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

Two different approaches of microbial community structure characterization in riverine epilithic biofilms under multiple stressors conditions: Developing molecular indicators

(2021) Lorenzo Pin et al.   Molecular Ecology Resources

Assessing the Ecological Status of European Rivers and Lakes Using Benthic Invertebrate Communities: A Practical Catalogue of Metrics and Methods

(2021) Simon Vitecek et al.   Water

Sediment archives reveal irreversible shifts in plankton communities after World War II and agricultural pollution

(2021) Raffaele Siano et al.   CURRENT BIOLOGY

A Substrate-Independent Benthic Sampler (SIBS) for Hard and Mixed-Bottom Marine Habitats: A Proof-of-Concept Study

(2021) Nigel Keeley et al.   Frontiers in Marine Science

The network structure of intertidal meiofaunal communities from environmental DNA metabarcoding surveys in Northwest Iberia

(2021) Bruno Bellisario et al.   AQUATIC SCIENCES

Toward a reliable assessment of potential ecological impacts of deep‐sea polymetallic nodule mining on abyssal infauna

(2021) Lidia Lins et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Grab what you can—an evaluation of spatial replication to decrease heterogeneity in sediment eDNA metabarcoding

(2021) Jon T. Hestetun et al.   PeerJ

The Biodiversity and Distribution of Abyssal Benthic Foraminifera and Their Possible Ecological Roles: A Synthesis Across the Clarion-Clipperton Zone

(2021) Andrew J. Gooday et al.   Frontiers in Marine Science

Eukaryotic Biodiversity and Spatial Patterns in the Clarion-Clipperton Zone and Other Abyssal Regions: Insights From Sediment DNA and RNA Metabarcoding

(2021) Franck Lejzerowicz et al.   Frontiers in Marine Science

High concentrations of dissolved biogenic methane associated with cyanobacterial blooms in East African lake surface water

(2021) Stefano Fazi et al.   Communications Biology

Benthic eDNA metabarcoding provides accurate assessments of impact from oil extraction, and ecological insights

(2021) Anders Lanzén et al.   ECOLOGICAL INDICATORS

Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding

(2020) Fais Maria et al.   ESTUARINE COASTAL AND SHELF SCIENCE

High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes

(2020) Régis Vivien et al.   Scientific Reports

Marine Sediments Illuminate Chlamydiae Diversity and Evolution

(2020) Jennah E. Dharamshi et al.   CURRENT BIOLOGY

Evaluation of a eukaryote phylogenetic microarray for environmental monitoring of marine sediments

(2020) Katrine Lekang et al.   MARINE POLLUTION BULLETIN

Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes

(2020) Larissa Frühe et al.   MOLECULAR ECOLOGY

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

(2020) Tristan Cordier et al.   MOLECULAR ECOLOGY

Environmental DNA surveys detect distinct metazoan communities across abyssal plains and seamounts in the western Clarion Clipperton Zone

(2020) Olivier Laroche et al.   MOLECULAR ECOLOGY

Performance of the melting seawater‐ice elution method on the metabarcoding characterization of benthic protist communities

(2020) Albert Reñé et al.   Environmental Microbiology Reports

Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems

(2020) Joseph D. DiBattista et al.   Scientific Reports

The risks of using molecular biodiversity data for incidental detection of species of concern

(2020) John A. Darling et al.   DIVERSITY AND DISTRIBUTIONS

A microbial mandala for environmental monitoring: Predicting multiple impacts on estuarine prokaryote communities of the Bay of Biscay

(2020) Anders Lanzén et al.   MOLECULAR ECOLOGY

Deep-Sea Misconceptions Cause Underestimation of Seabed-Mining Impacts

(2020) Craig R. Smith et al.   TRENDS IN ECOLOGY & EVOLUTION

Assessing the response of micro-eukaryotic diversity to the Great Acceleration using lake sedimentary DNA

(2020) François Keck et al.   Nature Communications

An Assessment of Environmental Metabarcoding Protocols Aiming at Favoring Contemporary Biodiversity in Inventories of Deep-Sea Communities

(2020) Miriam I. Brandt et al.   Frontiers in Marine Science

The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA: A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda

(2020) René Dommain et al.   Frontiers in Ecology and Evolution

Nematodes as bioindicators of polluted sediments using metabarcoding and microscopic taxonomy

(2020) Janina Schenk et al.   ENVIRONMENT INTERNATIONAL

The role of metal contamination in shaping microbial communities in heavily polluted marine sediments

