The utility of DNA metabarcoding for studying the response of arthropod diversity and composition to land-use change in the tropics

Abstract

Metabarcoding potentially offers a rapid and cheap method of monitoring biodiversity, but real-world applications are few. We investigated its utility in studying patterns of litter arthropod diversity and composition in the tropics. We collected litter arthropods from 35 matched forest-plantation sites across Xishuangbanna, southwestern China. A new primer combination and the MiSeq platform were used to amplify and sequence a wide variety of litter arthropods using simulated and real-world communities. Quality filtered reads were clustered into 3,624 MOTUs at ≥97% similarity and the taxonomy of each MOTU was predicted. We compared diversity and compositional differences between forests and plantations (rubber and tea) for all MOTUs and for eight arthropod groups. We obtained ~100% detection rate after in silico sequencing six mock communities with known arthropod composition. Ordination showed that rubber, tea and forest communities formed distinct clusters. α-diversity declined significantly between forests and adjacent plantations for more arthropod groups in rubber than tea, and diversity of order Orthoptera increased significantly in tea. Turnover was higher in forests than plantations, but patterns differed among groups. Metabarcoding is useful for quantifying diversity patterns of arthropods under different land-uses and the MiSeq platform is effective for arthropod metabarcoding in the tropics.

One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies

“…On the contrary, samples from the tropics (feces of E. infrafasciatus from Africa and spider webs from South America) displayed a much lower taxonomic resolution generally corresponding to family level (Figure b). In megadiverse environments and regions, such as equatorial environments, our ability to identify sequences precisely (e.g., at species level) is indeed strongly restricted by relatively incomplete public databases (e.g., Cowart et al, ; Beng et al, ; Lopes et al, ; Stat et al, ). Our results therefore illustrate the role of completeness of public databases and the importance in investing into species inventories to better understand food web and species interactions.…”

“…Although false negatives often occur for rare taxa (e.g., Ficetola et al, 2015), they are also produced when the affinity between primer and primer-binding sites during polymerase chain reaction (PCR) is low (e.g., Elbrecht & Leese, 2017a;Vamos, Elbrecht, & Leese, 2017), which in turn will determine amplification success and hence the taxonomic coverage of a given primer set. Although there is growing use of control samples to assess levels of false positives (De Barba et al, 2014;Beng et al, 2016;Corse et al, 2017;Galan et al, 2018), no post hoc bioinformatic procedures can identify false negatives. Two primary strategies have been adopted to maximize the taxonomic coverage of primer sets used in metabarcoding studies.…”

A simplified DNA extraction protocol for unsorted bulk arthropod samples that maintains exoskeletal integrity

“…Studies have shown that metabarcoding can be used to identify arthropod taxa in bulk arthropod samples (e.g. Kocher et al, ; Liu et al, ; Morinière et al, ), and for example be applied to assess how arthropod diversity changes to different land‐uses (Beng et al, ). Metabarcoding has also been used to assess how invertebrates might leak DNA to their preservative ethanol which then potentially can serve as a mean to obtain sample diversity information (Erdozain et al, ; Hajibabaei, Spall, Shokralla, & Konynenburg, ).…”

“…Studies have shown that metabarcoding can be used to identify arthropod taxa in bulk arthropod samples (e.g. Kocher et al, 2017;Liu et al, 2013;Morinière et al, 2016), and for example be applied to assess how arthropod diversity changes to different land-uses (Beng et al, 2016).…”

Invertebrate DNA metabarcoding reveals changes in communities across mine site restoration chronosequences

“…Invertebrate DNA metabarcoding is a recent approach to monitoring that can effectively characterize invertebrate communities at a faster and cheaper rate than traditional morphological taxonomic identification (Yu et al ; Ji et al ; Beng et al ). DNA metabarcoding workflows consist of simultaneously amplifying standardized DNA fragments from the total DNA extracted from an environmental sample (Taberlet et al ).…”