Cawthron Institute

The application of environmental DNA (eDNA) and RNA (eRNA) technologies to aquatic ecosystem monitoring and management has increased rapidly in the last decade. These methods are providing many new and exciting opportunities for enhanced biodiversity assessment, ecological health evaluation, and species detection. This special issue of PeerJ Life and Environment brings together 20 innovative studies that collectively advance the eDNA toolkit. Four key themes are covered: (i) Methodological advancements, (ii) Ecological health assessments and biomonitoring, (iii) Species detection, and (iv) Application and management. The studies cover a suite of topics including; optimizing sample collection, developing species-specific assays, evaluating bioindicator species, assessing microbial activity, and biodiversity monitoring in diverse freshwater and marine habitats. Emerging applications, such as the use of genome skimming to identify new fish markers, showcase the many new advancements in this field. The studies in this issue also highlight challenges, including the need for standardized protocols and ethical considerations that must be addressed before these tools can be implemented or adopted for decision making at national or global scales. Together, these contributions demonstrate the transformative potential of environmental nucleic acids’ technologies for advancing aquatic conservation and management. By bridging methodological rigor with applied research, the studies in this special issue provide an important resource for researchers, policymakers, and practitioners committed to sustainable aquatic ecosystem stewardship.

Relational values feature prominently in recent international efforts to protect global biodiversity. In this article, we provide a conceptual approach for researchers, facilitators and policy‐makers to adequately represent place‐based relational values in assessments of nature's value that inform practice and policy. We suggest employing horizontal portability as an alternative and complement to the dominant mode of assessing nature's value via vertical subsumption. Vertical subsumption is a process through which particular values are generalised into overarching categories to conform to more general value concepts and thereby stripped of their place‐specific meanings. In contrast, horizontal portability is introduced here as a conceptual approach that maintains the contextual rootedness of place‐based local expressions of value while also communicating them across places, knowledge systems, and communities. The movement (i.e. ‘porting’) is ‘horizontal’ because it allows relational values rooted in a particular biocultural context to speak to different contexts on equal terms. We discuss how research on the value of nature and people –nature relationships can support horizontal portability. Finally, we provide recommendations for the application of horizontal portability that promotes more plurality and greater inclusion of place‐based relational values in research, policy and action. Read the free Plain Language Summary for this article on the Journal blog.

Digital PCR (dPCR) has increasingly been used as a primary measurement method for the characterization of nucleic acid reference materials. Nucleic acid reference materials are particularly useful when used for the validation and calibration of quantitative PCR (qPCR). In this study, we describe the development and characterization of Cyanobacteria DNA reference materials (RM) using dPCR. An international interlaboratory study involving 14 laboratories was conducted using the Cyanobacteria DNA RM in combination with a lyophilized PCR reagent designed for the monitoring of Cyanobacteria bloom events. Of the 55 scored study results obtained using qPCR-based techniques, 62% were within the 8% relative expanded uncertainty based on dPCR measurements, while 100% of the study results returned satisfactory z scores calculated using a set performance coefficient of variation equivalent to one Ct value. The study participants' results indicate that the cyanobacteria DNA RM is fit for the purpose of method validation and quality control of the qPCR format used for monitoring toxic cyanobacteria algae bloom events. Most importantly, the study results demonstrated that the use of standardized reagents combined with highly characterized nucleic acid RMs allows qPCR-based DNA quantification technology to reach levels of accuracy and reproducibility comparable to those achieved with digital PCR technology.

