Biology subjects

Jalabert, L.

Publications and source records attributed to Jalabert, L..

3 recordsLinked to original sources

bioRxiv2024

Ubiquity of inverted 'gelatinous' ecosystem pyramids in the global ocean

Summary paragraphPlankton are essential in marine ecosystems. However, our knowledge of overall community structure is sparse due to inconsistent sampling across their very large organismal size range. Here we use diverse imaging methods to establish complete plankton inventories of organisms spanning five orders of magnitude in size. Plankton community size and trophic structure variation validate a long-held theoretical link between organism size-spectra and ecosystem trophic structures. We found that predator/grazer biomass and biovolume unexpectedly exceed that of primary producers at most (55%) locations, likely due to our better quantification of gelatinous organisms. Bottom- heavy ecosystems (the norm on land) appear to be rare in the ocean. Collectively, gelatinous organisms represent 30% of the total biovolume (8-9% of carbon) of marine plankton communities from tropical to polar ecosystems. Communities can be split into three extreme typologies: diatom/copepod-dominated in eutrophic blooms, rhizarian/chaetognath-dominated in oligotrophic tropical oceans, and gelatinous-dominated elsewhere. While plankton taxonomic composition changes with latitude, functional and trophic structures mostly depend on the amount of prey available for each trophic level. Given future projections of oligotrophication of marine ecosystems, our findings suggest that rhizarian and gelatinous organisms will increasingly dominate the apex position of planktonic ecosystems, leading to significant changes in the oceans carbon cycle.

ecology↗

bioRxiv2022

Silicon as a microfluidic material for imaging and incubation of droplets

Droplet microfluidics has become a powerful tool in life sciences, underlying digital assays, single-cell sequencing or directed evolution, and it is making foray in physical sciences as well. Imaging and incubation of droplets are crucial, yet they are encumbered by the poor optical, thermal and mechanical properties of PDMS - the de facto material for microfluidics. Here we show that silicon is an ideal material for droplet chambers. Si chambers pack droplets in a crystalline and immobile monolayer, are immune to evaporation or sagging, boost the number of collected photons, and tightly control the temperature field sensed by droplets. We use the mechanical and optical benefits of Si chambers to image [~]1 million of droplets from a multiplexed digital assay - with an acquisition rate similar to the best in-line methods. Lastly, we demonstrate their applicability with a demanding assay that maps the thermal dependence of Michaelis-Menten constants with an array of [~]150,000. The design of the Si chambers is streamlined to avoid complicated fabrication and improve reproducibility, which makes Silicon a complementary material to PDMS in the toolbox of droplet microfluidics. Significance StatementAs the technological engine behind single-cell sequencing and digital assays, droplets microfluidics has revolutionized life science and molecular diagnosis, and is making foray into physical sciences as well. Observing droplets in a controlled manner is becoming crucial, but PDMS - the de facto material of microfluidics - hampers imaging and incubation. Here we revisit silicon as a microfluidic material and show that its superior mechanical, optical and thermal performances improve the throughput and operation of droplets assay.

biochemistry↗

bioRxiv2022

Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems

AbstractThe Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58,000 samples. The expedition was designed to systematically study warm coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps but also through a global analysis allowing the comparison with known environmental large-scale structures. Such a wide released datasets opens the perspective to address a wide range of scientific questions.

ecology↗