Biology subjects

Ducret, H.

Publications and source records attributed to Ducret, H..

5 recordsLinked to original sources

bioRxiv2025

Proteomic insights into the photobiology of the Hawaiian rice coral Montipora capitata in response to decreased light intensity

Reef-building corals are sessile marine organisms that inhabit a wide range of light habitats along depth gradients. As coral biology is often studied in the context of global change and changing temperatures, knowledge gaps persist in our understanding of the molecular and cellular pathways involved in the responses to other factors than temperature, such as light intensity, which decreases exponentially in the water column and gradually changes the environment. To fill this gap, we tested the response of the Hawaiian rice coral Montipora capitata to decreased light intensity in a field experiment in K[a]neohe Bay, Oahu, Hawaii, using Data-Independent Acquisition (DIA) proteomics. There was a significant effect of light intensity on both the coral and zooxanthellae proteomes. In the M. capitata host, 69 proteins differed significantly in abundance between light levels after two years. The 50 proteins identified as significantly more abundant in the control condition were mostly involved in mRNA and RNA processing, pointing toward a positive correlation between metabolic activity, growth rates and increased light levels. The 19 proteins identified as significantly more abundant in the shade treatment were associated with calcium transport and with the structure of key cellular components, such as cell membrane and cytoskeleton. By contrast, zooxanthellae showed only minor changes in protein abundances, with photosynthesis proteins more abundant in the shade treatment and enzymes involved in fatty acid metabolism more abundant in the control treatment. Overall, these findings establish a baseline for our understanding of the cellular and metabolic processes driving Montipora capitatas acclimatization potential to different light intensities.

ecology↗

bioRxiv2025

Nature vs nurture? Light availability drives phenotypic plasticity within a reef coral species

Scleractinian corals exhibit wide intra-specific phenotypic variations. However, the extent to which these variations are explained by genotypic variation or phenotypic plasticity remains unclear. To elucidate this question, we devised a replicated experiment in which nine Montipora capitata coral colonies were cut into six pieces each, three of which were placed in shaded conditions (with a 73% reduction in light intensity) whereas the other three were kept in natural conditions as a control. After one year, we detected statistically significant morphological differences between corals of the same genotypes grown in different light environments, but no significant change in symbiont community structure. Colonies kept in control conditions exhibited high surface complexity and converged towards more digitate or corymbose morphs compared to shaded corals, which exhibited planar-like surfaces and converged toward laminar and foliose forms. Our data demonstrate the high level of light-driven phenotypic plasticity of Montipora capitata and suggest a trade-off between the amount of biomass per space area and the amount of absorption of incident light.

ecology↗

bioRxiv2025

A rapid and inexpensive universal PCR protocol for DNA (meta)barcoding using a one-tube, 2-step PCR

DNA barcoding has become a widespread technique for species identification through the amplification of standardized gene regions. These include the cytochrome c oxy-dase subunit I (COI) for metazoans, ITS for fungi and plants or the 16S rRNA for bacteria and archaea. It has been shown to be more accurate than more traditional methods such as morphology, making it a now widespread method for species delimitation. The development of new sequencing methods such as Nanopore sequencing becoming more affordable and accurate has led to a growing use of those methods and a need for fast, standardized and cheap protocol. Although Sanger sequencing has become super-seded by next-generation sequencing for most genomic applications, using second or third-generation sequencing for amplicons remains an expensive and time-consuming approach, especially for laboratories that analyse many different markers. Amplicon sequencing typically occurs in the context of either DNA barcoding (sequencing one or a few markers of interest for each specimen in a collection) or DNA metabarcoding (investigating the composition of a community by using universal primers targeting a whole group of organisms). Pooling the resulting PCR products for e.g. Nanopore sequencing requires the use of barcodes that are generally added to amplicons once they are amplified (using either ligation or a second round of amplification), and these supplementary steps are time-consuming, expensive and prone to contamination. To alleviate these issues, we present here a quick, single-tube two-step PCR with four primers: two internal primers with tails, and two external barcode primers that anneal on the tails during the second phase of the PCR. we show an improved 4 primers PCR protocol by using a single tube "drop in the lid" method. 8 DNA extract from Asellus. sp were obtained and amplified using both, 2-step PCR and the 1-step PCR. Results shows a clear enhancement of PCR product using the 2-step PCR for both ITS and CO1 marker compare to the 1-Step protocol. Method SummaryTo maximize the cost and effectiveness of barcoding approaches, we developed barcodes based on the Native Barcoding Kit 96 V14 of Oxford Nanopore Technologies (ONT). This step allows to tag samples within the PCR rather than through the use of ligase enzymes. To avoid primer interaction between the inner primer and the barcodes, the latter were added within the PCR cycles through the implementation of a hold step between the inner primer cycles and the barcoding cycles. For this purpose, barcodes are dried on the lid, avoiding the opening PCR tubes and preventing potential contamination.

genomics↗

bioRxiv2024

Shading does not lower thermal tolerance in the coral Montipora capitata: implications for conservation intervention

Marine heatwaves trigger severe coral bleaching events that result in dramatic losses of coral reefs worldwide. An increasingly common method used to mitigate coral bleaching is to shade portions of reefs. However, as shaded corals become less exposed to environmental stress, shading has also been hypothesized to lower their thermal tolerance, which would be detrimental for their survival. Here, we investigated how long-term shading modifies the response of Montipora capitata to both light and temperature stressors. After two years of growth, we used the Coral Bleaching Automated Stress System (CBASS) to compare responses of 73% shaded and unshaded corals during 1) temperature stress under ambient light, 2) temperature stress under low light, and 3) ambient temperature with light stress. Results show that shaded corals are less resistant than control ones to light stress and to heat stress under high light, but not to heat stress under low light, where no difference was detected. We further demonstrate that low light intensity during heat stress reduces the decline of photosynthetic efficiency when compared to heat stress at ambient light, regardless of the light history of the coral colonies. Our data support light-mediated stress, both independent of and synergistic with heat-induced stress, and suggest that light and heat stresses trigger different molecular and cellular pathways. We hereby confirm the benefits of coral shading under both short- and long-term temperature stress, and underline the importance of light acclimation in the conservation and restoration of coral reefs.

ecology↗

bioRxiv2021

Strong genetic structure and limited connectivity among populations of Clark's Anemonefish (Amphiprion clarkii) in the centre of marine biodiversity

Populations of anemonefish species often show signs of local isolation due limited dispersal potential and oceanographic conditions. Additionally, anthropogenic pressure, such as overharvesting and coral reef exploitation causes reduced population size, eventually leading to local extinction. The understanding of the genetic population structure, as well as the influence of both historical and current connectivity, is required to design effective marine protected area (MPA) networks. In this study, the genetic structure of Clarks Anemonefish (Amphiprion clarkii) populations of the Indo-Malay Archipelago (IMA) is assessed through mitochondrial control region (mtCR) sequences and nuclear microsatellites. Results provided evidence of a significant genetic structure (mtCR: {Phi}st = 0.42039, {Phi}ct = 0.63852; microsatellites: Fst = 0.01449, Fct = 0.05199). Genetic breaks were identified among Western (Padang Karimunjawa), Central (Sulawesi, Borneo, Bali, Komodo, Timor), and Eastern (Biak) IMA populations, which matches with patterns obtained for congeneric and other coral reef taxa. Due to the restricted connectivity among these three regions, it is suggested to consider them as separate management areas in the design of MPA networks.

molecular biology↗