# Environmental DNA (eDNA) Technology in Biodiversity and Ecosystem Health Research: Advances and Prospects

## TL;DR

eDNA technology is a noninvasive method for monitoring biodiversity and ecosystem health by detecting genetic material in environmental samples, with potential for large-scale and cost-effective ecological research.

## Contribution

This review systematizes standardized eDNA workflows and guidelines to enhance reproducibility and addresses key challenges in eDNA applications.

## Key findings

- eDNA is effective for detecting rare, endangered, and invasive species across multiple ecosystems.
- Standardized sampling and analysis methods improve the reliability and comparability of eDNA research.
- Challenges include database gaps, contamination risks, and limitations in quantifying species abundance.

## Abstract

Environmental DNA (eDNA) technology, as a minimally invasive or noninvasive monitoring approach, has been increasingly applied in biodiversity surveys and ecosystem health assessment by detecting genetic material in environmental samples. This approach exhibits high sensitivity for identifying rare, endangered, and invasive species, with broad applicability across aquatic, terrestrial, and atmospheric ecosystems. Moreover, eDNA metabarcoding enables large‐scale detection of microbial community structure and function. By systematically synthesizing multi‐environment case studies, this review evaluates optimized eDNA workflows, including sampling (0.22–0.45 μm filtration for aquatic systems, PCI/DNeasy methods for soils, and MD8 samplers for air), DNA extraction, and bioinformatic analysis, integrating standardized guidelines to enhance research reproducibility and comparability. Despite advantages such as reduced field labor and cost efficiency, eDNA applications still face critical challenges, such as reference database gaps, full‐process quality control risks, methodological inconsistencies, and limitations in abundance quantification. Future advancements in sequencing technologies, bioinformatics, and interdisciplinary integration (machine learning, remote sensing) are expected to expand eDNA's role in tackling global change issues such as climate adaptation, pollution tracking, and ecological restoration.

This review synthesizes over 15 years of advancements in eDNA technology by systematizing standardized guidelines for sampling, extraction, and bioinformatics, thereby enhancing the reproducibility of eDNA‐based research. It highlights eDNA's transformative role in noninvasively detecting rare, endangered, and invasive species, as well as its value in ecosystem health assessment, while also addressing critical challenges facing eDNA applications, including methodological inconsistencies, limitations in species abundance quantification, and contamination risks to broaden the technology's field utility. Additionally, the review explores future advancements in eDNA research, focusing on the integration of sequencing technologies, bioinformatics, and machine learning to further expand eDNA's application in climate adaptation and ecological monitoring.