[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 …

Functional trait‐based approaches as a common framework for aquatic ecologists

S Martini, F Larras, A Boyé, E Faure… - Limnology and …, 2021 - Wiley Online Library
Aquatic ecologists face challenges in identifying the general rules of the functioning of
ecosystems. A common framework, including freshwater, marine, benthic, and pelagic …

Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

F Keck, RC Blackman, R Bossart… - Molecular …, 2022 - Wiley Online Library
DNA metabarcoding is increasingly used for the assessment of aquatic communities, and
numerous studies have investigated the consistency of this technique with traditional …

Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses

F Keck, M Couton, F Altermatt - Molecular Ecology Resources, 2023 - Wiley Online Library
Assessment of biodiversity using metabarcoding data, such as from bulk or environmental
DNA sampling, is becoming increasingly relevant in ecology, biodiversity sciences and …

MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences

M Leray, N Knowlton, RJ Machida - Environmental DNA, 2022 - Wiley Online Library
Abstract Analysis of environmental DNA is increasingly used to characterize ecological
communities, but the effectiveness of this approach depends on the accuracy of taxonomic …

A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses

A Hakimzadeh, A Abdala Asbun… - Molecular Ecology …, 2024 - Wiley Online Library
Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for
monitoring biodiversity in ecology. However, taxa identifications produced through …

Freshwater phytoplankton diversity: models, drivers and implications for ecosystem properties

G Borics, A Abonyi, N Salmaso, R Ptacnik - Hydrobiologia, 2021 - Springer
Our understanding on phytoplankton diversity has largely been progressing since the
publication of Hutchinson on the paradox of the plankton. In this paper, we summarise some …

[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 …

[HTML][HTML] Benthic algae assessments in the EU and the US: Striving for consistency in the face of great ecological diversity

DF Charles, MG Kelly, RJ Stevenson, S Poikane… - Ecological …, 2021 - Elsevier
Freshwaters face multiple environmental problems including eutrophication, acidification,
salinization, and climate-change, all of which can lead to impairment of ecosystem structure …