. and Boss, Emmanuel S. and Picheral, Marc and Guidi, Lionel and Pesant, St{\'e}phane and Scanlan, David J. and Wincker, Patrick and Acinas, Silvia G. and Kehoe, David M. and Garczarek, Laurence}
}
@article {Baines2012,
	title = {Significant silicon accumulation by marine picocyanobacteria},
	journal = {Nature Geoscience},
	volume = {5},
	number = {12},
	year = {2012},
	note = {arXiv: 9605103 [cs] ISBN: 1752-08941?752-0908 Publisher: Nature Publishing Group tex.arxivid: cs/9605103 tex.mendeley-tags: rcc1084,rcc1086,rcc752},
	pages = {886{\textendash}891},
	abstract = {The marine silicon cycle is thought to be intimately tied to the carbon cycle through its effect on the growth of diatoms. These unicellular algae form substantial blooms in cold, nutrient-rich waters. Their dense, siliceous cell walls promote the sinking of particulate matter, and all the carbon and nutrients contained therein1. As such, diatoms are thought to be the primary organisms responsible for the low levels of dissolved silicon observed in the surface ocean and the export of mineral silica to depth. Here, we use synchrotron X-ray fluorescence microscopy to determine the elemental composition of individual diatoms and cyanobacterial cells from the eastern equatorial Pacific and the Sargasso Sea.We show that cells of Synechococcus, a small unicellular marine cyanobacterium that dominates in nutrient-depleted waters2, can exhibit cellular ratios of silicon to sulphur, and silicon to phosphorus, approaching those detected in diatoms in the same location. Silicon accumulation was also observed in cultured Synechococcus strains. We estimate that the water column inventory of silicon in Synechococcus can exceed that of diatomsinsomecases.We suggest that picocyanobacteriamay exert a previously unrecognized influence on the oceanic silicon cycle, especially in nutrient-poorwaters.},
	keywords = {rcc1084, RCC1086, rcc752},
	issn = {1752-0894},
	doi = {10.1038/ngeo1641},
	url = {http://www.nature.com/doifinder/10.1038/ngeo1641},
	author = {Baines, Stephen B. and Twining, Benjamin S. and Brzezinski, Mark a. and Krause, Jeffrey W. and Vogt, Stefan and Assael, Dylan and McDaniel, Hannah}
}
