Environmental DNA (eDNA) techniques offer sensitive monitoring tools for the early detection of aquatic invasive species, which is increasingly needed to prevent their establishment and spread. We compared the eDNA sensitivities of high-volume plankton tow net water sampling to conventional low-volume water filtration methods in three lakes of known recent zebra mussel (Dreissena polymorpha) infestations. Paired filtration and tow net samples were analyzed for Dreissena DNA where higher yields of Dreissena eDNA (more DNA copies) were recovered from plankton tow than from filtered samples in all 33 paired comparisons.

We tune in on the importance of understanding eDNA taphonomy and sediment provenance for the field of eDNA research. We use atomic force microscopy to show how interfacial geochemical interactions drive DNA adsorption behavior on mineral surfaces and combine mineralogic composition with experimental adsorption data to outline a way forward to increase the scope and resolution of biodiversity inferences from eDNA.

We developed and employed a species-specific eDNA assay to detect humpback whale DNA from flukeprints. We detected humpback whales in ~30% of samples and determined there was no difference between instant and delayed filtration on detection.

Successful integration of a new method into a standard management regime requires understanding both its relative efficacy and cost-effectiveness when compared against conventional sampling methods. We successfully detected M. temminckii in Louisiana streams using both eDNA surveys and conventional trapping with eDNA surveys yielding 5.55 times higher detection rates, 40% fewer labor hours per detection, and 84% more streams surveyed per year than conventional trapping. Our results suggest that eDNA presents a promising and cost-efficient technique for M. temminckii surveys.

The plant resources supporting arthropods in natural and agricultural landscapes are of increasing interest, largely because of the global decline in arthropod abundance and species diversity, as well as the increasing recognition of wild native pollinators as important contributors to crop yields. We demonstrate that eDNA metabarcoding of pan trap water can be used to identify the plant resources arthropods rely on. This approach complements long-standing survey methods and may potentially improve the characterization of plant–animal interactions in agroecosystems.

We performed relative expression analysis for environmental RNA released from Japanese medaka, using quantitative PCR. We found that genes frequently used as reference genes in conventional expression analysis correlated well with each other and some of them showed low variability.

In this study, we make use of hatchery net pens containing >46 million juvenile chum salmon (Oncorhynchus keta) in nearshore Southeast Alaska to test for dispersion of eDNA and the effects of tide. We collected and filtered surface water every 80 m along a 2 km transect to test eDNA attenuation over surface distance during incoming and outgoing tides on a single day. We found that surface samples showed a consistent signal of decreasing chum salmon eDNA across the 2 km transect, with the majority of eDNA detections within 1.5 km of the net pens and higher concentrations of DNA throughout during incoming tide.

We use a metabarcoding approach to describe oomycetes' diversity and report that anthropogenic activities shape their diversity, while plantations can act as a gateway for invading natural forests. Our results suggested that the P. europaea cluster might already have crossed this boundary, advocating the importance of improved surveillance of oomycete diversity in various environments.

The manuscript examines whether Proteinase K (ProK), a standard and expensive ingredient in DNA extraction protocols, is necessary for protein-limited marine eDNA samples. We tested the effect of varying levels of ProK on DNA yield, ZOTU diversity, community composition and found no significant differences in diversity metrics among ProK quantities. Our results suggest that rare ZOTUs and eDNA patchiness are driving overall community differences as opposed to extraction ingredients.

Environmental DNA technology has been used to identify rare sturgeons in the Ural River. The study found sturgeons at all sites in spring and autumn, confirming their semi-anadromous ecology. This is the first documented eDNA detection of sturgeon specimens in the Ural River.

