eDNA Monitoring & Diversity
Overview
Our eDNA-Based Population Monitoring & Genetic Diversity Solution introduces a transformative, non-invasive method for biodiversity research and conservation. By capturing and analyzing trace DNA from environmental sources such as water, soil, and air—coupled with high-throughput sequencing and tailored bioinformatics—we enable detailed species detection and genetic diversity assessment at an ecosystem scale.
Our eDNA-Based Population Monitoring & Genetic Diversity Solution Empowers Your Research and Conservation with:
- Comprehensive biological insights:
We not only precisely monitor the distribution and population dynamics of target species, but also deeply analyze their genetic diversity levels, obtaining dual key data on the "presence or absence" and "health status" of the population at one time.
- Efficient and Scalable Monitoring
eDNA sampling simplifies fieldwork, requiring minimal equipment and time compared to trapping, tagging, or visual surveys. One sample can reflect biodiversity at a scale previously requiring intensive effort—making it ideal for remote, large-scale, or long-term ecological studies.
- Tailored to Your Research Questions
Our bioinformatics pipelines are fully customizable. Whether you're conducting a broad biodiversity audit or a focused population study, we adapt our analysis to your specific goals, for instance, by designing a panel that simultaneously tracks coral reef macrofauna and their symbiotic microbes for a holistic health assessment.
What Is eDNA Monitoring & Diversity
eDNA monitoring and diversity analysis is a revolutionary environmental genomics technology. It can identify species by capturing DNA (i.e. eDNA) shed by organisms from environmental samples such as water, soil or air, without direct contact with the organisms.
This technology can not only precisely monitor the existence and distribution of specific species (such as endangered or invasive species), but also utilize high-throughput sequencing to deeply analyze the genetic diversity of populations. By assessing the richness of genetic variations, scientists can understand the health status, adaptability and survival potential of populations, providing crucial scientific basis for biodiversity conservation, ecosystem management and the recovery of endangered species.
How We Deliver This Solution
Sample Collection & Preparation
- Professional sampling plan design: Our technical expert team will tailor the optimal sampling strategy for you based on your specific research goals, water body type and environmental conditions, including point layout, sampling volume and repeat Settings.
- Pollution-free on-site collection: We provide detailed standardized operation guidelines and professional sterile sampling equipment support for the project. The core of on-site operation lies in eliminating contamination: sterile gloves must be worn throughout the process and changed in a timely manner at different sampling points. At the same time, it is essential to collect on-site blank and filter blank samples.
- Efficient eDNA enrichment and stabilization: Our solution is based on a leading solid-phase adsorption membrane filtration method to efficiently enrich eDNA in water samples. Compared with traditional centrifugal precipitation, it can handle larger water volumes and capture more DNA. After filtration, the membrane is immediately placed into a stabilizing solution and stored at low temperature, effectively preventing DNA degradation.
- Standardized sample management and logistics: From sample labels, collection records to the entire low-temperature cold chain transportation, we implement strict standard operating procedures to ensure that each sample maintains the integrity and traceability of its biological information before arriving at the laboratory.
Sequencing
1. Multi-Marker Metabarcoding Approach
We utilize a multi-marker metabarcoding strategy that targets several conserved genetic regions—such as 16S rRNA for bacteria, 18S rRNA for eukaryotes, COI for animals, and ITS for fungi—from a single environmental sample. This allows us to detect and identify species across a wide range of taxonomic groups simultaneously. Our PCR methods are optimized to reduce bias while maintaining high sensitivity, even for low-abundance organisms.
Application: This method is particularly valuable for comprehensive biodiversity inventories and ecosystem health assessments. In conservation projects, we use multi-marker metabarcoding to establish baseline biodiversity metrics, monitor changes in community structure following disturbance events, and detect the presence of endangered species without direct observation. The approach also effectively identifies invasive species early in their establishment phase.
2. Shotgun Metagenomics for Functional Insights
We apply shotgun metagenomic sequencing. This method captures all genomic content within a sample, free from PCR amplification, and reveals taxonomic identity alongside functional genes and metabolic pathways.
Application: Shotgun metagenomics enables us to move beyond species lists to understand ecosystem functioning. In agricultural monitoring, we use this approach to profile soil microbial communities and their nutrient-cycling capabilities. In marine environments, it helps track how microbial functional profiles shift in response to pollution, providing early warning signs of ecosystem stress before visible impacts emerge.
Bioinformatics
1. Data quality control and precise species identification
First, we conduct strict quality control on the original sequencing data, including denoising, removing chimeras, and eliminating contaminated sequences that appear in blank controls to ensure the purity and reliability of the data. Subsequently, through multi-label macro barcode analysis, we compared high-quality sequences with international authoritative databases to achieve precise species identification and community analysis at multiple trophic levels, ranging from bacteria, fungi to animals and plants.
2. Population level in-depth analysis
Beyond community composition, we conduct more in-depth single-species analyses using specific loci. By identifying single nucleotide polymorphisms (SNPs), we can analyze the population genetic structure of a specific target species, assess its genetic diversity and inbreeding level, and even estimate the relative number of individuals at the population level through individual identification techniques.
3. Advanced Statistics and Visualization
We offer comprehensive statistical analysis services, including α and β diversity calculations, community difference significance tests, and environmental factor association analyses. All results are presented visually through professional charts (such as species composition bar charts, PCoA ranking charts, heat maps, etc.), allowing the data to "speak for itself" and helping you quickly grasp the core discoveries.
