DNA metabarcoding as monitoring tool
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In the context of global change, molecular methods offer promising tools for lifting some of the taxonomic impediments and thus allowing for sound and low-cost biological monitoring. Molecular approaches present several advantages: first, individuals and species can often be identified by sequencing standard gene regions (DNA barcodes) – for animals most often their cytochrome c oxidase subunit I (COI) gene. COI-based clusters also allow for interim taxonomic nomenclature, by e.g. using the Barcode Index Number (BIN). Second, samples including many individuals and species can be treated by bulk methods and COI amplicons analyzed using high-throughput sequencing, “DNA metabarcoding”. This represents a powerful approach for screening numerous environmental samples rich in species, and new solutions for spatial and temporal monitoring.
With most of our common insect species at Barro Colorado Island in Panama being characterized by their own BIN, we can now move towards monitoring the probable 25,000 arthropod species on the island by DNA metabarcoding. We have demonstrated proof of concept with the soil fauna (ants, termites and Collembola) and are now analyzing results obtained with Malaise and light traps.
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., Montejo Cruz, M., Arango Galván, A. & Barrios, H. (2022). Comparison of traditional and DNA metabarcoding samples for monitoring tropical soil arthropods (Formicidae, Collembola and Isoptera). Scientific Reports, 12, 10762. https://doi.org/10.1038/s41598-022-14915-2
Basset, Y., Donoso, D.A., Hajibabaei, M., Wright, M.T.G., Perez, K.H.J., Lamarre, G.P.A., De León, L.F., Palacios-Vargas, J.G., Castaño-Meneses, G., Rivera, R., Perez, F., Bobadilla, R., Lopez, Y., Ramirez, J.A. & Barrios, H. 2020. Methodological considerations for monitoring soil/litter arthropods in tropical rainforests using DNA metabarcoding, with a special emphasis on ants, springtails and termites. Metabarcoding and Metagenomics, 4, 151-163.
Basset, Y., Palacios-Vargas, J.G., Donoso, D.A., Castaño-Meneses, G., Decaëns, T., Lamarre, G.P., De León, L.F., Rivera, M., García-Gómez, A., Perez, F., Bobadilla, R., Lopez, Y., Ramirez, J.A., Cruz, M.M., Galván, A.A., Mejía-Recamier, B.E. & Barrios, H. 2020. Enemy-free space and the distribution of ants, springtails and termites in the soil of one tropical rainforest. European Journal of Soil Biology, 99, 103193.