D. G. Mann and P. Vanormelingen, An inordinate fondness? The number, distributions and origins of diatom species, J. Eukaryot. Microbiol, vol.60, pp.414-420, 2013.

R. J. Stevenson, Ecological assessments with algae: a review and synthesis, J. Phycol, vol.50, pp.437-461, 2014.

J. P. Smol and E. F. Stoermer, The Diatoms: Applications for the Environmental and Earth Sciences, vol.667, 2010.

R. Kolkwitz and M. Marson, Okologie der pflanzliche Saprobien, Ber. Dtsch. Bot. Ges, vol.26, pp.505-519, 1908.

R. W. Butcher, Studies in the ecology of rivers. IV. The algae of organically enriched water, J. Ecol, vol.35, pp.186-191, 1947.

F. Hustedt, Die Diatomeenflora des Flusssystems der Weser im Gebiet der Hansestadt Bremen, Abh. Nat. Ver. Bremen, vol.34, pp.181-440, 1957.

M. Zelinka and P. Marvan, Zur Prazisierung der biologischen Klassifikation der Reinheit fliessender Gewasser, Arch. Hydrobiol, vol.57, pp.389-407, 1961.

F. Rimet, Recent views on river pollution and diatoms, Hydrobiologia, vol.683, pp.1-24, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02651508

, Directive 2000/60/EC of the European Parliament and of the Council of 23rd October 2000 establishing a framework for Community action in the field of water policy, Official Journal of the European Communities, vol.327, pp.1-72, 2000.

M. T. Barbour, J. Gerritsen, and B. D. Snyder, Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic Macroinvertebrates and Fish, 1999.

F. Round, C. G. Crawford, and D. G. Mann, The diatoms. Biology and Morphology of the Genera, vol.747, 1990.

;. Afnor, Qualit e de l'eau-Guide pour l'identification et le d enombrement des echantillons de diatom ees benthiques de rivières, et leur interpr etation. Afnor, pp.1-13, 2004.

A. Besse-lotoskaya, P. Verdonschot, and J. Sinkeldam, Uncertainty in diatom assessment: sampling, identification and counting variation, Hydrobiologia, vol.566, pp.247-260, 2006.

P. Hebert, A. Cywinska, and S. L. Ball, Biological identifications through DNA barcodes, Proc. Biol. Sci, vol.270, pp.313-321, 2003.

K. M. Evans and D. G. Mann, A proposed protocol for nomenclaturally effective DNA barcoding of microalgae, Phycologia, vol.48, pp.70-74, 2009.

M. B. Moniz and I. Kaczmarska, Barcoding diatoms: is there a good marker?, Mol. Ecol. Resour, vol.9, pp.65-74, 2009.

F. Pompanon, E. Coissac, and P. Taberlet, Metabarcoding a new way to analyze biodiversity, Biofutur, vol.30, pp.30-32, 2011.

L. Kermarrec, A. Franc, and F. Rimet, Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms, Mol. Ecol. Resour, vol.13, pp.607-619, 2013.
URL : https://hal.archives-ouvertes.fr/bioemco-00840234

J. Zimmermann, G. Gl?-ockner, and R. Jahn, Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies, Mol. Ecol. Res, vol.15, pp.526-542, 2014.

L. Guillou, D. Bachar, and S. Audic, The protist ribosomal reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy, Nucleic Acids Res, vol.41, pp.597-604, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01253994

C. Quast, E. Pruesse, and P. Yilmaz, The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Res, vol.41, pp.590-596, 2013.

L. Kermarrec, A. Franc, and F. Rimet, A next-generation sequencing approach to river biomonitoring using benthic diatoms, Freshw. Sci, vol.33, pp.349-363, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02632667

A. Bouchez, L. Kermarrec, and F. Rimet, Abstract ID:14368, session 029 Aquatic Species Investigation: Environmental DNA Applications For Aquatic Ecosystems, Joint Aquatic Sciences Meeting, pp.18-23, 2014.

D. A. Benson, M. Cavanaugh, and K. Clark, GenBank. Nucleic Acids Res, vol.41, pp.36-42, 2013.

K. M. Evans, A. H. Wortley, and D. G. Mann, An assessment of potential diatom "barcode" genes (cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta), Protist, vol.158, pp.349-364, 2007.

