Environmental DNA in Biodiversity Studies

Field-derived temperature correction compromises eDNA-based abundance inference

This study shows that using field-derived temperature corrections in eDNA data reduces its ability to predict fish abundance, as it removes both temperature and abundance signals.

Full-length COI barcodes improve eDNA metabarcoding data denoising relative to mini-barcodes

This study compares COI barcode lengths in eDNA metabarcoding, finding that 658 bp is optimal for balancing accuracy and ecological interpretation.

Changing Pacific salmon nursery lake ecosystem dynamics over centuries to millennia: insights from sedimentary DNA metabarcoding

This study uses sedimentary DNA metabarcoding to track changes in lake ecosystems over centuries, identifying shifts in algal communities and potential drivers like land-use changes and climate factors.

eDNA sampling reveals no negative effects of beaver recolonisation on the catchment-scale distribution of migratory fish

The paper uses eDNA metabarcoding to assess the impact of beaver recolonisation on migratory fish distribution across a catchment, finding no negative effects on salmon or lamprey but a positive association with eel.

TRIDENT (Taxonomic Resolution and IDentification using Environmental dNa Traces): An Optimized Algorithm for Vertebrate Taxonomic Assignments in eDNA Metabarcoding, Integrating Molecular, Taxonomic, and Ecological Criteria

TRIDENT improves taxonomic assignments in eDNA metabarcoding by integrating molecular, taxonomic, and ecological criteria, reducing errors and increasing efficiency.

Comparison of environmental DNA and bulk DNA metabarcoding for assessing terrestrial arthropod diversity across three habitat types on Guam

This study compares bulk DNA metabarcoding and environmental DNA (eDNA) methods for assessing arthropod diversity in three Guam habitats, finding both methods detect significant taxa with eDNA offering a non-destructive alternative.

Accuracy of occurrence and abundance estimates from insect metabarcoding

This study evaluates how lysis methods, spike-ins, and sample processing affect the accuracy of insect metabarcoding for species occurrence and abundance.

Automated eDNA and eRNA Profiling for Biodiversity Monitoring in Marine and Freshwater Ecosystems

This study tests an automated eDNA sampler in various aquatic environments, showing it can effectively profile eukaryotes, prokaryotes, and fish using ribosomal RNA genes and detect taxonomic groups and antimicrobial resistance genes.

Assessing the degradation dynamics of sugar kelp in anaerobic marine sediment using environmental DNA

The paper uses eDNA to study sugar kelp degradation in anaerobic marine sediment, finding rapid eDNA loss in some cases and increased eDNA in buried holdfasts.

Let the prey speak: Using PNA clamps to silence predator DNA in marine faecal diet studies

This study introduces a PNA clamp to suppress predator DNA in faecal diet studies, increasing prey sequence recovery and maintaining prey community composition accuracy.

From egg to adult: comprehensive (e)DNA metabarcoding monitoring of fish diversity in a temperate estuary

The paper evaluates DNA metabarcoding's effectiveness in identifying fish species and detecting seasonal variations in a temperate estuary using ichthyoplankton and water samples.

First genetic detection and ongoing eDNA monitoring of the golden mussel (Limnoperna fortunei) in California

The paper reports the first genetic confirmation of golden mussels in North America and develops eDNA monitoring procedures for early detection of invasive species.

A practical evaluation of sampling filtration and preservation of environmental DNA samples for the water column monitoring.

This paper evaluates filter types and preservatives for eDNA sampling and conservation in offshore water column monitoring, finding that filter choice has less impact than preservation methods on eDNA quality.

A Practical and Cost-Effective Approach to Long-Fragment eDNA Sequencing for High-Resolution Genetic Diversity Assessment

This paper develops a low-cost method for long-fragment eDNA sequencing to assess genetic diversity, finding it effective for high-resolution phylogeographic analysis.

The marine microbiome can accurately predict its chemical and biological environment

This study uses DNA metabarcoding to predict environmental parameters and plankton communities in the Baltic Sea, showing its effectiveness compared to traditional methods.

