The soil fauna of the tropics remains one of the least known components of the biosphere. Long-term monitoring of this fauna is hampered by the lack of taxonomic expertise and funding. These obstacles may potentially be lifted with DNA metabarcoding. To validate this approach, we studied the ants, springtails and termites of 100 paired soil samples from Barro Colorado Island, Panama. The fauna was extracted with Berlese-Tullgren funnels and then either sorted with traditional taxonomy and known, individual DNA barcodes ("traditional samples") or processed with metabarcoding ("metabarcoding samples"). We detected 49 ant, 37 springtail and 34 termite species with 3.46 million reads of the COI gene, at a mean sequence length of 233 bp. Traditional identification yielded 80, 111 and 15 species of ants, springtails and termites, respectively; 98%, 37% and 100% of these species had a Barcode Index Number (BIN) allowing for direct comparison with metabarcoding. Ants were best surveyed through traditional methods, termites were better detected by metabarcoding, and springtails were equally well detected by both techniques. Species richness was underestimated, and faunal composition was different in metabarcoding samples, mostly because 37% of ant species were not detected. The prevalence of species in metabarcoding samples increased with their abundance in traditional samples, and seasonal shifts in species prevalence and faunal composition were similar between traditional and metabarcoding samples. Probable false positive and negative species records were reasonably low (13-18% of common species). We conclude that metabarcoding of samples extracted with Berlese-Tullgren funnels appear suitable for the long-term monitoring of termites and springtails in tropical rainforests. For ants, metabarcoding schemes should be complemented by additional samples of alates from Malaise or light traps.

Agriculture and Environment Department Harper Adams University Newport TF10 8NB Shropshire UK

Biology Centre of the Czech Academy of Sciences Institute of Entomology 370 05 Ceske Budejovice Czech Republic

CEFE University of Montpellier CNRS EPHE IRD University Paul Valéry Montpellier 3 Montpellier France

Centre for Biodiversity Genomics Biodiversity Institute of Ontario and Department of Integrative Biology University of Guelph 50 Stone Road East Guelph ON N1G2W1 Canada

Centro de Biodiversidad y Descubrimiento de Drogas Instituto de Investigaciones Científicas y Servicios de Alta Tecnología P O Box 0843 01103 Panamá 5 Panama

Centro de Investigación de la Biodiversidad y Cambio Climático Universidad Tecnológica Indoamérica EC170103 Quito Ecuador

Departamento de Biología Escuela Politécnica Nacional Quito Ecuador

Department of Biology University of Massachusetts Boston 100 Morrissey Blvd Boston MA 02125 USA

Department of Biotechnology Acharya Nagarjuna University Guntur Andhra Pradesh 522 510 India

Department of Ecology Faculty of Science Charles University Vinicna 7 128 44 Prague Czech Republic

Department of Ecology Swedish University of Agricultural Sciences P O Box 7044 750 07 Uppsala Sweden

Department of Integrative Biology University of Guelph Guelph ON N1G2W1 Canada

Faculty of Science University of South Bohemia 370 05 Ceske Budejovice Czech Republic

ForestGEO Smithsonian Tropical Research Institute Apartado 0843 03092 Balboa Ancon Panamá Panama

Fort Lauderdale Research and Education Center 3205 College Avenue Davie FL 33314 USA

Laboratorio de Ecología y Sistemática de Microartrópodos Departamento de Ecología y Recursos Naturales Facultad de Ciencias Universidad Nacional Autónoma de México 04510 Mexico City Mexico

Maestría de Entomología Universidad de Panamá 080814 Panama City Republic of Panama

Unidad Multidisciplinaria de Docencia e Investigación Facultad de Ciencias Universidad Nacional Autónoma de México Campus Juriquilla Juriquilla 76230 Querétaro Mexico

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