S. E. Hamsher, K. M. Evans, and D. G. Mann, Barcoding diatoms: exploring alternatives to COI-5P, Protist, vol.162, pp.405-422, 2011.

L. Kermarrec, A. Bouchez, and F. Rimet, First evidence of the existence of semi-cryptic species and of a phylogeographic structure in the Gomphonema parvulum (K? utzing) K? utzing complex (Bacillariophyta), Protist, vol.164, pp.686-705, 2013.

J. Zimmermann, R. Jahn, and B. Gemeinholzer, Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols, Org. Divers. Evol, vol.11, pp.173-192, 2011.

E. J. Cox, The use of chloroplast and other features of living cell in the taxonomy of naviculoid diatoms. 6th Diatom Symposium, K? onigstein, pp.115-133, 1981.

F. Rimet and A. Bouchez, Life-forms, cell-sizes and ecological guilds of diatoms in European rivers, Knowl. Manag. Aquat. Ecosyst, vol.406, pp.1-14, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02650771

C. Lecointe, M. Coste, and J. Prygiel, Omnidia": software for taxonomy, calculation of diatom indices and inventories managment, Hydrobiologia, vol.269, pp.509-513, 1993.

H. Van-dam, A. Mertens, and J. Sinkeldam, A coded checklist and ecological indicator values of freshwater diatoms from the Netherlands, Neth. J. Aquat. Ecol, vol.28, pp.117-133, 1994.

M. G. Kelly and B. A. Whitton, The trophic diatom index: a new index for monitoring eutrophication in rivers, J. Appl. Phycol, vol.7, pp.433-444, 1995.

M. Kahlert and A. Jarlman, Påv? axt i rinnande vattenkiselalgsanalys, Handledning f? or milj? o? overvakning, 2009.

. Metoder, Programområ de: S? otvatten. Version 3:1. In: Milj? o? overvakningens metoder och unders? okningstyper inom programområde S? otvatten. Havs-och vattenmyndighetens online document, vol.19

. Cemagref, Etude des m ethodes biologiques quantitative d'appr eciation de la qualit e des eaux, vol.218, 1982.

F. Keck, A. Bouchez, A. Franc, and F. Rimet, Linking phylogenetic similarity and pollution sensitivity to develop ecological assessment methods: a test with river diatoms (microalgae), Journal of Applied Ecology, 2016.

M. D. Guiry and G. M. Guiry, AlgaeBase. World-wide electronic publication, 2014.

W. H. Kusber, N. Abarca, and O. Skibbe, Reference library of DNA-barcoded diatoms-A use case for publishing data via the GBIF database AlgaTerra. Book of abstracts of the 22nd International Diatom Symposium, p.65, 2012.

A. Franc, A primer for MIAB INRA UMR, INRA, vol.31, 2014.

T. F. Smith and M. S. Waterman, Identification of common molecular subsequences, J. Mol. Biol, vol.147, pp.195-197, 1981.

T. M. Fruchterman and E. M. Reingold, Graph drawing by force-directed placement, Software-Pract. Exper, vol.21, pp.1129-1164, 1991.

M. Gouy, S. Guindon, and O. Gascuel, SeaView Version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building, Mol. Biol. Evol, vol.27, pp.221-224, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511794

K. Tamura, D. Peterson, and N. Peterson, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol. Biol. Evol, vol.28, pp.2731-2739, 2011.

O. Monnier, M. Coste, and J. Rosebery, Une classification des taxons de l'Indice Biologique Diatom ees (IBD, norme AFNOR NF T90-354, d ecembre, Diatomania, vol.13, pp.17-47, 2007.

L. Kermarrec, L. Ector, and F. Rimet, A preliminary phylogenetic analysis of the Cymbellales based on 18S rDNA gene sequencing, Diatom Res, vol.26, pp.305-315, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02648431

F. Rimet, L. Kermarrec, and A. Bouchez, Molecular phylogeny of the family Bacillariaceae based on 18S rDNA sequences: focus on freshwater Nitzschia of the Lanceolatae section, Diatom Res, vol.26, pp.273-291, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00956037

F. Rimet, R. Trobajo, and D. G. Mann, When is sampling complete? The effects of geographical range and marker choice on perceived diversity in Nitzschia palea (Bacillariophyta), Protist, vol.165, pp.245-259, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02640347

F. Larras, F. Keck, and B. Montuelle, Linking diatom sensitivity to herbicides to phylogeny: a step forward for biomonitoring?, Environ. Sci. Technol, vol.48, pp.1921-1930, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02636747

M. L. Macgillivary and I. Kaczmarska, Survey of the efficacy of a short fragment of the rbcL gene as a supplemental DNA barcode for diatoms, J. Eukaryot. Microbiol, vol.58, pp.529-536, 2011.

