4.7 Article

DNA metabarcoding and morphological methods show complementary patterns in the metacommunity organization of lentic epiphytic diatoms

Related references

Note: Only part of the references are listed.
Article Biodiversity Conservation

The potential of exact sequence variants (ESVs) to interpret and assess the impact of agricultural pressure on stream diatom assemblages revealed by DNA metabarcoding

Kalman Tapolczai et al.

Summary: This study assessed the impact of land-use on diatom assemblages using DNA metabarcoding and tested a taxonomy-free approach for a better interpretation of agricultural stress. Results showed that the taxonomy-free approach provided better insights into the effects of agricultural land use and could lead to the development of more efficient indices. Furthermore, it demonstrated the importance of retaining ecological information by using exact sequence variants without taxonomic assignment.

ECOLOGICAL INDICATORS (2021)

Article Biodiversity Conservation

Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities

Wengang Kang et al.

Summary: This study experimentally evaluated the effects of sediment sample quantity and bioinformatics pipelines on the metabarcoding data of diatoms, demonstrating minimal impact of sample quantity and high consistency among different bioinformatics pipelines. Taxonomic mismatches between metabarcoding and microscopy results were identified, potentially due to database incompleteness and taxonomic inconsistencies. Community analysis confirmed consistent results between microscopy and metabarcoding, highlighting the viability of metabarcoding in identifying diatom-environment relationships.

ECOLOGICAL INDICATORS (2021)

Article Environmental Sciences

Large-scale geographical and environmental drivers of shallow lake diatom metacommunities across Europe

Omar Rodriguez-Alcala et al.

SCIENCE OF THE TOTAL ENVIRONMENT (2020)

Article Biodiversity Conservation

Biotic interactions hold the key to understanding metacommunity organisation

Jorge Garcia-Giron et al.

ECOGRAPHY (2020)

Article Environmental Sciences

Evaluation and sensitivity analysis of diatom DNA metabarcoding for WFD bioassessment of Mediterranean rivers

Javier Perez-Burillo et al.

SCIENCE OF THE TOTAL ENVIRONMENT (2020)

Article Biodiversity Conservation

Development of a novel metric for evaluating diatom assemblages in rivers using DNA metabarcoding

M. G. Kelly et al.

ECOLOGICAL INDICATORS (2020)

Article Fisheries

Resilience of benthic diatom communities in Mediterranean streams: role of endangered species

E. Falasco et al.

MARINE AND FRESHWATER RESEARCH (2019)

Review Ecology

DNA barcoding - A new device in phycologist's toolbox

Zuzanna Kowalska et al.

ECOHYDROLOGY & HYDROBIOLOGY (2019)

Article Limnology

Are dead stems suitable substrata for diatom-based monitoring in Mediterranean shallow ponds?

Maria Borrego-Ramos et al.

FUNDAMENTAL AND APPLIED LIMNOLOGY (2019)

Review Ecology

Fifteen important questions in the spatial ecology of diatoms

Janne Soininen et al.

FRESHWATER BIOLOGY (2019)

Article Marine & Freshwater Biology

Metabarcoding of lake benthic diatoms: from structure assemblages to ecological assessment

S. F. Rivera et al.

HYDROBIOLOGIA (2018)

Article Plant Sciences

PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives

Leho Tedersoo et al.

NEW PHYTOLOGIST (2018)

Review Plant Sciences

Ecology and applications of freshwater epiphytic diatoms - review

Marketa Letakova et al.

CRYPTOGAMIE ALGOLOGIE (2018)

Article Biochemistry & Molecular Biology

Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units' ecological profiles

Francois Keck et al.

MOLECULAR ECOLOGY RESOURCES (2018)

Article Evolutionary Biology

Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes

Frederic Rimet et al.

ORGANISMS DIVERSITY & EVOLUTION (2018)

Article Environmental Sciences

Development of a diatom-based multimetric index for acid mine drainage impacted depressional wetlands

Luisa Riato et al.

