Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data

Joana Amorim Visco; Laure Apothéloz-Perret-Gentil; Arielle Cordonier; Philippe Esling; Loïc Pillet; Jan Pawlowski

doi:10.1021/es506158m

Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data

Joana Amorim Visco ¹ Laure Apothéloz-Perret-Gentil ¹ Arielle Cordonier ² Philippe Esling ^{3, 1} Loïc Pillet ^{1, 4} Jan Pawlowski ^{1, *}

* Corresponding author

1 University of Geneva [Switzerland]

2 Water Ecology Service

3 Repmus - Représentations musicales

STMS - Sciences et Technologies de la Musique et du Son

4 DIPO - Diversité et Interactions au sein du Plancton Océanique

ADMM - Adaptation et diversité en milieu marin

Abstract : Diatoms are widely used as bioindicators for the assessment of water quality in rivers and streams. Classically, the diatom biotic indices are based on the relative abundance of morphologically identified species weighted by their autoecological value. Obtaining such indices is time-consuming, costly, and requires excellent taxonomic expertise, which is not always available. Here we tested the possibility to overcome these limitations using a next-generation sequencing (NGS) approach to identify and quantify diatoms found in environmental DNA and RNA samples. We analyzed 27 river sites in the Geneva area (Switzerland), in order to compare the values of the Swiss Diatom Index (DI-CH) computed either by microscopic quantification of diatom species or directly from NGS data. Despite gaps in the reference database and variations in relative abundance of analyzed species, the diatom index shows a significant correlation between morphological and molecular data indicating similar biological quality status for the majority of sites. This proof-of-concept study demonstrates the potential of the NGS approach for identification and quantification of diatoms in environmental samples, opening new avenues toward the routine application of genetic tools for bioassessment and biomonitoring of aquatic ecosystems.

Document type :

Journal articles

Domain :

Environmental Sciences / Biodiversity and Ecology

Liste complète des métadonnées

https://hal.sorbonne-universite.fr/hal-01245156
Contributor : Gestionnaire Hal-Upmc <>
Submitted on : Wednesday, December 16, 2015 - 6:18:06 PM
Last modification on : Sunday, December 2, 2018 - 1:23:37 AM

Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data

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Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data

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