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How do microalgae perceive light in a high-rate pond? Towards more realistic Lagrangian experiments.

ABSTRACT: Hydrodynamics in a high-rate production reactor for microalgae cultivation affects the light history perceived by cells. The interplay between cell movement and medium turbidity leads to a complex light pattern, whose forcing effects on photosynthesis and photoacclimation dynamics are non-trivial. Hydrodynamics of high density algal ponds mixed by a paddle wheel has been studied recently, although the focus has never been on describing its impact on photosynthetic growth efficiency. In this multidisciplinary downscaling study, we first reconstructed single cell trajectories in an open raceway using an original hydrodynamical model offering a powerful discretization of the Navier-Stokes equations tailored to systems with free surfaces. The trajectory of a particular cell was selected and the associated high-frequency light pattern was computed. This light pattern was then experimentally reproduced in an Arduino-driven computer controlled cultivation system with a low density Dunaliella salina culture. The effect on growth and pigment content was recorded for various frequencies of the light pattern, by setting different paddle wheel velocities. Results show that the frequency of this realistic signal plays a decisive role in the dynamics of photosynthesis, thus revealing an unexpected photosynthetic response compared to that recorded under the on/off signals usually used in the literature. Indeed, the light received by a single cell contains signals from low to high frequencies that nonlinearly interact with the photosynthesis process and differentially stimulate the various time scales associated with photoacclimation and energy dissipation. This study highlights the need for experiments with more realistic light stimuli to better understand microalgal growth at high cell densities. An experimental protocol is also proposed, with simple, yet more realistic, step functions for light fluctuations.

SUBMITTER: Demory D

PROVIDER: S-EPMC5990726 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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How do microalgae perceive light in a high-rate pond? Towards more realistic Lagrangian experiments.

Demory David D Combe Charlotte C Hartmann Philipp P Talec Amélie A Pruvost Eric E Hamouda Raouf R Souillé Fabien F Lamare Pierre-Olivier PO Bristeau Marie-Odile MO Sainte-Marie Jacques J Rabouille Sophie S Mairet Francis F Sciandra Antoine A Bernard Olivier O

Royal Society open science 20180530 5

Hydrodynamics in a high-rate production reactor for microalgae cultivation affects the light history perceived by cells. The interplay between cell movement and medium turbidity leads to a complex light pattern, whose forcing effects on photosynthesis and photoacclimation dynamics are non-trivial. Hydrodynamics of high density algal ponds mixed by a paddle wheel has been studied recently, although the focus has never been on describing its impact on photosynthetic growth efficiency. In this mult ...[more]

PMID: 29892466

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Project description:BackgroundWith the continued development of new computational tools for multiple sequence alignment, it is necessary today to develop benchmarks that aid the selection of the most effective tools. Simulation-based benchmarks have been proposed to meet this necessity, especially for non-coding sequences. However, it is not clear if such benchmarks truly represent real sequence data from any given group of species, in terms of the difficulty of alignment tasks.ResultsWe find that the conventional simulation approach, which relies on empirically estimated values for various parameters such as substitution rate or insertion/deletion rates, is unable to generate synthetic sequences reflecting the broad genomic variation in conservation levels. We tackle this problem with a new method for simulating non-coding sequence evolution, by relying on genome-wide distributions of evolutionary parameters rather than their averages. We then generate synthetic data sets to mimic orthologous sequences from the Drosophila group of species, and show that these data sets truly represent the variability observed in genomic data in terms of the difficulty of the alignment task. This allows us to make significant progress towards estimating the alignment accuracy of current tools in an absolute sense, going beyond only a relative assessment of different tools. We evaluate six widely used multiple alignment tools in the context of Drosophila non-coding sequences, and find the accuracy to be significantly different from previously reported values. Interestingly, the performance of most tools degrades more rapidly when there are more insertions than deletions in the data set, suggesting an asymmetric handling of insertions and deletions, even though none of the evaluated tools explicitly distinguishes these two types of events. We also examine the accuracy of two existing tools for annotating insertions versus deletions, and find their performance to be close to optimal in Drosophila non-coding sequences if provided with the true alignments.ConclusionWe have developed a method to generate benchmarks for multiple alignments of Drosophila non-coding sequences, and shown it to be more realistic than traditional benchmarks. Apart from helping to select the most effective tools, these benchmarks will help practitioners of comparative genomics deal with the effects of alignment errors, by providing accurate estimates of the extent of these errors.

Dataset Information

How do microalgae perceive light in a high-rate pond? Towards more realistic Lagrangian experiments.

Publications

How do microalgae perceive light in a high-rate pond? Towards more realistic Lagrangian experiments.

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