Article « Une « protection rapprochée » en France pour le puffin des Baléares, oiseau marin le plus menacé d’Europe » (pp.6-8)
1/ Pédenaud, G. (2024). Distribution et abondance du Puffin des Baléares au regard des conditions environnementales et des ressources trophiques de la mer d’Iroise (p. 107) [Mémoire de fin d’étude]. AgroParisTech.
2/ De La Cruz, A., Pereira, J. M., Arroyo, G. M., et al. (2025). Global distribution, threats and population trends of the critically endangered Balearic shearwater Puffinus mauretanicus. Biological Conservation, 305, 111047.
3/ Lewin, P.J., Wynn, J., Arcos, J.M., et al. Climate change drives migratory range shift via individual plasticity in shearwaters. Proceedings of the National Academy of Sciences, 2024, vol. 121, no 6, p. e2312438121.
Article « Le métabarcodage des diatomées : un outil pour optimiser l’évaluation de la qualité des milieux aquatiques » (pp.36-38)
1/ Adl, S.M., Bass, D., Lane, C.E., et al. (2019). Revisions to the classification, nomenclature, and diversity of eukaryotes. J Eukaryot Microbiol. 66, 4–119.
2/ Afnor (2016). Norme française NF T90-354 - Qualité de l’eau - Échantillonnage, traitement et analyse de diatomées benthiques en cours d’eau et canaux.121 p.
3/ Apothéloz‐Perret‐Gentil, L., Cordonier, A., Straub, F., et al (2017). Taxonomy‐free molecular diatom index for high‐throughput eDNA biomonitoring. Molecular ecology resources, 17(6), 1231-1242.
4/ Apothéloz‐Perret‐Gentil, L., Bouchez, A., Cordier, T., et al (2021). Monitoring the ecological status of rivers with diatom eDNA metabarcoding: A comparison of taxonomic markers and analytical approaches for the inference of a molecular diatom index. Molecular Ecology, 30(13), 2959-2968.
5/ Baricevic, A., Chardon, C., Kahlert, M., et al (2022). Recommendations for the preservation of environmental samples in diatom metabarcoding studies. Metabarcoding and Metagenomics (MBMG), 6, 349-365.
6/ Barinova, S. (2025). Database of Ecological Indicators of Freshwater Algae and Cyanobacteria. Ecology and Diversity, 2, 10003.
7/ Berthon, V., Bouchez, A., & Rimet, F. (2011). Using diatom life-forms and ecological guilds to assess organic pollution and trophic level in rivers: a case study of rivers in south-eastern France. Hydrobiologia, 673(1), 259-271.
8/ Blancher, P., Lefrançois, E., Rimet, F., et al (2022). A strategy for successful integration of DNA-based methods in aquatic monitoring. Metabarcoding and Metagenomics, 6, e85652.
9/ Blanco, S., Ector, L., Huck, V., et al (2008). Diatom assemblages and water quality assessment in the Duero Basin (NW Spain). Belgian Journal of Botany, 141, 39-50.
10/ Chonova, T., Rimet, F., Bouchez, A., et al (2023). Revisiting global diversity and biogeography of freshwater diatoms: New insights from molecular data. Environmental DNA, 5(6), 1505-1515.
11/ Coste, M., Boutry, S., Tison-Rosebery, J., & Delmas, F. (2009). Improvements of the Biological Diatom Index (BDI): description and efficiency of the new version (BDI-2006). Ecological indicators, 9(4), 621-650.
12/ European Commission (2000). Directive 2000/60/EC of the Europe¬an Parliament and of the Council of 23 October 2000 establish¬ing a framework for community action in the field of water policy.
13/ Field, C. B., Behrenfeld, M. J., Randerson, J. T., & Falkowski, P. (1998). Primary production of the biosphere: integrating terrestrial and oceanic components. Science, 281(5374), 237-240.
14/ Gregersen, R., Pearman, J. K., Atalah, J., et al (2023). A taxonomy-free diatom eDNA-based technique for assessing lake trophic level using lake sediments. Journal of Environmental Management, 345, 118885.
15/ Guiry, M. D. (2012). How many species of algae are there? Journal of phycology, 48(5), 1057-1063.
16/ Haye, R., Gassiole, G., & Monnier, O. (2025). Evaluation de la stabilité et de la robustesse de l’Indice diatomées Mayotte basé sur les traits (IDMtrait) et comparaison avec l’Indice diatomées Mayotte basé sur les espèces (IDMsp). Rapport Office français de la biodiversité.
17/ Heinry, L., Guéguen, J., Boutry, S., et al (2024). Assessment of river ecological status in the French West Indies based on diatom flora. Environmental Monitoring and Assessment, 196(9), 860.
18/ Keck, F., Vasselon, V., Rimet, F., et al (2018). Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles. Molecular Ecology Resources, 18(6), 1299-1309.
19/ Kelly, M. G., & Whitton, B. A. (1995). The Trophic Diatom Index : a new index for monitoring eutrophication in rivers. Journal of Applied Phycology, 7(4), 433 444.
20/ Kermarrec, L. (2012). Apport des outils de la biologie moléculaire pour l’utilisation des diatomées comme bioindicateurs de la qualité des écosystèmes aquatiques lotiques et pour l’étude de leur taxonomie (Doctoral dissertation, Université de Grenoble).
21/ Kermarrec, L., Franc, A., Rimet, F., et al (2013). Next‐generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms. Molecular ecology resources, 13(4), 607-619.
22/ Kermarrec, L., Franc, A., Rimet, F., et al (2014). A next-generation sequencing approach to river biomonitoring using benthic diatoms. Freshwater Science, 33(1), 349-363.
