Copepods Boost the Production but Reduce the Carbon Export Efficiency by Diatoms

The fraction of net primary production that is exported from the euphotic zone as sinking particulate organic carbon (POC) varies notably through time and from region to region. Phytoplankton containing biominerals, such as silicified diatoms have long been associated with high export fluxes. However, recent reviews point out that the magnitude of export is not controlled by diatoms alone, but determined by the whole plankton community structure. The combined effect of phytoplankton community composition and zooplankton abundance on export flux dynamics, were explored using a set of 12 large outdoor mesocosms. All mesocosms received a daily addition of minor amounts of nitrate and phosphate, while only 6 mesocosms received silicic acid (dSi). This resulted in a dominance of diatoms and dinoflagellate in the +Si mesocosms and a dominance of dinoflagellate in the -Si mesocosms. Simultaneously, half of the mesocosms had decreased mesozooplankton populations whereas the other half were supplemented with additional zooplankton. In all mesocosms, POC fluxes were positively correlated to Si/C ratios measured in the surface community and additions of dSi globally increased the export fluxes in all treatments highlighting the role of diatoms in C export. The presence of additional copepods resulted in higher standing stocks of POC, most probably through trophic cascades. However it only resulted in higher export fluxes for the +Si mesocosms. In the +Si with copepod addition (+Si +Cops) export was dominated by large diatoms with higher Si/C ratios in sinking material than in standing stocks. During non-bloom situations, the grazing activity of copepods decrease the export efficiency in diatom dominated systems by changing the structure of the phytoplankton community and/or preventing their aggregation. However, in flagellate-dominated system, the copepods increased phytoplankton growth, aggregation and fecal pellet production, with overall higher net export not always visible in term of export efficiency

Learning biophysically-motivated parameters for alpha helix prediction

<p>Abstract</p> <p>Background</p> <p>Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using parameterizable cost functions representing biological "pseudo-energies". Machine learning methods are applied to estimate the values of the parameters to correctly predict known protein structures.</p> <p>Results</p> <p>Focusing on the prediction of alpha helices in proteins, we show that a model with 302 parameters can achieve a Q_{<it>α </it>}value of 77.6% and an SOV_{<it>α </it>}value of 73.4%. Such performance numbers are among the best for techniques that do not rely on external databases (such as multiple sequence alignments). Further, it is easier to extract biological significance from a model with so few parameters.</p> <p>Conclusion</p> <p>The method presented shows promise for the prediction of protein secondary structure. Biophysically-motivated elementary free-energies can be learned using SVM techniques to construct an energy cost function whose predictive performance rivals state-of-the-art. This method is general and can be extended beyond the all-alpha case described here.</p

Differences in size distribution of marine phytoplankton in presence versus absence of jellyfish support theoretical predictions on top-down control patterns along alternative energy pathways

While theoretical food web studies highlight the importance of alternative energy pathways in shaping community response to bottom-up and top-down forcing, empirical insight on the relevance of the predicted patterns is largely lacking. In marine plankton food webs differences in food size spectra between ciliates and copepods lead to alternative energy pathways, one expanding from small phytoplankton over ciliates to copepods, the other from large edible phytoplankton directly to copepods. Correspondingly, predation pressure by copepods leads to an increase of small phytoplankton through top-down control of copepods on ciliates, but to a decrease of large phytoplankton through direct predation by copepods. Hence, food web theory predicts a shift from the dominance of large to small algae along an enrichment gradient. This prediction clearly deviates from the general assumption of a shift from small fast growing to larger slow-growing phytoplankton taxa with increasing nutrient availability. However, if copepods themselves are under top-down control by strong predation through planktivores such as fish or jellyfish, dominance of large algae is expected throughout the enrichment gradient. We tested these predictions by analyzing the phytoplankton composition from numerous marine lakes and lagoon sites located on the archipelago of Palau covering a wide range of nutrient levels, comparing sites lacking large numbers of higher trophic levels with sites harboring high densities of jellyfish. The observed patterns strongly support that higher trophic levels influence the phytoplankton size distribution along a nutrient enrichment gradient, highlighting the importance of alternate energy pathways in food webs for community responses

