Project Showcase

Practical environmental genomics projects for biodiversity monitoring and better environmental decisions.

OceanDNA System +

The OceanDNA System, developed under the Ocean Supercluster program, represents a significant advancement in the operationalization of environmental DNA for marine biodiversity monitoring and applied ecological assessment. At its core, the OceanDNA System leverages the principle that organisms continuously shed genetic material into their environment, allowing for the detection of complex biological communities from small volumes of seawater.

Through an integrated workflow encompassing sampling, nucleic acid extraction, amplification, sequencing, and bioinformatic analysis, the system enables robust identification of species and ecological patterns across a wide range of applications, including baseline biodiversity assessment, detection of invasive or endangered species, and monitoring of bioindicator taxa.

The current phase of the program focuses on scaling both laboratory and computational infrastructure to meet rapidly increasing demand. Laboratory capacity expansion is being achieved through the integration of robotic automation, which significantly enhances throughput, reduces human error, ensures reproducibility, and enables continuous processing. Complementary investments in computational infrastructure are required to address the exponential growth in sequencing data and reference databases, which are critical for accurate taxonomic assignment and ecological interpretation.

In parallel, the program emphasizes translation and deployment through targeted marketing and stakeholder engagement, as well as demonstration projects in collaboration with the Newfoundland and Labrador fishing industry. Notably, methodological innovation includes the development of DNA-absorbent sampling materials that eliminate the need for bulk water collection and enable room-temperature preservation, representing a substantial improvement in field logistics and scalability.

Collectively, these efforts position the OceanDNA System as a scalable, end-to-end platform for environmental genomics, bridging laboratory innovation, field deployment, and decision-making applications.

Key themes: Marine monitoring Automation EnviroSeq Scalable biodiversity data

Passive eDNA Sampling from Opportunistic Vessels +

The proposed solution is both simple and transformative: leveraging existing vessel traffic to passively collect eDNA samples. Rather than deploying dedicated sampling missions, this approach embeds biodiversity data collection directly into ongoing marine operations such as fisheries, coast guard, and shipping.

The key enabling innovation is a DNA-absorbent pod system that can be integrated into trawl lines or deployed in-flow, capturing environmental DNA without the need for active water collection, onboard filtration, or cold-chain logistics. This dramatically reduces both cost and operational burden while maintaining high-quality genomic outputs.

The project builds on prior work demonstrating that traditional vessel-based eDNA sampling, even when simplified, remains disruptive and impractical for routine use. The transition to passive, flow-through DNA capture represents a critical step change in usability and scalability.

The proposed deployment aboard the Polar Prince provides an ideal real-world testbed: a large-scale, opportunistic sampling platform spanning Atlantic Canada, including engagement with nine Indigenous Nations. This setting enables simultaneous optimization of device design, sampling materials, and training protocols, while generating a uniquely large and spatially extensive biodiversity dataset.

Scientifically, the project will generate multi-marker genomic data across 168 samples, enabling detection across major animal taxa and establishing a high-resolution baseline of marine biodiversity. Importantly, the preservation of DNA extracts for future re-analysis creates a long-term genomic archive, allowing retrospective studies and targeted species detection as analytical methods evolve.

From a systems perspective, this work represents a shift toward distributed, continuous biodiversity monitoring, where data collection is decoupled from dedicated field campaigns and instead integrated into existing infrastructure.

Key themes: Passive sampling Opportunistic vessels Low-cost monitoring Genomic archive

Monitoring Ecological Resilience in Northern Fisheries +

This project tackles a central challenge in modern fisheries science: the lack of scalable, ecosystem-level data needed to support sustainable ocean management in the face of rapid environmental change. While Canada and global partners are moving toward ecosystem-based approaches to fisheries management, current monitoring methods remain fundamentally inadequate—too slow, too narrow, and too expensive to capture the complexity and variability of marine ecosystems, particularly in the Arctic.

The proposed solution is the deployment of environmental genomics as a practical, field-ready system for ecosystem-scale observation. By leveraging eDNA, this project moves beyond single-species monitoring and enables simultaneous detection of entire biological communities, from microbes to marine mammals, using standardized sampling and analytical workflows.

The project is anchored in Northern fisheries systems, with a focus on ecologically and economically important regions along Eastern Baffin Island. These systems are undergoing rapid change driven by climate dynamics, yet remain among the least characterized globally.

By implementing a structured sampling program across seasons and depths, and integrating genomic data with abiotic measurements, the project will generate high-resolution biodiversity baselines, habitat models, and species interaction networks. These outputs are essential for understanding ecosystem resilience, predicting shifts in species distributions, and informing sustainable fisheries management.

A defining strength of the project is its community-based and multi-stakeholder design. The integration of Indigenous organizations, fisheries, government, and NGOs creates both scientific and operational capacity, while enabling local participation in data collection and interpretation.

