Main
François Keck
I am a community ecologist interested in using large datasets and computational methods to investigate ecological questions in the field of limnology. Broadly, my research activities are focussed on the links between environmental variation and community dynamics in diatoms. Because diatoms are important biological indicators, a significant part of my work involves developing ideas, methods and scientific principles to support environmental monitoring and management.
Education
Ph.D. Biodiversity, Ecology and Environment
University of Grenoble-Alpes
·
2016 - 2013
M.S. Ecology, Evolution and Biometry
University of Lyon
Lyon, FR
2011 - 2009
B.S. Biology and Population Ecology
University of Lyon
Lyon, FR
2009 - 2006
Professional experience
Postdoctoral researcher
Eawag
Zurich
2022 - 2020
Macroinvertebrate diversity in small catchments varying in agricultural land use intensity
Postdoctoral researcher
INRA
Thonon-les-Bains, FR
2019
Changes in lake micro-eukaryotic communities during the Anthropocene.
Postdoctoral researcher
SLU
Uppsala, SE
2018 - 2016
Diatom ecological niches and community structure.
PhD. Degree
University of Grenoble-Alpes
·
2016 - 2013
Assessing the links between phylogeny and ecological traits: new perspective for rivers bioassessment.
Ecological engineer
Charpentier Consultants
Montluel, FR
2012
Digital cartography of wetlands and methodological developments.
Ecological engineer
University of Lyon
Lyon, FR
2011
Analyses of ecological data as part of the Rhône river restauration project.
Ecological engineer
Charpentier Consultants
Montluel, FR
2008
Impact study as part of the Saône river restauration
Publications
Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment
Keck, F., Blackman, R. C., Bossart, R., Brantschen, J., Couton, M., Hürlemann, S., Kirschner, D., Locher, N., Zhang, H., Altermatt, F. (2022). Molecular Ecology, 31(6), 1820-1835.
Paleoreconstructions of ciliate communities reveal long-term ecological changes in temperate lakes
Barouillet, C., Vasselon, V., Keck, F., Millet, L., Etienne, D., Galop, D., Rius, D., Domaizon, I. (2022). Scientific Reports, 12(1), 7899.
A triad of kicknet sampling, eDNA metabarcoding, and predictive modeling to assess richness of mayflies, stoneflies and caddisflies in rivers
Keck, F., Hürlemann, S., Locher, N., Stamm, C., Deiner, K., Altermatt, F. (2022). Metabarcoding and Metagenomics, 6, e79351.
Co-occurrence, ecological profiles and geographical distribution based on unique molecular identifiers of the common freshwater diatoms Fragilaria and Ulnaria
Kahlert, M., Maaria Karjalainen, S., Keck, F., Kelly, M., Ramon, M., Rimet, F., Schneider, S., Tapolczai, K., Zimmermann, J. (2022). Ecological Indicators, 141, 109114.
Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb
Keck, F., Altermatt, F. (2022). Molecular Ecology Resources.
Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses
Keck, F., Couton, M., Altermatt, F. (2022). Molecular Ecology Resources.
The potential of exact sequence variants (ESVs) to interpret and assess the impact of agricultural pressure on stream diatom assemblages revealed by DNA metabarcoding
Tapolczai, K., Selmeczy, G. B., Szabó, B., B-Béres, V., Keck, F., Bouchez, A., Rimet, F., Padisák, J. (2021). Ecological Indicators, 122, 107322.
DNA metabarcoding reveals differences in distribution patterns and ecological preferences among genetic variants within some key freshwater diatom species
Pérez-Burillo, J., Trobajo, R., Leira, M., Keck, F., Rimet, F., Sigró, J., Mann, D. G. (2021). Science of The Total Environment, 798, 149029.
Assessing the response of micro-eukaryotic diversity to the Great Acceleration using lake sedimentary DNA
Keck, F., Millet, L., Debroas, D., Etienne, D., Galop, D., Rius, D., Domaizon, I. (2020). Nature Communications, 11(1), 3831.
Handling biological sequences in R with the bioseq package
Keck, F. (2020). Methods in Ecology and Evolution, 11(12), 1728-1732.
Key Questions for Next-Generation Biomonitoring
Makiola, A., Compson, Z. G., Baird, D. J., Barnes, M. A., Boerlijst, S. P., Bouchez, A., Brennan, G., Bush, A., Canard, E., Cordier, T., Creer, S., Curry, R. A., David, P., Dumbrell, A. J., Gravel, D., Hajibabaei, M., Hayden, B., van der Hoorn, B., Jarne, P., Jones, J. I., Karimi, B., Keck, F., Kelly, M., Knot, I. E., Krol, L., Massol, F., Monk, W. A., Murphy, J., Pawlowski, J., Poisot, T., Porter, T. M., Randall, K. C., Ransome, E., Ravigné, V., Raybould, A., Robin, S., Schrama, M., Schatz, B., Tamaddoni-Nezhad, A., Trimbos, K. B., Vacher, C., Vasselon, V., Wood, S., Woodward, G., Bohan, D. A. (2020). Frontiers in Environmental Science, 7.
