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De León LF, Silva B, Avilés-Rodríguez KJ, Buitrago-Rosas D. Harnessing the omics revolution to address the global biodiversity crisis. Curr Opin Biotechnol 2023; 80:102901. [PMID: 36773576 DOI: 10.1016/j.copbio.2023.102901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/10/2023] [Accepted: 01/18/2023] [Indexed: 02/12/2023]
Abstract
Human disturbances are altering global biodiversity in unprecedented ways. We identify three fundamental challenges underpinning our understanding of global biodiversity (namely discovery, loss, and preservation), and discuss how the omics revolution (e.g. genomics, transcriptomics, proteomics, metabolomics, and meta-omics) can help address these challenges. We also discuss how omics tools can illuminate the major drivers of biodiversity loss, including invasive species, pollution, urbanization, overexploitation, and climate change, with a special focus on highly diverse tropical environments. Although omics tools are transforming the traditional toolkit of biodiversity research, their application to addressing the current biodiversity crisis remains limited and may not suffice to offset current rates of biodiversity loss. Despite technical and logistical challenges, omics tools need to be fully integrated into global biodiversity research, and better strategies are needed to improve their translation into biodiversity policy and practice. It is also important to recognize that although the omics revolution can be considered the biologist's dream, socioeconomic disparity limits their application in biodiversity research.
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Affiliation(s)
- Luis F De León
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA.
| | - Bruna Silva
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Kevin J Avilés-Rodríguez
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA; Department of Biology, Fordham University, Bronx, NY, USA
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Basset Y, Hajibabaei M, Wright MTG, Castillo AM, Donoso DA, Segar ST, Souto-Vilarós D, Soliman DY, Roslin T, Smith MA, Lamarre GPA, De León LF, Decaëns T, Palacios-Vargas JG, Castaño-Meneses G, Scheffrahn RH, Rivera M, Perez F, Bobadilla R, Lopez Y, Ramirez Silva JA, Cruz MM, Galván AA, Barrios H. Comparison of traditional and DNA metabarcoding samples for monitoring tropical soil arthropods (Formicidae, Collembola and Isoptera). Sci Rep 2022; 12:10762. [PMID: 35750774 PMCID: PMC9232565 DOI: 10.1038/s41598-022-14915-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/15/2022] [Indexed: 11/09/2022] Open
Abstract
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.
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Affiliation(s)
- Yves Basset
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama.
- Faculty of Science, University of South Bohemia, 370 05, Ceske Budejovice, Czech Republic.
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, Ceske Budejovice, Czech Republic.
- Maestría de Entomología, Universidad de Panamá, 080814, Panama City, Republic of Panama.
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G2W1, Canada
| | - Michael T G Wright
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G2W1, Canada
| | - Anakena M Castillo
- 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, Guntur, Andhra Pradesh, 522 510, India
| | - David A Donoso
- Departamento de Biología, Escuela Politécnica Nacional, Quito, Ecuador
- Centro de Investigación de la Biodiversidad y Cambio Climático, Universidad Tecnológica Indoamérica, EC170103, Quito, Ecuador
| | - Simon T Segar
- Agriculture and Environment Department, Harper Adams University, Newport, TF10 8NB, Shropshire, UK
| | - Daniel Souto-Vilarós
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, Ceske Budejovice, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Vinicna 7, 128 44, Prague, Czech Republic
| | - Dina Y Soliman
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G2W1, Canada
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, P.O. Box 7044, 750 07, Uppsala, Sweden
| | - M Alex Smith
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Greg P A Lamarre
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, Ceske Budejovice, Czech Republic
| | - Luis F De León
- 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, USA
| | - Thibaud Decaëns
- CEFE, University of Montpellier, CNRS, EPHE, IRD, University Paul Valéry, Montpellier 3, Montpellier, France
| | - José G Palacios-Vargas
- 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
| | - Gabriela Castaño-Meneses
- Unidad Multidisciplinaria de Docencia e Investigación, Facultad de Ciencias, Universidad Nacional Autónoma de México, Campus Juriquilla, Juriquilla 76230, Querétaro, Mexico
| | - Rudolf H Scheffrahn
- Fort Lauderdale Research & Education Center, 3205 College Avenue, Davie, FL, 33314, USA
| | - Marleny Rivera
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
| | - Filonila Perez
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
| | - Ricardo Bobadilla
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
| | - Yacksecari Lopez
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
| | | | - Maira Montejo Cruz
- 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
| | - Angela Arango Galván
- 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
| | - Héctor Barrios
- Maestría de Entomología, Universidad de Panamá, 080814, Panama City, Republic of Panama
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