Environmental DNA (eDNA) is an emerging tool for wildlife biologists and citizen scientists to build local knowledge about biodiversity and detect invasive species. While single-species eDNA assays are widely used to detect cryptic species, metabarcoding approaches can simultaneously detect a wide range of taxa depending on the chosen genetic target. In a partnership pilot study between Traditional Owners, scientists, and Government, we used a 12S metabarcoding approach to identify the vertebrate prey consumed by predators in the Burragorang Valley on Gundungurra Country (NSW, Australia). Here, we report an incidental but important detection of an invasive fish species, Oriental Weatherloach Misgurnus anguillicaudatus, in multiple Red Fox Vulpes vulpes scats within the high conservation value landscape of the Burragorang Valley (encompassing the WaterNSW Warragamba Special Areas). Our eDNA identification of Oriental Weatherloach was later validated by a physical capture of the species. We reviewed public databases to better understand the distribution of this invasive species in the region and discovered that Oriental Weatherloach had been detected upstream of the Warragamba Special Area on the Wollondilly and Wingecarribee Rivers, expanding its range since the 1990s. However, this was the first detection within the strictly controlled inner conservation zone for Lake Burragorang, Sydney’s drinking water supply. The recent invasion of this exotic fish species was not widely known by Traditional Owners, local community, Government departments or conservation groups and is significant as it is within the Greater Blue Mountains World Heritage Area. Our preliminary study highlights the value of using eDNA metabarcoding on predator scats as a biomonitoring tool for the incidental detection of invasive species and shows that freshwater fish may play a more significant role in the diet of foxes than previously understood.

The only exclusively freshwater lineage of Sirenia, the Amazonian manatee (Trichechus inunguis) is listed by the IUCN as vulnerable, with populations projected to decline further during the coming decades. Given that illegal hunting, pollution, habitat disturbance and other impacts are ongoing, it is imperative to assess the distribution and abundance of this unique, elusive aquatic mammal. In this study, we used environmental DNA (eDNA) methods to test for T. inunguis presence at three locations along the longitudinal gradient of the Amazon River and its tributaries (Tefé, Manaus, Belém). At each location, water samples were collected at sites spanning a disturbance gradient from urban to protected reserves. We developed a field methodology to preserve DNA for up to 13 days or more without requiring freezing or cooling of samples. This method performed similarly to traditional cold-storage methods used for eDNA research. In the lab, DNA was extracted from the samples followed by PCR amplification, and Illumina sequencing. Detection of Amazonian manatee DNA was more than three times greater in the western Amazon (Tefé and Mamirauá Reserve) where human activity is low. Manatee DNA was detected at six sites in the central Amazon (Manaus) and in only two sites in the eastern Amazon near the coast (Belém) where human populations and impacts are greater. eDNA methodology was effective for detecting manatees and is expected to be useful for estimating their broader distribution as well as surveying other aquatic species in tropical rivers.

This study investigated the adult density, timing of migration, and biological characteristics of Pacific herring (Clupea pallasii) entering Jinhae Bay, South Korea, in winter, a major spawning ground for the species. A wideband autonomous transceiver (WBAT) was deployed from November 2022 to March 2023, and standardized gillnet surveys and environmental DNA (eDNA) were conducted concurrently. WBAT monitoring showed that C. pallasii school signals appeared predominantly from mid-January to mid-February, coinciding with the period during which herring were highly dominant in gillnet catches. Assessment of female reproductive maturity indicated that most individuals were ripe or spent, confirming that this period represented the peak spawning season. eDNA concentrations exhibited a sharp peak in mid-January in both surface and bottom waters and then declined steadily thereafter. Taken together, these results indicate that entry into the spawning ground begins in late-December, peaks in mid-to-late January, and declines toward late-February. By integrating acoustic, catch, and eDNA datasets, this study provides a comprehensive assessment of the timing, density, and spawning ecology of C. pallasii, offering evidence-based guidance for future resource management and spawning-ground protection in Jinhae Bay.

