Biology subjects

Robinet, T.

Publications and source records attributed to Robinet, T..

2 recordsLinked to original sources

bioRxiv2025

Reactive oxygen species drive downward vertical migration in diatom microphytobenthic biofilms as a strategy to cope with oxidative stress

Diatom-dominated intertidal microphytobenthic biofilms experience daily fluctuations in irradiance, which can lead to oxidative stress within the photosynthetic apparatus through the production and accumulation of reactive oxygen species. To maintain photosynthetic efficiency, benthic diatoms have developed protective strategies, including mobilization of the antioxidant xanthophyll cycle and the ability to migrate vertically through sediments. However, mechanistic understanding of signaling pathways underlying migration remains poorly characterized. This study investigated the triggering effect of reactive oxygen species on behavioral and photophysiological responses through the analysis of lipophilic pigments and fluorescence parameters. To this end, two microphytobenthic communities, one with sediment allowing vertical migration and another without sediment restricting it, were exposed to irradiance, cold atmospheric plasma, and hydrogen peroxide stresses. Results showed a consistent downward migration response under all oxidative stresses, highlighting the key role of reactive oxygen species, especially hydrogen peroxide, in triggering this microphytobenthic behavior. Moreover, a difference was observed between the pathways involved in vertical migration and those underlying photoprotective responses. Hydrogen peroxide and cold atmospheric plasma stresses highlighted the necessity for substantial microphytobenthic migration, whereas irradiance induced a specific and controlled response involving engagement of the xanthophyll cycle, acting in synergy with the migration strategy by showing stronger activation when migration was impaired. By establishing that a rapid and efficient migration could be induced by reactive oxygen species and could act in synergy with the xanthophyll cycle in epipelic cells, this study provides key insights into the molecular basis of microphytobenthic responses to cellular and environmental oxidative stresses.

ecology↗

bioRxiv2023

Nanopore long-reads reveal fine structure of prokaryotic communities in mangrove sediments, like Illumina short-reads but with twice more taxa

Following the development of high-throughput DNA sequencers, environmental prokaryotic communities were usually described by metabarcoding on short markers of the 16S domain. Among third generation sequencers, that offered the possibility to sequence the full 16s domain, the portable MinION from Oxford Nanopore was undervalued for metabarcoding because of its relatively higher error rate per read. Here we illustrate the limits and benefits of Nanopore sequencing devices by comparing the prokaryotic community structure in a mock community and 52 sediment samples from mangrove sites, inferred from full-length 16S long-reads (16S-FL, ca. 1.5 kpb) on a MinION device, with those inferred from partial 16S short-reads (16S- V4V5, ca. 0.4kpb, 16S-V4V5) on Illumina MiSeq. 16S-V4V5 and 16S-FL retrieved all the bacterial species from the mock, but Nanopore long-reads overestimated their diversity more than twice. Whether these supplementary OTUs were artefactual or not, they only accounted for ca. 10% of the reads. From the sediment samples, with a coverage-based rarefaction of reads and after singletons filtering, Mantel and Procrustean tests of co-inertia showed that bacterial community structures inferred from 16S-V4V5 and 16S- FL were significantly similar, showing both a comparable contrast between sites and a coherent sea-land orientation within sites. In our dataset, 84.7 and 98.8% of the 16S-V4V5 assigned reads were assigned strictly to the same species and genus, respectively, than those detected by 16S-FL. 16S-FL allowed to detect 92.2% of the 309 families and 87.7% of the 448 genera that were detected by the short 16S-V4V5. 16S-FL recorded 973 additional species and 392 genus not detected by 16S-V4V5 (31.5 and 10.4% of the 16S-FL reads, respectively, among which 67.8 and 79.3% were assigned), producted by both primer specificities and diffrent error rates. Thus, our results concluded to an overall similarity between 16S-V4V5 and 16S-FL sequencing strategies for this type of environmental samples.

molecular biology↗