Remote autonomous environmental DNA sampler and analyzer
Inventors
Pracheil, Brenda M. • CHESSER, Phillip C. • Griffiths, Natalie A. • Moody, Kristine • Post, Brian K. • Smith, Brennan T. • Wang, Peter • Carter, Caroline • Atkins, Celeste
Assignees
Publication Number
US-12247991-B2
Publication Date
2025-03-11
Expiration Date
2043-09-29
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Abstract
Systems and methods for operating an aquatic robot. The methods comprise: autonomously propelling the aquatic robot through a body of water to a location where a water sample is to be obtained; and performing operations by the aquatic robot to autonomously collect the water sample, cause the water sample to flow through a filter that retains eDNA, lyses and releases the eDNA to a create a lysate, process the lysate to obtain a product for eDNA sequencing, generate eDNA sequencing data using the product, and communicate the eDNA sequencing data to a remote external device.
Core Innovation
The invention provides an autonomous system and method for remotely collecting, processing, sequencing, and analyzing environmental DNA (eDNA) from aquatic environments using an aquatic robot. The aquatic robot is capable of autonomously propelling itself through a body of water to a designated sampling location, where it collects a water sample, passes it through a filter to retain eDNA, lyses cells to release the eDNA as a lysate, and subsequently processes the lysate to obtain a product for eDNA sequencing. The system can then generate eDNA sequencing data and communicate the data to a remote external device for further analysis.
This autonomous workflow is achieved with a combination of micro- or milli-fluidics, ambient stable molecular reagents, a genome sequencer, and telemetry, all integrated within the aquatic robot (also referred to as the eDNA-bot). The robot includes a filter integrated with a manifold for simplified filter changes, as well as a 3D-printed micro- or milli-fluidics system configured to perform key steps such as lysate cleaning, DNA purification, amplification, library construction, and delivery of the sample to the sequencer.
The core problem addressed is the inefficiency, high cost, human risk, and bias inherent in traditional biodiversity survey methods, which are also susceptible to sample contamination and often result in out-of-date or inaccurate species presence data. By automating eDNA collection and analysis, the eDNA-bot enables real-time, accurate, and cost-effective biodiversity assessments while reducing the need for human intervention and minimizing contamination risk.
Claims Coverage
The patent claims cover multiple inventive features including autonomous robotic sampling and analysis methods, integrated filter-manifold assemblies, advanced fluidics processing, and full system embodiments.
Autonomous aquatic robot for eDNA collection and sequencing
A method for operating an aquatic robot that: - Autonomously propels itself through a body of water to a location where a water sample is to be obtained. - Performs, in an autonomous manner, the following operations: collects a water sample, passes it through a filter that retains eDNA, lyses and releases eDNA to create a lysate, processes the lysate to obtain a product for eDNA sequencing, generates eDNA sequencing data using the product, and communicates the sequencing data to a remote external device. - Processes the lysate using a micro- or milli-fluidics system comprising a 3D printed part. - Uses fluid channels to transport the lysate to at least one mixing channel having a spiral shape that facilitates mixing with a cleaning solution.
Filter integrated with manifold and autonomous replacement
A method for operating an aquatic robot where: - The filter for retaining eDNA is integrated with a manifold into a single assembly, comprising a stationary part and a removable part that can be decoupled and re-coupled. - The assembly includes inlet and outlet channels around the circumference of the removable part to direct fluid to and from the filter. - The aquatic robot can autonomously decouple and replace the filter with another filter.
Micro- or milli-fluidics system with spiral mixing channels and controlled flow
The fluidics system uses: - A 3D printed part with at least one fluid channel to transport lysate to at least one spiral-shaped mixing channel for improved mixing with cleaning solutions. - A fluid holding area sized and shaped to control fluid flow to the mixing channel based on surface tension and internal pressure within the fluidics system. - Functionality to allow flow from the mixing channel through another filter to retain DNA, apply a release agent to the filter, and transport the released eDNA out of the system.
Complete system for autonomous aquatic eDNA sampling and sequencing
A system comprising: - A propulsion system. - An aquatic robot configured to autonomously control its movement, collect water samples, retain eDNA on a filter, produce a lysate, process the lysate for eDNA sequencing using a micro- or milli-fluidics system, generate sequencing data, and communicate that data to a remote device. - The robot is capable of sequential sampling at different locations, which may be selected randomly, by user-defined locations, or via machine learned information. - The robot includes an integrated filter/manifold assembly and systems for automated filter replacement.
The claims encompass autonomous robotic sampling and eDNA analysis workflows, integrated filter-manifold assemblies with automated filter replacement, advanced fluidics processing with spiral mixing and controlled fluid flow, and comprehensive systems for real-time, remote aquatic DNA monitoring.
Stated Advantages
Eliminates hands-on sample processing, reducing risk of contamination and increasing accuracy and confidence of results.
Provides real-time, cost-effective biodiversity assessments and rapid evaluation for conservation and management actions.
Reduces costs, contamination, and hazardous risk to human operators compared to traditional techniques.
Enables long-term and repeated sampling to collect time-series data crucial for monitoring changes in biodiversity.
Is adaptable for specific user needs, including rapid detection of changes such as new invasive species, and pathogen detection.
Facilitates non-intrusive monitoring, lowering risks of harm to both humans and wildlife.
Minimizes delays between sampling and data acquisition, improving the relevance of monitoring data for effective decision-making.
Documented Applications
Monitoring and assessing distributions, abundances, and community composition for biodiversity conservation.
Detection, delineation, and abundance estimation of rare, threatened, or endangered species.
Detection and monitoring of invasive species in aquatic environments.
Pathogen detection in natural systems and man-made infrastructure, such as wastewater and aquaculture.
Healthcare applications including real-time monitoring of new pathogenic variants and emerging infectious diseases.
Security and defense contexts involving tracking of biological agents or contaminants in water supplies.
Hydropower environmental assessments and other sectoral biodiversity evaluations.
Quantification of contaminants and pathogens in wastewater treatment facilities for improved human health policy decisions.
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