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Genetic barcoding of Ecuadorian epilithic diatom species suitable as water quality bioindicators
Comptes Rendus. Biologies, Tome 343 (2020) no. 1, pp. 41-52.
Résumé

L’identification des diatomées est une étape clé dans l’utilisation de ces microorganismes comme bioindicateurs de la qualité de l’eau. Le diagnostic morphologique est une tâche difficile en raison du nombre considérable d’espèces et de leur dimension microscopique. Il est possible de surmonter cette difficulté en utilisant des techniques moléculaires pour compléter le diagnostic. L’objectif principal de ce travail était d’obtenir le code-barre de l’ADN des diatomées épilithiques équatoriennes ayant une large distribution géographique, une niche écologique bien définie et des caractéristiques leur permettant d’être des espèces indicatrices fiables. Des cultures de diatomées unialgales ont été obtenues à partir d’échantillons environnementaux de cours d’eau des Andes équatoriennes. La caractérisation morphologique des cultures a été réalisée sous microscopie MEB. Pour la caractérisation moléculaire, les codes-barres 18SV4 et rbcL ont été séquencés à partir de chaque souche et comparés à la base de données GenBank. Pour chaque code-barres, un arbre phylogénétique a été construit à partir de la méthode ML comprenant des séquences de souches des espèces étudiées, provenant de différents lieux géographiques. Les résultats ayant montré que les cinq espèces suivantes étaient appropriées comme bioindicateurs, elles ont été isolées. Sellaphora seminulum (souche JA01b, c), Nitzschia fonticola (souche SP02a) et N. palea (souche CA01a) sont tolérantes à l’eutrophisation ; Eolimna minima (souche CH02a) est un bioindicateur d’eau mésotrophe, et Achnanthidium minutissimum (souche JA01a) est un bioindicateur d’eau oligotrophe. La comparaison avec la base de données GenBank des régions de code-barres a supporté leurs identifications morphologiques. Les séquences de code-barres des souches ont montré un pourcentage élevé d’identité génétique avec les séquences signalées dans les bases de données de l’INSDC pour la même espèce. La topologie des arbres phylogénétiques démontre que les diatomées épilithiques de l’Équateur sont étroitement liées à celles des mêmes espèces isolées d’autres régions géographiques. Cette étude est une première tentative d’établir une bibliothèque de référence morphologique et taxonomique moléculaire pour les diatomées néotropicales. Cette étude démontre qu’il serait possible d’utiliser les données de code-barres existantes pour les diatomées afin de développer des instruments moléculaires pour la bioévaluation des écosystèmes aquatiques dans la région andine équatorienne.

Compléments :
Des compléments sont fournis pour cet article dans le fichier séparé : crbiol-2-suppl.pdf

Reçu le : 2019-10-25
Révisé le : 2019-11-22
Accepté le : 2019-11-22
Publié le : 2020-06-05
DOI : https://doi.org/10.5802/crbiol.2
Mots clés: Bacillariophytae, Gène de l’ARNr 18SV4, Gène rbcL, Bibliothèques de référence de codes-barres, Biosurveillance, Équateur, Diatomées
@article{CRBIOL_2020__343_1_41_0,
     author = {Isabel Ballesteros and Pablo Castillejo and Adriana Paulina Haro and Cuthy Cristina Montes and Carla Heinrich and Eduardo Alexis Lobo},
     title = {Genetic barcoding of Ecuadorian epilithic diatom species suitable as water quality bioindicators},
     journal = {Comptes Rendus. Biologies},
     publisher = {Acad\'emie des sciences, Paris},
     volume = {343},
     number = {1},
     year = {2020},
     pages = {41-52},
     doi = {10.5802/crbiol.2},
     language = {en},
     url = {comptes-rendus.academie-sciences.fr/biologies/item/CRBIOL_2020__343_1_41_0/}
}
Isabel Ballesteros; Pablo Castillejo; Adriana Paulina Haro; Cuthy Cristina Montes; Carla Heinrich; Eduardo Alexis Lobo. Genetic barcoding of Ecuadorian epilithic diatom species suitable as water quality bioindicators. Comptes Rendus. Biologies, Tome 343 (2020) no. 1, pp. 41-52. doi : 10.5802/crbiol.2. https://comptes-rendus.academie-sciences.fr/biologies/item/CRBIOL_2020__343_1_41_0/

1. Introduction

Diatoms are an enormous group of microalgae containing more than 100,000 living species [1, 2]. A lot of work has been done to document diversity and relationships within the group. As a result, species-level taxonomy has become adequate to support the extensive and successful use of diatoms in biomonitoring based on their species-specific response to their environmental changes, especially organic pollution and eutrophication, with a broad spectrum of tolerance, from oligotrophic to eutrophic conditions [3, 4, 5].

