Detecting marine pests using environmental DNA and biophysical models

Advective Transport Drives Environmental DNA Dispersal in an Estuary

Environmental DNA (eDNA) is increasingly used for species detection and biodiversity monitoring in estuary and marine environments. The dynamic nature of these environments affects eDNA distribution relative to its source organisms, complicating the interpretation of eDNA observations and challenging the field sampling design. Here, an eDNA fate and transport model, built on an ocean model with Lagrangian particle tracking, provided a spatiotemporal estimate of the rapidly diluted eDNA shed by rare targets in an estuary environment before sampling. Based on the predicted particle densities, over 70% of the preselected stations detected the target eDNA. Despite potential variations in source strength and patchy distributions, the model explained approximately 40% of the observed variation in eDNA abundance; by comparison, eDNA concentration was uncorrelated with straight-line distance from the source or with a simplified oceanographic model. Our study revealed the extent of advective transport in shaping eDNA distribution and abundance and demonstrated the utility of ocean models and particle tracking in integrating marine eDNA observations with degradation, transport, and dilution processes; thus, it suggests broader applications to enhance understanding of eDNA signals and dispersal and optimize sampling strategies in other estuarine or marine environments.

Navigating uncertainty in environmental DNA detection of a nuisance marine macroalga

Early detection of nuisance species is crucial for managing threatened ecosystems and preventing widespread establishment. Environmental DNA (eDNA) data can increase the sensitivity of biomonitoring programs, often at minimal cost and effort. However, eDNA analyses are prone to errors that can complicate their use in management frameworks. To address this, eDNA studies must consider imperfect detections and estimate error rates. Detecting nuisance species at low abundances with minimal uncertainty is vital for successful containment and eradication. We developed a novel eDNA assay to detect a nuisance marine macroalga across its colonization front using surface seawater samples from Papahānaumokuākea Marine National Monument (PMNM), one of the world's largest marine reserves. Chondria tumulosa is a cryptogenic red alga with invasive traits, forming dense mats that overgrow coral reefs and smother native flora and fauna in PMNM. We verified the eDNA assay using site-occupancy detection modeling from quantitative polymerase chain reaction (qPCR) data, calibrated with visual estimates of benthic cover of C. tumulosa that ranged from < 1% to 95%. Results were subsequently validated with high-throughput sequencing of amplified eDNA and negative control samples. Overall, the probability of detecting C. tumulosa at occupied sites was at least 92% when multiple qPCR replicates were positive. False-positive rates were 3% or less and false-negative errors were 11% or less. The assay proved effective for routine monitoring at shallow sites (less than 10 m), even when C. tumulosa abundance was below 1%. Successful implementation of eDNA tools in conservation decision-making requires balancing uncertainties in both visual and molecular detection methods. Our results and modeling demonstrated the assay's high sensitivity to C. tumulosa, and we outline steps to infer ecological presence-absence from molecular data. This reliable, cost-effective tool enhances the detection of low-abundance species, and supports timely management interventions.

Genetic Evidence of Killer Whale Predation on White Sharks in Australia

Killer whales (Orcinus orca) have been documented to prey on white sharks (Carcharodon carcharias), in some cases causing localised shark displacement and triggering ecological cascades. Notably, a series of such predation events have been reported from South Africa over the last decade, with killer whales specifically targeting sharks' liver. However, observations of these interactions are rare, and knowledge of their frequency across the world's oceans remains limited. In October 2023, a 4.7 m (total length) white shark carcass washed ashore in southeastern Australia, coinciding with reports from citizen scientists of killer whales hunting a large, unidentified prey item in the area. Visual inspection of the carcass revealed that the liver, digestive, and reproductive organs were missing, and the presence of four distinctive bite wounds, one of which was characteristic of killer whale liver extraction as seen in South Africa. Genomic analyses performed on swabs taken from the bite wounds confirmed the presence of killer whale DNA in the major bite area, while the other bites were embedded with genetic material from the scavenging broadnose sevengill shark (Notorynchus cepedianus). These results provide confirmed evidence of killer whale predation on white sharks in Australia and the likely selective consumption of the liver, suggesting predations of this nature are more globally prevalent than currently assumed.

Environmental DNA reveals the spatiotemporal distribution and migration characteristics of the Yangtze finless porpoise, the sole aquatic mammal in the Yangtze River

The Yangtze Finless Porpoise (YFP) is one of the 13 global flagship species identified by the World Wildlife Fund and is classified as "Critically Endangered." It is also the only extant aquatic mammal in the Yangtze River. In this study, 44 sampling points were deployed across the middle and lower reaches of the Yangtze River, with vertical sampling sections established in four key areas. Using environmental DNA (eDNA) and species distribution model(SDM), we explored the spatiotemporal distribution of YFPs and predicted their potential suitable habitats. The results indicate that the YFP has a relatively wide distribution during the flood season but exhibits clustering behavior during the dry season, showing a patchy distribution and a migratory trend from the midstream to downstream of the main channel. Predictions using the MAXENT model reveal varying trends in suitable habitat under different scenarios. Overall, YFP's potential habitat is expected to expand by 2050, but due to rising temperatures, it will contract by 2070. Elevation (dem, 65.4%), human footprint index (hfp, 8.8%), and isothermality (bio3, 8%) are key factors influencing habitat suitability. These findings demonstrate that eDNA is an effective tool for monitoring large aquatic organisms and provide scientific evidence for the conservation of the YFP.

