A practical guide to DNA metabarcoding for entomological ecologists

M Liu, LJ Clarke, SC Baker, GJ Jordan… - Ecological …, 2020 - Wiley Online Library
1. DNA metabarcoding is a cost‐effective species identification approach with great potential
to assist entomological ecologists. This review presents a practical guide to help …

DNA metabarcoding for the characterization of terrestrial microbiota—pitfalls and solutions

D Francioli, G Lentendu, S Lewin, S Kolb - Microorganisms, 2021 - mdpi.com
Soil-borne microbes are major ecological players in terrestrial environments since they cycle
organic matter, channel nutrients across trophic levels and influence plant growth and …

Patterns of eukaryotic diversity from the surface to the deep-ocean sediment

T Cordier, IB Angeles, N Henry, F Lejzerowicz… - Science …, 2022 - science.org
Remote deep-ocean sediment (DOS) ecosystems are among the least explored biomes on
Earth. Genomic assessments of their biodiversity have failed to separate indigenous benthic …

Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding

MI Brandt, B Trouche, L Quintric… - Molecular Ecology …, 2021 - Wiley Online Library
Environmental DNA metabarcoding is a powerful tool for studying biodiversity. However,
bioinformatic approaches need to adjust to the diversity of taxonomic compartments targeted …

eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity

M Mousavi‐Derazmahalleh, A Stott… - Molecular Ecology …, 2021 - Wiley Online Library
Metabarcoding of environmental DNA (eDNA) when coupled with high throughput
sequencing is revolutionising the way biodiversity can be monitored across a wide range of …

[HTML][HTML] Encapsulated in sediments: eDNA deciphers the ecosystem history of one of the most polluted European marine sites

IB Angeles, ML Romero-Martínez, M Cavaliere… - Environment …, 2023 - Elsevier
The Anthropocene is characterized by dramatic ecosystem changes driven by human
activities. The impact of these activities can be assessed by different geochemical and …

APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data

D Buchner, TH Macher, F Leese - Bioinformatics, 2022 - academic.oup.com
DNA metabarcoding is an emerging approach to assess and monitor biodiversity worldwide
and consequently the number and size of data sets increases exponentially. To date, no …

[HTML][HTML] Diatom DNA metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries reveals the need for …

B Bailet, L Apothéloz-Perret-Gentil, A Baričević… - Science of the Total …, 2020 - Elsevier
Ecological assessment of lakes and rivers using benthic diatom assemblages currently
requires considerable taxonomic expertise to identify species using light microscopy. This …

Monitoring the ecological status of rivers with diatom eDNA metabarcoding: A comparison of taxonomic markers and analytical approaches for the inference of a …

L Apothéloz‐Perret‐Gentil, A Bouchez… - Molecular …, 2021 - Wiley Online Library
Recently, several studies demonstrated the usefulness of diatom eDNA metabarcoding as
an alternative to assess the ecological quality of rivers and streams. However, the choice of …

Microbial diversity alteration reveals biomarkers of contamination in soil-river-lake continuum

Z Bourhane, A Lanzén, C Cagnon, OB Said… - Journal of hazardous …, 2022 - Elsevier
Microbial communities inhabiting soil-water-sediment continuum in coastal areas provide
important ecosystem services. Their adaptation in response to environmental stressors …