François Keck

• PhD
• PostDoc Position at Swiss Federal Institute of Aquatic Science and Technology

Freshwaters worldwide face serious threats, making their protection increasingly important. Freshwater monitoring has historically produced valuable data and continues to develop. Rapid improvements to biomolecular techniques are revolutionizing the way scientists describe biological communities and are bringing about major changes in biomonitoring...

Diatoms include a great diversity of taxa and are recognized as powerful bioindicators in rivers. However using diatoms for monitoring programs is costly and time consuming because most of the methodologies necessitate species-level identification. This raises the question of the optimal trade-off between taxonomic resolution and bioassessment qual...

Human activities drive a wide range of environmental pressures, including habitat change, pollution and climate change, resulting in unprecedented effects on biodiversity1,2. However, despite decades of research, generalizations on the dimensions and extent of human impacts on biodiversity remain ambiguous. Mixed views persist on the trajectory of...

The contemporary ecological crisis calls for integration and synthesis of ecological data describing the state, change and processes of ecological communities. However, such synthesis depends on the integration of vast amounts of mostly scattered and often hard-to-extract information that is published and dispersed across hundreds of thousands of s...

Aquatic insects are iconic and ecologically highly relevant inhabitants of riverine ecosystems. They are also often the target of monitoring programs to assess the ecological status of these lotic habitats. Environmental DNA (eDNA) techniques have been widely and successfully implemented to investigate freshwater insects and other macroinvertebrate...

Anthropogenic land-cover changes are among the most pressing global threats to both aquatic and terrestrial ecosystems, jeopardising biodiversity and the critical connections between these systems. Resource flows and trophic interactions intricately link aquatic and terrestrial ecosystems, with terrestrial-derived detritus playing a foundational ro...

The rapid loss of biodiversity in freshwater systems asks for a robust and spatially explicit understanding of species' occurrences. As two complementing approaches, habitat suitability models provide information about species' potential occurrence, while environmental DNA (eDNA) based assessments provide indication of species' actual occurrence. I...

Aquatic macroinvertebrates, including many aquatic insect orders, are a diverse and ecologically relevant organismal group yet they are strongly affected by anthropogenic activities. As many of these taxa are highly sensitive to environmental change, they offer a particularly good early warning system for human-induced change, thus leading to their...

Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dyn...

The distribution of microorganisms has long been assumed to be cosmopolitan and primarily controlled by the environment, but recent studies suggest that microbes may also exhibit strong biogeographical patterns driven by dispersal limitation. Past attempts to study the global biogeography of freshwater diatoms have always encountered the great diff...

Diatom species identification with DNA metabarcoding is an economical, fast and reliable alternative to identification via light microscopy for river quality monitoring. Using a short DNA sequence of the rbcL gene and 'Diat.barcode', a reference barcode library, enables the identification of more than 90% of the environmental sequences to species l...

The current advances of environmental DNA (eDNA) bring profound changes to ecological monitoring and provide unique insights on the biological diversity of ecosystems. The very nature of eDNA data is challenging yet also revolutionizing how biological monitoring information is analysed. In particular, new metrics and approaches should take full adv...

Catchment urbanisation results in urban streams being exposed to a multitude of stressors. Notably, stressors originating from diffuse sources have received less attention than stressors originating from point sources. Here, advances related to diffuse urban stressors and their consequences for stream benthic communities are summarised by reviewing...

Assessment of biodiversity using metabarcoding data, such as from bulk‐ or eDNA sampling, is becoming increasingly relevant in ecology, biodiversity sciences, and monitoring. Thereby, the taxonomic identification of species from their DNA sequences relies strongly on reference databases that link genetic sequences to taxonomic names. These database...

DNA barcoding and metabarcoding are revolutionising the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be - and often has...

Diatom taxonomy has evolved in recent years, with many new species described and new approaches such as molecular genetics showing the existence of cryptic diversity within currently accepted species. This cryptic diversity is not well understood even for common freshwater genera such as Fragilaria and Ulnaria. The purpose of our study was to defin...

Ciliates are unicellular heterotrophic organisms that play a key role in aquatic planktonic and benthic food webs. Advances in sedimentary DNA (sed-DNA) analysis offer the possibility to integrate these bioindicators in paleoenvironmental reconstructions. In this study, we used the top–bottom paleolimnological approach and metabarcoding techniques...

Monitoring biodiversity is essential to understand the impacts of human activities and for effective management of ecosystems. Thereby, biodiversity can be assessed through direct collection of targeted organisms, through indirect evidence of their presence (e.g. signs, environmental DNA, camera trap, etc.), or through extrapolations from species d...

DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated the consistency of this technique with traditional morpho‐taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of aquatic organisms both in marine and freshwater s...

