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Towards a global barcode reference library for subterranean fauna.

Michelle T Guzik1, Jake Thornhill1, Mieke van der Heyde2

  • 1School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.

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Summary

Developing a global barcode reference library (BRL) for subterranean fauna is crucial for environmental DNA (eDNA) biodiversity assessments. A curated BRL significantly improves species identification in subterranean ecosystems, advancing biomonitoring efforts worldwide.

Keywords:
Barcode reference libraryBiodiversityDNADatabaseSubterranean faunaeDNA

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Area of Science:

  • Ecology
  • Genetics
  • Bioinformatics

Background:

  • Environmental DNA (eDNA) metabarcoding is a powerful tool for biodiversity discovery, particularly in subterranean ecosystems.
  • Accurate species identification from eDNA requires comprehensive barcode reference libraries (BRLs) with correct taxonomic metadata.
  • Existing databases may lack sufficient coverage for specialized environments like subterranean habitats.

Purpose of the Study:

  • To propose and test an open, globally accessible, and FAIR-compliant information resource for subterranean fauna eDNA biomonitoring.
  • To curate and analyze a BRL for subterranean fauna using multiple genetic markers.
  • To demonstrate the efficacy of a custom BRL in improving species identification in eDNA metabarcoding studies.

Main Methods:

  • Compiled a curated BRL for subterranean fauna from GenBank and BOLD databases, including sequences for COI, 18S, 12S, 28S, and 16S rRNA genes.
  • Generated eDNA metabarcoding data from an exemplar subterranean system at Bungaroo Creek, Australia.
  • Compared BLAST query results of eDNA Operational Taxonomic Units (OTUs) against the custom BRL and the general GenBank database.

Main Results:

  • The custom BRL successfully identified subterranean zero-radius OTUs (ZOTUs) that were unidentifiable using the GenBank database alone.
  • The custom BRL demonstrated superior performance when used in conjunction with GenBank, enhancing identification accuracy.
  • This study presents the first test of a subterranean BRL against real eDNA metabarcoding data.

Conclusions:

  • A curated, publicly accessible BRL is essential for robust eDNA biomonitoring of subterranean biodiversity.
  • The development of specialized BRLs significantly improves the resolution and accuracy of subterranean fauna identification.
  • This work proposes a six-stage plan for data infrastructure development and emphasizes collaborative efforts for a global BRL.