Biodiversity patterns of Arctic diatom assemblages in lakes and streams: Current reference conditions and historical context for biomonitoring
Kahlert, M., Rühland, K. M., Lavoie, I., Keck, F., Saulnier‐Talbot, E., Bogan, D., Brua, R. B., Campeau, S., Christoffersen, K. S., Culp, J. M., Karjalainen, S. M., Lento, J., Schneider, S. C., Shaftel, R., Smol, J. P. (2020). Freshwater Biology.
Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap
Cordier, T., Alonso‐Sáez, L., Apothéloz‐Perret‐Gentil, L., Aylagas, E., Bohan, D. A., Bouchez, A., Chariton, A., Creer, S., Frühe, L., Keck, F., Keeley, N., Laroche, O., Leese, F., Pochon, X., Stoeck, T., Pawlowski, J., Lanzén, A. (2020). Molecular Ecology.
Ecological correlates of riverine diatom and macroinvertebrate alpha and beta diversity across Arctic Fennoscandia
Brittain, J. E., Heino, J., Friberg, N., Aroviita, J., Kahlert, M., Karjalainen, S.-M., Keck, F., Lento, J., Liljaniemi, P., Mykrä, H., Schneider, S. C., Ylikörkkö, J. (2020). Freshwater Biology.
Community phylogenetic structure reveals the imprint of dispersal-related dynamics and environmental filtering by nutrient availability in freshwater diatoms
Keck, F., Kahlert, M. (2019). Scientific Reports, 9(1), 1-8.
Benthic Diatom Communities in an Alpine River Impacted by Waste Water Treatment Effluents as Revealed Using DNA Metabarcoding
Chonova, T., Kurmayer, R., Rimet, F., Labanowski, J., Vasselon, V., Keck, F., Illmer, P., Bouchez, A. (2019). Frontiers in Microbiology, 10.
Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status
Bailet, B., Bouchez, A., Franc, A., Frigerio, J.-M., Keck, F., Karjalainen, S.-M., Rimet, F., Schneider, S., Kahlert, M. (2019). Metabarcoding and Metagenomics, 3, e34002.
Connecting the morphological and molecular species concepts to facilitate species identification within the genus Fragilaria (Bacillariophyta)
Kahlert, M., Kelly, M. G., Mann, D. G., Rimet, F., Sato, S., Bouchez, A., Keck, F. (2019). Journal of Phycology.
Diatom DNA Metabarcoding for Biomonitoring: Strategies to Avoid Major Taxonomical and Bioinformatical Biases Limiting Molecular Indices Capacities
Tapolczai, K., Keck, F., Bouchez, A., Rimet, F., Kahlert, M., Vasselon, V. (2019). Frontiers in Ecology and Evolution, 7.
Disentangling the processes driving the biogeography of freshwater diatoms: A multiscale approach
Keck, F., Franc, A., Kahlert, M. (2018). Journal of Biogeography, 45(7), 1582-1592.
Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles
Keck, F., Vasselon, V., Rimet, F., Bouchez, A., Kahlert, M. (2018). Molecular Ecology Resources, 18(6), 1299-1309.
The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes
Rimet, F., Abarca, N., Bouchez, A., Kusber, W.-H., Jahn, R., Kahlert, M., Keck, F., Kelly, M. G., Mann, D. G., Piuz, A., Trobajo, R., Tapolczai, K., Vasselon, V., Zimmermann, J. (2018). Fottea, 18(1), 37-54.
River biofilm community changes related to pharmaceutical loads emitted by a wastewater treatment plant
Chonova, T., Labanowski, J., Cournoyer, B., Chardon, C., Keck, F., Laurent, É., Mondamert, L., Vasselon, V., Wiest, L., Bouchez, A. (2018). Environmental Science and Pollution Research, 25(10), 9254-9264.
Freshwater biomonitoring in the Information Age
Keck, F., Vasselon, V., Tapolczai, K., Rimet, F., Bouchez, A. (2017). Frontiers in Ecology and the Environment, 15(5), 266–274.
Can we predict diatoms herbicide sensitivities with phylogeny? Influence of intraspecific and interspecific variability
Esteves, S. M., Keck, F., Almeida, S. F. P., Figueira, E., Bouchez, A., Rimet, F. (2017). Ecotoxicology, 26(8), 1065-1077.
