AtlantECO-KER-IM-4

Thesis

Particles sinking from the surface to the deep ocean play a key role in the biological carbon pump, whose efficiency depends partly on sinking velocities. Over the last decade, in situ imaging has enabled critical advances in our understanding of particle dynamics in the ocean. Yet, in situ velocity measurements are scarce and often inferred only from the bulk population of particles. Here, we introduce the VisuTrap, a new tool to measure in situ velocities of marine particles. It consists of an Underwater Vision Profiler 6 (UVP6) camera inserted into different types of sediment traps, which isolate a volume of water. Continuous image acquisition during shortterm or long-term deployments enables reconstruction of particle tracks and estimation of their in situ vertical velocities. We detail the configuration and special UVP6 settings for this application, as well as the image processing and track analysis pipeline. Then, we present results from several experiments in the Mediterranean Sea to illustrate the VisuTrap's use as a new approach to understand the dynamical behavior of marine particles in situ. In light of the broad range of morphological data generated by the UVP6, we discuss technical additions to refine in situ velocity measurements and the possibility of integrating such data into carbon flux assessments.

Microfluidic technology can expedite nucleic acid testing by converting the functions of bulky laboratory instruments and protracted bench methodologies into easy-to-use and inexpensive miniaturised systems without compromising speed and reliability. We developed a lab-on-a-chip (LOC) platform that integrates a dimethyl adipimidate (DMA)-based functionalised silica DNA isolation and pre-concentration method with a rapid and real-time loop-mediated isothermal amplification (LAMP) for detecting domoic acid-producing phytoplankton, Pseudo-nitzschia. An optimised design of a lab on a chip extraction module achieved a maximum DNA capture capacity of 61.73 ± 0.98 ng μL−1. The DMA-based method reduced reagent costs per sample by 97% compared to a commercial nucleic acid isolation kit. A subsequent on-chip LAMP process was capable of sensitively quantifying cytochrome P450 homologous to the dabD gene, coding for a component of the domoic acid toxin production pathway, with a limit-of-detection of 10 cells per mL. LAMP-based detection of the target gene was achieved using dry-preserved reagents with a shelf-life of five months without refrigeration. There was no significant difference in assay performance between the preserved LAMP and freshly prepared LAMP mixtures. The total analysis time at the LOD of 10 cells per mL, from sample to result, was achieved within one hour. Our results demonstrate the long-term stability of assay reagents, rapid turnaround, and cost-effectiveness, offering a simple and economical approach to environmental monitoring and environmental bio-hazard diagnostics.

Microfluidic technology can expedite nucleic acid testing by converting the functions of bulky laboratory instruments and protracted bench methodologies into easy-to-use and inexpensive miniaturised systems without compromising speed and reliability. We developed a lab-on-a-chip (LOC) platform that integrates a dimethyl adipimidate (DMA)-based functionalised silica DNA isolation and pre-concentration method with a rapid and real-time loop-mediated isothermal amplification (LAMP) for detecting domoic acid-producing phytoplankton, Pseudo-nitzschia. An optimised design of a lab on a chip extraction module achieved a maximum DNA capture capacity of 61.73 ± 0.98 ng μL−1. The DMA-based method reduced reagent costs per sample by 97% compared to a commercial nucleic acid isolation kit. A subsequent on-chip LAMP process was capable of sensitively quantifying cytochrome P450 homologous to the dabD gene, coding for a component of the domoic acid toxin production pathway, with a limit-of-detection of 10 cells per mL. LAMP-based detection of the target gene was achieved using dry-preserved reagents with a shelf-life of five months without refrigeration. There was no significant difference in assay performance between the preserved LAMP and freshly prepared LAMP mixtures. The total analysis time at the LOD of 10 cells per mL, from sample to result, was achieved within one hour. Our results demonstrate the long-term stability of assay reagents, rapid turnaround, and cost-effectiveness, offering a simple and economical approach to environmental monitoring and environmental bio-hazard diagnostics.