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.

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.

Identifying antibiotic-resistance genes (ARGs) in marine systems traditionally relies on extensive laboratory-based analysis. Data-driven modelling of ARGs is an emerging and promising approach that could enable real-time water quality monitoring, reducing both field and lab work, and associated costs. This work demonstrates a combination of Squared Prediction Error (SPE), Kernel Principal Component Analysis (KPCA) and Gaussian Processes (GP) for marine monitoring. The work advances real-time decision-making for both when to sample and data-efficient modelling by identifying when environmental conditions are likely to be novel. This was quantified by the SPE-KPCA model as a difference between current water conditions and those previously sampled. By identifying already-sampled environmental conditions, the number of water samples that were collected was reduced. The modelling of the level of ARGs is based on the GP predictive model. The method adaptively updated SPE-KPCA and GP models as new data were collected. The proposed framework was validated on both synthetic and real-life data. The validation demonstrated that the GP model, using a subset of the data sequentially selected by the SPE-KPCA model, led to similar prediction accuracy to the case of using all data, showing the potential for reducing the costs of data acquisition in this problem.

Environmental DNA (eDNA) is increasingly used to monitor biodiversity, biosecurity and invasive species, providing insights into species presence across ecosystems. As eDNA datasets grow, interoperability and accessibility are crucial. OBIS Australia (OBIS-AU), Australia’s node of the United Nations Educational, Scientific and Cultural Organization (UNESCO) International Oceanographic Data and Information Exchange (IODE) Ocean Biodiversity Information System (OBIS), hosted by the Commonwealth Scientific and Industrial Research Organisation (CSIRO) National Collections and Marine Infrastructure (NCMI), promotes use of the DNA Derived Data Extension in Darwin Core (DwC) to standardise publication of eDNA and metabarcoding data Wieczorek et al. (2012), Abarenkov et al. (2023). OBIS-AU has published over 26 datasets with 21 million eDNA records to the OBIS. OBIS-AU is developing a scalable and interoperable eDNA data publishing pipeline that integrates tools such as the Findable, Accessible, Interoperable, Reusable eDNA (FAIRe) suite and the Global Biodiversity Information Facility (GBIF) Metabarcoding Data Toolkit (MDT) to transform diverse eDNA source data into Darwin Core Archives (DwC-A) for publication to OBIS, GBIF, and Atlas of Living Australia (ALA). By leveraging metadata standards including DwC, DNA Derived Data Extension, Minimum Information about any (X) Sequence (MIxS) and the FAIRe metadata checklist, the pipeline enables standardised, FAIR-compliant data publishing Takahashi et al. (2025), Meyer et al. (2023). It supports multiple transformation pathways, ensuring that eDNA datasets are consistent, reusable, and aligned with global biodiversity data infrastructures. The FAIR eDNA initiative enhances the FAIRness of eDNA data by extending standards like DwC and MIxS with eDNA-tailored metadata terms Takahashi et al. (2025). The FAIRe tools (FAIRe-ator, FAIRe-fier, and FAIRe2MDT) facilitate creation, validation, and conversion of standardised metadata to improve interoperability and reusability across platforms. The Metabarcoding Data Toolkit (MDT) is an open-source web tool that streamlines publishing of eDNA metabarcoding data by converting common data structures [e.g., Operational Taxonomic Unit (OTU) tables, taxonomy, metadata, Format for All Sequences from All Species (FASTA) files] into DwC-A GBIF Secretariat (2024). This modular design allows the pipeline to accommodate diverse data types and processing workflows while ensuring compatibility with global biodiversity data standards. The pipeline as shown in Fig. 1 provides four main pathways for converting source data into DwC-A and publishing them via the Integrated Publishing Toolkit (IPT): Directly publishing data already formatted as DwC-A; Transforming source data using a simple DwC pipeline with custom DwC transformation script; Generating DwC-A file from source data via the MDT tool; and Using FAIRe tools and converting it to DwC-A via the MDT tool or a custom transformation script. Directly publishing data already formatted as DwC-A; Transforming source data using a simple DwC pipeline with custom DwC transformation script; Generating DwC-A file from source data via the MDT tool; and Using FAIRe tools and converting it to DwC-A via the MDT tool or a custom transformation script. The Australian Microbiome (AM) Initiative is a national collaborative research program characterising microbial diversity across Australia’s terrestrial, freshwater, coastal, and marine environments. The AM data pipeline depicted in Fig. 2 transforms data stored in the AM Data Portal using the MDT tool to generate DwC-A for publication to global repositories. The Globalising Marine Biodiversity Observations (GLOMBO) Partnership is a collaboration between CSIRO and the Minderoo Foundation aimed at improving the large-scale monitoring of Australia’s vast marine ecosystems by deploying automated eDNA sampling systems to gather samples continuously during voyages, with the first installation taking place on CSIRO’s research vessel Investigator . This approach will be expanded through a network of “ships of opportunity,” encompassing research, commercial, and tourist vessels that contribute to a nationwide eDNA monitoring effort. The scalable data pipeline is proposed to automate, integrate, and disseminate eDNA datasets, enabling comprehensive, real-time insights into marine biodiversity across Australia’s oceans as illustrated in Fig. 3. Recording eDNA-derived species occurrences presents several challenges. One example is taxonomic ambiguity, often caused by incomplete reference databases like GenBank, World Register of Marine Species (WoRMS), Barcode of Life Data (BOLD), or SILVA. Linking eDNA sequence reads to biodiversity occurrence records is complex and requires expert knowledge and infrastructure integrating sequence data, metadata, and taxonomy. Technical barriers, limited engagement, and lack of incentives to make data accessible, hinder open access to eDNA data. OBIS-AU is addressing these challenges by exploring tools like GBIF’s MDT, OBIS’s Pacific Islands Marine bioinvasions Alert Network (PacMAN) pipeline, FAIRe tools, and AI-based tools as well as expert support and developing new automation pipelines to assist data publishers. OBIS-AU has published eDNA data using DwC Occurrence Core and DNA Derived Data Extension and is now testing a publication model with the DwC Event Core to better capture sampling context and improve integration, interoperability, and reuse of complex eDNA datasets. OBIS-AU intends to align with the new DwC Data Package to support modular publishing of marine biodiversity data.