SCIENCE OF THE TOTAL ENVIRONMENT (2018)

Review Plant Sciences

Mini review: Diatom species as seen through a molecular window

Linda K. Medlin

BRAZILIAN JOURNAL OF BOTANY (2018)

Article Ecology

Mapping the imprint of biotic interactions on β-diversity

Marc Ohlmann et al.

ECOLOGY LETTERS (2018)

Article Mathematical & Computational Biology

R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring

Frederic Rimet et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2016)

Article Multidisciplinary Sciences

VSEARCH: a versatile open source tool for metagenomics

Torbjorn Rognes et al.

PEERJ (2016)

Article Multidisciplinary Sciences

DNA Barcoding Green Microalgae Isolated from Neotropical Inland Waters

Samed I. I. A. Hadi et al.

PLOS ONE (2016)

Article Engineering, Environmental

Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data

Joana Amorim Visco et al.

ENVIRONMENTAL SCIENCE & TECHNOLOGY (2015)

Article Ecology

Contrasting species and functional beta diversity in montane ant assemblages

Tom R. Bishop et al.

JOURNAL OF BIOGEOGRAPHY (2015)

Article Microbiology

Genetic and Physiological Diversity in the Diatom Nitzschia inconspicua

Laia Rovira et al.

JOURNAL OF EUKARYOTIC MICROBIOLOGY (2015)

Article Biochemistry & Molecular Biology

Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

Jonas Zimmermann et al.

MOLECULAR ECOLOGY RESOURCES (2015)

Review Biodiversity Conservation

Biodiversity patterns in a macroinvertebrate community of a temporary pond network

Margarita Florencio et al.

INSECT CONSERVATION AND DIVERSITY (2014)

Review Biotechnology & Applied Microbiology

20 years since the introduction of DNA barcoding: from theory to application

Ziva Fiser Pecnikar et al.

JOURNAL OF APPLIED GENETICS (2014)

Article Biodiversity Conservation

Timing marine-freshwater transitions in the diatom order Thalassiosirales

Andrew J. Alverson

PALEOBIOLOGY (2014)

Article Ecology

Spatial extent, regional specificity and metacommunity structuring in lake macrophytes

Janne Alahuhta et al.

JOURNAL OF BIOGEOGRAPHY (2013)

Article Microbiology

An Inordinate Fondness? The Number, Distributions, and Origins of Diatom Species

David G. Mann et al.

JOURNAL OF EUKARYOTIC MICROBIOLOGY (2013)

Article Biochemistry & Molecular Biology

Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms

L. Kermarrec et al.

MOLECULAR ECOLOGY RESOURCES (2013)

Article Biochemical Research Methods

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

Nicholas A. Bokulich et al.

NATURE METHODS (2013)

Review Marine & Freshwater Biology

Recent views on river pollution and diatoms

Frederic Rimet

HYDROBIOLOGIA (2012)

Article Plant Sciences

Phytoplankton diversity during the spring bloom in the northwestern Mediterranean Sea

Isabella Percopo et al.

BOTANICA MARINA (2011)

Article Evolutionary Biology

Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols

Jonas Zimmermann et al.

ORGANISMS DIVERSITY & EVOLUTION (2011)

Article Ecology

Partitioning the turnover and nestedness components of beta diversity

Andres Baselga

GLOBAL ECOLOGY AND BIOGEOGRAPHY (2010)

Article Ecology

Species sorting in space and time-the impact of disturbance regime on community assembly in a temporary pool metacommunity

Bram Vanschoenwinkel et al.

JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY (2010)

Article Limnology

Diatom community structure along environmental and spatial gradients in lakes and streams

Janne Soininen et al.

FUNDAMENTAL AND APPLIED LIMNOLOGY (2009)

Article Biochemistry & Molecular Biology

Barcoding diatoms: Is there a good marker?

Monica B. J. Moniz et al.

MOLECULAR ECOLOGY RESOURCES (2009)

Review Engineering, Environmental

Understanding the influence of suspended solids on water quality and aquatic biota

G. S. Bilotta et al.

WATER RESEARCH (2008)

Article Biology

Biological identifications through DNA barcodes

PDN Hebert et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2003)