References
Anslan S, Bahram M, Hiiesalu I, Tedersoo L (2017) PipeCraft: flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data. Molecular Ecology Resources 17 , e234-e240.
Anslan S, Nilsson RH, Wurzbacher C, Baldrian P, Tedersoo L, Bahram M (2018) Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding. MycoKeys 39 , 29-40.
Apotheloz-Perret-Gentil L, Cordonier A, Straub F, Iseli J, Esling P, Pawlowski J (2017) Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring.Molecular Ecology Resources 17 , 1231-1242.
Baird DJ, Hajibabaei M (2012) Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next‐generation DNA sequencing. Molecular Ecology 21 , 2039-2044.
Battarbee R, Carvalho L, Jones V, Flower R, Cameron N, Bennion H, Juggins S (2001) Tracking Environmental Change Using Lake Sediments: Terrestrial, Algal and Siliceous Indicators. Kluwer Academic Publishers.
Brannock PM, Halanych KM (2015) Meiofaunal community analysis by high-throughput sequencing: Comparison of extraction, quality filtering, and clustering methods. Marine Genomics 23 , 67-75.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP (2016) DADA2: high-resolution sample inference from Illumina amplicon data. Nature Methods13 , 581.
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinformatics 10 , 421.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, … Gordon JI (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7 , 335-336.
Chen G, Shi H, Tao J, Chen L, Liu Y, Lei G, … Smol JP (2015) Industrial arsenic contamination causes catastrophic changes in freshwater ecosystems. Scientific Reports5 , 17419.
Clarke K, Gorley R (2006) PRIMER V6: User manual/tutorial. Primer-E Ltd. Plymouth, 192pp .
De Caceres M, Jansen F, De Caceres MM (2016) Package ‘indicspecies’. Relationship between species and groups of sites. R package version 1.7.6.
Deiner K, Altermatt F (2014) Transport distance of invertebrate environmental DNA in a natural river.PLoS ONE 9 , e88786.
Dixit SS, Smol JP, Kingston JC, Charles DF (1992) Diatoms - Powerful indicators of environmental change.Environmental Science & Technology 26 , 22-33.
Douglas MS, Smol JP (2010) Freshwater diatoms as indicators of environmental change in the High Arctic.The diatoms: applications for the environmental and earth sciences , 249.
Dulias K, Stoof-Leichsenring KR, Pestryakova LA, Herzschuh U (2017) Sedimentary DNA versus morphology in the analysis of diatom-environment relationships. Journal of Paleolimnology 57 , 51-66.
Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods 10 .
Edgar RC (2017) Accuracy of microbial community diversity estimated by closed-and open-reference OTUs.PeerJ 5 , e3889.
European-Committee-for-Standardization (2014) European Standard 13946. Water quality-Guidance for the routine sampling and preparation of benthic diatoms from rivers and lakes.
Flower RJ (1993) Diatom preservation: experiments and observations on dissolution and breakage in modern and fossil material, 473-484.
Frøslev TG, Kjøller R, Bruun HH, Ejrnæs R, Brunbjerg AK, Pietroni C, Hansen AJ (2017) Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates. Nature Communications 8 , 1188.
Geer LY, Marchler-Bauer A, Geer RC, Han L, He J, He S, … Bryant SH (2009) The NCBI biosystems database.Nucleic Acids Research 38 , D492-D496.
Hardge K, Neuhaus S, Kilias ES, Wolf C, Metfies K, Frickenhaus S (2018) Impact of sequence processing and taxonomic classification approaches on eukaryotic community structure from environmental samples with emphasis on diatoms. Molecular Ecology Resources 18 , 204-216.
Hermans SM, Buckley HL, Lear G (2018) Optimal extraction methods for the simultaneous analysis of DNA from diverse organisms and sample types. Molecular Ecology Resources18 , 557-569.
Keck F, Vasselon V, Rimet F, Bouchez A, Kahlert M (2018) Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles. Molecular Ecology Resources 18 , 1299-1309.
