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.
Highlights
Mock community No of reads No of reference genomes No of merged reads Reads passed filtering (%) No of unique sequences No of singletons OTUs_97% similarity assemblage composition along environmental gradients
Since the Miseq platform is more cost-efficient than Roche 454 for metabarcoding[6,22,23], and can produce up to ca. 15 times the number of reads produced by a Roche 454 FLX Titanium run[22,25,26], it may represent a promising alternative for efficient biodiversity assessment and monitoring
One limitation of metabarcoding is the efficiency of assigning taxonomy to molecular operational taxonomic units (MOTUs)
Summary
Mock community No of reads No of reference genomes No of merged reads Reads passed filtering (%) No of unique sequences No of singletons OTUs_97% similarity assemblage composition along environmental gradients. This information is critical for timely biodiversity monitoring, conservation management, land-use planning, and environmental impact assessment. Though the percentage of MOTUs assigned to order level is usually high, this is not the case for assignments at a lower taxonomic level (e.g. for insects; Order [96–99%], Family [17–37%], Genus [16–36%] and Species [16–35%]6) This problem is not due to the metabarcoding pipeline used, but rather to the lack of comprehensive and taxonomically reliable barcode databases for most taxa[6,27]. Which arthropod groups show significant changes across land-uses and deserve further attention?
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