High-resolution melting (HRM) curve analysis as a potential tool for the identification of earthworm species and haplotypes

PeerJ. 2022 Jun 28:10:e13661. doi: 10.7717/peerj.13661. eCollection 2022.

Abstract

Background: Earthworm communities are an important component of soil biodiversity and contribute to a number of ecosystem functions such as soil-nutrient cycling. Taxonomic identification is an essential requirement to assess earthworm biodiversity and functionality. Although morphological identification of species is labour-intensive, it is the most commonly used method due to a lack of cost-efficient alternatives. Molecular approaches to identify earthworms at species and haplotype level such as DNA barcoding are gaining popularity in science but are rarely applied in practice. In contrast to barcoding, the differentiation of PCR products based on their thermal denaturation properties using high-resolution melting (HRM) curve analysis is a fast and cost-efficient molecular closed-tube, post-PCR tool that allows identification of taxa.

Methods: We developed a HRM curve assay to identify eight earthworm species common to agricultural soils in Central Europe (Allolobophora chlorotica, Aporrectodea caliginosa, Apo. limicola, Apo. longa, Apo. rosea, Lumbricus castaneus, L. rubellus, and L. terrestris). For this, a new primer pair targeting a 158-bp long subregion of the cytochrome c oxidase I (COI) gene was designed. Our HRM assay was further tested for the differentiation of COI haplotypes using 28 individuals of the earthworm species Allo. chlorotica. Furthermore, we developed a novel extraction method for DNA from earthworm tissue that is fast and requires minimal consumables and laboratory equipment.

Results: The developed HRM curve assay allowed identifying all eight earthworm species. Performing the assay on 28 individuals of the earthworm species Allo. chlorotica enabled the distinction among different COI haplotypes. Furthermore, we successfully developed a rapid, robust, scalable, and inexpensive method for the extraction of earthworm DNA from fresh or frozen tissue.

Conclusions: HRM curve analysis of COI genes has the potential to identify earthworm species and haplotypes and could complement morphological identification, especially for juvenile or damaged individuals. Our rapid and inexpensive DNA extraction method from earthworm tissue helps to reduce the costs of molecular analyses and thereby promote their application in practice.

Keywords: COI; Earthworm identification; Earthworm taxonomy; Haplotypes; High-resolution melting (HRM) curve analysis; Real-time PCR; Species.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • DNA / genetics
  • Ecosystem
  • Haplotypes / genetics
  • Oligochaeta* / genetics
  • Polymerase Chain Reaction
  • Soil

Substances

  • DNA
  • Soil

Grants and funding

This study was supported by the joint project MonViA - the German Farmland Biodiversity Monitoring that has been funded by the Federal Ministry of Food and Agriculture (BMEL). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.