Kelly M, Boonham N, Juggins S, Killie P, Mann D, Pass D, … Glover R (2018) A DNA based Diatom Metabarcoding Approach for Water Framework Directive Classification of Rivers.
Kermarrec L, Franc A, Rimet F, Chaumeil P, Humbert J-F, Bouchez A (2013) Next‐generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms. Molecular Ecology Resources 13 , 607-619.
Kociolek J, You Q, Wang Q, Liu Q (2015) A consideration of some interesting freshwater gomphonemoid diatoms from North America and China, and the description of Gomphosinica gen. nov. Nova Hedwigia 144 , 175-198.
Krammer K, Lange-Bertalot H (1986-1991) Bacillariophyceae, vol. 2 (1–4). Süsswasserflora von Mitteleuropa, Gustav Fischer Verlag, Stuttgart/Jena .
Lange-Bertalot H, Hofmann G, Werum M, Cantonati M, Kelly MG (2017) Freshwater benthic diatoms of Central Europe: over 800 common species used in ecological assessment Koeltz Botanical Books Schmitten-Oberreifenberg.
Li G, Dong H, Hou W, Wang S, Jiang H, Yang J, Wu G (2016) Temporal Succession of Ancient Phytoplankton Community in Qinghai Lake and Implication for Paleo-environmental Change. Scientific Reports 6 , 19769.
Li Y, Lange-Bertalot H, Metzeltin D (2013) Sichuaniella (Li Yanling, Lange-Bertalot et Metzeltin) nom. nov. - a new name for Sichuania (Li Yanling et al). Diatoms of Europe: Diatoms of the European inland waters and comparable habitats. Vol7 , 5-12.
Liaw A, Wiener M (2002) Classification and regression by randomForest. R news 2 , 18-22.
Majaneva M, Hyytiäinen K, Varvio SL, Nagai S, Blomster J (2015) Bioinformatic amplicon read processing strategies strongly affect eukaryotic diversity and the taxonomic composition of communities. PLoS ONE 10 , e0130035.
Mann DG (1999) The species concept in diatoms. Phycologia 38 , 437-495.
Medlin L, Yang I, Sato S (2012) Evolution of the diatoms. VII. Four gene phylogeny assesses the validity of selected araphid genera. Nova Hedwig 141 , 505-513.
Mohan J, Stone JR, Nicholson K, Neumann K, Dowling C, SHARMA S (2018) Lindavia biswashanti, a new diatom species (Bacillariophyta) from Gokyo Cho, Himalayan Range, Nepal.Phytotaxa 364 , 101-107.
Morales EA, Wetzel CE, Novais MH, Buczkó K, Morais MM, Ector L (2019) Morphological reconsideration of the araphid genus Pseudostaurosira (Bacillariophyceae), a revision of Gedaniella, Popovskayella and Serratifera, and a description of a new Nanofrustulum species. Plant Ecology and Evolution 152 , 262-284.
Mortágua A, Vasselon V, Oliveira R, Elias C, Chardon C, Bouchez A, … Almeida SF (2019) Applicability of DNA metabarcoding approach in the bioassessment of Portuguese rivers using diatoms. Ecological Indicators 106 , 105470.
Nascimento FJ, Lallias D, Bik HM, Creer S (2018) Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing. Scientific Reports 8 .
Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’hara R, … Wagner H (2015) vegan: Community Ecology Package. R package version 2.4-2.http://CRAN.R-project.org/package=vegan .
Pan YD, Stevenson RJ, Hill BH, Herlihy AT, Collins GB (1996) Using diatoms as indicators of ecological conditions in lotic systems: A regional assessment. Journal of the North American Benthological Society 15 , 481-495.
Pauvert C, Buée M, Laval V, Edel-Hermann V, Fauchery L, Gautier A, … Vacher C (2019) Bioinformatics matters: the accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline. Fungal Ecology 41 , 23-33.
Pavlov A, Levkov Z, Williams DM, Edlund MB (2013) Observations on Hippodonta (Bacillariophyceae) in selected ancient lakes. Phytotaxa 90 , 1-53.