This study investigated the adult density, timing of migration, and biological characteristics of Pacific herring (Clupea pallasii) entering Jinhae Bay, South Korea, in winter, a major spawning ground for the species. A wideband autonomous transceiver (WBAT) was deployed from November 2022 to March 2023, and standardized gillnet surveys and environmental DNA (eDNA) were conducted concurrently. WBAT monitoring showed that C. pallasii school signals appeared predominantly from mid-January to mid-February, coinciding with the period during which herring were highly dominant in gillnet catches. Assessment of female reproductive maturity indicated that most individuals were ripe or spent, confirming that this period represented the peak spawning season. eDNA concentrations exhibited a sharp peak in mid-January in both surface and bottom waters and then declined steadily thereafter. Taken together, these results indicate that entry into the spawning ground begins in late-December, peaks in mid-to-late January, and declines toward late-February. By integrating acoustic, catch, and eDNA datasets, this study provides a comprehensive assessment of the timing, density, and spawning ecology of C. pallasii, offering evidence-based guidance for future resource management and spawning-ground protection in Jinhae Bay.

Understanding practical barriers to the global adoption of environmental DNA (eDNA) methods, tools, and standards.

Environmental DNA as a complementary tool for monitoring fish assemblages in coastal lagoons: Insights for conservation.

Characterizing seasonal persistence of low levels of Pseudo-nitzschia australis in the Gulf of Maine with environmental DNA.

Honey as an eDNA Reservoir: Detecting Spiroplasma apis and Spiroplasma melliferum in Australian honey bee populations.

With increasing human domination of ecosystems, wildlife must either relocate or adapt its behaviour to anthropogenic impacts in order to survive. Vervet monkeys (Chlorocebus pygerythrus), whose natural habitats have been progressively encroached upon by urban expansion, have successfully adapted to urbanised environments because of their flexible and generalist feeding behaviour. Characterising diet composition of vervet monkeys can therefore reveal how they exploit anthropogenic resources and uncover opportunistic foraging behaviours. However, accurately determining complete diets through direct observations is challenging. In this study, we used an environmental DNA (eDNA) approach investigating the DNA mixtures present in faecal samples as a non-invasive complementary method for assessing diet and foraging strategies. We identified the dietary components of vervet monkeys through DNA metabarcoding of 447 faecal samples collected from two monkey groups over 4 months in a semi-urban neighbourhood in South Africa. We further compared the results with observational data on foraging to describe how vervet monkeys exploit anthropogenic resources. Subsequently, we evaluated whether dietary patterns can be distinguished between groups and within matrilineal levels. We found DNA metabarcoding data to be consistent with observational data, but the former revealed a broader diversity of consumed taxa. Additionally, we detected a difference in diet between the two investigated groups, and a tendency for similar dietary patterns among matrilineal pairs compared to other group members. Our results support the use of the DNA metabarcoding methodology, both to determine the complex diet of omnivorous species in urbanised ecosystems and to address interindividual foraging behaviours.

Germplex PCR and massively parallel sequencing: A dynamic duo for detecting bacteria of biodefense and public health importance.

Flow conditions govern the efficiency of passive environmental DNA sampling.

Pharmabiome analyses in tandem with chemometrics can help trace the provenance of falsified medicines: A proof-of-concept study.

Variations in environmental DNA detection of aquatic plants across water body types: A case study of the Tokachi River

Towards a more concise understanding of different environmental DNA states in soils: Common challenges and future perspectives

