Environmental DNA in Biodiversity Studies

SSUplex is a tool for extracting and sorting small-subunit rRNA reads by origin, improving accuracy in environmental DNA metabarcoding.

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.

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

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.

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

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.

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

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.

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.

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

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

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

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.

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

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

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

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

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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

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