Ecological Diagnosis - DiagnosE

Ecological Diagnosis - DiagnosE

Coordinators :  
Dr. Jean Guillard, Research Engineer 
Dr. Frédéric Rimet, Research Engineer

Given the importance of ecological diagnoses in our scientific activities, this third, cross-cutting axis aims to formalize the development of innovative diagnostic tools and approaches that provide a privileged interface towards operational transfer. This cross-cutting axis, DiagnosE, is irrigated by some of the work of BIOTIC and MyCYCLE axes and in return provides tools and data applicable for their research topics.







Pursue the development, exploitation and transfer of innovative non-invasive and high-frequency tools for environmental diagnoses



integration of environmental DNA approaches for in-situ monitoring and ecological diagnoses

Development of autonomous devices (drones) for hydroacoustic monitoring (high spatial and temporal frequency)



Deploy, optimize and manage chemical sensors (e.g. CO2) for studies in aquatic ecology and biochemistry



Pursue and 'upgrade' evaluation tools for wetlands and coastal areas


Diagnostic methods and evaluation tools for ecological compensation and restoration

Consolidate participatory science approaches

Consolidation of fisheries data and monitoring by the development of a Smartphone application (amateur fishing)

Environmental DNA

Diat.barcode - DNA barcode reference library for diatoms

Diat.barcode is an open-access DNA barcode reference library for diatoms. Experts from several countries collaborate to complete and curate Diat.barcode. The database is accessible at:
F. Rimet 


Rivers and lakes play a fundamental role in the environment, not only by providing a habitat for all kinds of flora and fauna, but also by improving the landscape and quality of life. In order to implement actions to preserve aquatic areas, the SYNAQUA project proposes to use the genomic tools of bio-monitoring. The approach is based on a recognition of bio-indicator organisms present in the aquatic environment directly through their DNA. The environmental DNA analysis method developed by French and Swiss researchers in collaboration with professionals from public and private services will enable the development of robust and reliable tools and the optimization of current environmental bio-monitoring practices.
A. Bouchez was leader of this Interreg FR-CH projet with J. Pawlowski which ended in 2019. 


DNAquanet is EU COST Action (number CA15219): - international network of scientists & stakeholders advancing novel genetic tools for biomonitoring of Europe's aquatic ecosystems.
A. Bouchez is co-leader of this network with F. Leese. 


The main aim of Eco-AlpsWater is to improve the traditional monitoring approaches (Water Framework Directive 2000/60/EC-EU WFD and, in Switzerland, the Water Protection Ordinance-WPO) by using advanced DNA sequencing techniques such as metabarcoding. The new approach will make use of Next Generation Sequencing (NGS) to analyze environmental DNA in waterbodies (which allow rapid species identification at low costs, from fish to bacteria), and smart technologies (automation in data processing, data storage, information retrieval).
I. Domaizon is part of this Alpine-Space Interreg projet. 


Development of a tool using eDNA for the identification of phytoplankton and application in French overseas departments. This project is financed by the OFB (Office Français de la Biodiversité) since 2020.


Harle: Hydroacoustic autonomous boat for Remote fish detections in lake
J. Guillard, C. Goulon


FISHOLA is a smartphone application allowing you to inform your fishing trips and your catches on the large alpine lakes (Lake Geneva, Lake Annecy, Lake Le Bourget and Lake Aiguebelette). By providing this information, you participate in the understanding and preservation of the lakes, but also in the knowledge of the amateurs fishing and its practice. 
C. Goulon, J. Guillard  


Méthode Nationale d'évaluation des fonctions des zones humides (financée OFB, CD38) (Partenaires: UMS PatriNat, Cerema, Tour du Valat)  :
Cette méthode, rapide à mettre en œuvre sur le terrain, permet en outre de vérifier que certains principes de la compensation sont bien respectés. La version 2 est en cours de finalisation, elle inclura entre autres de nouveaux indicateurs, les ZH littorales et une interface de dimensionnement.
J.C. Clément


(financé ZABR-AE RMC) (Partenaires (Lab. Ecol. Microbienne INRAE/Lyon 1, Biotope, UMS PatriNat, INRAE Grenoble, UMR CITERES, Biotope, ) : Élaboration d’un outil opérationnel pour évaluer, préserver ou restaurer les fonctions biogéochimiques en zones humides répondant aux enjeux de qualité des eaux et de biodiversité.
J.C. CLément

High-frequency sensors

Using open-source hardware for a better spatial and temporal resolution of lake monitoring: towards an autonomous sensor network
V. Tran-Khac

Modification date: 28 June 2023 | Publication date: 04 October 2019 | By: ED