Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects.
Cytochrome c oxidase I (COI) is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable primer binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. The 16S primers amplified three more insect species than the Folmer COI primers and amplified more equally, probably due to decreased primer bias. Estimation of biomass might be less biased with 16S than with COI, although variation in read abundances of two orders of magnitudes is still observed. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of insects will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey the 16S marker, which requires building a local reference database, or optimised degenerated COI primers could be more appropriate.
Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, Bochum, Germany; Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany.
Vasco
V
Elbrecht
Laboratoire d'Ecologie Alpine (LECA), CNRS, Grenoble, France; Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Grenoble, France.
Pierre
P
Taberlet
SPYGEN , Le Bourget du Lac , France.
Tony
T
Dejean
SPYGEN , Le Bourget du Lac , France.
Alice
A
Valentini
Lab Interdisciplinaire des Environnements Continentaux (LIEC), Université de Lorraine , Metz , France.
Philippe
P
Usseglio-Polatera
Ecole Nationale du Génie de l'Eau et de l'Environnement de Strasbourg, Strasbourg, France; UMR CNRS 7362-LIVE, Université de Strasbourg, Strasbourg, France.
Jean-Nicolas
JN
Beisel
Laboratoire d'Ecologie Alpine (LECA), CNRS, Grenoble, France; Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Grenoble, France.
Eric
E
Coissac
Laboratoire d'Ecologie Alpine (LECA), CNRS, Grenoble, France; Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Grenoble, France.
Frederic
F
Boyer
Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany; Centre for Water and Environmental Research (ZWU) Essen, University of Duisburg-Essen, Essen, Germany.
Florian
F
Leese
Biodiversity assessment; DNA metabarcoding; Freshwater invertebrates; High throughput sequencing; Illumina sequencing; Method testing; Primer bias; Small ribosomal subunit; Stream ecosystems; Stream monitoring