Monitoring freshwater biodiversity is essential to understand the impacts of human activities and for effective management of ecosystems. Thereby, biodiversity can be assessed through direct collection of targeted organisms, through indirect evidence of their presence (e.g. signs, environmental DNA, camera trap, etc.), or through extrapolations fro...

Ciliates are unicellular heterotrophic organisms that play a key role in the planktonic and benthic food webs of lakes, and represent a great potential as bioindicator. In this study, we used the top-bottom paleolimnological approach to compare the recent and past (i.e. prior to major anthropogenic impacts) ciliate communities of 48 lakes located a...

Our study evaluates differences in the distribution and ecology of genetic variants within several ecologically important diatom species that are also key for Water Framework Directive monitoring of European rivers: Fistulifera saprophila (FSAP), Achnanthidium minutissimum (ADMI), Nitzschia inconspicua (NINC) and Nitzschia soratensis (NSTS). We use...

Assessment of the diversity and composition of biological communities is central to studies in ecology as well as for ecological monitoring. Historically, individual taxonomic groups have been assessed separately, while for an understanding of the state and change of biodiversity under ongoing global change an integrated assessment would be necessa...

Diatoms (Bacillariophyta) are ubiquitous microalgae, which present a huge taxonomic diversity, changing in correlation with differing environmental conditions. This makes them excellent ecological indicators for various ecosystems and ecological problematics (ecotoxicology, biomonitoring, paleo-environmental reconstruction …). Current standardized...

Diatom biomonitoring and ecological studies can greatly benefit from DNA metabarcoding compared to conventional microscopical analysis by potentially providing more reliable and accurate data in a cost- and time-efficient way. A conventional strategy for the bioinformatic treatment of sequencing data involves the clustering of quality filtered sequ...

The high-dispersal rates of microorganisms have driven to the expectation of their cosmopolitan geographic distribution. However, recent studies demonstrate that microorganisms instead show particular biogeography. Despite the existence of cosmopolitan species, geographically limited microbial groups have been found in aquatic and terrestrial envir...

Reference databases of sequences that have been taxonomically assigned are a key element for DNA-based identification of organisms. Accurate and complete reference databases are necessary to associate a correct taxonomic name to the sequences obtained in studies using metabarcoding. Today many research projects using DNA metabarcoding include the d...

Land-use imposes an important potential threat on the aquatic ecosystems of riverine habitats. In this study, DNA metabarcoding was used to assess the effect of land-use on diatom assemblages, with a special focus on cropland area as an integrative proxy for several direct-acting pressures. The so-called taxonomy-free approach was tested using exac...

With the democratization of molecular biology, more and more ecologists are required to analyse complex datasets including biological sequences. I present the R package bioseq , a comprehensive toolset to handle biological sequences in R. The package implements three classes to work with DNA, RNA and amino acid sequences. Biological sequences are s...

• Arctic freshwaters support biota adapted to the harsh conditions at these latitudes, but the climate is changing rapidly and so are the underlying environmental filters. Currently, we have limited understanding of broad‐scale patterns of Arctic riverine biodiversity and the correlates of α‐ and β‐diversity. • Using information from a database set...

Long-term time series have provided evidence that anthropogenic pressures can threaten lakes. Yet it remains unclear how and the extent to which lake biodiversity has changed during the Anthropocene, in particular for microbes. Here, we used DNA preserved in sediments to compare modern micro-eukaryotic communities with those from the end of the 19t...

A decade after environmental scientists integrated high‐throughput sequencing technologies in their toolbox, the genomics‐based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, tec...

Comprehensive assessments of contemporary diatom distributions across the Arctic remain scarce. Furthermore, studies tracking species compositional differences across space and time, as well as diatom responses to climate warming, are mainly limited to paleolimnological studies due to a lack of routine monitoring in lakes and streams across vast ar...

A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on biodiversity and ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental DNA and RNA to cost-efficiently and accurate...

Classical biomonitoring techniques have focused primarily on measures linked to various biodiversity metrics and indicator species. Next-generation biomonitoring (NGB) describes a suite of tools and approaches that allow the examination of a broader spectrum of organizational levels—from genes to entire ecosystems. Here, we frame 10 key questions t...

Recent years provided intense progression in the implementation of molecular techniques in a wide variety of research fields in ecology. Biomonitoring and bioassessment can greatly benefit from DNA metabarcoding and High-Throughput Sequencing (HTS) methods that potentially provide reliable, high quantity and quality standardized data in a cost- and...

Despite important progress, uncertainty persists regarding the ecological forces driving microbial community assembly. Here, we present the first study to use phylogenetic information to interpret the structure and diversity of diatom communities. We examined local phylogenetic divergence and beta- phylogenetic diversity in a large dataset of 595 f...