Science shows mounting global health risks associated with plastics life cycle pollution. Leveraging evidence and streamlining research to inform policy is critical to safeguarding people and planet. We conducted an electronic survey questionnaire, between 16th April and 16th August 2024, amongst United Nations government delegates developing the Global Plastics Treaty. We explored (1) perceptions and prioritisation of human health evidence, (2) preferred plastic pollution mitigation strategies, and (3) priorities for health research. Responses were collected in Qualtrics and analysed using summary statistics, the Fisher’s Exact Test, and thematically mapped to the Policy Cycle Framework. We received 27 survey responses, balanced by gender and career stage, including 23 countries and all World Bank country income classifications and regions, but greater representation from high-income and European countries. Human health was the highest-ranking concern related to plastics risks (Sum of rank scores (SRS) = 54). Most delegates expressed strong conviction in evidence of risks associated with plastics chemicals, polymers, products, microplastics and broader life cycle emissions. Reducing plastics production (SRS = 53) and eliminating chemicals, polymers and products of concern (SRS = 53) were prioritised, even amongst those affiliated with waste management departments or less convinced of health risks. We found the least regard for recycling as a strategy to protect health (SRS = 4–5) and eliminating open burning was the most prioritised downstream measure (SRS = 15). Generating quantitative, causal data on risks across plastics life cycles, identifying emerging health hazards, defining criteria, safe lists and substitutes for chemicals, polymers and products were government delegate priorities for research, alongside tools to track policy impacts on health and greater bilateral communication between scientists and delegations. Health risks of all forms of plastic pollution were a concern for most delegates responding to our survey. We identified key priorities for policy-driven research to strengthen the science-policy interface and support evidence-based plastics policy that protects human health.

Passive environmental DNA (eDNA) samplers offer a cost-effective and scalable approach to marine biodiversity monitoring, potentially aiding detections of non-indigenous species. This study explored the efficiency of passive eDNA samplers to detect a variety of globally problematic marine invasive species in field conditions: Sabella spallanzanii , Styela clava , Bugula neritina and Undaria pinnatifida . Four passive sampler substrates, nylon filters, positively charged nylon discs, nylon mesh, and artificial sponges, were tested across six submergence times, ranging from 10 to 720 min, against standard filtration-based approaches. Our results demonstrated that passive samplers could achieve comparable or even higher eDNA yields than traditional active filtration methods, indicating their potential for biosecurity surveillance. Species-specific droplet-digital PCR (ddPCR) assays provided sensitive and quantifiable eDNA signals, though assay validation remains crucial to avoid false negatives. Significant variation in eDNA signal detection highlighted the importance of considering both material selection and submersion time, depending on the targeted organisms. Furthermore, 18S rRNA metabarcoding was undertaken to assess how the overall detected biodiversity might interfere with species-specific detections. Certain sessile organisms, such as ascidians and polychaetes, dominated early representation on the passive filters but did not interfere with species-specific detection. By optimizing material selection, submersion time, and assay validation, passive eDNA sampling can enhance the sensitivity and reliability of eDNA-based monitoring, contributing to improved marine biosecurity and conservation efforts.

Bioactive venoms and toxins are emerging as a promising source of drug leads. Optimized through evolution, these compounds display remarkable selectivity and ligand affinity toward a range of relevant pharmacological targets. The successful development of new drugs from toxins is hampered in some areas by the chemical complexity of the active compounds, which limits the possibility of using chemical synthesis or recombinant strategies for drug lead generation. Marine paralytic shellfish toxins produced by marine microalgae is one such family of compounds. These compounds are highly potent blockers of voltage-gated ion channels, involved in regulating a range of physiological processes and thus versatile targets for drug development. To overcome the supply issue, the current paper describes the development of a scalable production method to generate gram amounts of gonyautoxin-1,4 by mass cultivation of the dinoflagellate Alexandrium pacificum in artificial seawater. By selecting a high-producing strain and running a series of growth optimization experiments, we have scaled up production from 100 mL to 1150 L, with cellular yields of toxin 30 times higher than in a natural bloom. This allows commercial production of gram amounts of these promising compounds, thereby enabling their use in a range of applications beyond the analytical scale.

The bacterial skin disease tenacibaculosis, caused by Tenacibaculum species, affects numerous economically important marine fish, including salmonids. This study reports the ability of three Tenacibaculum maritimum strains, belonging to different molecular O‐AGC types, and a single Tenacibaculum dicentrarchi strain to induce tenacibaculosis in farmed Chinook salmon ( Oncorhynchus tshawytscha , Walbaum 1792) in Aotearoa New Zealand. Naïve Chinook salmon were exposed to T. maritimum (2 × 10 ⁸ cells/mL) and T. dicentrarchi (2 × 10 ⁷ cells/mL) by immersion using natural seawater. Clinical signs of tenacibaculosis were apparent in all T. maritimum strains used in the challenged fish. Of these, 100% of the fish challenged with O‐AGC Type 2‐1 and Type 3‐2 strains became moribund, whereas only 60% of the O‐AGC Type 3‐0 challenged fish became moribund. Fish exposed to T. dicentrarchi showed more severe symptoms, exposing musculature in 51% of the challenged population, with 28% of fish becoming moribund. Gross pathological signs of fin rot, scale loss, skin ulcers and haemorrhagic skin spots were observed for both Tenacibaculum species and were consistent with those observed on farmed fish. Pure T. maritimum and T. dicentrarchi cultures were reisolated from epidermal damage of challenged fish. Tenacibaculum species was not isolated from the anterior kidney of affected fish, which indicates no systemic infection in Chinook salmon.