23/ Kulaš, A., Lemonnier, C., Alric, B., et al (2025). Can genetic diversity in microalgae species be explained by climate: an overview of metabarcoding with diatoms. ISME communications, 5(1), ycaf171.
24/ Lange-Bertalot, H. (1979). Pollution tolerance of diatoms as a criterion for water quality estimation. Nova Hedwigia Beiheft, 64, 285-304.
25/ Mann, D. G., & Vanormelingen, P. (2013). An inordinate fondness? The number and origins of diatom species. Journal of eukaryotic microbiology, 60(4), 414-420.
26/ Nelson, D. M., Tréguer, P., Brzezinski, M. A., et al (1995). Production and dissolution of biogenic silica in the ocean: revised global estimates, comparison with regional data and relationship to biogenic sedimentation. Global biogeochemical cycles, 9(3), 359-372.
27/ Passy, S. I. (2007). Diatom ecological guilds display distinct and predictable behavior along nutrient and disturbance gradients in running waters. Aquatic botany, 86(2), 171-178.
28/ Patrick, R. (1963). The structure of diatom communities under varying ecological conditions. Annals of the New York Academy of Sciences, 108(2), 359-365.
29/ Prygiel, J., & Coste, M. (1999). Progress in the use of diatoms for monitoring rivers in France. Use of algae for monitoring rivers III. Prygiel, J., Whitton, B.A., Bukowska, J. (Eds), 165-179.
30/ Rimet, F., Gusev, E., Kahlert, M., et al (2019). Diat. barcode, an open-access curated barcode library for diatoms. Scientific Reports, 9(1), 15116.
31/ Rimet, F., Lemonnier, C., Alric, B., et al (2025). Omics to study and manage aquatic environments: a snapshot from the AquaEcOmics meeting (Evian-les-Bains, 2025). Molecular Ecology, 34, e70041.
32/ Rivera, S., Vasselon, V., Chardon, C., et al (2019). Bioindication diatomées : comparaison microscopie / barcoding ADN. Etude nationale DREALs 2016-2017, Projet INRA-AFB N° 15000239 / A30. Rapport final.
33/ Rivera, S. F., Vasselon, V., Bouchez, A., & Rimet, F. (2020). Diatom metabarcoding applied to large scale monitoring networks: Optimization of bioinformatics strategies using Mothur software. Ecological indicators, 109, 105775.
34/ Rivières sauvages, Scimabio-Interface & Inrae (2022). Séminaire de restitution de l’étude ADN environnemental des diatomées sur les sites « rivières sauvages » de France.
35/ Round, F.E., Crawford, R.M. & Mann, D.G. (1990). The Diatoms. Biology and morphology of the genera. Cambridge University Press, Cambridge.
36/ Smucker, N. J., Pilgrim, E. M., Nietch, C. T., et al (2024). Using DNA metabarcoding to characterize national scale diatom-environment relationships and to develop indicators in streams and rivers of the United States. Science of the Total Environment, 939, 173502.
37/ Soininen, J. (2007). Environmental and spatial control of freshwater diatoms-a review. Diatom Research. 22, 473–490.
38/ Tapolczai, K., Keck, F., Bouchez, A., et al (2019). Diatom DNA metabarcoding for biomonitoring: strategies to avoid major taxonomical and bioinformatical biases limiting molecular indices capacities. Frontiers in Ecology and Evolution, 7, 409.
39/ Vasselon, V. (2017). Barcoding et bioindication: développement du metabarcoding des diatomées pour l'évaluation de la qualité des cours d'eau (Doctoral dissertation, Université Grenoble Alpes).
40/ Vasselon, V., Rimet, F., Tapolczai, K., & Bouchez, A. (2017). Assessing ecological status with diatoms DNA metabarcoding: Scaling-up on a WFD monitoring network (Mayotte island, France). Ecological Indicators, 82, 1-12.
41/ Vasselon, V., Bouchez, A., Rimet, F., et al (2018). Avoiding quantification bias in metabarcoding: Application of a cell biovolume correction factor in diatom molecular biomonitoring. Methods in Ecology and Evolution, 9(4), 1060-1069.
42/ Vasselon, V., Rimet, F., Domaizon, I., et al (2019a). Évaluer la pollution des milieux aquatiques avec l’ADN des diatomées : où en sommes-nous ? Techniques Sciences Méthodes, 5, 53–70.
43/ Vasselon, V., Rimet, F., Domaizon, I., et al (2019b). Assessing pollution of aquatic environments with diatoms' DNA metabarcoding: experience and developments from France Water Framework Directive networks. Metabarcoding and Metagenomics, 2019, 3.
44/ Vasselon, V. (2022). Utilisation de l’ADN environnemental des diatomées comme outil de biomonitoring pour la conservation des Rivières Sauvages (2020-2022). Application au bassin versant de la Gioune et du Pic. Rapport Rivières Sauvages, Scimabio Interface.
45/ Vasselon, V., Rivera, S., Ács, É., et al (2025). Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring. Metabarcoding and Metagenomics, 9, e133264.
46/ Vidaković, D., Mayombo, N. A. S., Castellanos, A. B., et al (2024). Diatom metabarcoding as a tool to assess the water quality of two large tributaries of the Danube River. Ecological Indicators, 168, 112793.
47/ Vitte, I., Peres, F., Vasselon, V., Jouanillou, A. (2023). Projet Méta-IBD - Indice biologique diatomées : évaluation de la mise en routine de la méthode de métabarcoding à l'échelle locale (Sud-ouest de la France). Rapport Agence de l’eau Adour-Garonne, Laboratoire des Pyrénées et des Landes, Scimabio Interface, Artemis.
48/ Wu, J. T. (1999). A generic index of diatom assemblages as bioindicator of pollution in the Keelung River of Taiwan. Hydrobiologia, 397, 79-87.