Persisting roadblocks in arthropod monitoring using non-destructive metabarcoding from collection media of passive traps.

Autor: Sire L; Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR7261 CNRS - Université de Tours, Tours, France.; Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR7205 Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France., Schmidt Yáñez P; Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany., Bézier A; Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR7261 CNRS - Université de Tours, Tours, France., Courtial B; INRAE, UR0633 Zoologie forestière, Orléans, France., Mbedi S; Museum für Naturkunde -Leibniz Insitute for Evolution and Biodiversity Science, Berlin, Germany.; Berlin Center for Genomics in Biodiversity Research, Berlin, Germany., Sparmann S; Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.; Berlin Center for Genomics in Biodiversity Research, Berlin, Germany., Larrieu L; Université de Toulouse, INRAE, UMR DYNAFOR, Castanet-Tolosan, France.; CRPF Occitanie, Tarbes, France., Rougerie R; Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR7205 Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France., Bouget C; INRAE 'Forest Ecosystems' Research Unit Domaine des Barres, Nogent-sur-Vernisson, France., Monaghan MT; Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.; Berlin Center for Genomics in Biodiversity Research, Berlin, Germany.; Institut für Biologie, Freie Universität Berlin, Berlin, Germany., Herniou EA; Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR7261 CNRS - Université de Tours, Tours, France., Lopez-Vaamonde C; Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR7261 CNRS - Université de Tours, Tours, France.; INRAE, UR0633 Zoologie forestière, Orléans, France.
Jazyk: angličtina
Zdroj: PeerJ [PeerJ] 2023 Oct 10; Vol. 11, pp. e16022. Date of Electronic Publication: 2023 Oct 10 (Print Publication: 2023).
DOI: 10.7717/peerj.16022
Abstrakt: Background: Broad-scale monitoring of arthropods is often carried out with passive traps ( e.g., Malaise traps) that can collect thousands of specimens per sample. The identification of individual specimens requires time and taxonomic expertise, limiting the geographical and temporal scale of research and monitoring studies. DNA metabarcoding of bulk-sample homogenates has been found to be faster, efficient and reliable, but the destruction of samples prevents a posteriori validation of species occurrences and relative abundances. Non-destructive metabarcoding of DNA extracted from collection medium has been applied in a limited number of studies, but further tests of efficiency are required with different trap types and collection media to assess the consistency of the method.
Methods: We quantified the detection rate of arthropod species when applying non-destructive DNA metabarcoding with a short (127-bp) fragment of mitochondrial COI on two combinations of passive traps and collection media: (1) water with monopropylene glycol (H 2 O-MPG) used in window-flight traps (WFT, 53 in total); (2) ethanol with monopropylene glycol (EtOH-MPG) used in Malaise traps (MT, 27 in total). We then compared our results with those obtained for the same samples using morphological identification (for WFTs) or destructive metabarcoding of bulk homogenate (for MTs). This comparison was applied as part of a larger study of arthropod species richness in silver fir ( Abies alba Mill., 1759) stands across a range of climate-induced tree dieback levels and forest management strategies.
Results: Of the 53 H 2 O-MPG samples from WFTs, 16 produced no metabarcoding results, while the remaining 37 samples yielded 77 arthropod MOTUs in total, of which none matched any of the 343 beetle species morphologically identified from the same traps. Metabarcoding of 26 EtOH-MPG samples from MTs detected more arthropod MOTUs (233) than destructive metabarcoding of homogenate (146 MOTUs, 8 orders), of which 71 were shared MOTUs, though MOTU richness per trap was similar between treatments. While we acknowledge the failure of metabarcoding from WFT-derived collection medium (H 2 O-MPG), the treatment of EtOH-based Malaise trapping medium remains promising. We conclude however that DNA metabarcoding from collection medium still requires further methodological developments and cannot replace homogenate metabarcoding as an approach for arthropod monitoring. It can be used nonetheless as a complementary treatment when enhancing the detection of soft-bodied arthropods like spiders and Diptera.
Competing Interests: The authors declare there are no competing interests.
(©2023 Sire et al.)
Databáze: MEDLINE
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