Diatom taxonomy is based almost exclusively on the morphological features of the silica frustules [6] and, even after training and long experience, diatomists often find it difficult to agree about identifications. Moreover, morphological treatment is a time-consuming process and costly. In contrast, DNA-based identification has been proposed as an alternative method to complement or even replace traditional identification methods of species [7]. DNA barcoding is based on DNA sequences that are linked to morphologically identified specimens. It is considered a faster and universally applicable approach and also has the potential for refined analyses [8, 9]. Consequently, DNA barcoding deserves careful consideration as a means of improving the reliability of identifications and discovering species and also of increasing the quality and quantity of other taxonomic information. DNA-based methods are being used for assessing biodiversity in environmental samples, the so-called DNA metabarcoding [10], which allows one to determine a species’ presence and abundance from bulk samples of soil, water, or air [11]. Several studies have demonstrated that metabarcoding may be an applicable tool for ecological monitoring based on epilithic diatoms [12, 13, 14, 15, 16]. The preferred barcoding markers in these studies were 18S rRNA and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase).

The basis for a reliable identification with molecular methods is a comprehensive reference library where molecular and morphological data are tied together with a taxonomic name. However, the taxonomic consistency of the sequence information in these databases is very low for diatoms [17]. Rimet et al. [18] developed the R-syst::diatom barcoding library in open-access (http://www.rsyst.inra.fr/) that includes barcodes for microalgae strains of the culture collection maintained in INRA (Institut National de la Recherche Agronomique, France). Another limitation to DNA-based identification approaches is the natural intraspecific divergence of the barcoding marker in specimens from different geographic origins. To date, no information on barcoding sequences has been reported for diatom species from Ecuador. This is a constraint on the application of these methods in freshwater diversity studies and in biomonitoring.

In this context, this research aimed at obtaining the barcodes of Ecuadorian epilithic diatoms with a wide geographical distribution, a well-defined ecological range and characteristics that allow them to be reliable indicator species [19, 20, 21]. This study is a humble first step towards coupling the morphological and molecular data of benthic diatoms in Ecuador. We have therefore studied morphology as a diagnostic feature of each unialgal diatom strain via light and scanning electron microscopies and also determined the DNA barcode 18SV4 rRNA [9, 22] as well as rbcL [23, 24] in order to establish the foundation of a reference library. The original strains are kept alive in the Universidad de las Américas’ epilithic diatoms collection. By publishing these data online, we are contributing to a morphological and molecular taxonomic reference library for neotropical diatoms, making them available for comparative studies. Thus, we expect this to be a key step in developing a trophic water quality index based on a molecular biology analysis of epilithic diatoms in Ecuador.

2. Materials and methods

2.1. Sample collection

Samples were collected under the MAE-DNB-CM-2018-093 authorization conceded by the Environment Ministry of Ecuador. Epilithic diatom samples were collected from four freshwater streams within the Andean region of Ecuador (Figure 1; Table 1). Three of them characterized as páramo (highland wilderness) landscapes at the Iliniza Volcano (SP), Chimborazo volcano (CH) and Cajas national park (CA). The fourth one is located at the Jambelí stream, in the parish of Machachi, surrounded by agricultural livestock mosaics (Table 1). Location data were taken with a GPS navigator (WGS 84 UTM Zone 17 with 5 meters of precision). The sampling design aimed to capture indicator species from pristine streams (SP, CH and CA) and a eutrophic stream (JA) from the Ecuadorian Andean region (Figure 1).

Figure 1.

Location of sampling sites along Ecuadorian Andes. JA: Jambeli River at Pichincha province. SP: San Pedro River at Illiniza Ecological Reserve. CH: stream at Chimborazo Ecological Reserve. CA: stream at Cajas National Park.

Table 1.

Location of the sampled streams in the central Ecuadorian Andean Region with geographical coordinates, altitude (masl) and the code assigned to samples collected in each stream

CodeProvinceDescription LatitudeLongitudeAltitude
SPPichinchaIlliniza Ecological Reserve−0.58661−78.673433601 masl
JAPichinchaQuito−0.57296−78.594183162 masl
CHChimborazoChimborazo Ecological Reserve−1.41337−78.864583978 masl
CAAzuayCajas National Park−2.84271−79.141823165 masl

The physical and chemical variables analyzed were water temperature, pH, turbidity, dissolved oxygen (DO) and conductivity, measured in the field with a multiparameter analyzer, and nitrate and phosphate, measured in the laboratory. Diatom samples were scrubbed off the upper surface of three to five submerged stones, 10 to 20 cm in diameter, using a toothbrush [25]. Diatom and water samples were kept cold until they were transferred to the laboratory.

2.2. Isolation and culturing

The environmental samples were cultured on BBM agar plates [26] supplemented with sodium silicate (10 mM) at 15–18 °C, light intensity of 50 μEm-2 s-1 and 12/12 hr light/dark regime. Individualized macroscopic colonies on agar plates were inoculated into liquid media and grown until they turned brown. This process was repeated until unialgal cultures were obtained. The achievement of unialgal cultures was checked by light microscopy using an Olympus BX51 microscope. Diatom strains were maintained on agar plates and liquid medium.