Automated, remotely deployable in situ molecular systems have the potential to significantly improve phytoplankton research and monitoring. Being automated and remotely deployable, they can cut observation costs and drastically improve spatial and temporal resolution of observations. Using molecular methods, they can provide high taxonomic resolution and potentially target genes related to toxin production. In this chapter, we summarize the current state of the art of the main components (sampling, sample preparation, and detection) of such systems, focusing on technologies at reasonable technology readiness. The environmental sample processor has been applied through a range of projects to study phytoplankton ecology and dynamics, illustrating the potential of the approach.

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.

A point of care device utilising Lab-on-a-Chip technologies that is applicable for biological pathogens was designed, fabricated and tested showing sample in to answer out capabilities. The purpose of the design was to develop a cartridge with the capability to perform nucleic acid extraction and purification from a sample using a chitosan membrane at an acidic pH. Waste was stored within the cartridge with the use of sodium polyacrylate to solidify or gelate the sample in a single chamber. Nucleic acid elution was conducted using the RPA amplification reagents (alkaline pH). Passive valves were used to regulate the fluid flow and a multiplexer was designed to distribute the fluid into six microchambers for amplification reactions. Cartridges were produced using soft lithography of silicone from 3D printed moulds, bonded to glass substrates. The isothermal technique, RPA is employed for amplification. This paper shows the results from two separate experiments: the first using the RPA control nucleic acid, the second showing successful amplification from Chlamydia Trachomatis. Endpoint analysis conducted for the RPA analysis was gel electrophoresis that showed 143 base pair DNA was amplified successfully for positive samples whilst negative samples did not show amplification. End point analysis for Chlamydia Trachomatis samples was fluorescence detection that showed successful detection of 1 copy/μL and 10 copies/μL spiked in a MES buffer.

Algae are considered to be a good source of alternative renewable energy for biofuel as up to 60% of the world is covered in water and contains algae, chlorophyll and plankton, where each of these absorbs light and fixes carbon dioxide through photosynthesis [1]. Wavelength of the light source plays an important role in the algal growth. In this study, the experimental arrangement implemented to study the effects of using blue lasers as coherent light sources on the growth of Algae is explained in comparison to that of the white light LED irradiation. Three individual lasers having the following wavelengths (405 nm, 450 nm and 473 nm) were employed to generate photons with emission spectra matching the pigments' absorption spectra of Chlamydomonas reinhardtii algae; this was with a view to improving transportation of electrons within photosystems II and I, thus expecting an increase in cell division rate. C. reinhardtii algae effectively grew under exposure to both the blue lasers and that of the white light LED when each was applied individually. The best laboratory results were obtained by using the 473 nm blue laser as it increased the rate of cell division by twice that of the white light LED; this was followed by the 405 nm laser with 1.8 times enhancement. For the wavelength 450 nm, the white light LED performed better (1.5 times that of the 450 nm laser). In comparison to the open pond under natural daylight cycles, the 405 nm, 450 nm and 473 nm lasers showed enhancement of 3.9, 1.5 and 4.3 times respectively. The pH was maintained between 7.0 and 7.7, with temperatures maintained between 19.00 and 25.00 °C.

