Biodiv Sci ›› 2022, Vol. 30 ›› Issue (12): 22252.  DOI: 10.17520/biods.2022252

Special Issue: 土壤生物与土壤健康

• Technology and Methodology • Previous Articles     Next Articles

Performance evaluation of molecular taxonomy assignment tools for soil invertebrates

Cong Xu1, Feiyu Zhang1, Daoyuan Yu2, Xin Sun3, Feng Zhang1,*()   

  1. 1. College of Plant Protection, Nanjing Agricultural University, Nanjing 210095
    2. College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095
    3. Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 130102
  • Received:2022-05-09 Accepted:2022-08-18 Online:2022-12-20 Published:2022-11-25
  • Contact: *E-mail:


Aims: Soil invertebrate communities are of extremely high diversity but still poorly studied in DNA-based diversity assessments. Since traditional morphological identifications have trouble in completing thousands of taxonomy assignments accurately with limited time, more and more biodiversity surveys turn to molecular taxonomy assignments. To promote biodiversity surveys on soil invertebrates, we made a comprehensive comparison for five popular taxonomy assignment tools (VSEARCH, HS-BLASTN, EPA-NG, RAPPAS and APPLES) targeting on different molecular markers (COI, 16S and 18S). Four soil invertebrate groups (Collembola, Acari, Clitellata and Chromadorea) were selected in the comparison representing three representative phyla of varied body-sizes.
Methods: The databases of four soil invertebrate groups using three molecular markers were built with a filtering step. The commands of five taxonomy assignment tools were integrated into a script which would finally output the taxonomic information of query sequences. All of assignment accuracy, running speed and memory usage of five tools were estimated and compared.
Results: Our results indicated that EPA-NG performed best in accuracy for most cases, especially for COI. VSEARCH and HS-BLASTN remained high accuracy and showed similar accuracy performance when utilizing 16S and 18S markers. Moreover, shorter running time and lower memory usage made VSEARCH more popular applying in 16S and 18S than EPA-NG. RAPPAS and APPLES showed unstable performances in accuracy and were often too conservative to identify some species at generic or familial levels.
Conclusion: This study concluded that molecular taxonomy assignment could accomplish identifications of soil invertebrates in an accurate and efficient manner. COI marker is the most recommended marker applied in molecular taxonomy assignment for soil invertebrates because of its abundant repositories of reference sequences reflected in all of species, genus and family levels. When COI is utilized as marker, EPA-NG is the most recommended tool unless the reference database is too large. When 16S or 18S is utilized as marker, VSEARCH is most highly recommended.

Key words: taxonomy assignment, soil invertebrate, bioinformatics tool, identification, biodiversity