Phytoplankton distribution during two contrasted summers in a Mediterranean harbour: combining automated submersible flow cytometry with conventional techniques

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Comparative study of three analysis methods (TTGE, flow cytometry and HPLC) for xenobiotic impact assessment on phytoplankton communities

International audienceThe impacts of the fungicide Opus® (epoxiconazole) on marine phytoplankton communities were assessed in a 12-day field experiment using in situ microcosms maintained underwater at 6 m depth. Three community analysis methods were compared for their sensitivity threshold in fungicide impact detection. When phytoplankton communities were exposed to 1 μg l−1 of epoxiconazole, no effects could be demonstrated using TTGE (Temporal Temperature Gradient gel Electrophoresis), flow cytometry or HPLC. When exposed to 10 μg l−1, TTGE fingerprints from PCR amplified 18S rDNA of communities exhibited significant differences compared with controls (ANOSIM, P = 0.028). Neither flow cytometry counts, nor HPLC pigment profiles allowed to show significant differences in microcosms exposed to 10 μg l−1 of epoxiconazole. When exposed to 100 μg l−1, all three methods allowed to detect significant differences in treated microcosms, as compared to controls. The TTGE analysis appears in this study as the most sensitive method for fungicide impact assessment on eukaryote microbial communities

Effets de l'hydroclimat local sur les groupes de phytoplancton dans l'estuaire de la Charente

Cette étude s’inscrit dans le cadre du projet TOPHYPAC (2011-2014) financé par le programme “Pesticides” du Ministère de l’Écologie, du Développement durable et de l’Énergie. Ce travail vise à décrire les variations saisonnières des abondances de phytoplancton en lien avec l'environnement physique et chimique (nutriments et métaux) de l'estuaire de la Charente de 2011 à 2014. À partir des données d'abondances de groupes phytoplanctoniques déterminés par microscopie et par cytométrie de flux, les contributions relatives des variables environnementales sur la dynamique du phytoplancton ont été évaluées : dans ce but, une analyse PLS multibloc a été réalisée. Celle-ci souligne une contribution importante de l'environnement physique (température, salinité et rayonnement photosynthétiquement actif (PAR)) sur l'abondance globale du phytoplancton. Les données de température et de salinité haute fréquence enregistrées ont permis de distinguer deux périodes hydroclimatiques : la première (2011 et début 2012) correspondant à des masses d’eau plus chaudes et plus salées que la seconde (du printemps 2012 au début de 2014). Dans ce contexte hydroclimatique, les variations saisonnières inter-annuelles des groupes de phytoplancton et des nutriments et oligo-éléments ont été analysées grâce à des analyses triadiques partielles. On note que l'occurrence des picoeucaryotes apparaît différemment entre l'année 2011 et les années 2012 et 2013 (comme pour la silice, le cadmium et le nickel). Les occurrences d'autres groupes phytoplanctoniques montrent quant à elles des différences entre l'année 2013 et les années 2011 et 2012, à l'image du cuivre et des phosphates. Le décalage entre les périodes hydroclimatiques et la réponse des principaux groupes phytoplanctoniques étudiés suggère que leur développement et leur succession pourraient dépendre des conditions environnementales du début de l'année (période hivernale). Enfin, les relations des groupes de phytoplancton avec certains nutriments et métaux (mises en évidence par la méthode STATICO) révèlent que les concentrations en phosphate et en cuivre peuvent contribuer à la structuration des communautés de phytoplancton dans l'estuaire de la Charente