2.3. Morphology-based analysis

One fraction of each unialgal culture was used for morphological analysis. Living cells as well as cleaned frustules were examined and photographed by light microscopy. To remove organic material, the cells were oxidized with 50% nitric acid at 80 °C for an hour and rinsed several times with H2O [27]. Permanent slides were mounted with the high refraction index mounting medium Naphrax®. For scanning with the electron microscope, a few drops were dried on stubs and sputter-coated with gold using a Quorum Tech Q150RES. SEM images were taken using an ultra-high-resolution analytical field emission (FE) scanning electron microscope Tescan MIRA3, operated at 10 kV.

Species identification was performed using a microscope Olympus BX-40 according to the following taxonomic references [4, 28, 29, 30].

Table 2.

Sequence identity of the closest relative of each isolated strain found in GenBank using BLASTn

Strain 18SV4 % identityN hits Closest match rbcL % identityN hits Closest match
CA01aNitzschia palea99–100% 37KU341755.1Nitzschia palea98–100% 104 HF675122
CH02aEolimna minima95–100%7KM084877.1Eolimna minima 95–97%3KM084939.1
JA01aAchnanthidium minutissimum93–100% 24 KY863464Achnanthidium minutissimum97–100%15KY863482.1
JA01bSellaphora seminulum93–100%6KR150677.1Sellaphora seminulum95–100%4KM084937.1
JA01cSellaphora seminulum93–100%5KR150677.1Sellaphora seminulum95–100%4KM084937.1
SP02aNitzschia fonticola 90–98%3 AJ867022.1Nitzschia fonticola99–100%4HF675068.1

2.4. Molecular-based analysis

A second fraction of each unialgal culture was used to extract total genomic DNA. Cells were pelleted by centrifugation of 1 mL culture medium at 8000 g for 2 min and disrupted using ceramic beads by vortexing. The extraction method was then performed according to Edwards et al. [31]. The rbcL and 18SV4 rRNA regions were submitted to PCR amplification using GoTaq® Green Master Mix by Promega with 0.2 μM of each primer. The V4 region of the 18S rRNA was amplified with the primer pair DIV4for/DIV4rev3 [13, 32]. Primer used for the rbcL fragment were Diat_rbcL_708F [33] and reverse primer R3 [34]. The selected primer pairs amplify a fragment around 300 pb and have been used previously for DNA metabarcoding analysis [12, 14, 24]. PCR regime included an initial denaturation at 95 °C for 2 min, then 35 cycles of denaturation at 95 °C for 45 s, annealing at 50 °C for 45 s, elongation at 72 °C for 30 s, and a final elongation at 72 °C for 2 min. Sequence reactions were performed with an Applied Biosystems® 3130 Genetic Analyzer. Sequences were edited with MEGA 7 software [35] and blasted against the GenBank database at NCBI (National Center for Biotechnology Information). Sequences of strains of the studied species from different geographical locations were downloaded from GenBank (Supplementary Tables S1 and S2) and aligned with barcoding sequences from Ecuadorian strains using the Muscle Algorithm [36]. Bolidomonas pacifica was used as an outgroup taxon, due to its genetic proximity to diatoms [37]. The ends of the alignments were trimmed to minimize missing characters. Tree topologies and branch lengths were computed separately for the two markers with the maximum-likelihood method (ML) using Tamura-Nei distance [38] with gamma distributed rates among sites followed by a statistical test of the tree topologies with 500 bootstrap replications.

3. Results

Five suitable bioindicator species were sampled from the Ecuadorian Andean Region (Table 1): Sellaphora seminulum (Grunow) D. G. Mann (strain JA01b, c), Nitzschia fonticola (Grunow) Grunow (strain SP02a) and N. palea (Kützing) W. Smith (strain CA01a) are tolerant to eutrophication; Eolimna minima (Grunow) Lange-Bertalot (strain CH02a) is a mesotrophic water bioindicator and Achnanthidium minutissimum (Kützing) Czarnecki (strain JA01a) is an oligotrophic water bioindicator. The comparison with the GenBank database of the barcoding regions obtained supported the morphological identification. Blasting results against NCBI are shown in Table 2. N. palea had the most hits (37 sequences for 18SV4; 104 for rbcL) followed by A. minutissimum (24 sequences for 18SV4; 15 for rbcL). GenBank accession numbers for 18SV4 rRNA and rbcL sequences from this study are MN589666-MN589670 and MN603956-MN603960 respectively.

