From a Droplet to a Healthier Ecosystem:
How eDNA Is Changing Biodiversity Research
The latest 2025 State of the Climate report confirms Earth’s climate is at its most imbalanced state on record—the hottest 11 years, soaring ocean heat, and shrinking polar ice. Beneath these alarming trends lies a hidden crisis: biodiversity loss. As ecosystems face mounting pressure from warming waters and shifting habitats, our ability to monitor and protect them has never been more critical.
Enter environmental DNA (eDNA)—a revolutionary technology that enables rapid, non-invasive biodiversity monitoring. By analysing DNA traces in water, soil, or air, eDNA provides a powerful window into the health of our natural world, empowering scientists and conservationists to act with speed and precision.
In recent years, MGI’s DNBSEQ platforms and automated solutions have supported scientists across a wide range of major projects, each tackling unique environmental challenges. Together, these technologies are making biodiversity science faster, deeper, and more actionable.
1. eDNA Empowering Ecosystem Restoration & Monitoring
Yangtze River Basin, China
In the Yangtze River basin, routine monitoring using eDNA technology documented a net increase of over 20 aquatic species across 19 national monitoring sections over a five-year period. Species of conservation interest, including small cetaceans and native fish, were consistently identified through their genetic signatures. This wasn’t a one-time experiment—it reflects a broader integration of eDNA into routine environmental monitoring workflows to track species diversity, identify rare or endangered aquatic life, and provide quantitative evidence of ecosystem recovery.
Behind these results is a complete technical workflow designed by MGI for consistency and scalability. The process starts with a portable eDNA sampler, enabling field collection with minimal contamination risk. Samples are then processed through automated nucleic acid extraction and library preparation—steps that were historically manual and time-consuming. High-throughput sequencing is performed on compact, high-accuracy platforms, followed by bioinformatics analysis that translates raw sequence data into species-level identification.
What makes this approach particularly valuable for long-term monitoring is its ability to deliver standardised, repeatable results across sites and over time. The combination of automation, integrated reagent systems, and dedicated analysis software allows monitoring agencies and research teams to move from sample collection to actionable data in a fraction of the time previously required.
Biodiversity Guardians of Thai Mangroves
Reference genome databases were established for 15 mangrove species in Thailand using the DNBSEQ-G400RS platform. RAD-seq and RNA-seq were applied to assess genetic diversity and inform conservation strategies for the Thai Department of Marine and Coastal Resources.
Fish Diversity Monitoring in East Lake, Wuhan, China
A total of 51 fish species across 16 families and 36 genera were identified via eDNA metabarcoding, including economically important species (common carp, silver carp, bighead carp, crucian carp) and the invasive mosquito fish (Gambusia affinis). From eDNA extraction (MGIEasy kit) to library preparation (ATOPlex, 2-step PCR) and sequencing on the DNBSEQ-G99 platform, the entire process was completed in just 12 hours.
Comparative analysis of two 12S rRNA primers (Mifish and Metafish) showed that the Mifish primer more accurately reflects local fish community composition, making it more suitable for routine fish diversity monitoring in East Lake.
2. Extreme Environments & Basic Research
Biodiversity Research Across Extremes: Deep Sea, Antarctica & Coral Reefs
Five high-impact studies using DNBSEQ platforms have explored deep-sea, polar, and coral reef ecosystems for environmental and biodiversity research. Key achievements include the discovery of 7,564 prokaryotic species (89.4% novel) in the Mariana Trench, a completed 13.92 Gb chromosome-level genome of a deep-sea amphipod, 6,000-year sedimentary DNA records of penguin populations tracing evolution in the Antarctic Ross Sea, and the identification of synergistic adaptations between hosts and symbionts in coral reef environments. An upgraded eDNA metabarcoding and metagenomics solution was also introduced.
Unveiling the Microbial Dark Matter of Mangrove Sediments
A total of 2,965 microbial genomes were reconstructed from mangrove sediments in Guangxi, China, using the DNBSEQ-T1+ platform. This generated 10.3 TB of data, covering 78 microbial phyla and revealing key microbial drivers of biogeochemical cycles.
3. Invasive Species & Fisheries Management
eDNA Surveillance of Black-Chinned Tilapia in Thailand
The Thai Department of Fisheries partnered with BIOTEC to deploy an eDNA-based surveillance approach targeting the invasive black-chinned tilapia (Sarotherodon melanotheron), which threatens both natural aquatic ecosystems and the fish farming industry. Using MGI’s ATOPlex Mifish panel, E25 sequencer, and MetaSIS analysis software, the team successfully detected the species across multiple natural water sources, with results matching expectations.
The study demonstrates the power of portable, rapid eDNA workflows for early warning of invasive species and ecosystem protection. A full article is currently in preparation.
4. Rapid Viable Bacteria Detection for Water Safety
This work was awarded a Gold Medal at the 51st International Exhibition of Inventions of Geneva, this work introduced a fully automated PMA-qPCR system for viable bacteria detection in water, reducing detection time from 1–2 days to within 2 hours. The portable solution integrates an eDNA sampler, automated extractor, and rapid qPCR module, demonstrating high correlation (r > 0.99) with plate culture methods.
For those working at the intersection of life science tools and environmental conservation, these real-world applications carry a clear message: the technology is ready. It’s scalable. And it’s already delivering evidence that helps guide conservation decisions.
Intelligent Automation for eDNA Monitoring
Beyond individual instruments, MGI delivers end-to-end automation for eDNA monitoring. By integrating automated extraction, library preparation, and data analysis into a unified workflow, MGI enables scalable, high-throughput solutions that minimise manual steps, improve data consistency, and support the shift towards intelligent, lights-out environmental monitoring.
A Next Step: Supporting MGI EU & AF eDNA Projects
Building on these proven applications, the next question is clear: how do we accelerate adoption where it’s needed most?
To address this, a new eDNA grant is being prepared to support researchers, conservation practitioners, and monitoring programmes in applying eDNA technology to critical environmental questions. Whether focused on freshwater biodiversity, coastal ecosystem health, or novel applications of environmental genomics, the aim is to lower barriers and enable impactful work.
If you’re working on eDNA-based conservation or biodiversity monitoring, stay tuned.
More details will follow in April.
Published 4 April 2026