The aquaculture industry can be impacted by mortality events triggered by marine heatwaves, pathogens, and other environmental factors. Aquaculture managers would benefit from advanced warning of mortality events so they can make decisions to maximise production and profitability. To help monitor fish health and performance, finfish farms are often equipped with an array of cameras and environmental sensors. However, analysing and interpreting all this information can be difficult. Decision support systems (DSSs) can help by simplifying multiple data sources into a single output for quick interpretation and action. Here, we present a DSS capable of providing salmon farmers with 4 wk warning of an impending mortality event. This DSS was trained on a suite of data routinely collected by New Zealand salmon farmers and provides an alert if weekly mortality is predicted to exceed 0.5%. In the final model, present mortality, water temperature, and standardised feeding rate were all found to be significantly correlated with the probability of a future mortality event. The model performed well when tested on data not included in the model-building process, suggesting that the DSS could be useful to farm managers. This study shows that even limited information can be used to construct a DSS capable of providing some advanced warning of elevated mortality risk. Given the ease with which DSSs can be adapted to ingest and predict other parameters, we see strong potential for future development and adoption of these tools by the aquaculture industry and other sectors.

Understanding biodiversity is crucial for protecting unique environments, but acquiring this knowledge is challenging in isolated areas due to limited availability of easy-to-implement biomonitoring tools. To determine optimal sampling strategies in remote regions, environmental DNA and RNA (eDNA and eRNA) sampling workflows were evaluated at 12 sites in three fiords within Fiordland National Park, Aotearoa-New Zealand. For f iltration comparison, a modified cruising speed net was used to concentrate eDNA/eRNA onto 20 μ m nylon f ilters, while water from the net’s cod-end was filtered through a 5 μ m Smith-Root self-preserving filter using the eDNA Citizen Scientist Sampler. To compare preservation methods, Smith-Root filters were cut in half, with one half preserved in the self-preserving unit and the other in DNA/RNA Shield™ buffer. Biodiversity screening was performed by sequencing the 18S rRNA gene for eukaryotes and two mitochondrial 16S rRNA genes for fish and marine vertebrates. Comparable amplicon sequence variant (ASVs) richness was observed between methods, yet samples preserved with buffer showed higher richness of fish and marine vertebrate taxa and higher PCR amplification success. There was little variation in community composition, except for 16S rRNA targeting fish, where distinct patterns emerged based on preservation methods. Overall, sampling workflows showed similar community composition and alpha diversity across both nucleic acids. These results confirm that enhancing eDNA/eRNA yields for sparse taxa requires consideration of collection and preservation methods. However, abundant taxa biodiversity is captured consistently, allowing for adjustments without compromising robustness. These insights support streamlined eDNA/eRNA sampling, emphasizing adaptive strategies based on targeted taxa.

Comparative genomic studies of closely related taxa are important for our understanding of the causes of divergence on a changing Earth. This being said, the genomic resources available for marine intertidal molluscs are limited and currently, there are few publicly available high‐quality annotated genomes for intertidal species and for molluscs in general. Here we report transcriptome assemblies for six species of Patellogastropoda and genome assemblies and annotations for three of these species ( Scurria scurra , Scurria viridula and Scurria zebrina ). Comparative analysis using these genomic resources suggest that and recently diverging lineages (10–20 Mya) have experienced similar amounts of contractions and expansions but across different gene families. Furthermore, differences among recently diverged species are reflected in variation in the amount of coding and noncoding material in genomes, such as amount of repetitive elements and lengths of transcripts and introns and exons. Additionally, functional ontologies of species‐specific and duplicated genes together with demographic inference support the finding that recent divergence among members of the genus Scurria aligns with their unique ecological characteristics. Overall, the resources presented here will be valuable for future studies of adaptation in molluscs and in intertidal habitats as a whole.

