Ecosystems monitoring powered by environmental genomics: a review of current strategies with an implementation roadmap

T Cordier, L Alonso‐Sáez… - Molecular …, 2021 - Wiley Online Library
A decade after environmental scientists integrated high‐throughput sequencing
technologies in their toolbox, the genomics‐based monitoring of anthropogenic impacts on …

Toward a global reference database of COI barcodes for marine zooplankton

A Bucklin, KTCA Peijnenburg, KN Kosobokova… - Marine Biology, 2021 - Springer
Abstract Characterization of species diversity of zooplankton is key to understanding,
assessing, and predicting the function and future of pelagic ecosystems throughout the …

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 …

New high-tech flexible networks for the monitoring of deep-sea ecosystems

J Aguzzi, D Chatzievangelou, S Marini… - … science & technology, 2019 - ACS Publications
Increasing interest in the acquisition of biotic and abiotic resources from within the deep sea
(eg, fisheries, oil–gas extraction, and mining) urgently imposes the development of novel …

Eutrophication decrease compositional dissimilarity in freshwater plankton communities

Y Li, M Geng, J Yu, Y Du, M Xu, W Zhang… - Science of the Total …, 2022 - Elsevier
Human activities, such as land use change and eutrophication, threaten freshwater
biodiversity and ecosystem function. In this study, we examined both the α-and β-diversity of …

Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities?

A Antich, C Palacín, E Cebrian, R Golo… - Molecular …, 2021 - Wiley Online Library
In the marine realm, biomonitoring using environmental DNA (eDNA) of benthic
communities requires destructive direct sampling or the setting‐up of settlement structures …

From metabarcoding to metaphylogeography: separating the wheat from the chaff

X Turon, A Antich, C Palacín, K Præbel… - Ecological …, 2020 - Wiley Online Library
Metabarcoding is by now a well‐established method for biodiversity assessment in
terrestrial, freshwater, and marine environments. Metabarcoding data sets are usually used …

Multi-marker DNA metabarcoding for precise species identification in ichthyoplankton samples

AO Ferreira, OM Azevedo, C Barroso, S Duarte… - Scientific Reports, 2024 - nature.com
Ichthyoplankton monitoring is crucial for stock assessments, offering insights into spawning
grounds, stock size, seasons, recruitment, and changes in regional ichthyofauna. This study …

DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity

JM Casey, E Ransome, AG Collins… - Environmental …, 2021 - Wiley Online Library
DNA metabarcoding is an increasingly popular technique to investigate biodiversity;
however, many methodological unknowns remain, especially concerning the biases …

Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA

MI Brandt, F Pradillon, B Trouche, N Henry… - Scientific Reports, 2021 - nature.com
Despite representing one of the largest biomes on earth, biodiversity of the deep seafloor is
still poorly known. Environmental DNA metabarcoding offers prospects for fast inventories …