Comparison of traditional and DNA metabarcoding samples for monitoring tropical soil arthropods (Formicidae, Collembola and Isoptera)
Por:
Basset Y., Hajibabaei M., Wright M.T.G., Castillo A.M., Donoso D.A., Segar S.T., Souto-Vilarós D., Soliman D.Y., Roslin T., Smith M.A., Lamarre G.P.A., De León L.F., Decaëns T., Palacios-Vargas J.G., Castaño-Meneses G., Scheffrahn R.H., Rivera M., Perez F., Bobadilla R., Lopez Y., Ramirez Silva J.A., Cruz M.M., Galván A.A., Barrios H.
Publicada:
1 ene 2022
Categoría:
Multidisciplinary
Resumen:
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. © 2022, The Author(s).
Filiaciones:
Basset Y.:
ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
Faculty of Science, University of South Bohemia, Ceske Budejovice, 370 05, Czech Republic
Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, 370 05, Czech Republic
Maestría de Entomología, Universidad de Panamá, Panama City, 080814, Panama
Hajibabaei M.:
Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G2W1, Canada
Wright M.T.G.:
Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G2W1, Canada
Castillo A.M.:
Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), P.O. Box 0843-01103, Panamá 5, Panama
Department of Biotechnology, Acharya Nagarjuna University, Andhra Pradesh, Guntur, 522 510, India
Donoso D.A.:
Departamento de Biología, Escuela Politécnica Nacional, Quito, Ecuador
Centro de Investigación de la Biodiversidad y Cambio Climático, Universidad Tecnológica Indoamérica, Quito, EC170103, Ecuador
Segar S.T.:
Agriculture and Environment Department, Harper Adams University, Shropshire, Newport, TF10 8NB, United Kingdom
Souto-Vilarós D.:
Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, 370 05, Czech Republic
Department of Ecology, Faculty of Science, Charles University, Vinicna 7, Prague, 128 44, Czech Republic
Soliman D.Y.:
Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G2W1, Canada
Roslin T.:
Department of Ecology, Swedish University of Agricultural Sciences, P.O. Box 7044, Uppsala, 750 07, Sweden
Smith M.A.:
Department of Integrative Biology, University of Guelph, Guelph, ON N1G2W1, Canada
Lamarre G.P.A.:
ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, 370 05, Czech Republic
De León L.F.:
Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), P.O. Box 0843-01103, Panamá 5, Panama
Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, United States
Decaëns T.:
CEFE, University of Montpellier, CNRS, EPHE, IRD, University Paul Valéry, Montpellier 3, Montpellier, France
Palacios-Vargas J.G.:
Laboratorio de Ecología y Sistemática de Microartrópodos, Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
Castaño-Meneses G.:
Unidad Multidisciplinaria de Docencia e Investigación, Facultad de Ciencias, Universidad Nacional Autónoma de México, Campus Juriquilla, Juriquilla 76230, Querétaro, Mexico
Scheffrahn R.H.:
Fort Lauderdale Research & Education Center, 3205 College Avenue, Davie, FL 33314, United States
Rivera M.:
ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
Perez F.:
ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
Bobadilla R.:
ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
Lopez Y.:
ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
Ramirez Silva J.A.:
ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
Cruz M.M.:
Laboratorio de Ecología y Sistemática de Microartrópodos, Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
Galván A.A.:
Laboratorio de Ecología y Sistemática de Microartrópodos, Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
Barrios H.:
Maestría de Entomología, Universidad de Panamá, Panama City, 080814, Panama
Green Published, gold, Gold, Green
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