Data and code from: Establishing DNA-based strategies for soil biodiversity assessment: Insights from carabid beetles

Molecular-based methods offer valuable opportunities for assessing soil biodiversity in different ecosystems. However, their reliability and large-scale applicability depend on developing, optimizing protocols, and establishing high-quality, curated local reference databases. This study aimed to evaluate key steps in the soil macroinvertebrate metabarcoding workflow, including the sample decontamination process and the efficiency of taxa recovery. Specifically, we sought to: (1) determine the impact of sample decontamination, (2) validate species-level recovery efficiency of the metabarcoding pipeline spiked with a curated mock community of morphologically identified and barcoded carabid beetles, and (3) compare traditional morphological identification and metabarcoding for specimens’ taxonomic assignment and recovery. Our results showed that the commonly used decontamination process did not significantly impact OTU richness, suggesting it is not essential for this fauna. Compared to mo...,
Sample Collection and Processing
This study, conducted under the CULTIVAR project in Idanha-a-Nova, Portugal, monitored soil macrofauna across 24 plots, each containing nine pitfall traps. A total of 216 traps were set up from late November to early December 2022, remaining in the field for 13 to 17 days. Traps were filled with ethylene glycol as a preservative and covered with lids to prevent dilution by rain. Collected specimens were preserved in 96 % ethanol until further analysis. Under low-power microscopy, organisms were counted and identified, per sample, to the lowest possible taxonomic level using morphology-based keys and literature. These community samples were stored at 96 % ethanol.

Establishing a COI Barcode Reference Database
Carabidae specimens were identified to the species level using morphological traits. To crete a local barcode reference base, one to two identified specimens were bleached, washed, and DNA was extracted using a Qiagen DNeasy® kit. For smaller speci..., , # Data and code from: Establishing DNA-based strategies for soil biodiversity assessment: Insights from carabid beetles

[https://doi.org/10.5061/dryad.g1jwstr28](https://doi.org/10.5061/dryad.g1jwstr28)

## Description of the data and file structure

This repository contains the data and the scripts from a study conducted as part of the CULTIVAR project in Idanha-a-Nova, Portugal. The research focused on monitoring soil macrofauna diversity through a combination of traditional morphological identification and advanced molecular techniques, such as barcoding and metabarcoding.

## Study Overview

* **Sample Collection**:\
Soil macrofauna were collected from 24 plots using 216 pitfall traps set up from late November to early December 2022. Specimens were preserved in 96 % ethanol and sorted under low-power microscopy.
* **COI Barcode Reference Database**:\
Carabidae specimens were identified morphologically and DNA barcoded using Folmer primers to establish a local COI reference data...,