Sustained observations of microbial dynamics are rare, especially in southern hemisphere waters. The Australian Marine Microbial Biodiversity Initiative (AMMBI) provides methodologically standardized, continental scale, temporal phylogenetic amplicon sequencing data describing Bacteria , Archaea and microbial Eukarya assemblages. Sequence data is linked to extensive physical, biological and chemical oceanographic contextual information. Samples are collected monthly to seasonally from multiple depths at seven sites: Darwin Harbour (Northern Territory), Yongala (Queensland), North Stradbroke Island (Queensland), Port Hacking (New South Wales), Maria Island (Tasmania), Kangaroo Island (South Australia), Rottnest Island (Western Australia). These sites span ~30 ° of latitude and ~38 ° longitude, range from tropical to cold temperate zones, and are influenced by both local and globally significant oceanographic and climatic features. All sequence datasets are provided in both raw and processed fashion. Currently 952 samples are publically available for bacteria and archaea which include 88,951,761 bacterial (72,435 unique) and 70,463,079 archaeal (24,205 unique) 16 S rRNA v1-3 gene sequences, and 388 samples are available for eukaryotes which include 39,801,050 (78,463 unique) 18 S rRNA v4 gene sequences.

This paper presents the design of a modular point of care test platform that integrates a proprietary sample collection device directly with a microfluidic cartridge. Cell lysis, within the cartridge, is conducted using a chemical method and nucleic acid purification is done on an activated cellulose membrane. The microfluidic device incorporates passive mixing of the lysis-binding buffers and sample using a serpentine channel. Results have shown extraction efficiencies for this new membrane of 69% and 57% compared to the commercial Qiagen extraction method of 85% and 59.4% for 0.1ng/µL and 100ng/µL salmon sperm DNA respectively spiked in phosphate buffered solution. Extraction experiments using the serpentine passive mixer cartridges incorporating lysis and nucleic acid purification showed extraction efficiency around 80% of the commercial Qiagen kit. Isothermal amplification was conducted using thermophillic helicase dependant amplification and recombinase polymerase amplification. A low cost benchtop real-time isothermal amplification platform has been developed capable of running six amplifications simultaneously. Results show that the platform is capable of detecting 1.32×10(6) of sample DNA through thermophillic helicase dependant amplification and 1×10(5) copy numbers Chlamydia trachomatis genomic DNA within 10min through recombinase polymerase nucleic acid amplification tests.

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.

Background/introduction Brunel DoCLab is part of the eSTI2 Consortium which is developing electronic self-testing and portable instruments for sexually transmitted infections using nucleic acid amplification test technologies. We have designed a point of care test platform that integrates a proprietary sample collection device directly with a microfluidic cartridge. A low cost benchtop real-time isothermal amplification platform has been developed capable of running six amplifications simultaneously. Aim(s)/objectives To evaluate the sample preparation and isothermal amplification within the low cost diagnostic platform. Methods The microfluidic device incorporates passive mixing of the lysis-binding buffers and sample. Cell lysis, within the cartridge, is conducted using a chemical method and nucleic acid purification is done on an activated cellulose membrane. Isothermal amplification was conducted using recombinase polymerase amplification (RPA). Results Preliminary results have shown extraction efficiencies for this new membrane of 69% and 57% compared to the commercial Qiagen extraction method of 85% and 59.4% for 0.1 ng/µL and 100 ng/µL salmon sperm DNA respectively spiked in phosphate buffered solution. Extraction experiments in the passive mixer cartridges with lysis and nucleic acid purification showed extraction efficiency around 80% of the commercial Qiagen kit. The platform is capable of detecting Chlamydia trachomatis genomic DNA within 10 min using RPA for 100,000 copies/µL. Discussion/conclusion The work presented here shows a low cost, rapid nucleic acid extraction, isothermal amplification and detection platform for diagnosing C. trachomatis. Work is on-going to fully integrate the sample-in to result platform for rapid diagnosis of STIs using genital samples.

