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. 2022 Feb 1:10:e12845.
doi: 10.7717/peerj.12845. eCollection 2022.

Unearthing soil arthropod diversity through DNA metabarcoding

Monica R Young  1   2 , Paul D N Hebert  1   2
Affiliations

Unearthing soil arthropod diversity through DNA metabarcoding

Monica R Young et al. PeerJ. .

Abstract

DNA metabarcoding has the potential to greatly advance understanding of soil biodiversity, but this approach has seen limited application for the most abundant and species-rich group of soil fauna-the arthropods. This study begins to address this gap by comparing information on species composition recovered from metabarcoding two types of bulk samples (specimens, soil) from a temperate zone site and from bulk soil samples collected at eight sites in the Arctic. Analysis of 22 samples (3 specimen, 19 soil) revealed 410 arthropod OTUs belonging to 112 families, 25 orders, and nine classes. Studies at the temperate zone site revealed little overlap in species composition between soil and specimen samples, but more overlap at higher taxonomic levels (families, orders) and congruent patterns of α- and β-diversity. Expansion of soil analyses to the Arctic revealed locally rich, highly dissimilar, and spatially structured assemblages compatible with dispersal limited and environmentally driven assembly. The current study demonstrates that DNA metabarcoding of bulk soil enables rapid, large-scale assessments of soil arthropod diversity. However, deep sequence coverage is required to adequately capture the species present in these samples, and expansion of the DNA barcode reference library is necessary to improve taxonomic resolution of the sequences recovered through this approach.

Keywords: Arthropods; Biodiversity; Environmental DNA; Metabarcoding; NGS; Soil.

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Conflict of interest statement

The authors declare there are no competing interests.

Figures

Figure 1
Figure 1. Map showing the 11 Canadian sites where soil samples were collected and the three sites where specimen samples were also obtained.
Figure 2
Figure 2. Taxonomic breakdown of the classified reads and OTUs generated from (A) 22 samples including three specimen and 19 soil samples, and (B) the subset of six paired specimen and soil samples.
Figure 3
Figure 3. OTU diversity recovered by DNA metabarcoding 22 soil samples (3 specimen, 19 soil) and the proportion of known and novel OTUs based on comparison with the BOLD reference library.
Comparisons are provided for (A) 6 major taxonomic groups, (B) 8 invertebrate phyla, and (C) 23 arthropod orders.
Figure 4
Figure 4. OTU accumulation curves (with 1,000 randomizations) across eight extraction replicates summarized for all taxa combined and all arthropods detected for the three paired specimen and soil samples, and all 19 soil samples.
Figure 5
Figure 5. Taxonomic recovery of arthropod orders and families from three paired samples of specimens and soil analysed by DNA metabarcoding compared to taxa detected through morphological analysis of vouchers from the specimen samples.
Figure 6
Figure 6. Hierarchical clustering of pairwise Sorensen dissimilarity values for arthropod and mite OTUs detected from three paired specimen and soil samples.
Figure 7
Figure 7. Hierarchical clustering of pairwise Sorensen dissimilarity values for arthropod and mite OTUs detected from 19 soil samples from 11 sites and three ecoregions.
(TA, Taiga/Arctic Cordillera transition; TF, Temperate Forest; TU, Tundra) within Canada.
See this image and copyright information in PMC

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