Biology subjects

Bouly, J.-P.

Publications and source records attributed to Bouly, J.-P..

4 recordsLinked to original sources

bioRxiv2026

Microdiversity drives resilience and niche partitioning in the bloom forming cyanobacteria Limnospira platensis

The intraspecific evolutionary mechanisms of adaptation in blooming cyanobacteria, particularly those occurring on small spatial and temporal scales, remain poorly understood. Here, we used the unique properties of Lake Dziani Dzaha, which hosts a persistent population of Limnospira platensis inhabiting distinct macro-habitats, to explore the spatial and temporal dynamics of microevolution. The Lake Dziani Dzaha (Mayotte), very stable at least since 2010, has experienced a seismo-volcanic crisis from May 2018 to November 2019, characterized by CO2 outgassing that led to the mixing of the initially seasonally stratified water column, as well as changes in numerous physicochemical parameters. Phylogenomic analysis of 108 strains isolated during sampling campaigns in 2010, 2014, 2022, and 2024 revealed a population that remained highly phylogenetically cohesive over time. In 2022, genomic expansion was observed, characterized by an increase in genome size due to the proliferation of insertion sequences and a subsequent loss of adaptive genes. By 2024, a rapid recovery of the 2010-2014 genetic content took place through multiple independent events of horizontal gene transfer. At the spatial scale, although no significant differences in gene content were detected, distinct subpopulations were identified based on allele frequencies. Some alleles were specifically fixed and subject to different selection pressures among the subpopulations, suggesting the existence of distinct ecotypes. Overall, this study highlights the role of microdiversity in rapid resilience of blooming cyanobacteria populations within dynamic environments and in their adaptation through niche partitioning.

microbiology↗

bioRxiv2024

Circadian regulation of key physiological processes by the RITMO1 clock protein in the marine diatom Phaeodactylum tricornutum

O_LIPhasing biological and physiological processes to periodic light-dark cycles is crucial for the life of most organisms. Marine diatoms, as many phytoplanktonic species, exhibit biological rhythms, yet their molecular timekeepers remain largely uncharacterized. Recently, the bHLH-PAS protein RITMO1 has been proposed to act as a regulator of circadian rhythms. C_LIO_LIIn this study, we first determined the physiological conditions to monitor circadian clock activity and its perturbation in the diatom model species Phaeodactylum tricornutum by using cell fluorescence as a circadian output. Employing ectopic overexpression, targeted gene mutagenesis, and functional complementation, we then investigated the role of RITMO1 in various circadian processes. C_LIO_LIOur findings reveal that RITMO1 significantly influences the P. tricornutum circadian rhythms not only of cellular fluorescence, but also of photosynthesis and of the expression of clock-controlled genes, including transcription factors and putative clock input/output components. RITMO1 effects on rhythmicity are unambiguously detectable under free running conditions. C_LIO_LIBy uncovering the complex regulation of biological rhythms in P. tricornutum, these results provide a key step in understanding the endogenous regulators of phytoplankton physiological responses to environmental changes. Furthermore, these studies position diatoms as instrumental and novel model systems for elucidating key mechanistic principles of oscillator functions in marine ecosystems. C_LI

molecular biology↗

bioRxiv2023

Diatom phytochromes integrate the entire visible light spectra for photosensing in marine environments

Aquatic life is strongly structured by light gradients, with gradual decrease in light intensity and differential attenuation of sunlight wavelengths with depth. How phytoplankton perceive these variations is unknown. By providing the first in vivo quantitative assessment of the action of marine diatom phytochrome photoreceptors (DPH), we show that they efficiently trigger photoreversible responses across the entire light spectrum, unlike current models of phytochrome photosensing. The distribution and activity of DPHs in the environment indicate that they are extremely sensitive detectors of spectral light variations related to depth and optical properties of the water column in temperate and polar oceans, revealing a completely novel view of how light is perceived in the marine environment.

plant biology↗

bioRxiv2019

ProfileView: multiple probabilistic models resolve protein families functional diversity

Sequence functional classification has become a critical bottleneck in understanding the myriad of protein sequences that accumulate in our databases. The great diversity of homologous sequences hides, in many cases, a variety of functional activities that cannot be anticipated. Their identification appears critical for a fundamental understanding of living organisms and for biotechnological applications. ProfileView is a sequence-based computational method, designed to functionally classify sets of homologous sequences. It relies on two main ideas: the use of multiple probabilistic models whose construction explores evolutionary information in available databases, and a new definition of a representation space where to look at sequences from the point of view of probabilistic models combined together. ProfileView classifies families of proteins for which functions should be discovered or characterised within known groups. We validate ProfileView on seven classes of widespread proteins, involved in the interaction with nucleic acids, amino acids and small molecules, and in a large variety of functions and enzymatic reactions. ProfileView agrees with the large set of functional data collected for these proteins from the literature regarding the organisation into functional subgroups and residues that characterize the functions. Furthermore, ProfileView resolves undefined functional classifications and extracts the molecular determinants underlying protein functional diversity, showing its potential to select sequences towards accurate experimental design and discovery of new biological functions. ProfileView proves to outperform three functional classification approaches, CUPP, PANTHER, and a recently developed neural network approach based on Restricted Boltzmann Machines. It overcomes time complexity limitations of the latter.

bioinformatics↗