Effect of local hydroclimate on phytoplankton groups in the Charente estuary

00001 ăWOS:000386406500033International audienceThis study aimed to describe seasonal variations of phytoplankton abundances in relation to the physical and chemical (nutrients and metals) environment under the influence of freshwater input in the Charente river estuary (Marennes-Oleron bay, France) over three years, from 2011 to 2014. Phytoplankton abundances were determined using microscopy and flow cytometry. Considering high frequency temperature and salinity data, breakpoints in each series led to the identification of two local hydroclimatic periods: the first (2011 and early 2012) being warmer and higher in salinity than the second (from spring 2012 to the beginning of 2014). A multiblock PLS analysis highlighted the significant contribution of the physical environment (temperature, salinity and Photosynthetically Active Radiation (PAR)) on phytoplankton abundances. Two partial triadic analyses (PTA) were run in order to visualize seasonal variations of i) phytoplankton groups and ii) nutrients and trace elements, irrespective of spatial gradient: picoeukaryote occurrence showed a difference between year 2011 and the years 2012 and 2013 (as did cadmium, nickel and silica levels). However, both PTA revealed greater differences between year 2013 and the years 2011 and 2012, as shown by occurrences of cryptophytes, dinoflagellates and nano-eukaryotes, as well as copper and phosphate levels. These results showed a shift between the hydro climate breakpoint and some phytoplankton responses, suggesting that their development and succession might depend on conditions early in the year. Finally, a STATICO analysis was performed on the paired PTA in order to examine the relations of phytoplankton with nutrients and metals more closely. Most phytoplankton groups were represented on the first axis, together with cadmium on the one hand, and nitrates, silica and nickel on the other. This analysis revealed the separation of phytoplankton groups on the second axis that represented phosphates and copper. Hydroclimatic conditions and the nature of freshwater inputs, especially phosphates and copper content, might be key factors driving phytoplankton structure in the Charente estuary

Benthic Diatoms: What Makes Them Unique

International audienceDiatoms are found in almost all aquatic environments as long as light is available for their photosynthesis. In coastal ecosystems, pelagic diatoms are extensively studied, but their benthic counterparts, more discreet and more difficult to access, are often ignored. Yet living at much lower light intensities, they are a key compartment of coastal ecosystems functioning, being able to produce as much biomass as pelagic diatoms that live in the well-lit surface waters. Benthic diatoms differ considerably from pelagic forms on several aspects: First, pelagic and benthic diatoms do not follow the same seasonal dynamics: In the bay of Brest, we showed that benthic diatoms are the first to bloom in the season, providing food and energy to the ecosystem right from the beginning of spring (with 60% of the total biomass until April). The system then moves from a system dominated by benthic biomass in early spring to a system where the pelagic biomass dominates. Regarding biodiversity, most benthic diatoms species are different from those found in the water column, they are mostly pennate forms and are far more diverse. On the physiological side, benthic diatoms are incredibly well adapted to low light intensities. However, the mechanisms which result in this adaptation remain unclear. We search for the role of the nanostructure of the frustule in the capture of light, but no difference between pelagic and benthic diatoms could be highlighted so far. Of particular interest is that benthic diatoms able to migrate into the sediment, are adapted to the high Si(OH)4 concentrations found in their surrounding and evidence a multiphasic Si uptake with very high half saturation constant (KS). Their capacity to reverse benthic Si(OH)4 fluxes at the interface indicate the important role they also play in the coastal silica cycle and particularly in controlling the pelagic diatom production. It remains to examine the coupling between carbon and silica at the water/ sediment interface and to determine which factors control the benthic production. Further studies are also needed to understand which evolution has allowed pennate diatoms to colonize so successfully the benthic habitat

TOPHYPAC. Tolérance des communautés phytoplanctoniques aux phytosanitaires dans le panache de la Charente. Programme Évaluation et réduction des risques liés à l’utilisation des Pesticides