(2020) Andrea Di Cesare et al.   ENVIRONMENTAL POLLUTION

Including sediment in European River Basin Management Plans: twenty years of work by SedNet

(2020) Jos Brils   JOURNAL OF SOILS AND SEDIMENTS

Chemical contamination can promote turnover diversity of benthic prokaryotic assemblages: The case study of the Bagnoli-Coroglio bay (southern Tyrrhenian Sea)

(2020) M. Tangherlini et al.   MARINE ENVIRONMENTAL RESEARCH

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

(2020) Laure Apothéloz‐Perret‐Gentil et al.   MOLECULAR ECOLOGY

Global diversity of microbial communities in marine sediment

(2020) Tatsuhiko Hoshino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

qPCR-based assessment of microfaunal indicators of oil for monitoring benthos around oil and gas platforms

(2020) Adriana Krolicka et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

(2020) Sofia Duarte et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Advances in the Detection of Toxic Algae Using Electrochemical Biosensors

(2020) Linda K. Medlin et al.   Biosensors-Basel

Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding

(2020) Naiara Guimarães Sales et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring

(2020) M. Sagova-Mareckova et al.   WATER RESEARCH

Exploring the capacity of aquatic biofilms to act as environmental DNA samplers: Test on macroinvertebrate communities in rivers

(2020) Sinziana F. Rivera et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Responses of foraminifera communities to aquaculture-derived organic enrichment as revealed by environmental DNA metabarcoding

(2019) Xiaoping He et al.   MOLECULAR ECOLOGY

Fungi in aquatic ecosystems

(2019) Hans-Peter Grossart et al.   NATURE REVIEWS MICROBIOLOGY

Retrospective eDNA assessment of potentially harmful algae in historical ship ballast tank and marine port sediments

(2019) Jennifer L. A. Shaw et al.   MOLECULAR ECOLOGY

Multi-marker eDNA metabarcoding survey to assess the environmental impact of three offshore gas platforms in the North Adriatic Sea (Italy)

(2019) Tristan Cordier et al.   MARINE ENVIRONMENTAL RESEARCH

Fungal diversity in the deep-sea hadal sediments of the Yap Trench by cultivation and high throughput sequencing methods based on ITS rRNA gene

(2019) Wei Xu et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Bacterial community pattern along the sediment seafloor of the Arctic fjorden (Kongsfjorden, Svalbard)

(2019) Xiao-Mei Fang et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Comparison of two DNA extraction methods widely used in aquatic microbial ecology

(2019) Erick Mateus-Barros et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Rapid and in-situ detection of fecal indicator bacteria in water using simple DNA extraction and portable loop-mediated isothermal amplification (LAMP) PCR methods

(2019) Seunguk Lee et al.   WATER RESEARCH

Natural and anthropogenic disturbances shape benthic phototrophic and heterotrophic microbial communities in the Po River Delta system

(2019) Tamara Cibic et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Can Environmental RNA Revolutionize Biodiversity Science?

(2019) Melania E. Cristescu   TRENDS IN ECOLOGY & EVOLUTION

Metagenomic Sequencing Identifies Highly Diverse Assemblages of Dinoflagellate Cysts in Sediments from Ships’ Ballast Tanks

(2019) Shang et al.   Microorganisms

Testing different (e)DNA metabarcoding approaches to assess aquatic oligochaete diversity and the biological quality of sediments

(2019) Régis Vivien et al.   ECOLOGICAL INDICATORS

Exploring bacterial pathogen community dynamics in freshwater beach sediments: A tale of two lakes

(2019) Danielle VanMensel et al.   ENVIRONMENTAL MICROBIOLOGY

Release and degradation of environmental DNA and RNA in a marine system

(2019) Susanna A. Wood et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water

(2019) Luke E. Holman et al.   Scientific Reports

Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies

(2019) Ryan P. Kelly et al.   Scientific Reports

New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality

(2019) C. Giguet-Covex et al.   Scientific Reports

Relating Metatranscriptomic Profiles to the Micropollutant Biotransformation Potential of Complex Microbial Communities

(2019) Stefan Achermann et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Prokaryotic community composition and distribution in coastal sediments following a Po river flood event (northern Adriatic Sea, Italy)

(2019) Stefano Fazi et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Testing the efficiency of a bacterial community-based index (microgAMBI) to assess distinct impact sources in six locations around the world

(2018) Angel Borja   ECOLOGICAL INDICATORS

Metabarcoding of benthic ciliate communities shows high potential for environmental monitoring in salmon aquaculture