Environmental DNA and RNA can serve as molecular tools for biodiversity monitoring, yet questions about their persistence and dynamics within the field and in storage conditions remain. In our study seawater collected near a Sabella spallanzanii colony, was deployed in dialysis bags in a marina, with a subset of bags being stored on ice. Species-specific ddPCR results defied traditional decay models, revealing inconsistent eDNA/eRNA signal detection patterns over 24 h. Bioanalyzer results revealed an increase in larger fragments in field conditions, and preliminary results using long-read sequencing by Oxford Nanopore Technologies uncovered microbial eDNA growth in in-field samples, while ice-stored samples showed limited growth. These findings provide insights into total eDNA dynamics and its potential impact on targeted eDNA concentration and detection.

In this study, we collected eDNA samples from distinct micro-habitats in a rocky intertidal ecosystem over their exposure period in a tidal cycle. Using a well-established eukaryotic (cytochrome oxidase subunit I) metabarcoding assay, we detected 415 species across 28 phyla and identified unique eDNA signals from the different micro-habitats sampled. Our results demonstrate that eDNA biomonitoring can differentiate micro-habitats in the rocky intertidal only 40 m apart, that these differences reflect known ecology in the area, and that physical connectivity informs the degree of differentiation possible.

Metabarcoding of automatic light traps in a tropical forest reveals great diversity. Comparing metabarcoding to local long-term monitoring program reveals this to be successful at capturing known diversity of focal species.

Using microcosms and bioassay experiments to determine the impacts of limnological water quality measurements on the rate of environmental DNA degradation. Results show that chlorophyll-a is a key parameter that impacts the rate of degradation of eDNA in lake environments.

Choice of lysis buffer and DNA isolation approach impacts yield and fragment composition in aeDNA extracts from marine sediments. Created with BioRender.com.

Environmental DNA (eDNA) is a powerful tool for resource management and conservation but currently requires specialized expertise and laboratory conditions to perform. The research seeks to expand the use of eDNA to field biologists by developing a streamside CRISPR/Cas12a detection technology for Chinook salmon eDNA. The method proved to be sensitive and specific and was able to successfully detect Chinook salmon in stream samples from the Snake River in the USA.

This study provides the first evidence of dietary partitioning of three common pseudochromid species in the Red Sea using a combination of (i) visual stomach content analysis, (ii) stomach content DNA metabarcoding (18S, COI), and (iii) stable isotope analysis (δ¹⁵N, δ¹³C). Our results revealed that Pseudochromis flavivertex, P. fridmani, and P. olivaceus present different dietary specializations and low dietary niche overlap among species. Our analysis highlights the importance of combining several approaches (short-term: visual analysis and DNA metabarcoding; and long-term: isotope analysis) when assessing the feeding habits of coral reef fishes, as they provide complementary information necessary to delimit their niches and understand the role that small mesopredators play in coral reef ecosystems.

It can be challenging to ensure that eDNA assays are specific to their intended targets, particularly when biodiversity is high and the geographic area is large. Here, we use an accurate machine-learning-based PCR model to streamline validation of 46 qPCR assays targeting invasive species throughout the continental United States. We present an overview of our validation framework and trends in assay performance, along with detailed records of validation for each assay in an appendix.

We developed two independent sets of generic quality control qPCR assays (QCqPCR) targeting abundant endogenous plant DNA in the environment. Unlike exogenous controls, our QCqPCR assays enable the monitoring of the entire eDNA workflow. We recommend incorporating either one of the QCqPCR assays into qPCR-based eDNA analysis to detect potential false negatives and improve the reliability of eDNA surveys.

Using metabarcoding, we analyze the diet of the European turtle dove (Streptopelia turtur) in different sites, both breeding and wintering. We identified a diverse range of taxa in the diet and little overlap in the food consumed in breeding and wintering grounds. The roles of wild and cultivated food in the diet and implications for species management were considered.

We measured eDNA shedding and degradation rates of three freshwater mussel species, including one federally endangered species. We tested how biomass, feeding, and temperature affected shedding rate and found shedding rates were generally low for mussels compared with previous reports of shedding rates in fish. Degradation rates of eDNA were similar to those reported in the literature for other taxa.