Unearthing soil arthropod diversity through DNA metabarcoding

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

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Arthropods* / genetics
  • Biodiversity
  • DNA / genetics
  • DNA Barcoding, Taxonomic
  • Humans
  • Soil

Substances

  • Soil
  • DNA

Grants and funding

This project was supported by grants from NSERC, the Ontario Ministry of Research, Innovation and Science, Polar Knowledge Canada, and the Canada Foundation for Innovation to Paul D. N. Hebert. Support was also provided by Canada C3, the Northern Scientific Training Program, and NSERC’s Canada Graduate Scholarship to Monica R. Young. This study represents a contribution to the “Food From Thought” programme which is supported by the Canada First Research Excellence Fund. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.