Environmental DNA in Biodiversity Studies

Invasive terrestrial invertebrate detection in water and soil using a targeted eDNA approach

This study demonstrates that eDNA from terrestrial invasive invertebrates can be detected in adjacent waterbodies and soil, with purification steps improving detection rates.

Environmental DNA phylogeography: successful reconstruction of phylogeographic patterns of multiple fish species from a cup of water

This study demonstrates that eDNA analysis can accurately reconstruct phylogeographic patterns of multiple fish species from water samples, reducing the effort required for traditional phylogeographic surveys.

Maximizing the reliability and the number of species assignments in metabarcoding studies

This study improves species assignment reliability and detection in metabarcoding by combining a regional library with a public repository and optimal assignment methods.

Non-destructive DNA metabarcoding of arthropods using collection medium from passive traps

This study evaluates non-destructive DNA metabarcoding from collection media in passive traps for arthropod species detection, finding it effective for soft-bodied species but less so for others.

COInr and mkCOInr: Building and customizing a non-redundant barcoding reference database from BOLD and NCBI using a lightweight pipeline.

The paper introduces COInr, a non-redundant COI reference database built from BOLD and NCBI, and mkCOInr, a tool to customize it for metabarcoding applications.

Can we sort states of environmental DNA (eDNA) from a single sample?

This study evaluates methods to separate different states of eDNA from a single sample, finding that the membrane-bound state is best isolated with minimal contamination.

Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring

The paper compares eDNA sources from water, bivalves, sponges, and ethanol to assess their utility for biodiversity monitoring, finding sponges are reliable while bivalves are not.

Niche overlap between two large herbivores across landscape variability using dietary eDNA metabarcoding

The paper uses dietary eDNA metabarcoding to assess how landscape variability affects niche overlap between Red deer and European bison in the Bialowieza Forest.

Air-seq: Measuring air metagenomic diversity in an agricultural ecosystem

The paper introduces Air-seq, a method to monitor agricultural ecosystem biodiversity using airborne DNA, showing it can detect pathogens and track their abundance over time.

It`s raining species: Rainwash eDNA metabarcoding as a minimally invasive method to assess tree canopy invertebrate diversity

The paper demonstrates that rainwash eDNA metabarcoding can detect canopy invertebrate diversity, revealing species not present in water samples and showing host-specific patterns.

Non-invasive real-time genomic monitoring of the critically endangered kakapo

This study uses non-invasive genomic methods to monitor kakapo populations, enabling individual identification through environmental DNA sequencing and providing insights into genomic diversity and inbreeding.

EukRibo: a manually curated eukaryotic 18S rDNA reference database to facilitate identification of new diversity

EukRibo provides a curated 18S rDNA database for accurate taxonomic annotation of environmental metabarcoding data, focusing on eukaryotic diversity.

Introducing an rbcL and trnL reference library to aid in the metabarcoding analysis of foraged plants from semi-arid eastern South African savannas

This paper creates rbcL and trnL DNA barcode reference datasets for plants in semi-arid eastern South African savannas to improve metabarcoding accuracy.

MetaWorks: A flexible, scalable bioinformatic pipeline for high-throughput multi-marker biodiversity assessments

MetaWorks provides a bioinformatic pipeline for processing multi-marker metabarcoding data across different domains of life, supporting various markers and taxonomic assignments.

Environmental DNA reflects common haplotypic variation

This study shows that environmental DNA can effectively detect common haplotypes in blackfoot pua but rarely captures rare ones, supporting its use for non-invasive population genetic monitoring.

Elasmobranchs' metabarcoding requires a pragmatic approach to reach its promises

The paper tests metabarcoding for elasmobranch monitoring using published primers and identifies practical constraints and adjustments needed for effective application.

Non-invasive fecal DNA yields whole genome and metagenomic data for species conservation

This paper presents a non-invasive molecular pipeline using fecal DNA to generate whole genome and metagenomic data for African savanna elephants, demonstrating its utility for conservation.

Spatio-temporal monitoring of lake fish spawning activity using environmental DNA metabarcoding

This study uses environmental DNA metabarcoding to track the spatial and temporal patterns of Arctic charr spawning in a lake, confirming its effectiveness compared to traditional methods.

Comparing the accuracy and efficiency of third generation DNA barcode sequencing: Oxford Nanopore Technologies versus Pacific Biosciences

This study compares the accuracy and efficiency of DNA barcode sequencing using Oxford Nanopore Technologies and Pacific Biosciences, finding ONT's R10 & Q20+ chemistry combination provides the highest success rate.

Optimised DNA isolation from marine sponges for natural sampler DNA (nsDNA) metabarcoding

This study optimises DNA isolation from marine sponges for metabarcoding, finding that blotting tissue dry and using a non-commercial protocol improves taxon recovery and sequence reads.

Multi-marker DNA metabarcoding detects suites of environmental gradients from an urban harbour

The paper uses DNA metabarcoding to detect environmental gradients in an urban harbour, showing greater variation in species rank assessments compared to morphological methods.

Fast processing of environmental DNA metabarcoding sequence data using convolutional neural networks

This paper uses convolutional neural networks to process eDNA metabarcoding data, achieving faster speeds than OBITools while maintaining comparable accuracy.

Shotgun metagenomics of soil invertebrate communities reflects taxonomy, biomass and reference genome properties

This study evaluates how shotgun metagenomics captures composition and biomass in artificial soil invertebrate communities, showing taxon-specific biases and the influence of reference genome properties.

The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind

This study evaluates the use of universal primers as capture probes to isolate or remove DNA from eDNA samples, finding that COI capture probes fail to exclude bacterial DNA while 16S capture misses metazoans.

Best practice recommendations for sample preservation in metabarcoding studies: a case study on diatom environmental samples

This study compares three preservation protocols for diatom samples over different storage durations, finding that DNA quality and diversity are largely unaffected, but rare taxa vary, highlighting the importance of method choice for detecting low-density species.

A non-invasive eDNA tool for detecting sea lamprey larvae in river sediments: analytical validation and field testing in a low abundance ecosystem

This paper develops and validates an eDNA assay to detect sea lamprey larvae in river sediments, showing it can effectively detect low-abundance larvae.

Leveraging eDNA metabarcoding to characterize nearshore fish communities in Southeast Alaska: Do habitat and tide matter?

This study uses eDNA metabarcoding to assess nearshore fish communities in Southeast Alaska, finding that habitat type significantly influences species richness and composition, while tide effects are more subtle and habitat-dependent.

Environmental DNA sequencing data from algal blooms in Lake Erie using Oxford Nanopore MinION

The paper describes a portable sequencing pipeline for detecting harmful algal blooms using environmental DNA from Lake Erie, showing significant differences in HAB-associated taxa abundance before and after a bloom.

Passive sampling of environmental DNA in aquatic environments using 3D-printed hydroxyapatite samplers

This paper introduces 3D-printed hydroxyapatite samplers for passive environmental DNA collection, showing they efficiently recover DNA but with variable results.

Recommendations for tissue homogenisation and extraction in DNA metabarcoding of Malaise trap samples

This paper compares two DNA extraction methods for metabarcoding Malaise trap samples, finding that wet material processing is more efficient and less prone to contamination.