Applicability and perspectives for DNA barcoding of soil invertebrates

Area of Science:

• Soil ecology
• Molecular ecology
• Taxonomy

Background:

• Belowground invertebrate communities are dominated by microarthropods requiring extensive taxonomic expertise.
• Molecular methods like metabarcoding offer potential for rapid analysis of these cryptic communities.
• Accurate species-level assignment using metabarcoding remains a challenge for abundant soil microarthropods such as Collembola and Oribatida.

Purpose of the Study:

• To investigate the presence and utility of a barcoding gap in the cytochrome oxidase I (COI) gene for Collembola and Oribatida.
• To assess the accuracy of automated species assignment using molecular data for these soil microarthropods.
• To identify factors influencing the success of molecular species identification in Collembola and Oribatida.

Main Methods:

• Collected COI sequences for Collembola and Oribatida from BOLD and NCBI databases.
• Focused on species with wide geographic sampling to capture intraspecific genetic variation.
• Analyzed intra- and interspecific genetic distances and evaluated automated taxonomic assignment methods.

Main Results:

• Overlapping intra- and interspecific genetic distances in COI were observed in most species, hindering accurate assignment.
• When present, the barcoding gap varied significantly between species and often exceeded standard thresholds.
• Automated assignment revealed multiple genetic lineages within species, causing ambiguous results; phylogenetic methods showed limited success, especially for Collembola.
• Parthenogenetic species exhibited lower genetic variance and more accurate assignments compared to sexual species.

Conclusions:

• A single standard gene and genetic threshold are likely insufficient for molecular species identification in many Collembola and Oribatida.
• Deep evolutionary distances contribute to varying genetic diversity patterns among species.
• Improved metabarcoding requires additional genes, long-read sequencing, and development of pan-barcodes for species lacking clear barcoding gaps.