A State-of-the-Art Review of Aquatic eDNA  Sampling Technologies and Instrumentation: Advancements, Challenges, and Future  Prospects

IntroductionRoutine monitoring of biological communities is integral to characterizing ecosystem health, biodiversity, and providing information necessary for public health and resource management (Canonico et al., 2019; Forio and Goethals, 2020). Traditionally, researchers have relied on labor-intensive and invasive techniques, such as netting, trapping, and visual identifications, to identify and quantify species presence. While effective, these conventional methods often present limitations, including constrained spatial coverage, inadequate temporal resolution, disturbance to sensitive habitats, and inability to capture the breadth of organisms present in the environment. In addition, the expertise and methodology required to conduct surveys is highly dependent on the organisms in question. In recent years, environmental DNA (eDNA) analysis has emerged as a complementary approach to traditional observational techniques (Rourke et al., 2022; Stat et al., 2017; Wang et al., 2024; Westgaard et al., 2024).eDNA analysis involves the collection and analysis of genetic material shed by organisms into their surrounding environment (Taberlet et al., 2018). Multicellular organisms release DNA and RNA in a myriad of ways, such as by shedding skin cells, scales, mucus, feces, and gametes, all of which can be extracted and sequenced to identify species present within a given ecosystem. This approach offers several advantages over traditional survey techniques, including non-invasiveness, high sensitivity, and capacity to detect rare or elusive species—particularly those that are difficult to observe visually (Gold et al., 2021; Holman et al., 2019; Noble-James et al., 2023). Moreover, eDNA analysis enables comprehensive assessments of biodiversity over large spatial and temporal scales, providing valuable insights into community composition, species richness, and ecological dynamics (Preston et al., 2024; Searcy et al., 2022; Thomsen et al., 2012).One of the main benefits of aquatic-based omics’ research, responsible for its expanding uptake, is the simplicity in collecting samples from diverse habitats. However, this is also a pivotal challenge to collect samples over relevant temporal and spatial scales. Traditional biological observations are labor and resource-intensive, and while analysis of eDNA data can be complex, eDNA filtration and preservation is universally-accessible. Coverage using conventional eDNA sampling techniques can be comprehensive in marine settings (e.g., coastal) accessible by humans, but laborious as it typically involves sampling in the field with time consuming filtrations in the lab. In contrast, sampling in remote environments requiring crewed ships, e.g., remains limited in spatial and temporal resolution, hindering the characterization of aquatic ecosystems. To address these challenges and leverage the ease of eDNA sample collection, autonomous samplers andin situ biomolecular sensors have emerged, offering a paradigm shift in understanding ecosystem dynamics broadly(McQuillan and Robidart, 2017)(McQuillan and Robidart, 2017; Woods Hole Oceanographic Institution, 2023). These new technologies not only enhance the precision and frequency of data collection but also enable researchers to delve deeper into the molecular mechanisms governing aquatic life in remote locations.A critical but often overlooked consideration in the development of these technologies is the alignment between the diversity of end-user needs and the diversity of sampling systems. No single technology can meet the demands of all applications, and design choices often reflect trade-offs between performance, usability, and cost. For instance, real-time detection capabilities are particularly valuable for event-based sampling, such as during harmful algal blooms or pathogen outbreaks, whereas they are less critical for long-term biodiversity surveys. High-capacity, autonomous sampling systems are better suited for extended deployments or high-frequency data collection, but may be excessive for short-term missions such as ROV-based exploration. Likewise, affordability is a key driver for community science and resource-limited monitoring programs, while fit-for-purpose tools may be prioritized by structured research initiatives, including long-term ecosystem observatories or oceanographic expeditions. Recognizing this diversity of applications, sampling environments and technology helps clarify why no single approach is universally optimal, and highlights the importance of a flexible and interoperable instrumentation landscape.This review summarizes information shared during the Marine ‘Omics Technology and Instrumentation Workshop which was held October 10-12, 2023, supplemented with a subsequent literature review to synthesize the state of autonomous eDNA sampling technology and instrumentation. We explore the latest advancements in autonomous sampling instrumentation, including their design and capabilities, but limit this review to automated samplers, without consideration of the parallel expansion of passive eDNA sampling technologies (Bessey et al., 2021). Additionally, we discuss the integration of these sampling devices with various platforms, advanced in situ analytical capabilities, environmental sensors, and imaging technologies, that collectively enhance the effectiveness and utility of the sampling systems. Finally, we examine current challenges and opportunities associated with autonomous eDNA sampling, including applications, validation, and standardization, all of which are required for a coordinated and larger scale adoption of eDNA (Agersnap et al., 2022; Kelly et al., 2024).