Penton CR, Gupta VV, Yu J, Tiedje JM (2016) Size matters: assessing optimum soil sample size for fungal and bacterial community structure analyses using high throughput sequencing of rRNA gene amplicons. Frontiers in Microbiology 7 , 824.
Piredda R, Sarno D, Lange CB, Tomasino MP, Zingone A, Montresor M (2017) Diatom resting stages in surface sediments: A pilot study comparing Next Generation Sequencing and Serial Dilution Cultures. Cryptogamie, Algologie 38 , 31-47.
R-Core-Team (2015) R Foundation for Statistical Computing; 2015. R: A language and environment for statistical computing .
Rimet F, Abarca N, Bouchez A, Kusber W-H, Jahn R, Kahlert M, … Piuz A (2018) The potential of high throughput sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes.Fottea 18 , 37-54.
Rimet F, Chaumeil P, Keck F, Kermarrec L, Vasselon V, Kahlert M, … Bouchez A (2016) R-Syst:: diatom: an open-access and curated barcode database for diatoms and freshwater monitoring. Database 2016 .
Rimet F, Vasselon V, Barbara A, Bouchez A (2018) Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes. Organisms Diversity & Evolution 18 , 51-62.
Rivera SF, 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.
Rivera SF, Vasselon V, Jacquet S, Bouchez A, Ariztegui D, Rimet F (2018) Metabarcoding of lake benthic diatoms: from structure assemblages to ecological assessment.Hydrobiologia 807 , 37-51.
Rognes T, Flouri T, Nichols B, Quince C, Mahé F (2016) VSEARCH: a versatile open source tool for metagenomics.PeerJ 4 , e2584.
Ruppert KM, Kline RJ, Rahman MS (2019) Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Global Ecology and Conservation17 .
Schiebelhut LM, Abboud SS, Gómez Daglio LE, Swift HF, Dawson MN (2017) A comparison of DNA extraction methods for high-throughput DNA analyses. Molecular Ecology Resources 17 , 721-729.
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, … Weber CF (2009) Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. Applied and Environmental Microbiology 75 , 7537-7541.
Sinha R, Abu-Ali G, Vogtmann E, Fodor AA, Ren B, Amir A, … Abnet CC (2017) Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Nature Biotechnology .
StatSoft I (2004) STATISTICA (data analysis software system), version 7. www.statsoft.com.
Taberlet P, Bonin A, Coissac E, Zinger L (2018) Environmental DNA: For biodiversity research and monitoring Oxford University Press.
Tapolczai K, Keck F, Bouchez A, Rimet F, Vasselon V (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.
Tapolczai K, Vasselon V, Bouchez A, Stenger‐Kovács C, Padisák J, Rimet F (2019) The impact of OTU sequence similarity threshold on diatom‐based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean). Ecology and Evolution9 , 166-179.
Vasselon V, Bouchez A, Rimet F, Jacquet S, Trobajo R, Corniquel M, … Domaizon I (2018) Avoiding quantification bias in metabarcoding: application of a cell biovolume correction factor in diatom molecular biomonitoring. Methods in Ecology and Evolution 9 , 1060-1069.
Vasselon V, Domaizon I, Rimet F, Kahlert M, Bouchez A (2017) Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter? Freshwater Science 36 , 162-177.
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.
Visco JA, Apothéloz-Perret-Gentil L, Cordonier A, Esling P, Pillet L, Pawlowski J (2015) Environmental monitoring: inferring the diatom index from next-generation sequencing data. Environmental Science & Technology 49 , 7597-7605.
Wang R, Dearing JA, Langdon PG, Zhang E, Yang X, Dakos V, Scheffer M (2012) Flickering gives early warning signals of a critical transition to a eutrophic lake state.Nature 492 , 419.
Zimmermann J, Glöckner G, Jahn R, Enke N, Gemeinholzer B (2015) Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies.Molecular Ecology Resources 15 , 526-542.