TOPHYPAC is a field study that was conducted in the Charente river estuary (Marennes-Oléron bay). The main goal was to assess the possible impact of chemical contamination with copper and pesticides on phytoplankton communities. Physical, chemical (nutrients, metals and pesticides) and biological (phytoplankton community) parameters were monitored in the field during three years, from 2011 to 2014. In 2012 and 2013, field sampling was coupled with experimental exposure of phytoplankton communities to copper and to an herbicide cocktail, after transportation to the lab: the effects were assessed using photosynthesis endpoint and cellular densities. TOPHYPAC allowed to set the framework of Charente estuary contamination with pesticides: herbicides glyphosate (and its metabolite AMPA) and metolachlor were almost permanently found at the most upstream station (Fort Lupin) from the studied area. The most elevated concentrations were noticed during the first part of each year. Samples from spring and early summer also exhibited other herbicide substances: dimethenamid, acetochlor, bentazon, mesotrion, metamitron. Phytoplankton evolution in the natural environment was studied as a whole but also on the following community subsets: micro-phytoplankton, nano-phytoplankton, pico-phytoplankton and cyanobacteria Synechococcus sp.. The most influent driver on the whole phytoplankton community abundance was shown to be temperature, related to seasons; however other variables such as salinity, tubidity and solar radiation were also significant drivers for the community subsets. The analysis model used highlighted an abnormal low abundance period for Synechococcus sp. during spring 2012. At the same time, a massive freshwater discharge that brought pesticides was also noticed: this event was not identified as responsible for this drop, but it could weaken the communities. The experimental part of the study showed a marked sensitivity of phytoplankton communities that were exposed to copper during the year 2012: especially, Synechococcus sp. were shown to be impacted by copper, at concentrations at the µg.L-1 level. The herbicide cocktail used during the year 2012 (glyphosate, metolachlor and mesotrion) induced no significant effect on phytoplankton communities, whatever the concentration tested and the season. During the year 2013, the modified cocktail (glyphosate, S-metolachor, dimethenamid and metamitron) led to significant but slight effects on photosynthesis with no variation related to stations or seasons. Tests run from spring to autumn during two years did not demonstrate phytoplankton sensitivity towards the tested herbicides at environmental relevant concentrations.TOPHYPAC est une étude sur l’estuaire de la Charente (bassin de Marennes-Oléron). L’objectif général du projet était d’évaluer l’impact éventuel de la contamination chimique par le cuivre et les pesticides sur les communautés phytoplanctoniques. Un suivi environnemental comportant des paramètres physiques, chimiques tels que les nutriments, métaux et pesticides, et biologiques (phytoplancton) a été réalisé de 2011 à 2014 ; ce suivi a été couplé, en 2012 et 2013, à une approche expérimentale sur les communautés de phytoplancton transplantées en laboratoire et exposées au cuivre et à deux mélanges d’herbicides. Les effets des contaminants testés ont été recherchés sur la photosynthèse et les abondances du phytoplancton. Le projet TOPHYPAC a permis de dresser un état des lieux de la contamination de l’estuaire par les pesticides : les analyses ont révélé une présence quasiment permanente des herbicides glyphosate (et son métabolite l’AMPA) et métolachlore au niveau de la station la plus en amont (Fort Lupin) du site d’étude. Les concentrations les plus importantes sont retrouvées dans la première partie de l’année. La période de printemps et début d’été est également celle où d’autres herbicides sont présents dans l’environnement tels que : diméthénamide, acétochlore, bentazone, mésotrione, métamitron. L’évolution du phytoplancton dans son milieu naturel a été analysée de manière globale mais aussi sur des sous-groupes : micro-phytoplancton, nano-phytoplancton, pico-phytoplancton et les cyanobactéries Synechococcus sp. L’influence prépondérante de la température, liée à la saisonnalité, a été démontrée sur l’abondance globale de la communauté ; cependant des paramètres tels que la salinité ou la turbidité, ainsi que le rayonnement, influencent aussi notablement les différents sous-groupes. Le modèle utilisé a mis en évidence une période pendant laquelle les Synechococcus sp. étaient anormalement peu abondants, au printemps 2012. La survenue concomitante d’une importante dessalure accompagnée de pesticides ne semble pas être en cause, mais pourrait constituer un facteur fragilisant les communautés. Au niveau expérimental, les expositions des communautés au cuivre ont montré une sensibilité plus importante de celles-ci en 2012 : en particulier, une sensibilité très marquée des Synechococcus sp. au cuivre a été démontrée, avec des valeurs seuils d’effets parfois de l’ordre du µg.L-1. Le mélange d’herbicides utilisé en 2012 (glyphosate, métolachlore et mésotrione) n’a conduit à aucun effet significatif aux concentrations testées sur les communautés, quelle que soit la période. En 2013, le mélange, quelque peu différent (glyphosate, S-métolachore, diméthénamide et métamitron), a entraîné des effets significatifs modérés, uniquement sur la photosynthèse, et relativement stables au niveau spatial (stations) et temporel (saisons). Il semble que les essais réalisés du printemps à l’automne au cours de deux années consécutives ne permettent pas de conclure à une sensibilité particulière du phytoplancton aux concentrations environnementales des herbicides testés