JA01b strain presents linear valves with rounded apices. The axial area is narrow, linear. The central area is wide, rectangular. The raphe is filiform with the terminal fissures curved to the same side of the valve with distinct central pores. Striae are radiate, multiseriate, and more distant and curved near the central area, with 2 or 3 shorter striae. The areolas are rounded. Valve dimensions: Length: 9–12 μm; Width: 3–3.5 m, 20–22 striae in 10 μm (Figure 2i–l). This result is consistent with S. seminulum description [39]. Morphological description of JA01c strain also matches S. seminulum although its length ranges from 6 to 10 μm and width reaches up to 4.5 μm (Figure 2m–p). Thus, JA01c strain presents elliptical valve shape while JA01b has linear valves. Despite the morphological differences, both strains have 100% identity for 18SV4 and rbcL sequences. The number of 18S and rbcL sequences for Sellaphora seminulum in the GenBank database is scarce. There are strains from the Geneva basin [32] Seoul and Reunion Island [40] with a homology of 98% with 18SV4 and rbcL. Evans et al. [41] and Kermarrec et al. [24] described two strains of S. seminulum from United Kingdom and Mayotte Island at the Komora Archipelago, with a homology below 95%. There is a third case in the GenBank for a strain from Berlin that presents 100% of identity with rbcl, but less than 95% with 18SV4 [17].

Figure 2.

Isolated diatoms under SEM: a–d: strain CA01a (N. palea (Kützing) W. Smith); e–h: strain SP02 (Nitzschia fonticola (Grunow) Grunow); a, i–l: strain JA01b (Sellaphora seminulum (Grunow) D. G. Mann); m–p: JA01c (Sellaphora seminulum (Grunow) D. G. Mann); q–t, u: JA01a (Sellaphora seminulum (Grunow) D. G. Mann); v–y: CH02a (Eolimna minima (Grunow) Lange-Bertalot). Scale bar  = 1 μm.

The morphological traits of strain SP02 match the species Nitzschia fonticola [42]: linear-lanceolate valves, acutely rounded apices, eccentric, marginal raphe, uniseriate striae on the valvar face and biseriate in the canal of the raphe, practically equidistant fibulae, except in the central area that presents two fibulae more distant from the others. Valve dimensions: Lenght: 15–18 μm; width: 2.5–3 μm; 10–14 fibulae in 10 μm (Figure 2e–h). The sequences obtained from this strain have higher identity with rbcL sequences (99–100%) than with 18SV4 sequences (90–98%) uploaded to the GenBank. There is no strain described as N. fonticola with both rbcL an 18SV4 barcodes reported. The sequences matching rbcL belong to strains collected from the United Kingdom, Spain, and Reunion Island [17, 40] while 18SV4 matches only one sequence (from France, data not published) with over 98% similarity. There are two other sequences for 18SV4 with less than 90% similarity from microorganisms isolated from karstic-stream biofilms in Germany (data unpublished).

CA01a strain, described as Nitzschia palea [43], presents linear-lanceolate valves, rostral apices, eccentric raphe, marginal, very thin uniseriate striae, equidistant fibulae including the central pair. Valve dimensions: Lenght: 25–27 μm; width: 2.8–3 μm; 16 fibulae in 10 μm (Figure 2a–d). There are plenty of sequences for N. palea [32, 37, 44] in the GenBank from all around the world, most of them with over 99% identity with CA01a strain for both rbcL and 18SV4 barcodes.

CH02a strain shows elliptical valves with rounded apices. The axial area is narrow, linear. The central area is little expanded, slightly rectangular, limited by the irregular size of the median striae. The raphe is filiform, straight, with proximal ends slightly flexed. The central pores are small. Striae are radiate, uniseriate, with irregular sizes near the central area, composed of rounded areolas (Figure 2v–y). Valve dimensions: Length: 6–10 μm; Width: 3–4 μm; 25–26 stretch marks in 10 μm. This is consistent with the morphological description of E. minima [45]. The closest match with both barcodings belongs to the Eolimna genera, but it is not identified at a species level [17]. There are other strains reported with a 99% identity match for 18SV4 described as Eolimna, Sellaphora and Navicula minima, which are homotypic synonyms. The rbcL sequence obtained showed 96% similarity with a strain identified as E. minima from Germany [17].

JA01a morphological traits are consistent with Achnantidium minutissimum [46]. It shows linear-lanceolate valves, rounded and rostrate ends, narrow axial area, linear, widening towards the center, straight raphe, filiform, curved terminal fissures, radiate striae, more widely spaced in the central area of the valve. Valve dimensions: Length: 6–7 m; Width: 2–3 m; 30–32 striae in 10 m. (Figure 2q–u). Blast results for both barcodes show from 98 to 100% identity with A. minutissimum from Europe, Asia and North America [9, 32, 37, 40]. There are a few strains from Japan and Île de Reunion that have less than 96% identity for 18SV4 (Data unpublished).

Phylogenetic trees were constructed based on 18SV4 and rbcL regions separately due to the lack of strains with both barcode sequences deposited in INSDC databases. The phylogenetic analyses include sequence representatives of each species from different geographical locations reported previously. In the phylogeny, both barcode sequences of the same species clustered into one clade (Figures 3 and 4). Species level clades are well supported statistically. Short branches in species clades mean low divergence between the Ecuadorian strains and their homologous strains. In the phylogenetic tree based on the 18SV4 region (Figure 3), N. fonticola sequences are in the same clade as E. minima and S. seminulum but separated from N. palea. However bifurcations representing the relationship between the species are not well supported by bootstrap values. Nevertheless, in the phylogeny of rbcL (Figure 4), sequences belonging to Nitzschia genera clustered together. E. minima and S. seminulum are grouped in the same clade in both phylogenetic analyses.