Service flowchart
Figure 1: How We Deliver This Solution: eDNA Monitoring & Diversity Workflow
Our Advantages
No Prior Species-Specific Knowledge Required
Our approach works even for poorly studied or novel taxa, as it relies on universal PCR primers or shotgun sequencing rather than pre-designed species-specific markers. This makes it invaluable for biodiversity surveys in understudied regions or for emerging conservation priorities.
Efficient and sensitive non-invasive monitoring
eDNA sampling greatly simplifies fieldwork and requires less equipment and time compared with traditional methods such as trapping, marking or visual investigation. This method has extremely high sensitivity and can detect traces of rare, endangered or concealed species, achieving low-interference and non-invasive monitoring of target organisms.
Full-process integrated solution
We support the entire chain from sampling scheme design and standardized sample handling to experimental wet lab processing and bioinformatics analysis. This integrated approach ensures high data quality and traceability, while minimizing information loss and risks that can arise from fragmented outsourcing.
Applications
Ecosystem Health Assessment and Restoration: By synchronously identifying multiple species in environmental samples, a rapid and comprehensive investigation of the entire community can be achieved. By analyzing the genetic diversity of key species or indicator species, assess ecosystem functions, detect signs of degradation at an early stage, and measure the effectiveness of restoration projects (such as reforestation and wetland restoration).
Biodiversity census and ecosystem assessment: Conduct rapid and comprehensive biodiversity background surveys in specific areas (such as nature reserves, national parks, oceans, etc.) to assess the health status and restoration effectiveness of ecosystems. Through multi-label macro barcode technology, we can obtain a comprehensive species list from microorganisms to large animals at one time, greatly enhancing the efficiency of investigations and the completeness of species discovery, and providing a solid data foundation for ecological assessment.
Monitoring of rare, endangered and hidden species: In vast or hard-to-reach habitats, track the distribution and activity traces of rare, endangered or hidden species that are difficult to observe directly, such as giant pandas, finless porpoises and amphibians. With extremely high detection sensitivity, we achieve non-invasive and low-disturbance monitoring, providing crucial evidence for the formulation of conservation strategies for endangered species, habitat selection, and effectiveness assessment.
Aquatic ecology and fishery resources management: Assess the impact of dam construction, channel dredging and other projects on aquatic biological communities; Monitor the population dynamics and spatial distribution of important economic fish species and other aquatic organisms. To offer a more economical and comprehensive community monitoring method than traditional methods such as net fishing and acoustic investigation, accurately assess engineering impacts, and provide a scientific basis for the sustainable utilization and management of fishery resources.
Demo
Figure 2: Accumulation of rainwash eDNA diversity with increasing sampling effort for plants and insects. (Zinger, 2025)
Case Study
Effectiveness assessment of using riverine water eDNA to simultaneously monitor the riverine and riparian biodiversity information.
Journal: Sci Rep
Published：2021
The high cost, time consumption, and taxonomic expertise required by conventional biodiversity surveys fundamentally limit their spatiotemporal resolution and scope. This data gap impedes a deeper understanding of ecosystem dynamics and the development of effective conservation policies. An additional challenge is the unresolved efficacy of riverine eDNA as a unified tool for monitoring both aquatic and terrestrial biota. Critical unknowns include how detection rates are modulated by seasonal fluctuations, precipitation events, and taxon-specific eDNA degradation kinetics.
To address these challenges, we leverage the efficiency and standardization of eDNA metabarcoding and high-throughput sequencing, enabling high-resolution and large-scale biodiversity monitoring. We define the watershed biological information flow (WBIF) to approximate the transportation effectiveness of biodiversity information from land to river and upstream to downstream. By assessing the WBIF's transport capacity, degradation rate, and environmental filtration under different seasons and weather conditions for various taxonomic communities, we propose a framework to evaluate the effectiveness of using riverine water eDNA for comprehensive biodiversity monitoring.
This study developed an innovative monitoring method that integrates eDNA meta-barcodes and WBIF, significantly enhancing the standardization and efficiency of monitoring. By using this system, we have clarified the combined influence of environmental factors such as season and weather, as well as the specific degradation rate of taxonomic groups, on the monitoring effect of eDNA in river water, providing a key scientific basis for the precise assessment of biodiversity.
Figure 3: Comparison of the performances of 96 KASP marker panel and GBS in evaluating the RP genome recovery in the selected BC3F4 introgression lines.
FAQ
No. Our solution uses universal PCR primers (for metabarcoding) or shotgun sequencing, which do not require pre-existing genomic resources. This makes it applicable to non-model organisms, newly discovered species, or ecosystems with limited genetic data.
References
- Zinger L, Benoiston AS, Cuenot Y, et al. Elusive tropical forest canopy diversity revealed through environmental DNA contained in rainwater.Sci Adv. 2025 Aug 15;11(33):eadx4909. doi: 10.1126/sciadv.adx4909.
- Yang H, Du H, Qi H, et al. Effectiveness assessment of using riverine water eDNA to simultaneously monitor the riverine and riparian biodiversity information. Sci Rep. 2021 Dec 20;11(1):24241. doi: 10.1038/s41598-021-03733-7.
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