The field of environmental DNA (eDNA) analysis has revolutionized our ability to detect and monitor biodiversity in aquatic and terrestrial ecosystems. However, traditional eDNA sampling methods often present limitations in terms of temporal and spatial coverage, resulting in a loss of resolution associated with infrequent events or those prohibitive to onsite fieldwork. In recent years, the emergence of autonomous eDNA sampling technology has provided researchers with a powerful tool for collecting high‐resolution genetic data, overcoming many of the challenges associated with manual sample acquisition. This review focuses exclusively on eDNA technologies designed for the collection and preservation of water samples, to provide a comprehensive overview of the current landscape of aquatic autonomous eDNA sampling technology and instrumentation. A new era of instrument development and capabilities is emerging; the result of knowledge gained through experience with long‐tested marine biological observation instrumentation. Lastly, we highlight current research to develop an in situ eDNA analytical capability, as well as explore the challenges and future prospects associated with this rapidly evolving field.

Advances in microfluidics and the introduction of isothermal nucleic acid amplification assays have resulted in a range of solutions for nucleic acid amplification tests suited for point of care and field use. However, miniaturisation of instrumentation for such assays has not seen such rapid advances and fluorescence based assays still depend on complex, bulky and expensive optics such as fluorescence microscopes, photomultiplier tubes and sensitive lens assemblies. In this work we demonstrate a robust, low cost platform for isothermal nucleic acid amplification on a microfluidic device. Using easily obtainable materials and commercial off-the-shelf components, we show real time fluorescence detection using a low cost photodiode and operational amplifier without need for lenses. Temperature regulation on the device is achieved using a heater fabricated with standard printed circuit board fabrication methods. These facile construction methods allow fabrications at a cost compatible with widespread deployment to resource poor settings.

Antimicrobial resistance (AMR) is threatening modern medicine. While the primary cost of AMR is paid in the healthcare domain, the agricultural and environmental domains are also reservoirs of resistant microorganisms and hence perpetual sources of AMR infections in humans. Consequently, the World Health Organisation and other international agencies are calling for surveillance of AMR in all three domains to guide intervention and risk reduction strategies. Technologies for detecting AMR that have been developed for healthcare settings are not immediately transferable to environmental and agricultural settings, and limited dialogue between the domains has hampered opportunities for cross-fertilisation to develop modified or new technologies. In this feature, we discuss the limitations of currently available AMR sensing technologies used in the clinic for sensing in other environments, and what is required to overcome these limitations.

Amoebic gill disease (AGD), caused by Neoparamoeba perurans , is a challenge for Atlantic salmon aquaculture. Research has, therefore, focused on detecting/monitoring N. perurans loads within/around fish pens. Recently, molecular methods to detect N. perurans have been used to reduce labour‐intensive sampling, inconsistency, and stress on stock while complementing gill scoring and histology methods for AGD assessment. Molecular detection depends on reliable and cost‐effective sample collection. Recent studies have demonstrated the potential for utilising naturally occurring filter‐feeding animals as a mechanism for collecting DNA from the environment (i.e., ‘natural samplers’) for use in downstream molecular assays. This opens the possibility of sampling with minimal training or expertise, offering the potential to easily integrate this sampling within normal farm operations. We evaluated, through aquarium‐based experiments, the utility of the Pacific oyster ( Magallana gigas ) to collect N. perurans DNA from the water column. In aquaria inoculated with N. perurans , total water column amoeba load decreased significantly over time in the presence of oysters. Despite this decrease, no correlation between the level of amoeba accumulation within oysters and the decrease in the water column was observed. N. perurans was detected in every oyster organ type tested (mantle, gill, palp, and digestive gland), though with high variation. The detection of N. perurans DNA within the digestive gland indicates that oysters ingested amoeba. Oysters were found to be viable environmental DNA (eDNA) samplers for N. perurans , providing a useful collection method.