Introduction Rapid and accurate field diagnostics have potential to impact on the burden of STIs in resource poor settings. Microfluidic and nano technologies offer opportunities to create molecular detection platforms but costs may be prohibitive. We present a low cost isothermal amplification, point of care test for rapid identification of sexually transmitted infections. Sample collection integrates directly with a microfluidic device for automated sample preparation, isothermal amplification and optical detection. Methods Cell lysis, within the microfluidic cartridge, is conducted using a chemical method and nucleic acid purification is achieved on activated cellulose membrane. The microfluidic device incorporates passive mixing of lysis-binding buffers and sample using a serpentine channel. Isothermal amplification is conducted using thermophillic helicase dependent amplification (tHDA) and recombinase polymerase amplification (RPA). A low cost real-time isothermal amplification platform has been developed capable of running six amplifications simultaneously. Results Results have shown extraction efficiencies for the new membrane of 69% and 57% compared to commercial Qiagen extraction of 85% and 59.4% for 0.1 ng/µL and 100 ng/µL salmon sperm DNA respectively spiked in phosphate buffered solution. Extraction experiments using the serpentine passive mixer cartridges incorporating lysis and nucleic acid purification showed extraction efficiency around 80% of the commercial Qiagen kit. The platform is capable of detecting 1.32 × 106 copies of target DNA through thermophillic helicase dependent amplification and 1 × 105 copies of Chlamydia trachomatis genomic DNA within 10 min through RPA. Conclusion We have produced a low cost, rapid nucleic acid extraction, isothermal amplification and detection platform consistent with use remote resource poor settings. The simple optics setup demonstrated high sensitivity and rapid detection of the tHDA and RPA reactions removing the requirement for expensive dichroic filters and lenses. Diagnostic performance of the device is currently being undertaken. Disclosure of interest statement No Disclosure of interest.

A method has been developed using chitosan impregnated on membranes reducing the complexity of nucleic acid extraction. This can be automated in a microfluidic system prior to nucleic acid amplification and detection. The procedure is pH dependent and involves the binding of DNA at pH 5.0 with DNA release at pH 9.0. The results showed extraction efficiencies of 63% and 82% for input samples of 100ng/µL and 0.1ng/µL respectively in comparison to benchtop Qiagen extraction results of 59% and 85%.

This paper presents a holistic methodology for the design of medical device software, which encompasses of a new way of eliciting requirements, system design process, security design guideline, cloud architecture design, combinatorial testing process and agile project management. The paper uses point of care diagnostics as a case study where the software and hardware must be robust, reliable to provide accurate diagnosis of diseases. As software and software intensive systems are becoming increasingly complex, the impact of failures can lead to significant property damage, or damage to the environment. Within the medical diagnostic device software domain such failures can result in misdiagnosis leading to clinical complications and in some cases death. Software faults can arise due to the interaction among the software, the hardware, third party software and the operating environment. Unanticipated environmental changes and latent coding errors lead to operation faults despite of the fact that usually a significant effort has been expended in the design, verification and validation of the software system. It is becoming increasingly more apparent that one needs to adopt different approaches, which will guarantee that a complex software system meets all safety, security, and reliability requirements, in addition to complying with standards such as IEC 62304. There are many initiatives taken to develop safety and security critical systems, at different development phases and in different contexts, ranging from infrastructure design to device design. Different approaches are implemented to design error free software for safety critical systems. By adopting the strategies and processes presented in this paper one can overcome the challenges in developing error free software for medical devices (or safety critical systems).

Nucleic Acid Testing (NAT) promises rapid, sensitive and specific diagnosis of infectious, inherited and genetic disease. The next generation of diagnostic devices will interrogate the genetic determinants of such conditions at the point-of-care, affording clinicians prompt reliable diagnosis from which to guide more effective treatment. The complex biochemical nature of clinical samples, the low abundance of nucleic acid targets in the majority of clinical samples and existing biosensor technology indicate that some form of nucleic acid amplification will be required to obtain clinically relevant sensitivities from the small samples used in point-of-care testing (POCT). This publication provides an overview and thorough review of existing technologies for nucleic acid amplification. The different methods are compared and their suitability for POCT adaptation are discussed. Current commercial products employing isothermal amplification strategies are also investigated. In conclusion we identify the factors impeding the integration of the methods discussed in fully automated, sample-to-answer POCT devices.