Figure 3.

Phylogram constructed using 18SV4 rRNA sequences. The phylogram was constructed using the maximum-likelihood method with Tamura-Nei protocol. Numerical values at the nodes of the branches indicate bootstrap values above 50%. Accession number and geographical origin is indicated for each sequence (Supplementary Table S1).

Figure 4.

Phylogram constructed using rbcL sequences. The phylogram was constructed using the maximum-likelihood method with Tamura-Nei protocol. Numerical values at the nodes of the branches indicate bootstrap values above 50%. Accession number and geographical origin is indicated for each sequence (Supplementary Table S2).

4. Discussion

To the best of our knowledge, this study is the first attempt to establish a barcode reference library for epilithic diatoms from Andean streams of Ecuador. Five strains considered as water quality bioindicators have been cultured and sequenced for rbcL and 18SV4 barcodes. N. palea, N. fonticola and S. seminulum are tolerant to organic pollution and eutrophication. N. palea regularly occurs downstream of sewage treatment plants [47]. E. minima is abundant in mesotrophic water. A. seminulum is a small monoraphid diatoms of oligo/mesosaprobic rivers [47]. These species are very important from an ecological point of view, since they are often among the most abundant benthic species in freshwater systems. Furthermore, N. palea, A. minutissimum and E. minima have been used to assess sensitivity to herbicides [37, 48] and metals [49].

The occurrence and/or abundance of epilithic diatoms to define ecological status through morphological characteristics has some limitations [7]. The use of DNA sequences could potentially alleviate these limitations [50]. The barcoding sequences of the strains presented here have a high percentage of identity with the sequences reported in INSDC databases for the same species. Hence, DNA barcoding, based on 18SV4 and rbcL, emerges as a useful tool for diatom species identification in Andean streams. Nonetheless, we found that there are reported sequences for the same species with a divergence of at least 5%. This could be due to an inaccurate identification, since there are poor circumscriptions and a lack of reliable information about the epithets ‘minima’, and ‘seminulum’ even though they are apparently well–established and often referred to in ecological and taxonomic literature [51, 52, 53]. For instance, E. minima can barely be identified using light microscopy (LM) and the lack of illustrations from a scanning electron microscope (SEM) is a major impediment [7]. Moreover, there are identification problems derived from isolation and culturing, which are needed to obtain barcodes, given that some species experience cell size reduction in culture [54]. That could be the case for S. seminulum strains, JA01b and c, which are different in size but identical for rbcL and 18SV4 sequences. This supports the necessity of barcode reference libraries that couple morphological and molecular data for comparative analyses [12, 17].

The usefulness of 18SV4 and rbcL barcodes to assess phylogenetic relationships in diatoms has been proven extensively [6, 17, 18, 55, 56]. The topology of the phylogenetic trees demonstrates that epilithic diatoms from Ecuador show close relatedness to those of same species isolated from other geographical regions. This could mean low phylogeographic variability in diatoms. However, the E. minima clade presents the highest divergences, but this could be due to identification problems related with this species. The genera clades are congruent with previous analysis where Sellaphora falls into one group with Eolimna [17] and these are separate from Nitzschia and Achnantidium [18].

This research highlights the complementary aspects of classical taxonomy and DNA barcoding. All reference sequences presented here are linked to morphological detailed images in order to initiate a complete barcode reference library for diatoms in the neotropical region. In addition, this study demonstrates that it would be feasible to use the existing barcoding data for diatoms to develop molecular tools for bioassessment of aquatic ecosystems in the Ecuadorian Andean region.

Acknowledgements

This study was funded by the Universidad de Las Américas [grant number: BIO.IBR.19.05], Quito, Ecuador. Access to collection resources was granted by means of the Framework agreement for Access to genetic resources: MAE-DNB-CM-2018-0093 celebrated between the Environment Ministry, Ecuador and the Universidad de Las Américas, Ecuador. Thanks to Miguel Martínez-Fresneda Mestre for helping with the maps.

Supplementary data

Supporting information for this article is available on the journal’s website under https://doi.org/10.5802/crbiol.2 or from the author.