Abstract Purpose: This review examines the effects of wildfires in Mediterranean and contrasted ecosystems (e.g. in terms of topography, vegetation cover, wildfire history) through the prism of ecosystem components. This approach considers the multiple components of the ecosystem, including soils and sediments, water, and biota, as well as external stressors such as chemical contaminants, to assess the multiple impacts of wildfires. These impacts, which spread from upper to lower catchment areas, affect all ecosystem components, physical, biological, and functional, in a cumulative process along the entire trajectory. Their extent and nature depend on both the intrinsic characteristics of the environment, such as topography, vegetation cover, soil type, and hydrological connectivity, and the characteristics of the wildfire, including its intensity, severity, extent, and frequency. By investigating erosion processes, biodiversity changes and their impacts via environmental DNA analysis, the redistribution of fire retardants, and sediment transport, the aim is to provide a comprehensive understanding of wildfire effects. The main objective of the current review is to synthesize existing knowledge and to identify critical gaps in our understanding of the interactions between these factors, including wildfire, biodiversity, erosion, and contaminants. Methods: Relevant journal articles were extracted from the Clarivate Web of Science database as of September 9, 2025. A total of 161 publications were analyzed, and their findings were categorized into three thematic axes related to wildfire effects: post-wildfire erosion and sediment dynamics, biodiversity assessment using environmental DNA (eDNA), and the transfer of contaminants such as flame retardants and Polycyclic Aromatic Hydrocarbons (PAHs). Results and Conclusion: The results highlighted the complex relationships between wildfire-induced erosion, sediment dynamics, biodiversity and the effects of contaminant transfers in impacted areas. Accordingly, the need to implement comprehensive long-term research, conducted over more than two decades and conducted at integrative spatial scales (e.g. at the catchment level), to improve our understanding of ecological connectivity, sediment transport dynamics, and the cumulative effects of wildfires is demonstrated.

Traditional biodiversity monitoring methods often struggle to detect elusive, rare, or cryptic species due to their reliance on direct observation and specimen collection. In an era of accelerating habitat loss and climate change, there is an urgent need for rapid, reliable, and non-invasive tools to assess biodiversity across ecosystems. This review aims to synthesize the emerging field of environmental DNA (eDNA) and metabarcoding, focusing on their principles, methodologies, and transformative applications in ecological monitoring, species detection, and conservation management. We summarize global research developments on eDNA collection from environmental matrices such as soil, water, and air, explain the integration of PCR-based metabarcoding with high-throughput sequencing, and analyze bioinformatics pipelines used for taxonomic identification and community composition assessment. Additionally, we highlight advances in combining eDNA with remote sensing, machine learning, and conservation genomics. The synthesis demonstrates that eDNA metabarcoding provides a cost-effective, scalable, and highly sensitive framework for biodiversity assessment, enabling detection of rare, invasive, and cryptic species. Its integration with ecological and bioinformatics tools bridges molecular data with environmental management, offering a transformative frontier for global biodiversity monitoring and conservation planning under changing climatic and anthropogenic pressures.

Whole-genome sequencing has boosted our ability to explore microbial diversity by enabling the recovery of metagenome-assembled genomes (MAGs) directly from environmental DNA. As a result, the vast availability of sequencing data has prompted the development of numerous bioinformatics pipelines for MAG reconstruction, along with challenges to identify the most suitable pipeline to perform the analysis according to the user needs. This report briefly discusses the computational requirements of these pipelines; presents the variety of interfaces, workflow managers, and package managers they feature; and describes the typical modular structure. Also, it provides a compacted technical overview of 41 publicly available pipelines or platforms to build MAGs starting from short and/or long sequences. Moreover, recognizing the overwhelming number of factors to consider when selecting an appropriate pipeline, we introduce an interactive decision-support web application, 2Pipe, that helps users to identify a suitable workflow based on their input data characteristics, desired outcomes, and computational constraints. The tool presents a question-driven interface to customize the recommendation, a pipeline gallery to offer a summarized description, and a pipeline comparison based on key factors used for the questionnaire. Beyond this and foreseeing the release of novel pipelines in the near future, we include a quick form and detailed instructions for developers to append their workflow in the application. Altogether, this review and the application equip the researchers with a general outlook of the growing metagenomics pipeline landscape and guide the users toward deciding the workflow that best fits their expectations and infrastructure.