K. Bruder and L. K. Medlin, Morphological and molecular investigations of Naviculoid Diatoms. II. selected genera and families, Diatom Res, vol.23, pp.283-329, 2008.

, Database, vol.2016

K. Bruder and L. K. Medlin, Morphological and molecular investigations of Naviculoid Diatoms, Diatom Res, vol.23, pp.331-347, 2008.

L. K. Medlin, A Review of the evolution of the diatoms from the origin of the lineage to their populations, pp.93-118, 2011.

E. C. Theriot, M. P. Ashworth, and T. Nakov, Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling, Mol. Phylogenet. Evol, vol.89, pp.28-36, 2015.

L. Medlin, H. J. Elwood, and S. Stickel, The characterization of enzymatically amplified eukaryotic 16S rRNA-coding regions, Gene, vol.71, pp.491-499, 1988.

E. C. Theriot and K. Serieyssol, Phylogenetic systematics as a guide to understanding features and potential morphological characters of the centric diatom family Thalassiosiraceae, Diatom Res, vol.9, pp.429-450, 1994.

T. A. Shcherbakova, S. V. Kiril'chik, and E. V. Likhoshvai, Phylogenetic position of diatom algae of the genus Aulacoseira from Lake Baikal based on the results of the comparison of 18S rRNA gene nucleotide sequences, Mol. Biol. Moscow, vol.32, pp.735-740, 1998.

S. M. Edgar and E. C. Theriot, Phylogeny of Aulacoseira (Bacillariophyta) based on molecules and morphology, J. Phycol, vol.40, pp.772-788, 2004.

L. K. Medlin and I. Kaczmarska, Evolution of diatoms: V. Morphological and cytological support for the major clade and a taxonomic reivsion, Phycologia, vol.43, pp.245-270, 2004.

A. J. Alverson, R. K. Jansen, and E. C. Theriot, Bridging the rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms, Mol. Phylogenet. Evol, vol.45, pp.193-210, 2007.

I. A. Luddington, I. Kaczmarska, and C. Lovejay, Distance and character-based evaluation of the V4 region of the 18S rRNA Gene for the identification of diatoms (Bacillariophyceae), 2012.

, PLoS One, vol.7, pp.1-11

K. Whittaker, D. Rignanese, and R. Olson, Molecular subdivision of the marine diatom Thalassiosira rotula in relation to geographic distribution, genome size, and physiology, BMC Evol. Biol, vol.12, pp.1-14, 2013.

H. Kaeriyama, E. Katsuki, and M. Otsubo, Effects of temperature and irradiance on growth of strains belonging to seven Skeletonema species isolated from Dokai Bay, southern Japan, Eur. J. Phycol, vol.46, pp.113-124, 2011.

A. J. Alverson, L. Kolnick, W. Kooistra, D. Sarno, and S. Balzano, Intragenomic nucleotide polymorphism among small subunit (18s) rdna paralogs in the diatom genus Skeletonema (Bacillariophyta), Global diversity and biogeography of Skeletonema species (Bacillariophyta), vol.41, pp.1248-1257, 2005.

, Protist, vol.159, pp.177-193

R. Trobajo, E. Clavero, and V. Chepurnov, Morphological, genetic and mating diversity within the widespread bioindicator Nitzschia palea (Bacillariophyceae), 2009.

, Phycologia, vol.48, pp.443-459

R. Trobajo, D. G. Mann, and E. Clavero, The use of partial cox1, rbcL and LSU rDNA sequences for phylogenetics and species identification within the Nitzschia palea species complex (Bacillariophyceae), Eur. J. Phycol, vol.45, pp.413-425, 2010.