Phylogenetic signal in diatom ecology: Perspectives for aquatic ecosystems biomonitoring
Keck, F., Rimet, F., Franc, A., Bouchez, A. (2016). Ecological Applications, 26(3), 861–872.
Linking phylogenetic similarity and pollution sensitivity to develop ecological assessment methods: a test with river diatoms
Keck, F., Bouchez, A., Franc, A., Rimet, F. (2016). Journal of Applied Ecology, 53(3), 856–864.
phylosignal: an R package to measure, test, and explore the phylogenetic signal
Keck, F., Rimet, F., Bouchez, A., Franc, A. (2016). Ecology and Evolution, 6(9), 2774–2780.
Separate treatment of hospital and urban wastewaters: A real scale comparison of effluents and their effect on microbial communities
Chonova, T., Keck, F., Labanowski, J., Montuelle, B., Rimet, F., Bouchez, A. (2016). Science of The Total Environment, 542, 965-975.
R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring
Rimet, F., Chaumeil, P., Keck, F., Kermarrec, L., Vasselon, V., Kahlert, M., Franc, A., Bouchez, A. (2016). Database, 2016, baw016.
Linking Diatom Sensitivity to Herbicides to Phylogeny: A Step Forward for Biomonitoring?
Larras, F., Keck, F., Montuelle, B., Rimet, F., Bouchez, A. (2014). Environmental Science & Technology, 48(3), 1921-1930.
Can we predict nutrient limitation in streams and rivers?
Keck, F., Lepori, F. (2012). Freshwater Biology, 57(7), 1410–1421.
Effects of Atmospheric Nitrogen Deposition on Remote Freshwater Ecosystems
Lepori, F., Keck, F. (2012). AMBIO: A Journal of the Human Environment, 41(3), 235-246.
Selected presentation
From DNA sequences to operational reference databases. An opinionated approach using R
1st DNAqua-net conference (online, 2021).
Patterns and drivers of phylogenetic diversity in freshwater diatom communities of Sweden
25th International Diatom Symposium (Berlin, Germany, 2018).
Developing phylogenetically based biomonitoring methods: a test with diatoms
9th Use of Algae for Monitoring RIvers and comparable habitats (Trentino, Italy, 2015).
Linking phylogenetic similarity and pollution sensitivity to develop ecological assessment methods: a test with diatoms
9th Symposium for European Freshwater Sciences (Geneva, Switzerland, 2015).
Linking Diatoms Ecological Preferences To Phylogeny: New Perspectives for Aquatic Ecosystems Bioassessment
Joint Aquatic Sciences Meeting (Portland, Oregon, 2014).
Linking diatoms polluosensitivity to phylogeny: New perspectives for aquatic ecosystems bioassessment
7th Central European Diatoms meeting (Thonon-les-Bains, France, 2013).
Can we predict nitrogen limitation in streams and rivers? A meta-analysis
7th Symposium for European Freshwater Sciences (Gerona, Spain, 2011).
Software Development
Lead developer of two R packages available on CRAN
- rleafmap: Interactive maps with R and leaflet.
- phylosignal: Assessing and exploring the phylogenetic signal with R.
Other open source contributions: https://github.com/fkeck
Invited at the R hackathon Hackout 2: Graphical Resources for Infectious Disease Epidemiology in R (Imperial College, London, 2015).
Activity as Reviewer
Scientific articles
The ISME journal, Environmental Science & Technology, BMC Evolutionary Biology, Freshwater Science, Molecular Ecology , Metabarcoding & Metagenomics, Journal of Biogeography, Harmful Algae.
Research proposals
Funding scheme HARMONIA for the National Science Centre of Poland.
Prizes & Awards
Best student presentation award. 7th Central European Diatoms Meeting.
Outstanding Ph.D. thesis award. University of Grenoble-Alpes (1500 €).
Best ECR oral presentation. 1st DNAqua-net conference (500 €).
References
Dr Florian Altermatt
Professor, Eawag & University of Zurich
Dpt. of Aquatic Ecology,
Überlandstrasse 133,
CH-8600 Dübendorf – Switzerland
+41 58 765 5592
florian.altermatt@eawag.ch
Dr Maria Kahlert
Associate Professor, SLU
Dpt. of Aquatic Sci. & Assessment,
Box 7050,
75007 Uppsala – Sweden
+46 018-673145
maria.kahlert@slu.se
Dr Agnès Bouchez
Research Director, INRA
UMR CARRTEL,
75 avenue de Corzent,
74200 Thonon-les-Bains – France
+33 4 50 26 78 60
agnes.bouchez@inra.fr
Dr Fabio Lepori
Senior Researcher, SUPSI
Institute of Earth Sciences,
Via Trevano, Blocco,
6952 Canobbio – Switzerland
+41 058 666 62 29
fabio.lepori@supsi.ch