Diatoms are known to be efficient bioindicators for water quality assessment because of their rapid response to environmental pressures and their omnipresence in water bodies. The identification of benthic diatoms communities in the biofilm, coupled with quality indices such as the Indice de polluosensibilité spécifique (IPS) can be used for biomon...

This paper explores the diversity and taxonomy of species within Fragilaria sensu stricto, an abundant and ecologically important diatom genus, taking advantage of cultured and DNA‐barcoded material. The goal is to facilitate identification of European taxa within this complex, providing a unified view on morphological and molecular diversity. Ther...

Freshwater ecosystems are continuously affected by anthropogenic pressure. One of the main sources of contamination comes from wastewater treatment plant (WWTP) effluents that contain wide range of micro- and macropollutants. Chemical composition, toxicity levels and impact of treated effluents (TEs) on the recipient aquatic ecosystems may strongly...

CAFF Circumpolar Biodiversity Monitoring Program State of Arctic Freshwater Biodiversity Report.

Sötvatten (www.havochvatten.se/sotvatten17). Authors: Maria Kahlert, Bonnie Bailet & Francois Keck, SLU (2018) In Swedish. About the recent developments of metabarcoding for environmental assessment and diversity analyses, with a focus on diatoms and Swedish monitoring programs.

DNA metabarcoding has been introduced as a revolutionary way to identify organisms and monitor ecosystems. However, the potential of this approach for biomonitoring remains partially unfulfilled because a significant part of the sampled DNA cannot be affiliated to species due to incomplete reference libraries. Thus, biotic indices which are based o...

Wastewater treatment plants (WWTP) are the main sources of a broad spectrum of pharmaceuticals found in freshwater ecosystems. These pollutants raise environmental health concerns because of their highly bioactive nature and their chronic releases. Despite this, pharmaceuticals' effects on aquatic environments are poorly defined. Biofilms represent...

Diatoms are used routinely to assess pollution level in rivers and lakes. Current methods are based on identification by light microscopy, which is laborious. An alternative is to identify species based on short DNA fragments and High–Throughput Sequencing (HTS). However a potential limitation is the incomplete coverage of species in reference barc...

Aim 1. To disentangle the effects of local environmental conditions and space at multiple scales in order to uncover and explain biogeographical signals in microbial communities of freshwater diatoms. 2. To assess the role of species traits related to dispersal capacities in diatom biogeography. Location Rivers and streams of Sweden sampled over a...

Diatoms are used as indicators of freshwater ecosystems integrity. Developing diatom-based tools to assess impact of herbicide pollution is expected by water managers. But, defining sensitivities of all species to multiple herbicides would be unattainable. The existence of a phylogenetic signal of herbicide sensitivity was shown among diatoms and s...

Les diatomées sont des micro-algues largement utilisées pour évaluer la qualité écologique des milieux aquatiques. La grande majorité des indices biotiques utilisant les diatomées sont basés sur la sensibilité à la pollution des espèces. Cela constitue un frein à leur utilisation car l’identification taxonomique au niveau de l’espèce est complexe,...

Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of...

Phylogenetic signal is the tendency for closely related species to display similar trait values as a consequence of their phylogenetic proximity. Ecologists and evolutionary biologists are becoming increasingly interested in studying the phylogenetic signal and the processes which drive patterns of trait values in the phylogeny. Here, we present a...

Diatoms include a great diversity of taxa and are recognized as powerful bioindicators of freshwater quality. However, using diatoms for bioassessment is costly and time‐consuming, because most of the indices necessitate species‐level identification. Simplifying diatom‐based assessment protocols has focused the attention of water managers and resea...

Hospital wastewaters (HWW) contain wider spectrum and higher quantity of pharmaceuticals than urban wastewaters (UWW), but they are generally discharged in sewers without pretreatment. Since traditional urban wastewater treatment plants (WWTP) are not designed to treat HWWs, treated effluents may still contain pollutants that could impair receiving...

Phylogeny has not yet been fully accepted in the field of ecotoxicology, despite studies demonstrating its potential for developing environmental biomonitoring tools, as it can provide an a priori assessment of the sensitivity of several indicator organisms. We therefore investigated the relationship between phylogeny and sensitivity to herbicides...

1. Anthropogenic impacts on the biogeochemical cycles of nitrogen (N) and phosphorus (P) affect natural ecosystems worldwide. Modelling is required to predict where and when these key nutrients limit primary production in freshwaters. 2. We reviewed 382 nutrient-enrichment experiments to examine which factors promote limitation of microphytobentho...

We review known and hypothesized effects of nitrogen (N) deposition owing to human activities on the chemistry, organisms, and ecosystem processes of remote oligotrophic freshwaters. Acidification is the best-known effect of N deposition on water chemistry, but additional effects include increased nutrient availability and alteration of the balance...