The old pipe gives the sweetest smoke: A phylogenetic turn for eDNA metabarcoding

The paper introduces a phylogenetic approach to eDNA metabarcoding to improve biodiversity monitoring by using phylogenetic diversity metrics instead of taxonomic metrics.

Charting the insect biodiversity of Crete: insights from a pilot metabarcoding survey

This study uses DNA metabarcoding to survey insect biodiversity in Crete, revealing many new species and highlighting gaps in reference databases.

Complementary Insights from Environmental DNA and Environmental RNA Metabarcoding for Marine Biodiversity Assessment Around San Andres Island, Colombia

This paper compares eDNA and eRNA metabarcoding in marine environments, finding eRNA better captures active communities and reveals habitat-specific differences.

The overall and sequence-specific degradation of soil extracellular DNA fragments: rates and influential factors

The paper measures overall and sequence-specific degradation rates of extracellular DNA fragments in soil and identifies factors influencing these rates.

Benchmarking the quantitative performance of metabarcoding and shotgun sequencing using mock communities of marine nematodes

This study benchmarks metabarcoding and shotgun sequencing for quantifying marine nematode communities using mock communities, finding shotgun sequencing more reliable for cross-taxon abundance comparisons.

Taxon-resolved sources of organic carbon preserved in lake sediments using the sedaDNA GenC pipeline

The paper develops the genC pipeline to estimate taxonomically resolved organic carbon sources in lake sediments and finds that environmental conditions, especially warming, drive OC variation, with terrestrial sources dominating.

Environmental DNA analysis to search for an endangered desert fish

The paper uses eDNA metabarcoding to survey for an endangered fish in Mexican rivers, finding no evidence of its presence and identifying non-native species in some areas.

Benchmarking full-length ITS metabarcoding across Illumina 2x500, PacBio, and Oxford Nanopore sequencing using mock and soil communities

The paper benchmarks full-length ITS metabarcoding across Illumina, PacBio, and Oxford Nanopore platforms using mock and soil communities, finding PacBio has the lowest error rate and recommends standard pipelines for biodiversity assessments.

Towards the reliable use of aerial eDNA for ecosystem monitoring

This study generates and analyzes year-round aerial eDNA metabarcoding data to improve species detection and monitoring, identifying limitations and best practices for airborne eDNA collection.

Variable performances of commercial eDNA inventories challenge their use for surveying stream fish communities

This paper compares eDNA metabarcoding results from four companies to an exhaustive fish inventory, finding significant variation in species detection rates and highlighting challenges for ecological assessments.

Detecting terrestrial insects from naturally exuding tree sap using environmental DNA: a pilot study

This study tests tree sap and sap-mimicking traps as substrates for detecting insect DNA in forest ecosystems using environmental DNA, finding that fermenting sap yields insect eDNA while non-fermenting sap does not.

Comparative analysis of metabarcoding and metagenomics for fish biodiversity estimates using standard and novel high-flow filtration methods

This study compares metabarcoding and metagenomics for fish biodiversity using standard and high-flow filtration methods, finding metagenomics detects more species in field settings and reveals methylation patterns.

Biodiversity effects of beaver activity in a semi-natural enclosure revealed by eDNA

This study uses eDNA metabarcoding to show that beaver dams increase beta diversity and macroinvertebrate gamma diversity in freshwater systems.

Molecular Star Gazing: Development and Validation of an Environmental DNA Assay for the Imperiled Sunflower Sea Star (Pycnopodia helianthoides)

The paper develops and validates an eDNA assay for the sunflower sea star to monitor its populations and assess recovery efforts.

Semi-Annual Cycles in the Biotic Communities of Temperate Aquatic Habitats

The paper detects a semi-annual biotic cycle in temperate aquatic communities using machine learning on DNA metabarcoding data, linking it to insolation patterns and photoautotrophs.