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Bonnie Bailet

My doctoral project aims to develop new methods improving the water management. The project focus on exploring the role of diatoms in ecosystems and developing DNA metabarcoding techniques for investigating the structure and function of algal biofilms.


New methods improving the water management - The role of diatoms in ecosystems:

This PhD project focusses on the biodiversity of benthic diatoms, quantified not only at the species and higher levels, but also at the level of the genotype, and encompassing the diversity of functional traits. 

The project aims to investigate how these different biodiversity aspects underpin the phenotypic plasticity and environmental tolerances of benthic diatoms, and to link intraspecific, species, and functional diversity measures with important ecosystem functions mediated by diatoms.  To achieve its goals, the project involves the development and evaluation of two novel methodologies: DNA metabarcoding as a new, cost-effective approach for quantifying diatom biodiversity for routine use in both research and bioassessment, and functional trait classifications of diatoms, to develop enable a predictive framework linking diatom species with key ecosystem functions including primary productivity and nutrient uptake. 

Finally, the project ensures coverage of broad gradients in environmental parameters and genetic and phenotypic variability by exploiting new and existing data-sets, samples and cultures in both Fennoscandia and France.


The present project is designed as PhD project at SLU in collaboration with the Swedish Agency for Marine and Water Management (Havs- och Vattenmyndigheten, HaV) and with international partners which embed the research results in a wider context.

This project is funded by Stiftelsen Oscar och Lili Lamms Minne and by The Swedish Agency for Marine and Water management

Please read more about the project here:

Benthic Diatoms with dNA - Method development

Benthic Diatoms with DNA - Method development (in english)


New methods improving freshwater conservation and management


Others co-projects:

DNAqua (CA COST Action CA15219)

Developing new genetic tools for bioassessment of aquatic ecosystems in Europe
The protection, preservation and restoration of aquatic ecosystems and their functions is of global importance. For European states it became legally binding mainly through the EU-Water Framework Directive (WFD). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water body. The quantified mismatch thus obtained determines the extent of potential management actions. The current approach to biodiversity assessment is based on morpho-taxonomy. This approach has many drawback such as being time consuming, limited in temporal and spatial resolution, and error-prone due to variation of individual taxonomic expertise of the analysts. Novel genomic tools can overcome many of the aforesaid problems and could complement or even replace traditional bioassessment. Yet, a plethora of approaches are independently developed in different institutions, thereby hampering any concerted routine application. The goal of this Action is to nucleate a group of researchers across disciplines with the task to identify gold-standard genomic tools and novel eco-genomic indices for routine application for biodiversity assessments of European water bodies. Furthermore, DNAqua-Net will provide a platform for training of the next generation of European researchers preparing them for the new technologies. Jointly with water managers, politicians and other stakeholders, the group will develop a conceptual framework for the standard application of eco-genomic tools as part of legally binding assessments.

EU-founded program COST  (European Cooperation in Science & Technology)



Chair of the Action:
Prof Florian LEESE (DE)

Vice Chair of the Action:

Science officer of the Action:
Dr Mafalda QUINTAS

Administrative officer of the Action:


DESTRESS Project (DisEntangling the impacts of multiple Stressors on stream ecosystems)

Aim: Investigation of interactions between multiple stressors and their ecological effects on watercourses.

Brendan McKie


INRA UMR CARRTEL - Centre Alpin de Recherche sur les Reseaux Trophiques des Ecosystemes limniques.

INRA UMR BIOGECO - Biodiversite Genes et Communautes.


2013-2015: Oceanography master specialized in marine biology and ecology (Aix-Marseille University, France). Advanced Microbiology, Genomic evolution and bioinformatics, Protection, Restoration and sustainable management.

2012-2013: Marine and Freshwater Biology Bachelor degree (Edinburgh Napier University, UK). Populations and communities’ ecology, environmental toxicology, microbiology, marine mammals’ biology.

2010-2012: DUT in Biological Engineering specialized in Environmental engineering (Aix-Marseille University, France)