Environmental DNA (eDNA)-derived data, particularly DNA sequences and species occurrence records, are powerful resources for various applications, including biodiversity monitoring, biosecurity, and agricultural bio-surveillance. An important part of eDNA data’s value lies in its reusability, which can be enhanced through the use of metadata that adheres to FAIR (Findable, Accessible, Interoperable, Reusable) data principles (Wilkinson et al. 2016, Abarenkov et al. 2023). While FAIR practices are gaining recognition within the eDNA community, adoption remains limited. A key barrier is that existing data standards, including Darwin Core (DwC, Darwin Core Task Group 2009) and the Minimum Information about any (x) Sequence (MIxS), lack sufficient terms to fully describe eDNA workflows, from sampling and processing to bioinformatic outputs (Takahashi et al. 2025). To address this challenge, we have initiated a collaborative eDNA Task Group supported by the Biodiversity Information Standards (TDWG) and the Genomic Standards Consortium (GSC) organisations. We build upon current standardisation efforts to develop a comprehensive and interoperable eDNA metadata checklist for formal integration into the MIxS and DwC frameworks. See the task group descriptions at TDWG*2 and GSC.*1 Our goal is to ensure compatibility with, and seamless adoption by, major biodiversity and sequence data infrastructures, such as Global Biodiversity Information Facility (GBIF), Ocean Biodiversity Information System (OBIS), and International Nucleotide Sequence Database Collaboration (INSDC). This talk will present progress of the TDWG/GSC joint eDNA initiative, including our collaborative efforts with related working groups and initiatives, such as eDNAqua-plan, the Darwin Core Data Package, DNA-derived data extension to DwC, Minimum Information about any Ancient Sequence (MInAS), and the FAIR eDNA (FAIRe) initiatives (Takahashi et al. 2025). We invite contributions and collaboration to help shape a shared metadata framework that supports the growth, reuse, and long-term utility of eDNA data worldwide.

Understanding how synthetic chemicals affect biodiversity is essential for informing ecological risk assessments and supporting global biodiversity targets. Yet, current risk assessments rely mainly on linear extrapolations from laboratory toxicity tests and rarely capture multifaceted biodiversity, particularly genetic diversity, at the watershed scale. We integrated high-throughput mass spectrometry and environmental DNA (eDNA) metabarcoding to assess cumulative chemical stressor impacts on multitrophic communities (protozoa, algae, fungi, invertebrate metazoan, and fish) across streams, rivers, and lakes of the 40,000 km2 Tai Lake Basin, eastern China. A total of 132 chemicals were detected, and cumulative ecological risk thresholds were exceeded at >70% of sites, indicating basin-wide chemical stress. Spatial heterogeneity in chemical composition and ecological risk were strongly associated with land-use intensity, particularly agricultural and urban development. eDNA metabarcoding revealed that community composition and sequence diversity mirrored chemical stressor distribution across sites. Sites with higher chemical stressors exhibited reduced sequence diversity and increased community similarity, while taxonomic diversity remained stable. Structural equation modeling showed that chemical effects on beta diversity were mediated through reduced sequence diversity, with no significant direct effects. These findings underscore the need to incorporate sequence-based biodiversity metrics into ecological risk frameworks and develop biodiversity-informed thresholds for freshwater ecosystems.

Coral reefs in tropical and subtropical oceans are complex ecosystems characterized by high biodiversity. Zooxanthellate scleractinians are a major component of these reefs. However, the factors influencing coral community establishment and the diversity of coral genera remain poorly understood. A scleractinian-specific environmental DNA metabarcoding (Scl-eDNA-M) method offers a comprehensive and comparative approach to analyzing coral communities across different reef sites. In this study, 10 reef sites in the Republic of Palau, each with distinct geographic features, were monitored using the Scl-eDNA-M system. This system is technically capable of identifying all 69 known scleractinian coral genera in Palau; approximately 60 genera were detected in this study. Acropora , Porites , Montipora , Pocillopora , Goniastrea , and Merulina were the dominant genera, while Leptoria , Platygyra , Pavona , Favites , Isopora , Cyphastrea , and Hydnophora were sub-dominant. The visual census method supported the eDNA metabarcoding results. Clustering analysis based on coral diversity at the genus level indicated that the 10 sites could be grouped into three categories, primarily based on the dominance of Acropora , Porites , Montipora , or Pocillopora . These community profiles were not associated with geographic features such as north versus south or east versus west, but rather with geological features such as lagoons, moats, or reef slopes. In contrast, several genera were identified only at specific geographic locations, including the western outer reefs. Although a larger-scale survey is needed, this study provides an insight into how coral communities in the Palau Islands may have formed in relation to geographic and geological factors.