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Navigating the seven seas of arthropod collection protocols: Metabarcoding arthropod diversity in a tropical forest

Daniel Souto‐Vilarós,Eduardo Navarro‐Valencia,Ana Cecilia Zamora,Yahir Campusano,G. P. Lamarre,Filonila Perez,Yacksecari Lopez,Ricardo M. Bobadilla,José Alejandro Ramírez Silva,Milan Janda,Jeremy R. deWaard,M. Leponce,Héctor Barrios,Yves Basset

Published 2025 in Methods in Ecology and Evolution

ABSTRACT

Insects and other arthropods represent one of the most diverse groups of life on Earth, with an estimated 70% of species awaiting discovery. Advances in DNA‐based tools have accelerated species discovery, while high‐throughput sequencing has enabled large‐scale biodiversity surveys. Arthropods also exhibit immense ecological, habitat and distributional diversity, requiring multiple sampling methods to effectively capture this variation. Comparisons of results provided by these methods, once the samples are processed by DNA metabarcoding, have rarely been evaluated. To address this gap, we employed seven of the most widely used arthropod bulk‐sampling protocols across 25 subplots (20 × 20 m) in a tropical rainforest on Barro Colorado Island, Panama, during the wet and dry seasons. We used Berlese‐Tullgren funnels, Winkler extractors and pitfall traps to target soil and leaf litter fauna; beating to sample arthropods resting on vegetation; and polytraps, Malaise and light traps to survey flying fauna. All 350 samples were processed with COI metabarcoding, and resulting sequences were assigned to known Barcode Index Numbers (BINs) using the mBRAVE platform. Beyond documenting the magnitude of arthropod richness in one of the world's most biodiverse ecosystems, our study aimed to identify the most cost‐efficient sampling methods (USD/BIN) for capturing broad arthropod diversity in a complex environment. We detected ca. 10,000 arthropod species within a combined hectare of tropical lowland rainforest, with each sampling subplot revealing significant diversity (2227 ± 28 BINs). Our findings highlight the utility of method‐specific targeting, from Berlese‐Tullgren funnels efficiently detecting soil micro‐arthropods to generalist approaches such as light traps, which captured a broad diversity of well‐studied taxa (e.g. moths). Our results demonstrate that DNA metabarcoding enhances species recovery beyond the target taxa. Based on our findings, we recommend a combined approach using flight‐intercept and soil‐targeting traps, with Malaise traps effectively capturing flying and ground dwelling/emerging arthropods. Pitfall traps, comparatively simple and inexpensive, recover a wide range of arthropods and offer a practical starting point for baseline surveys.

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