(2018) Thorsten Stoeck et al.   ECOLOGICAL INDICATORS

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

(2018) Nigel Keeley et al.   ECOLOGICAL INDICATORS

Risk assessment of pesticides in estuaries: a review addressing the persistence of an old problem in complex environments

(2018) Nagore Cuevas et al.   ECOTOXICOLOGY

eDNA-based bioassessment of coastal sediments impacted by an oil spill

(2018) Yuwei Xie et al.   ENVIRONMENTAL POLLUTION

The Response of Cultured Meiofaunal and Benthic Foraminiferal Communities to Lead Exposure: Results from Mesocosm Experiments

(2018) Fabrizio Frontalini et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

A Comparison of Different Ciliate Metabarcode Genes as Bioindicators for Environmental Impact Assessments of Salmon Aquaculture

(2018) Dominik Forster et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

The use of metabarcoding for meiofauna ecological patterns assessment

(2018) Laiza Cabral de Faria et al.   MARINE ENVIRONMENTAL RESEARCH

Chemical characteristics of dissolved mercury in the pore water of Minamata Bay sediments

(2018) Akito Matsuyama et al.   MARINE POLLUTION BULLETIN

Assessing the effect of mercury pollution on cultured benthic foraminifera community using morphological and eDNA metabarcoding approaches

(2018) Fabrizio Frontalini et al.   MARINE POLLUTION BULLETIN

Perturbation of seafloor bacterial community structure by drilling waste discharge

(2018) Tan T. Nguyen et al.   MARINE POLLUTION BULLETIN

A cross-taxa study using environmental DNA/RNA metabarcoding to measure biological impacts of offshore oil and gas drilling and production operations

(2018) Olivier Laroche et al.   MARINE POLLUTION BULLETIN

Environmental DNA metabarcoding of benthic bacterial communities indicates the benthic footprint of salmon aquaculture

(2018) Thorsten Stoeck et al.   MARINE POLLUTION BULLETIN

Optimal extraction methods for the simultaneous analysis of DNA from diverse organisms and sample types

(2018) Syrie M. Hermans et al.   Molecular Ecology Resources

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

(2018) Tristan Cordier et al.   Molecular Ecology Resources

Interactive effects of multiple stressors revealed by sequencing total (DNA) and active (RNA) components of experimental sediment microbial communities

(2018) Simone C. Birrer et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Global Carbon Cycling on a Heterogeneous Seafloor

(2018) Paul V.R. Snelgrove et al.   TRENDS IN ECOLOGY & EVOLUTION

Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive

(2018) Daniel Hering et al.   WATER RESEARCH

Extracellular DNA as a genetic recorder of microbial diversity in benthic deep-sea ecosystems

(2018) C. Corinaldesi et al.   Scientific Reports

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity

(2018) David López-Escardó et al.   Scientific Reports

Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks

(2018) Eva Aylagas et al.   ECOLOGICAL INDICATORS

Impact of an artificial structure on the benthic community composition in the southern North Sea: assessed by a morphological and molecular approach

(2018) Lise Klunder et al.   ICES JOURNAL OF MARINE SCIENCE

Meiobenthic community composition and biodiversity along a 5500 km transect of Western Antarctica: a metabarcoding analysis

(2018) PM Brannock et al.   MARINE ECOLOGY PROGRESS SERIES

Comparison of environmental DNA and bulk-sample metabarcoding using highly degenerate cytochrome c oxidase I primers

(2018) Jan-Niklas Macher et al.   Molecular Ecology Resources

Implementing Morpholino-Based Nucleic Acid Sensing on a Portable Surface Plasmon Resonance Instrument for Future Application in Environmental Monitoring

(2018) Andrea Bagi et al.   SENSORS

First insights into the living groundwater mycobiome of the terrestrial biogeosphere

(2018) Ali Nawaz et al.   WATER RESEARCH

Impacts of DNA extraction and PCR on DNA metabarcoding estimates of soil biodiversity

(2018) Andrew Dopheide et al.   Methods in Ecology and Evolution

Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing

(2018) Francisco J. A. Nascimento et al.   Scientific Reports

Limited congruence exhibited across microbial, meiofaunal and macrofaunal benthic assemblages in a heterogeneous coastal environment

(2018) Sorcha Cronin-O’Reilly et al.   Scientific Reports

A comparative analysis of metabarcoding and morphology-based identification of benthic communities across different regional seas

(2018) Abigail E. Cahill et al.   Ecology and Evolution

Considerations for incorporating real-time PCR assays into routine marine biosecurity surveillance programmes: a case study targeting the Mediterranean fanworm (Sabella spallanzanii) and club tunicate (Styela clava)