Priorities for improving predictions of vessel-mediated marine invasions

Nonindigenous marine species are impacting the integrity of marine ecosystems worldwide. The invasion rate is increasing, and vessel traffic, the most significant human-assisted transport pathway for marine organisms, is predicted to double by 2050. The ability to predict the transfer of marine species by international and domestic maritime traffic is needed to develop cost-effective proactive and reactive interventions that minimise introduction, establishment and spread of invasive species. However, despite several decades of research into vessel-mediated species transfers, some important knowledge gaps remain, leading to significant uncertainty in model predictions, often limiting their use in decision making and management planning. In this review, we discuss the sequential ecological process underlying human-assisted biological invasions and adapt it in a marine context. This process includes five successive stages: entrainment, transport, introduction, establishment, and the subsequent spread. We describe the factors that influence an organism's progression through these stages in the context of maritime vessel movements and identify key knowledge gaps that limit our ability to quantify the rate at which organisms successfully pass through these stages. We then highlight research priorities that will address these knowledge gaps and improve our capability to manage biosecurity risks at local, national and international scales. We identified four major data and knowledge gaps: (1) quantitative rates of entrainment of organisms by vessels; (2) the movement patterns of vessel types lacking maritime location devices; (3) quantifying the release (introduction) of organisms as a function of vessel behaviour (e.g. time spent at port); and (4) the influence of a species' life history on establishment success, for a given magnitude of propagule pressure. We discuss these four research priorities and how they can be addressed in collaboration with industry partners and stakeholders to improve our ability to predict and manage vessel-mediated biosecurity risks over the coming decades.

Development and Testing of Species-Specific Primers for Detecting the Presence of the Northern Pacific Sea Star (Asterias amurensis) from Environmental DNA

The starfish Asterias amurensis, a well-known predator of molluscan species in intertidal ecosystems, has caused substantial ecological and economic losses in North China such as offshore Qingdao. Effective monitoring and prevention measures are urged to minimize its negative impacts. Compared with traditional biomonitoring methods, environmental DNA technology has emerged as a powerful and cost-efficient tool for inferring species' presence and abundance. In this study, we developed a pair of species-specific primers (i.e., Ast-F and Ast-R) for the A. amurensis mitochondrial COI gene and tested its utility in amplifying and quantifying the DNA fragments from environmental samples under both laboratory and field conditions. The results of controlled water tank experiments demonstrated that the amount of eDNA released by A. amurensis was positively related to its biomass; after the removal of the starfish, the eDNA degraded significantly in 24 h and remained detectable for 8 days. The number of eDNA copies enriched tended to increase with smaller pore size of filter membrane and larger volume of filtered water. For field tests, we confirmed the validation of our approach in six locations in Qingdao by filtering 1000 ml water per sample with a 0.45-µm pore size filtration. All the amplification products generated a single and bright band via gel electrophoresis, and the quantitative PCR results unveiled significant differences in eDNA copies. This study provided an eDNA-based approach for investigating the distribution and biomass of A. amurensis, which may help to formulate early warning and management strategies in coastal Qingdao and other regions.

Environmental DNA and remote sensing datasets reveal the spatial distribution of aquatic insects in a disturbed subtropical river system

Biodiversity datasets with high spatial resolution are critical prerequisites for river protection and management decision-making. However, traditional morphological biomonitoring is inefficient and only provides several site estimates, and there is an urgent need for new approaches to predict biodiversity on fine spatial scales throughout the entire river systems. Here, we combined the environmental DNA (eDNA) and remote sensing (RS) technologies to develop a novel approach for predicting the spatial distribution of aquatic insects with high spatial resolution in a disturbed subtropical Dongjiang River system of southeast China. First, we screened thirteen RS-based vegetation indices that significantly correlated with the eDNA-inferred richness of aquatic insects. In particular, the green normalized difference vegetation index (GNDVI) and normalized difference red-edge2 (NDRE2) were closely related to eDNA-inferred richness. Second, using the gradient boosting decision tree, our data showed that the spatial pattern of eDNA-inferred richness could achieve a high spatial resolution to 500 m reach and accurate prediction of more than 80%, and the prediction efficiency of the headwater streams (Strahler stream order = 1) was slightly higher than the downstream (Strahler stream order >1). Third, using the random forest algorithm, the spatial distribution of aquatic insects could reach a prediction rate of over 70% for the presence or absence of specific genera. Overall, this study provides a new approach to achieving high spatial resolution prediction of the distribution of aquatic insects, which supports decision-making on river diversity protection under climate changes and human impacts.