N. Abarca, R. Jahn, and J. Zimmermann, Does the cosmopolitan diatom Gomphonema parvulum (Kutzing) Kutzing Have a Biogeography?, PLoS One, vol.9, pp.1-18, 2014.

K. M. Evans, V. A. Chepurnov, and H. J. Sluiman, Highly differentiated populations of the freshwater diatom Sellaphora capitata suggest limited dispersal and opportunities for allopatric speciation, Protist, vol.160, pp.386-396, 2009.

K. M. Evans, A. H. Wortley, and G. E. Simpson, A molecular systematic approach to explore diversity within the Sellaphora pupula species complex (Bacillariophyta), J. Phycol, vol.44, pp.215-231, 2008.

D. G. Mann, S. M. Mcdonald, and M. M. Bayer, The Sellaphora pupula species complex (Bacillariophyceae): morphometric analysis, ultrastructure and mating data provide evidence for five new species, Phycologia, vol.43, pp.459-482, 2004.

N. Lundholm, S. S. Bates, and K. A. Baugh, Cryptic and pseudo-cryptic diversity in diatoms with descriptions of Pseudo-Nitzschia hasleana Sp Nov and P. fryxelliana Sp Nov, J. Phycol, vol.48, pp.436-454, 2012.

N. Lundholm, O. Moestrup, and Y. Kotaki, Inter-and intraspecific variation of the Pseudo-nitzschia delicatissima complex (Bacillariophyceae) illustrated by rRNA probes, morphological data and phylogenetic analyses, J. Phycol, vol.42, pp.464-481, 2006.

B. Beszteri, E. Acs, and J. Makk, Phylogeny of six naviculoid diatoms based on 18S rDNA sequences, Int. J. Syst. Evol. Microbiol, vol.51, pp.1581-1586, 2001.

K. Bruder, S. Sato, and L. K. Medlin, Morphological and molecular investigations of naviculoid diatoms IV. Pinnularia Vs, Caloneis Diatom, vol.24, pp.8-24, 2008.

K. Bruder and L. K. Medlin, Molecular assessment of phylogenetic relationships in selected species/genera in the naviculoid diatoms (Bacillariophyta). I. The genus Placoneis, Nova Hedwigia, vol.85, pp.331-352, 2007.

C. Souffreau, H. Verbruggen, and A. Wolfe, A time-calibrated multi-gene phylogeny of the diatom genus Pinnularia, Mol. Phylogenet. Evol, vol.61, pp.866-879, 2011.

F. Rimet, Benthic diatom assemblages and their correspondence with ecoregional classifications: case study of rivers in north-eastern France, Hydrobiologia, vol.636, pp.137-151, 2009.

M. G. Kelly, S. Juggins, and R. Guthrie, Assessment of ecological status in UK rivers using diatoms, Freshw. Biol, vol.1111, pp.1365-2427, 2007.

L. King, G. Clarke, and H. Bennion, Use of diatom lifeforms and ecological guilds to assess pollution in rivers: case study of south-eastern french rivers, J. Appl. Phycol, vol.18, pp.259-271, 2006.

S. I. Passy, Diatom ecological guilds display distinct and predictable behavior along nutrient and disturbance gradients in running waters, Aquat. Bot, vol.86, pp.171-178, 2007.

J. Zimmermann, N. Abarca, and N. Enke, Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research, PLoS One, vol.9, pp.1-24, 2014.

. Cen, Water quality-Technical report for the management of diatom barcodes for ecological status assessment, European Committee for Standardization, vol.7, 2014.

L. Kermarrec, Apport des outils de la biologie mol eculaire pour l'utilisation des diatom ees comme bioindicateurs de la qualit e des ecosystèmes aquatiques lotiques et pour l' etude de leur taxonomie, vol.297, 2012.

R. Trobajo, L. Rovira, and L. Ector, Morphology and identity of some ecologically important small Nitzschia species, Diatom Res, vol.28, pp.37-59, 2013.

M. G. Kelly, R. Trobajo, and L. Rovira, Characterizing the niches of two very similar Nitzschia species and implications for ecological assessment, Diatom Res, vol.30, pp.27-33, 2015.

D. J. Baird and M. Hajibabaei, Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing, Mol. Ecol, vol.8, pp.2039-2044, 2012.