[HTML][HTML] Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

J Pawlowski, K Bruce, K Panksep, FI Aguirre… - Science of the Total …, 2022 - Elsevier
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for
identification of whole communities within a targeted group) is revolutionizing the field of …

[HTML][HTML] The future of biotic indices in the ecogenomic era: Integrating (e) DNA metabarcoding in biological assessment of aquatic ecosystems

J Pawlowski, M Kelly-Quinn, F Altermatt… - Science of the Total …, 2018 - Elsevier
The bioassessment of aquatic ecosystems is currently based on various biotic indices that
use the occurrence and/or abundance of selected taxonomic groups to define ecological …

[HTML][HTML] Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring

M Sagova-Mareckova, J Boenigk, A Bouchez… - Water research, 2021 - Elsevier
Bioindication has become an indispensable part of water quality monitoring in most
countries of the world, with the presence and abundance of bioindicator taxa, mostly …

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 …

Embracing environmental genomics and machine learning for routine biomonitoring

T Cordier, A Lanzén, L Apothéloz-Perret-Gentil… - Trends in …, 2019 - cell.com
Genomics is fast becoming a routine tool in medical diagnostics and cutting-edge
biotechnologies. Yet, its use for environmental biomonitoring is still considered a futuristic …

Predicting the ecological quality status of marine environments from eDNA metabarcoding data using supervised machine learning

T Cordier, P Esling, F Lejzerowicz, J Visco… - … science & technology, 2017 - ACS Publications
Monitoring biodiversity is essential to assess the impacts of increasing anthropogenic
activities in marine environments. Traditionally, marine biomonitoring involves the sorting …

Supervised machine learning outperforms taxonomy‐based environmental DNA metabarcoding applied to biomonitoring

T Cordier, D Forster, Y Dufresne… - Molecular ecology …, 2018 - Wiley Online Library
Biodiversity monitoring is the standard for environmental impact assessment of
anthropogenic activities. Several recent studies showed that high‐throughput amplicon …

Life in a drop: Sampling environmental DNA for marine fishery management and ecosystem monitoring

J Gilbey, G Carvalho, R Castilho, I Coscia… - Marine Policy, 2021 - Elsevier
Science-based management of marine fisheries and effective ecosystem monitoring both
require the analysis of large amounts of often complex and difficult to collect information …

Advantages and limitations of environmental DNA/RNA tools for marine biosecurity: management and surveillance of non-indigenous species

A Zaiko, X Pochon, E Garcia-Vazquez… - Frontiers in Marine …, 2018 - frontiersin.org
To enable successful management of marine bioinvasions, timely and robust scientific
advice is required. This knowledge should inform managers and stakeholders on the …

Development and preliminary validation of a multi-trophic metabarcoding biotic index for monitoring benthic organic enrichment

N Keeley, SA Wood, X Pochon - Ecological Indicators, 2018 - Elsevier
Sea-based fish farms are associated with strong, benthic enrichment gradients and routine
monitoring is usually required by regulation. This has traditionally been based on benthic …