From a systems perspective, this work establishes a framework for next-generation ocean monitoring—one that is distributed, data-rich, and aligned with the objectives of the UN Decade of Ocean Science for Sustainable Development.

Ultimately, this project is not just about generating data—it is about redefining how we observe, understand, and manage marine ecosystems.

Key themes: Northern fisheries Community monitoring Climate change Ecosystem resilience

Scalable Monitoring of Invasive Species and Harmful Algae +

This project evaluates the use of environmental DNA for the detection and monitoring of aquatic invasive species and harmful algae across coastal Newfoundland, with a focus on Placentia Bay and adjacent inshore environments.

The work demonstrates how multi-marker metabarcoding combined with occupancy modeling can provide a scalable and sensitive framework for biodiversity surveillance and early detection of high-risk taxa.

Across water, sediment, and plankton samples collected over spatial and seasonal gradients, eDNA analysis detected six invasive species and thirteen harmful algal species, alongside a broad background of biodiversity spanning multiple trophic levels.

Known invasive species, including Carcinus maenas and Ciona intestinalis, were reliably detected at established invasion sites, validating the method’s ability to capture biologically meaningful signals. At the same time, widespread detection of certain harmful algae across sites and seasons highlights the capacity of eDNA to reveal persistent and system-wide ecological risks.

The project also demonstrates strong seasonal structuring of biodiversity and target species detections, with clear shifts in community composition from spring through fall. This has direct implications for monitoring design: single time-point sampling is inadequate, and temporal replication is essential to capture ecosystem dynamics and improve detection of species with seasonal signals.

Importantly, the application of multi-species occupancy modeling provides a quantitative framework to address one of the central challenges of eDNA—imperfect detection. By estimating both species occurrence and probability of capture, the study moves beyond presence/absence reporting and enables statistically robust interpretation of detection data.

Beyond target species, the dataset reveals extensive biodiversity, with detections spanning dozens of phyla and hundreds of taxa, highlighting the broader value of eDNA as an ecosystem-scale monitoring tool.

Key themes: Invasive species Harmful algae Occupancy modeling Coastal biosecurity

Enhancing Aquaculture Productivity with Environmental Genomics +

This project leverages advanced environmental genomics to transform aquaculture monitoring and management by addressing two critical challenges: environmental sustainability and disease risk in salmon farming. Through a strategic partnership between eDNAtec and Mowi, the world’s largest producer of farmed salmon, the initiative applies high-resolution eDNA sequencing to simultaneously characterize local biodiversity and detect pathogenic organisms in marine farm environments. By capturing genetic signals from water and sediment samples, the approach enables early detection of disease-causing agents such as Tenacibaculum spp., while also providing comprehensive insights into ecosystem dynamics within and around aquaculture sites.

Beyond detection, the project integrates molecular data with predictive modeling to develop early warning systems for disease outbreaks and to quantify environmental impacts with unprecedented precision. This represents a shift from proxy-based monitoring toward direct, data-rich assessment of ecosystem health and fish production conditions. The resulting platform is designed to scale operationally across aquaculture systems, offering both improved environmental stewardship and enhanced production efficiency. With strong commercial and global deployment potential, the project positions environmental genomics as a core technology for the sustainable growth of the blue economy.

Key themes: Aquaculture Disease detection Predictive modeling Environmental genomics Blue economy

Atlantic Ports Baseline Biodiversity Project +

This project establishes a next-generation environmental genomics framework for biodiversity monitoring in marine ports, addressing the growing need for scalable and comprehensive assessment of ecosystem health in high-traffic coastal environments. Focusing on four strategically selected ports across Atlantic Canada, the initiative applies environmental DNA (eDNA) metabarcoding to generate baseline biodiversity inventories from water samples, capturing organisms across trophic levels—from microbes to fish—in a single, non-invasive workflow. By integrating automated sampling technologies with standardized molecular and bioinformatic pipelines, the project evaluates the feasibility of routine, high-resolution biodiversity surveillance in operational port settings, where traditional monitoring approaches are often limited in scope and scalability.

Beyond baseline characterization, the project is designed to build operational capacity within port authorities and enable the transition toward continuous, data-driven environmental monitoring. The resulting datasets provide critical insights into ecosystem composition, including the detection of invasive, commercially important, and culturally significant species, while supporting regulatory compliance and sustainability initiatives such as Green Marine certification. By combining advanced genomics with deployable sampling systems and decision-oriented data products, this initiative demonstrates how eDNA can be integrated into real-world monitoring programs to improve environmental stewardship and inform long-term management of coastal infrastructure.

Key themes: Ports Baseline biodiversity eDNA monitoring Invasive species Green Marine