Intracellular, free‐floating and biofilm‐forming bacterial pathogens have been implicated in summer mortality of farmed Chinook salmon, Oncorhynchus tshawytscha , in New Zealand. A mortality event in 2022 in the Pelorus Sound, Marlborough, was linked to high water temperatures (> 18°C), and bacterial skin disease associated with Piscirickettsia spp. (= Rickettsia ‐like organisms) and Tenacibaculum species. To understand the progression of infection and potential drivers of the mortality, simulation of the event was conducted using a networked susceptible, infectious and recovered (SIR) model. Parameter exploration shows that reconstruction of observed mortality rates across three affected farm sites was possible. The best SIR simulations identified plausible values for key drivers of disease, which are consistent with previously estimated disease parameter ranges for Piscirickettsia salmonis . Our modelling shows the 2022 Pelorus Sound event likely experienced spread of bacterial pathogens within healthy fish populations at salmon farm sites over a 10‐week long incubation period, before elevated mortality was observed. We show evidence that vaccine use at one site likely prevented 10% higher mortality and that an alternative site for the vaccination could have further reduced mortalities. This result highlights the importance of future vaccine developments in aquaculture and the potential to improve vaccine efficacy through considered site selection.

Ciguatera poisoning (CP) is caused by the consumption of marine products contaminated with ciguatoxins (CTXs) produced by dinoflagellates of the genus Gambierdiscus. Analytical methods for CTXs, involving the extraction/purification of trace quantities of CTXs from complex matrices, are numerous in the literature. However, little information on their effectiveness for nonpolar CTXs is available, yet these congeners, contributing to the risk of CP, are required for the establishment of effective food safety monitoring programs. An evaluation of six extraction/purification protocols, performed with CTX3C spiked on fish flesh and a neuroblastoma cell-based assay (CBA-N2a), revealed recoveries from 6 to 45%. This led to the development of an optimized 3-day protocol designed for a large number of samples, with CTX1B and CTX3C eluting in a single fraction and showing recoveries of 73% and 70%, respectively. In addition, a reduction in adverse matrix effects in the CBA-N2a analyses was demonstrated with naturally contaminated specimens, increasing the sensitivity of the method, which now meets the very low guidance level recommended by international agencies. However, efforts are still required to reduce the signal suppression observed in LC-MS/MS analysis. This optimized protocol contributes to the technological advancement of detection methods, promoting food safety and improving CP risk assessment in marine products.

Photosynthetic eukaryotic microalgae are key primary producers in the Antarctic sea ice environment. Anticipated changes in sea ice thickness and snow load due to climate change may cause substantial shifts in available light to these ice-associated organisms. This study used a laboratory-based experiment to investigate how light levels, simulating different sea ice and snow thicknesses, affect fatty acid (FA) composition in two ice associated microalgae species, the pennate diatom Nitzschia cf. biundulata and the dinoflagellate Polarella glacialis. FA profiling and transcriptomic analyses were used to compare the impact of three light levels: High (baseline culturing conditions 90 ± 1 μmol photons m⁻² s⁻¹), mid (10 ± 1 μmol photons m⁻² s⁻¹); and low (1.5 ± 1 μmol photons m⁻² s⁻¹) on each isolate. Both microalgal isolates had altered growth rates and shifts in FA composition under different light conditions. Nitzschia cf. biundulata exhibited significant changes in specific saturated and monounsaturated FAs, with a notable increase in energy storage-related FAs under conditions emulating thinner ice or reduced snow cover. Polarella glacialis significantly increased production of polyunsaturated FAs (PUFAs) in mid light conditions, particularly octadecapentaenoic acid (C18:5N-3), indicating enhanced membrane fluidity and synthesis of longer-chain PUFAs. Notably, C18:5N-3 has been identified as an ichthyotoxic molecule, with fish mortalities associated with other high producing marine taxa. High light levels caused down regulation of photosynthetic genes in N. cf. biundulata isolates and up-regulation in P. glacialis isolates. This and the FA composition changes show the variability of acclimation strategies for different taxonomic groups, providing insights into the responses of microalgae to light stress. This variability could impact polar food webs under climate change, particularly through changes in macronutrient availability to higher trophic levels due to species specific acclimation responses. Further research on the broader microalgal community is needed to clarify the extent of these effects.