Toward accurate species‐level metabarcoding of arthropod communities from the tropical forest canopy

• Main Authors: Thomas J. Creedy, Wui Shen Ng, Alfried P. Vogler
• Format: Article
• Language: English
• Published: Wiley 2019-03-01
• Series: Ecology and Evolution
• Subjects: arthropods; body size; compositionality; metabarcoding; sequencing bias; species diversity
• Online Access: https://doi.org/10.1002/ece3.4839

Abstract Metabarcoding of arthropod communities can be used for assessing species diversity in tropical forests but the methodology requires validation for accurate and repeatable species occurrences in complex mixtures. This study investigates how the composition of ecological samples affects the accuracy of species recovery. Starting with field‐collected bulk samples from the tropical canopy, the recovery of specimens was tested for subsets of different body sizes and major taxa, by assembling these subsets into increasingly complex composite pools. After metabarcoding, we track whether richness, diversity, and most importantly composition of any size class or taxonomic subset are affected by the presence of other subsets in the mixture. Operational taxonomic units (OTUs) greatly exceeded the number of morphospecies in most taxa, even under very stringent sequencing read filtering. There was no significant effect on the recovered OTU richness of small and medium‐sized arthropods when metabarcoded alongside larger arthropods, despite substantial biomass differences in the mixture. The recovery of taxonomic subsets was not generally influenced by the presence of other taxa, although with some exceptions likely due to primer mismatches. Considerable compositional variation within size and taxon‐based subcommunities was evident resulting in high beta‐diversity among samples from within a single tree canopy, but this beta‐diversity was not affected by experimental manipulation. We conclude that OTU recovery in complex arthropod communities, with sufficient sequencing depth and within reasonable size ranges, is not skewed by variable biomass of the constituent species. This could remove the need for time‐intensive manual sorting prior to metabarcoding. However, there remains a chance of taxonomic bias, which may be primer‐dependent. There will never be a panacea primer; instead, metabarcoding studies should carefully consider whether the aim is broadscale turnover, in which case these biases may not be important, or species lists, in which case separate PCRs and sequencing might be necessary. OTU number inflation remains an issue in metabarcoding and requires bioinformatic development, particularly in read filtering and OTU clustering, and/or greater use of species‐identifying sequences generated outside of bulk sequencing.