Bibliographie

[1] D. G. Mann; J. Droop Biodiversity, biogeography and conservation of diatoms, Hydrobiologia, Volume 336 (1996) no. 1–3, pp. 19-32 | Article

[2] D. Mann; P. Vanormelingen An inordinate fondness? The number, distributions, and origins of diatom species, J. Eukaryot. Microbiol., Volume 60 (2013) no. 4, pp. 414-420 | Article

[3] M. Kelly; L. King; B. Ní Chatháin The conceptual basis of ecological-statusassessments using diatoms, Biol. Environ. Proc. R. Irish Acad., Volume 109 (2009) no. 3, pp. 175-189 | Article

[4] E. A. Lobo; C. G. Heinrich; M. Schuch; C. E. Wetzel; L. Ector Diatoms as bioindicators in rivers, River Algae, Springer International Publishing, Cham, 2016, pp. 245-271 | Article

[5] E. A. Lobo; M. Schuch; C. G. Heinrich; A. B. da Costa; A. Düpont; C. E. Wetzel; L. Ector Development of the Trophic Water Quality Index (TWQI) for subtropical temperate Brazilian lotic systems, Environ. Monit. Assess., Volume 187 (2015) no. 6, 354 pages

[6] B. Beszteri; E. Acs; J. Makk; G. Kovács; K. Márialigeti; K. T. Kiss Phylogeny of six naviculoid diatoms based on 18S rDNA sequences, Int. J. Syst. Evol. Microbiol., Volume 51 (2001) no. Pt 4, pp. 1581-1586 | Article

[7] D. Hering; A. Borja; J. I. Jones; D. Pont; P. Boets; A. Bouchez; K. Bruce; S. Drakare; B. Hänfling; M. Kahlert; F. Leese; K. Meissner; P. Mergen; Y. Reyjol; P. Segurado; A. Vogler; M. Kelly Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive, Water Res., Volume 138 (2018), pp. 192-205 | Article

[8] P. D. N. Hebert; S. Ratnasingham; J. R. Dewaard Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species, Proc. Biol. Sci., Volume 270 (2003) no. Suppl 1, p. S96-S99

[9] J. Zimmermann; R. Jahn; B. Gemeinholzer Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols, Org. Divers. Evol., Volume 11 (2011) no. 3, pp. 173-192 | Article

[10] F. Pompanon; E. Coissac; P. Taberlet Metabarcoding a new way to analyze biodiversity, Biofutur, Volume 319 (2011), pp. 30-32

[11] K. M. Ruppert; R. J. Kline; M. S. Rahman Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: a systematic review in methods, monitoring, and applications of global eDNA, Glob. Ecol. Conserv., Volume 17 (2019) (e00547)

[12] D. Mora; N. Abarca; S. Proft; J. H. Grau; N. Enke; J. Carmona; O. Skibbe; R. Jahn; J. Zimmermann Morphology and metabarcoding: a test with stream diatoms from Mexico highlights the complementarity of identification methods, Freshw. Sci., Volume 38 (2019) no. 3, pp. 448-464 | Article

[13] L. Apothéloz-Perret-Gentil; A. Cordonier; F. Straub; P. Esling; J. Pawlowski Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring, Mol. Ecol. Resour., Volume 17 (2017) no. 6, pp. 1231-1242 | Article

[14] V. Vasselon; F. Rimet; K. Tapolczai; A. Bouchez Assessing ecological status with diatoms DNA metabarcoding: scaling-up on a WFD monitoring network (Mayotte island, France), Ecol. Indic., Volume 82 (2017), pp. 1-12 | Article

[15] J. Zimmermann; G. Glückner; R. Jahn; N. Enke; B. Gemeinholzer Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies, Mol. Ecol. Resour., Volume 15 (2015) no. 3, pp. 526-542 | Article

[16] L. Kermarrec; A. Franc; F. Rimet; P. Chaumeil; J. M. Frigerio; J. F. Humbert; A. Bouchez A next-generation sequencing approach to river biomonitoring using benthic diatoms, Freshw. Sci., Volume 33 (2014) no. 1, pp. 349-363 | Article

[17] J. Zimmermann; N. Abarca; N. Enke; O. Skibbe; W. H. Kusber; R. Jahn Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research, PLoS ONE, Volume 9 (2014) no. 9 (e108793) | Article

[18] F. Rimet; P. Chaumeil; F. Keck; L. Kermarrec; V. Vasselon; M. Kahlert; A. Franc; A. Bouchez R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring, Database (2016), pp. 1-21 (baw016)

[19] V. Geissler Experimentelle Untersuchungen zur Vari-abilität der Schalenmerkmale bei einigen zentrischenSü sswasser-Diatomeen, Nova. Hedwig. Beih., Volume 73 (1982), pp. 211-246

[20] M. Schuch; M. Oliveira; E. A. Lobo Spatial response of epilithic diatom communities to downstream nutrient increases, Water Environ. Res., Volume 87 (2015) no. 6, pp. 547-558 | Article

[21] P. Castillejo; S. Chamorro; L. Paz; I. Carrillo; J. Salazar; J. C. Navarro; C. Heinrich; E. A. Lobo Response of epilithic diatom communities to environmental gradients along an Ecuadorian Andean River, C. R. Biol., Volume 341 (2018) no. 4, pp. 256-263 | Article

[22] J. Pawlowski; F. Lejzerowicz; L. Apotheloz-Perret-Gentil; J. Visco; P. Esling Protist metabarcoding and environmental biomonitoring: time for change, Eur. J. Protistol., Volume 55 (2016), pp. 12-25 | Article

