Autonomous biomolecular sampling: enhancing the temporal and spatial resolution of ocean biodiversity observations

Abstract

On land, we can easily detect ecological changes through our senses, whether it’s hearing a new bird species or noticing fewer insects, and these sensory cues drive scientific inquiry. In contrast, changes in marine ecosystems are far less perceptible, making it challenging to notice and investigate ecological trends. Environmental DNA (eDNA) monitoring provides a powerful biomolecular tool to reveal these hidden trends, offering critical insight into the impacts of anthropogenic activities on marine ecosystems.

Traditional approaches to understanding these impacts often rely on micro- and mesocosm experiments, which may not accurately reflect natural marine communities. Long-term place-based monitoring is essential to observe cumulative effects and support adaptive management strategies. However, conventional visual monitoring in marine environments is costly, logistically challenging, and sometimes hazardous, limiting its ability to deliver the temporal and spatial resolution required to detect change.

Autonomous eDNA sampling technologies, such as the Robotic Cartridge Sampling Instrument (RoCSI), offer a promising solution. Although the initial investment is substantial, a network of these autonomous samplers could provide consistent, low-cost biodiversity data, that is resilient to funding fluctuations, due to the option to store samples in biobanks for future analysis.

This doctoral research explores how biomolecular monitoring and autonomous technologies like RoCSI can enhance marine biodiversity monitoring. Chapter 2 demonstrates the RoCSI's ability to autonomously collect samples via a ship’s underway system, increasing the spatial resolution of eDNA sampling. Chapter 3 focuses on the RoCSI's capability to capture high temporal resolution samples in a highly urbanised estuary. Chapter 4 optimises the RoCSI for long-term deployment by comparing different liquid nucleic acid preservatives. Chapter 5 discusses improvements in data management practices for biomolecular research, facilitating the integration of RoCSI data into a global/national scale observation network. Chapter 6 evaluates the Oxford Nanopore’s portable MinION sequencer for its potential use alongside the RoCSI.

Overall, this thesis validates the RoCSI as an effective tool for high-resolution temporal and spatial biodiversity monitoring, optimises it use for long-term deployments, and advances data management practices for large-scale biomolecular observations. The findings provide foundational evidence for establishing a national-scale ocean biomolecular observatory that combines both autonomous and manual methods to deliver consistent, long-term ecological data needed to inform adaptive, place-based management of marine ecosystems.

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Identifiers

ORCID for Robyn Mairin Samuel: orcid.org/0000-0001-5989-4588

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