Biology subjects

Guillemain, D.

Publications and source records attributed to Guillemain, D..

3 recordsLinked to original sources

bioRxiv2025

Separating faces in ARMS metabarcoding improves marine biodiversity monitoring: a comparison across protocols, experimental designs, and photographic surveys

Monitoring marine biodiversity requires approaches that capture its full complexity through space and time. DNA metabarcoding coupled with Autonomous Reef Monitoring Structures (ARMS) is increasingly used for this purpose, yet most applications still pool all sessile fractions and rarely benchmark molecular ouputs against photographic observations. Here, we combined photographic analysis with cytochrome c oxidase I (COI) metabarcoding across ten north-western Mediterranean sites to test, compare, and refine ARMS-based monitoring protocols. We first optimized laboratory procedures (DNA extraction and polymerase choice) and applied the control-driven, replicate-aware VTAM pipeline to minimize false positives and ensure full traceability. We then conducted the first face-by-face comparison of - and {beta}-diversity between imaging and eDNA in which each individual ARMS face was metabarcoded separately rather than pooled. Metabarcoding detected [~]15x higher site-level richness and revealed stronger correlations with geographic distance and environmental gradients, whereas photography provided complementary information on macro-taxa and surface cover. For metabarcoding, processing each face separately yielded much higher richness and markedly stronger {beta}-diversity-distance correlations than with the NOAA pooling protocol, demonstrating that pooling inflates sampling variance resulting in a loss of the ecological signal. Grouping faces into five structural categories offered a more operational alternative while further increasing -diversity and strengthening {beta}-diversity correlations. Overall, our results show that retaining ARMS microhabitat structure is critical for maximizing metabarcoding performance. Using five structural sessile fractions per ARMS combined with a control-driven bioinformatic workflow provides a reproducible, scalable framework for long-term eDNA monitoring and early detection of biodiversity change.

ecology↗

bioRxiv2025

Thriving Across Depths: How Blue Light Shapes a Large PSI Supercomplex and Specic Photosynthetic Traits in the seagrass Posidonia oceanica.

Photosynthetic organisms rely on finely tuned mechanisms to optimize photosynthesis under different light conditions. While these processes are well-characterized in land plants, the adaptive strategies of marine plants remain largely unexplored. The Mediterranean seagrass Posidonia oceanica (Alismatales), a key ecosystem engineer thriving from the surface up to 40m depth and one of the largest long-term blue carbon sinks in coastal environments. Here, we investigate how P. oceanica adjusts its photosynthetic apparatus in response to varying light spectra encountered at different seawater depths. Contrary to land plants, P. oceanica maintains a relatively high PSI/PSII ratio and a high content of the major light-harvesting complex II (LHCII), regardless of depth. Notably, the antenna size of the photosystems remains stable across depths, although we document significant depth-dependent reorganization of the thylakoid membrane ultrastructure. Moreover, we identify a novel large PSI-LHCII supercomplex (L-PSI-LHCII) in P. oceanica, characterized by additional Lhca proteins, reduced red-shifted absorption, and increased chlorophyll b content. Ultrafast spectroscopy reveals the distinct energy transfer dynamics within this complex. The presence of a similar supercomplex in other marine plants, such as Zostera marina, suggests a conserved adaptive strategy among seagrasses.

plant biology↗

bioRxiv2024

The Oscarella sponges genus: a hidden yet colorful diversity

The identification and classification of new taxa are crucial for understanding biodiversity. However, assigning samples to new taxa requires cautious and rigorous approaches. Historically, taxonomy has heavily relied on morphological traits, which can be subjective and may not always reflect underlying genetic divergence, particularly in organisms with few diagnostic morphological traits. A prime example is the sponge genus Oscarella (Homoscleromorpha), where species delimitation is challenged by the absence of spicules and limited morphological characters. Here, we address this gap by combining an extensive genetic dataset (192 specimens, five markers) with systematic photographic documentation. This approach enabled a robust assessment of Oscarella diversity in the Western Mediterranean, resulting in the identification of four species new to science. Multigene phylogenetic analyses also enabled us to propose an evolutionary scenario for color polymorphism. Moreover, our data highlighted critical limitations in current methodologies for studying Oscarella, including the low resolution of the widely used cytochrome c oxidase subunit I (cox1/COI) gene, the lack of genetic data for many species, and insufficient information on their geographical distribution. These issues, which mirror challenges across many taxa, highlight the urgent need for standardized genetic frameworks and comprehensive datasets to improve taxonomic resolution for each taxon.

evolutionary biology↗