Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities.
In marine and estuarine benthic communities, the inventory and estimation of species richness are often hampered by the need for broad taxonomic expertise across several phyla. The use of DNA metabarcoding has emerged as a powerful tool for the fast assessment of species composition in a diversity of ecological communities. Here, we tested the amplification success of five primer sets targeting different COI-5P regions by 454 pyrosequencing to maximize the recovery of two simulated macrobenthic communities containing 21 species (SimCom1 and SimCom 2). Species identification was first performed against a compiled reference library of macrobenthic species. Reads with similarity results to reference sequences between 70% and 97% were then submitted to GenBank and BOLD to attempt the identification of concealed species in the bulk sample. The combination of at least three primer sets was able to recover more species than any primer set alone, achieving 85% of represented species in SimCom1 and 76% in SimCom2. Our approach was successful to detect low-frequency specimens, as well as concealed species, in the bulk sample, indicating the potential for the application of this approach on marine bioassessment and inventory, including the detection of "hidden" biodiversity that would hardly be possible based on morphology only.
a CBMA-Centre of Molecular and Environmental Biology, Biology Department, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
Claudia
C
Hollatz
a CBMA-Centre of Molecular and Environmental Biology, Biology Department, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
Barbara R
BR
Leite
a CBMA-Centre of Molecular and Environmental Biology, Biology Department, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.|b MARE-Marine and Environmental Sciences Centre, Department of Environmental Sciences and Engineering, Faculty of Science and Technology, Lisbon New University, 2829-516 Monte de Caparica, Portugal.
Jorge
J
Lobo
c Next Generation Sequencing Unit, UC-Biotech-CNC, Biocant Park, 3060-197, Cantanhede, Portugal.
Hugo
H
Froufe
c Next Generation Sequencing Unit, UC-Biotech-CNC, Biocant Park, 3060-197, Cantanhede, Portugal.
Conceição
C
Egas
a CBMA-Centre of Molecular and Environmental Biology, Biology Department, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
Filipe O
FO
Costa
D000818:Animals; D000845:Annelida / Q000235:genetics; D001181:Arthropods / Q000235:genetics; D044822:Biodiversity; D018533:Biomass; D043344:Chordata / Q000235:genetics; D003063:Cnidaria / Q000235:genetics; D003198:Computer Simulation; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D017931:DNA Primers / Q000235:genetics*; D004447:Echinodermata / Q000235:genetics; D017753:Ecosystem; D003576:Electron Transport Complex IV / Q000235:genetics; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D008974:Mollusca / Q000235:genetics; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
D017931:DNA Primers; D003576:Electron Transport Complex IV
DNA barcoding; bioassessment; codage à barres de l’ADN; communauté marine macrobenthique; high-throughput sequencing; marine macrobenthos; séquençage à haut débit; évaluation de la biodiversité