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PhD Perception and measure of oceanic biodiversity through frugal planktonscopy: ergonomy and epistemology of a global citizen science project (m/w)

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Date Limite Candidature : lundi 30 mai 2022

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General information

Reference : UMR8129-VINGAU-020
Workplace : PARIS 05
Date of publication : Monday, May 9, 2022
Scientific Responsible name : giardino valeria
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 3 October 2022
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly

Description of the thesis topic

Current models aimed at predicting global ocean dynamics and interactions with the Earth system are fairly robust in terms of (bio)physics and chemistry. Indeed, measures of basic (bio)physical and chemical parameters have been performed for more than a century by the international float of oceanographic vessels equipped with uniform gears (e.g. Niskin bottles, CTD, ...) to probe the world ocean, and over the last three decades by continuous and automated ocean remote and in-situ sensing (e.g. satellites and floats) at planetary scale. However, by comparison, models are heavily oversimplified and unrealistic in terms of biology for a simple reason: ocean life, from viruses to animals, is highly complex and fragile, and the technologies to assess aquatic life's complexity are either emerging and semi-quantitative (e.g. meta-omics), or difficult to implement at sea, in particular in automated modes. Given that ocean ecosystems are driven by feedback loops between physical, chemical, and biological processes, today by far the greatest bottleneck in our understanding and ability to predict the ocean is the dramatic lack of consistent biocomplexity data across planetary spatial and time scales.


Protocols to consistently measure biodiversity from viruses to animals thriving in marine waters are now existing, as shown for instance by the suite of meta-genomics and meta-imaging procedures applied by the Tara Oceans consortium over the last decade. In order to make a step-change and reach the density of biological data needed to feed and constrain global ocean models, the question is rather how to implement these protocols in cost-effective and ergonomic instruments that can then be deployed across planetary scales. A huge challenge in ocean science where the watery realm is so hard to reach.


In the 'Plankton Planet' (P2) initiative, we propose to overcome this scalability barrier by developing a new generation of modular, user-friendly, open-source and cost-effective tools allowing any 'seatizen' to consistently collect, measure, and share plankton samples and data. By seatizen, we mean any citizen interested in discovering/measuring ocean invisible life, whether she is an oceanographer, a recreational or professional sailor, a crew member of a cargo or navy ship, a fisherman, oyster farmer, or coastal manager, etc.

The strategy is thus to (i) drastically lower the cost of tools (frugal) to collect plankton data; (ii) build tools that are handy, robust, and ergonomic enough to be used by seatizen and thus deployed globally in either coastal or open ocean contexts beyond academic constraints ; (iii) implement data flow, primary processing, and storage in appropriate public database for immediate and global sharing. Over the last years, P2 has proved the concept by achieving the first seatizen sailors-based planetary sampling of plankton for biodiversity assessment by DNA metabarcoding (de Vargas et al. 2020), and developed new tools to consistently sample (Coryphaena, Diodon, Fanon nets), measure (PlanktoScope and Lamprey), and store/analyze (in EcoTaxa and ENA web platforms) plankton data. The PlanktoScope (PS) is particularly promising; it is a miniaturized modular open source imaging platform (https://www.planktoscope.org) for quantitative, in-flux imaging of micro-plankton matching the quality of much larger and more expensive commercial instruments (Pollina et al. 2020). Its scientific robustness was validated recently along a trans-atlantic cruise on board Tara (Meriguet et al. 2022); we believe that its global deployment could provoke a paradigm shift in operational procedures for biological oceanography.


Today, we are at the critical stage where the first P2-kit for plankton biodiversity survey can be deployed amongst 'seatizen' and tested in real conditions. In particular, we will be able to build and distribute P2-kits to various communities of sea workers/lovers during two major planetary-biology programs to explore the land-sea interface along European coastlines (TREC and BIOcean5D, see below). Now, critical epistemological challenges confront a large-scale, marine frugal science project, challenges which require a collaboration between marine ecology and the social and cognitive sciences.

For P2 to generate good quality data, a thorough analysis of the ergonomy and the epistemology of the instrument is required. If in physics, (bio)chemistry, and terrestrial ecology, automatized tools made the scale change possible, in marine biology human samplers must be involved in relatively complex processes and data generated, and a deep understanding of the human-instrument interface is key. How can diverse seatizens appropriate the instrument and design sampling plans? How does it in turn modify their practices and their understanding of the marine environment?


Four challenges/objectives will delineate the research space of the epistemOcean project:

(1) An ergonomic study of the PS: acceptability, usability at sea, continuous upgrading to newer versions including sensors for contextual data, comparability of data across versions and seatizen samplers, feedback from users; (2) A comparative assessment of the viability and limits of marine frugal/citizen science, in particular with regard to existing land frugal and marine non-frugal approaches; (3) The outline of an epistemology of seatizen science, i.e. the study of biases and practices in knowledge generation: process quality, data quality, quality of results and knowledge visualization, deployment of collective intelligence; (4) A study of how the use of the PS changes both the data landscape and the users' perspective on the sea; with a set of measures for education.


By unveiling the basic ergonomic principles needed for field application of a frugal ocean science, but also by evaluating the cognitive changes in perception of the ocean (a soup of complex life through the PlanktoScope 'eyes') by the seatizen explorers engaged, epistemOcean is at the crossroad between SHS and SDV.

Work Context

The PhD project builds on, and consolidates, existing (and exciting!) structures and projects:


- The TREC - TRaversing European Coastlines - expedition and synergetic BIOcean5D EU project will deploy in 2023/24 mobile labs and research vessels including the schooner Tara through 21 coastal countries and 35 marine labs from the Mediterranean to Arctic seas to assess land-to-sea ecosystems (soil, aerosols, water, sediments), an ideal platform that will provide logistical and field/ and marine laboratory support to epistemOcean.

- The development/deployment of the PS is managed by a dedicated french NGO, 'Seatizens of Plankton Planet', which recruits and coordinates testers and sailors, interfaces with the general public in events and in educational and museal contexts, and scouts for industrial and institutional partners.

In the framework of the recently EU funded Biocean5D project (2023-2027), the project will take advantage of the recruitment of local communities along the path of the TREC expedition for organizing training and testing sessions.

- IJN developed a considerable expertise in online questionnaires (>600 studies and experiments on Qualtrics).

- Each of the two involved carriers (SBR and IJN) will provide access to facilities and resources (including mission expenditures), and integration in the respective intellectual environments, which include large national and international networks.

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