Biology subjects

Pochon, X.

Publications and source records attributed to Pochon, X..

4 recordsLinked to original sources

bioRxiv2025

Biofouling on aquaculture mesh: disentangling seasonal and environmental effects with eDNA

Biofouling presents ecological and economic challenges for marine industries, yet patterns of community development in relevant environments remain underexplored. In this study, we examined seasonal (winter vs summer) and spatial (sheltered vs exposed) patterns in eukaryotic biofouling across six coastal sites in New Zealand. Using standardised mesh substrates and environmental DNA (eDNA) metabarcoding with the 18S rRNA gene, we characterised over 10,000 Amplicon Sequence Variants (ASVs) across 216 samples, revealing 541 species from 249 taxonomic classes. Exposed sites exhibited marked seasonal contrasts: winter communities were dominated by hydroids (e.g., Coryne eximia), while summer samples shifted to amphipod-rich assemblages (e.g., Jassa slatteryi). Sheltered sites showed more stable biomass and diversity but greater site-level variability, especially in summer. Temperature and wind fetch emerged as key environmental drivers, with larger seasonal fluctuations observed under high-exposure conditions. Notably, several dominant species were non-native, underscoring the importance of early detection. These findings highlight the value of molecular monitoring for predicting biofouling risks and informing site-specific antifouling strategies in dynamic marine environments.

ecology↗

bioRxiv2024

CRISPR-based environmental biosurveillance assisted via artificial intelligence design of guide-RNAs

Environmental biosecurity challenges are worsening for aquatic ecosystems as climate change and increased anthropogenic pressures facilitate the spread of invasive species, thereby broadly impacting ecosystem composition, functioning, and services. Environmental DNA (eDNA) has transformed traditional biomonitoring through detection of trace DNA fragments left by organisms in their surroundings, primarily by application of the quantitative polymerase chain reaction (qPCR). However, qPCR presents challenges, including limited portability, reliance on precise thermal cycling, and susceptibility to inhibitors. To address these challenges and enable field-deployable monitoring, isothermal amplification techniques such as Recombinase Polymerase Amplification (RPA) paired with Clustered Regularly Interspaced Short Palindromic Repeats and associated proteins (CRISPR-Cas) have been proposed as alternatives. We report here the development of CORSAIR (CRISPR-based envirOnmental biosuRveillance aSsisted via Artificial Intelligence guide-RNAs), that harnesses the programmability of the CRISPR-Cas technology, RPA and the artificial intelligence (AI)-based tool Activity-informed Design with All-inclusive Patrolling of Targets (ADAPT) to deploy a swift RPA-CRISPR-Cas13a-based method that detects eDNA from two invasive species as proof of concept: Sabella spallanzanii and Undaria pinnatifida. CORSAIR showcased a robust, streamlined method augmented by ADAPT, reaching a high specificity when tested against co-occurring species and a 100% agreement with 12 PCR-benchmarked eDNA samples, reaching a sensitivity of 0.34 copies uL-1 in 1 hour with a cost of 3.5 USD per sample; thus highlighting CORSAIR as a powerful environmental biosurveillance platform for environmental nucleic acid detection. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/627849v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@b60942org.highwire.dtl.DTLVardef@119e924org.highwire.dtl.DTLVardef@1956bforg.highwire.dtl.DTLVardef@18e18b9_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

molecular biology↗

bioRxiv2024

A novel menthol-DCMU bleaching method for foraminifera: Generating aposymbiotic hosts for symbiosis research

Predicting the response and resilience of coral reefs to climate change can be achieved through better understanding the cellular symbiosis between coral reef holobionts and their associated endosymbiotic algae. Larger benthic foraminifera (LBF) are key calcium carbonate producers, of which two species were investigated for their suitability for menthol bleaching. The LBF Amphistegina lobifera, hosting diatoms, and Sorites orbiculus, hosting dinoflagellates of the family Symbiodiniaceae. This study aimed to rapidly generate symbiont-free (aposymbiotic) hosts via treatment with menthol and DCMU. The first experiment, Menthol Concentration Comparison (MCC), aimed to find a non-lethal and effective dose for both species. The second experiment, Menthol-bleaching Ecophysiology Assessment (MEA), used a larger sample size of both species to test the response to one concentration 0.19 mmol L-1 and measured growth, motility (an indicator for overall fitness) and mortality over a 4-week time frame. Menthol led to an aposymbiotic state in 100% of A. lobifera and only minimally impacted its motility and mortality. The method was effective for S. orbiculus, where an aposymbiotic state, defined as no visible remains of symbiont cells inside the host at the end of the experimental period, occurred in 66% of specimens of the MCC experiment. Growth was strongly impacted by the bleaching protocol in both species, allowing no new calcite to be formed during the acute exposure. This method can be applied for testing aspects of symbiosis establishment in LBF as well as their potential to take up different symbionts in a short-to medium time frame.

cell biology↗

bioRxiv2020

Plankton Planet: 'seatizen' oceanography to assess open ocean life at the planetary scale

In every liter of seawater there are between 10 and 100 billion life forms, mostly invisible, called plankton, which form the largest and most dynamic ecosystem on our planet, at the heart of global ecological and economic processes. While physical and chemical parameters of planktonic ecosystems are fairly well measured and modelled at the planetary scale, but biological data are still scarce due to the extreme cost and relative inflexibility of the classical vessels and instruments used to explore marine biodiversity. Here we introduce Plankton Planet, an initiative whose goal is to merge the creativity of researchers, makers, and mariners to (i) develop frugal scientific instrumentation and protocols to assess the genetic and morphological diversity of plankton life, and (ii) organize their systematic deployment through fleets of volunteer sailors, fishermen, or cargo-ships to generate comparable and open-access plankton data across global and long-term spatio-temporal scales. As proof-of-concept, we show how 20 crews of sailors ("planktonauts") were abl to sample plankton biomass from the world surface ocean in a single year, generating the first citizen-based, planetary dataset of plankton biodiversity based on DNA barcodes. The quality of this dataset is comparable to that generated by Tara Oceans and is not biased by the multiplication of samplers. This dataset has unveiled significant genetic novelty and can be used to explore the taxonomic and ecological diversity of plankton at both regional and global scales. This pilot project paves the way for construction of a miniaturized, modular, evolvable, affordable and open-source citizen field-platform that will allow systematic assessment of the eco/morpho/genetic variation of aquatic ecosystems across the dimensions of the Earth system.

ecology↗