[23] M. L. MacGillivary; I. Kaczmarska Survey of the efficacy of a short fragment of the rbcL gene as a supplemental DNA barcode for diatoms, J. Eukaryot. Microbiol., Volume 58 (2011) no. 6, pp. 529-536 | Article

[24] L. Kermarrec; A. Franc; F. Rimet; P. Chaumeil; J. F. Humbert; A. Bouchez Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms, Mol. Ecol. Resour., Volume 13 (2013) no. 4, pp. 607-619 | Article

[25] H. Kobayasi; S. Mayama Most pollution-tolerant diatoms of severely polluted rivers in the vicinity of Tokyo, J. Phycol., Volume 30 (1982), pp. 188-196

[26] R. A. Andersen; J. A. Berges; P. J. Harrison Recipes for freshwater and seawater media, Algal Culturing Techniques (R. A. Andersen, ed.), Elsevier Academic Press, London, 2005, pp. 429-538

[27] M. G. Potapova; D. F. Charles Benthic diatoms in USA rivers: distributions along spatial and environmental gradients, J. Biogeogr., Volume 29 (2002) no. 2, pp. 167-187 | Article

[28] D. Metzelin; H. Lange-Bertalot Tropical Diatoms of South America II. Special remarks on biogeographic disjunction, Iconogr. Diatomol., Volume 18 (2007), pp. 1-877

[29] D. Metzelin; F. Las García-Rodríguez Las diatomeas Uruguayas, División de Relaciones y Actividades Culturales (DI.R.A.C), Universidad de la República, Montevideo, Uruguay, 2003, pp. 1-207

[30] U. Rumrich; H. Lange-Bertalot; M. Rumrich Diatomeen der Anden. Von Venezuela bis Patagonien (Feuerland), Iconogr. Diatomol., Volume 9 (2000), pp. 1-649

[31] K. Edwards; C. Johnstone; C. Thompson A simple and rapid method for the preparation of plant genomic DNA for PCR analysis, Nucleic Acids Res., Volume 19 (1991) no. 6, 1349 pages | Article

[32] J. A. Visco; L. Apothéloz-Perret-Gentil; A. Cordonier; P. Esling; L. Pillet; J. Pawlowski Environmental monitoring: inferring the diatom index from next-generation sequencing data, Environ. Sci. Technol., Volume 49 (2015) no. 13, pp. 7597-7605 | Article

[33] K. R. Stoof-Leichsenring; L. S. Epp; M. H. Trauth; R. Tiedemann Hidden diversity in diatoms of Kenyan Lake Naivasha: a genetic approach detects temporal variation, Mol. Ecol., Volume 21 (2012) no. 8, pp. 1918-1930 | Article

[34] K. Bruder; L. K. Medlin Molecular assessment of phylogenetic relationships in selected species/genera in the naviculoid diatoms (Bacillariophyta). I. The genus Placoneis, Nova. Hedwigia., Volume 85 (2007) no. 3–4, pp. 331-352 | Article

[35] S. Kumar; G. Stecher; K. Tamura MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets, Mol. Biol. Evol., Volume 33 (2016) no. 7, pp. 1870-1874 | Article

[36] R. C. Edgar MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., Volume 32 (2004) no. 5, pp. 1792-1797 | Article

[37] S. M. Esteves; F. Keck; S. F. P. Almeida; E. Figueira; A. Bouchez; F. Rimet Can we predict diatoms herbicide sensitivities with phylogeny? Influence of intraspecific and interspecific variability, Ecotoxicology, Volume 26 (2017) no. 8, pp. 1065-1077 | Article

[38] K. Tamura; M. Nei Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees, Mol. Biol. Evol., Volume 10 (1993), pp. 512-526

[39] S. Blanco; C. Cejudo-Figueiras; I. Álvarez-Blanco; E. Bécares; L. Hoffmann; L. Ector (Atlas de las Diatomeas de la cuenca del Duero, Diatom atlas of the Duero Basin. 2010)

[40] F. Keck; F. Rimet; A. Franc; A. Bouchez Phylogenetic signal in Diatom ecology: perspectives for aquatic ecosystems biomonitoring, Ecol. Appl., Volume 26 (2016) no. 3, pp. 861-872 | Article

[41] K. M. Evans; A. H. Wortley; G. E. Simpson; V. A. Chepurnov; D. G. Mann A molecular systematic approach to explore diversity within the Sellaphora pupula species complex (Bacillariophyta), J. Phycol., Volume 44 (2008) no. 1, pp. 215-231 | Article

[42] R. Trobajo; D. G. Mann; V. A. Chepurnov; E. Clavero Taxonomy, life cycle, and auxosporulation of Nitzschia Fonticola (Bacillariophyta), J. Phycol., Volume 42 (2006), pp. 1353-1372 | Article