Current status and topical issues on the use of eDNA-based targeted detection of rare animal species

Animal detection through DNA present in environmental samples (eDNA) is a valuable tool for detecting rare species, that are difficult to observe and monitor. eDNA-based tools are underpinned by molecular evolutionary principles, key to devising tools to efficiently single out a targeted species from an environmental sample. Here, we present a comprehensive review of the use of eDNA-based methods for the detection of targeted animal species, such as rare, endangered, or invasive species, through the analysis of 549 publications (2008-2022). Aquatic ecosystems have been the most surveyed, in particular, freshwaters (74 %), and to a less extent marine (14 %) and terrestrial systems (10 %). Vertebrates, in particular, fish (38 %), and endangered species, have been the focus of most of these studies, and Cytb and COI are the most employed markers. Among invertebrates, assays have been mainly designed for Mollusca and Crustacea species (21 %), in particular, to target invasive species, and COI the most employed marker. Targeted molecular approaches, in particular qPCR, have been the most adopted (75 %), while eDNA metabarcoding has been rarely used to target single or few species (approx. 6 %). However, less attention has been given in these studies to the effects of environmental factors on the amount of shed DNA, the differential amount of shed DNA among species, or the sensitivity of the markers developed, which may impact the design of the assays, particularly to warrant the required detection level and avoid false negatives and positives. The accuracy of the assays will also depend on the availability of genetic data and vouchered tissue or DNA samples from closely related species to assess both marker and primers' specificity. In addition, eDNA-based assays developed for a particular species may have to be refined for use in a new geographic area taking into account site-specific populations, as well as any intraspecific variation.

Chromosome-level genome assembly of the northern Pacific seastar Asterias amurensis

Asterias amurensis has attracted widespread concern because of its population outbreaks, which has impacted fisheries and aquaculture, as well as disrupting local ecosystems. A high-quality reference genome is necessary to better investigate mechanisms of outbreak and adaptive changes. Combining PacBio HiFi and Hi-C sequencing data, we generated a chromosome-level A. amurensis genome with a size of 491.53 Mb. The contig N50 and scaffold N50 were 8.05 and 23.75 Mb, respectively. The result of BUSCO analysis revealed a completeness score of 98.85%. A total of 16,531 protein-coding genes were predicted in the genome, of which 94.63% were functionally annotated. The high-quality genome assembly resulting from this study will provide a valuable genetic resource for future research on the mechanism of population outbreaks and invasion ecology.

Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of seawater in reef environments

In tropical marine ecosystems, the coral-based diet of benthic-feeding reef fishes provides a window into the composition and health of coral reefs. In this study, for the first time, we compare multi-assay metabarcoding sequences of environmental DNA (eDNA) isolated from seawater and partially digested gut items from an obligate corallivore butterflyfish (Chaetodon lunulatus) resident to coral reef sites in the South China Sea. We specifically tested the proportional and statistical overlap of the different approaches (seawater vs gut content metabarcoding) in characterizing eukaryotic community composition on coral reefs. Based on 18S and ITS2 sequence data, which differed in their taxonomic sensitivity, we found that gut content detections were only partially representative of the eukaryotic communities detected in the seawater based on low levels of taxonomic overlap (3 to 21%) and significant differences between the sampling approaches. Overall, our results indicate that dietary metabarcoding of specialized feeders can be complimentary to, but is no replacement for, more comprehensive environmental DNA assays of reef environments that might include the processing of different substrates (seawater, sediment, plankton) or traditional observational surveys. These molecular assays, in tandem, might be best suited to highly productive but cryptic oceanic environments (kelp forests, seagrass meadows) that contain an abundance of organisms that are often small, epiphytic, symbiotic, or cryptic.

Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution

Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly 'distillation' of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.

Genetic Detection and a Method to Study the Ecology of Deadly Cubozoan Jellyfish

Cubozoan jellyfish pose a risk of envenomation to humans and a threat to many businesses, yet crucial gaps exist in determining threats to stakeholders and understanding their ecology. Environmental DNA (eDNA) provides a cost-effective method for detection that is less labour intensive and provides a higher probability of detection. The objective of this study was to develop, optimise and trial the use of eDNA to detect the Australian box jellyfish, Chironex fleckeri. This species was the focus of this study as it is known to have the strongest venom of any cubozoan; it is responsible for more than 200 recorded deaths in the Indo-Pacific region. Further, its ecology is poorly known. Herein, a specific and sensitive probe-based assay, multiplexed with an endogenous control assay, was developed, and successfully utilised to detect the deadly jellyfish species and differentiate them from closely related taxa. A rapid eDNA decay rate of greater than 99% within 27 h was found with no detectable influence from temperature. The robustness of the technique indicates that it will be of high utility for detection and to address knowledge gaps in the ecology of C. fleckeri; further, it has broad applicability to other types of zooplankton.