[43] E. Mora; D. Jiménez; J. Cantoral Epilithic diatoms in the Upper Laja River Basin, Guanajuato, Mexico, Rev. Mex. Biodivers., Volume 86 (2015), pp. 1024-1040

[44] F. Rimet.; R. Trobajo; D. G. Mann; L. Kermarrec; A. Franc; I. Domaizon; A. Bouchez When is sampling complete? The effects of geographical range and marker choice on perceived diversity in Nitzschia palea (Bacillariophyta), Protist, Volume 165 (2014) no. 3, pp. 245-259 | Article

[45] G. Moser; H. Lange-Bertalot; D. Metzeltin Insel der Endemiten Geobotanisches Phänomen Neukaledonien (Island of endemics New Caledonia - a geobotanical phenomenon), Bibl. Diatomol., Volume 38 (1998), 464 pages

[46] M. Potapova; P. B. Hamilton Morphological and ecological variation within the Achnanthidium minutissimum (Bacillariophyceae) species complex, J. Phycol., Volume 43 (2007) no. 3, pp. 561-575 | Article

[47] H. Van Dam; A. Mertens; J. Sinkeldam A coded checklist and ecological indicator values of freshwater diatoms from The Netherlands, Neth. J. Aquat. Ecol., Volume 28 (1994) no. 1, pp. 117-133

[48] S. Moisset; S. Kim Tiam; A. Feurtet-Mazel; S. Morin; F. Delmas; N. Mazzella; P. Gonzalez Genetic and physiological responses of three freshwater diatoms to realistic diuron exposures, Environ. Sci. Pollut. Res. Int., Volume 22 (2015) no. 6, pp. 4046-4055 | Article

[49] S. Kim Tiam; A. Feurtet-Mazel; F. Delmas; N. Mazzella; S. Morin; G. Daffe; P. Gonzalez Development of q-PCR approaches to assess water quality: effects of cadmium on gene expression of the diatom Eolimna minima, Water Res., Volume 46 (2012) no. 4, pp. 934-942 | Article

[50] J. Pawlowski; M. Kelly-Quinn; F. Altermatt; L. Apothéloz-Perret-Gentil; P. Beja; A. Boggero; A. Borja; A. Bouchez; T. Cordier; I. Domaizon; M. J. Feio; A. F. Filipe; R. Fornaroli; W. Graf; J. Herder; B. van der Hoorn; J. I. Jones; M. Sagova-Mareckova; C. Moritz; J. Barquín; J. J. Piggott; M. Pinna; F. Rimet; B. Rinkevich; C. Sousa-Santos; V. Specchia; R. Trobajo; V. Vasselon; S. Vitecek; J. Zimmerman; A. Weigand; F. Leese; M. Kahlert Science of the Total Environment The future of biotic indices in the ecogenomic era : integrating ( e ) DNA metabarcoding in biological assessment of aquatic ecosystems, Sci. Total Environ., Volume 638 (2018), pp. 1295-1310 | Article

[51] E. A. Lobo; H. Kobayasi Shannon’s diversity index applied to some freshwater diatom assemblages in the sakawa river system, Jpn. J. Phycol., Volume 38 (1990), pp. 229-243

[52] P. Siver; P. B. Hamilton Diatoms of North America: the Freshwater Flora of Waterbodies on the Atlantic Coastal Plain, Iconogr. Diatomol., Volume 22 (2011), pp. 1-916

[53] J. Żelezna-Wieczorek Diatom flora in springs of Łódź Hills (Central Poland), Biodiversity, Taxonomy, and Temporal Changes of Epipsammic Diatom Assemblages in Springs Affected by Human Impact (A. Witkowski, ed.) (Diatom Monographs), Gantner Verlag, Ruggell, Liechtenstein, 2011, 419 pages

[54] J. S. Ki; S. Y. Cho; T. Katano; S. W. Jung; J. Lee; B. S. Park; S. H. Kang; M. S. Han Comprehensive comparisons of three pennate diatoms, Diatoma tenuae, Fragilaria vaucheriae, and Navicula pelliculosa, isolated from summer Arctic reservoirs (Svalbard 79° N), by fine-scale morphology and nuclear 18S ribosomal DNA, Polar Biol., Volume 32 (2009) no. 2, pp. 147-159

[55] C. Santhosh Kumar; V. A. Prabu; C. P. Kumar DNA Barcode Genes (rbcL, 18s rRNA and ITS Phylogeny) in Skeletonema costatum Grevelli (Cleve, 1873), Int. J. Curr. Microbiol. Appl. Sci., Volume 4 (2015) no. 9, pp. 195-203

[56] L. Guo; Z. Sui; S. Zhang; Y. Ren; Y. Liu Comparison of potential diatom ‘barcode’ genes (The 18S rRNA gene and ITS, COI, rbcL) and their effectiveness in discriminating and determining species taxonomy in the Bacillariophyta, Int. J. Syst. Evol. Microbiol., Volume 65 (2015) no. 4, pp. 1369-1380 | Article