(2018) Susanna A. Wood et al.   GENOME

Environmental DNA metabarcoding studies are critically affected by substrate selection

(2018) Adam Koziol et al.   Molecular Ecology Resources

Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling

(2018) Fei Teng et al.   Scientific Reports

Simultaneous preservation of the DNA quality, the community composition and the density of freshwater oligochaetes for the development of genetically based biological indices

(2018) Régis Vivien et al.   PeerJ

Development and validation of a macroinvertebrate-based biomonitoring tool to assess fine sediment impact in small mountain streams

(2018) Alexander Gieswein et al.   SCIENCE OF THE TOTAL ENVIRONMENT

High diversity of benthic bacterial and archaeal assemblages in deep-Mediterranean canyons and adjacent slopes

(2018) Cinzia Corinaldesi et al.   PROGRESS IN OCEANOGRAPHY

Predicting the Ecological Quality Status of Marine Environments from eDNA Metabarcoding Data Using Supervised Machine Learning

(2017) Tristan Cordier et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Looking at biological community level to improve ecotoxicological assessment of freshwater sediments: report on a first French-Swiss workshop

(2017) Stéphane Pesce et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill

(2017) K M Handley et al.   ISME Journal

DNA-based methods in paleolimnology: new opportunities for investigating long-term dynamics of lacustrine biodiversity

(2017) Isabelle Domaizon et al.   JOURNAL OF PALEOLIMNOLOGY

Impact of a harbour construction on the benthic community of two shallow marine caves

(2017) Ettore Nepote et al.   MARINE POLLUTION BULLETIN

A bacterial community-based index to assess the ecological status of estuarine and coastal environments

(2017) Eva Aylagas et al.   MARINE POLLUTION BULLETIN

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

The Quest to Develop Ecogenomic Sensors: A 25-Year History of the Environmental Sample Processor (ESP) as a Case Study

(2017) Christopher Scholin et al.   OCEANOGRAPHY

Evaluation of metagenetic community analysis of planktonic copepods using Illumina MiSeq: Comparisons with morphological classification and metagenetic analysis using Roche 454

(2017) Junya Hirai et al.   PLoS One

Revealing higher than expected meiofaunal diversity in Antarctic sediments: a metabarcoding approach

(2017) V. G. Fonseca et al.   Scientific Reports

From the Surface to the Deep-Sea: Bacterial Distributions across Polymetallic Nodule Fields in the Clarion-Clipperton Zone of the Pacific Ocean

(2017) Markus V. Lindh et al.   Frontiers in Microbiology

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Consistent variability in beta-diversity patterns contrasts with changes in alpha-diversity along an onshore to offshore environmental gradient: the case of Red Sea soft-bottom macrobenthos

(2017) Zahra Alsaffar et al.   Marine Biodiversity

Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities

(2017) Olivier Laroche et al.   PeerJ

DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments

(2017) Anders Lanzén et al.   PLoS One

Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications

(2017) Xavier Pochon et al.   PLoS One

Using in situ bacterial communities to monitor contaminants in river sediments

(2016) Yuwei Xie et al.   ENVIRONMENTAL POLLUTION

First evaluation of foraminiferal metabarcoding for monitoring environmental impact from an offshore oil drilling site

(2016) Olivier Laroche et al.   MARINE ENVIRONMENTAL RESEARCH

Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea

(2016) John K. Pearman et al.   Marine Genomics

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

(2016) Alice Valentini et al.   MOLECULAR ECOLOGY

High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities

(2016) Anders Lanzén et al.   MOLECULAR ECOLOGY

Benthic algal assessment of ecological status in European lakes and rivers: Challenges and opportunities

(2016) Sandra Poikane et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Microbial source tracking in impaired watersheds using PhyloChip and machine-learning classification

(2016) Eric A. Dubinsky et al.   WATER RESEARCH

Benthic monitoring of salmon farms in Norway using foraminiferal metabarcoding

(2016) J Pawlowski et al.   Aquaculture Environment Interactions

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

(2016) C. Ryan Penton et al.   Frontiers in Microbiology

A multidisciplinary approach to study confined marine basins: the holobenthic and merobenthic assemblages in the Mar Piccolo of Taranto (Ionian Sea, Mediterranean)

(2016) L. Ferraro et al.   Marine Biodiversity

Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

(2016) Magdalena Guardiola et al.   PeerJ

High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany)

(2016) Christian Wurzbacher et al.   MycoKeys

Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems

(2016) R. Danovaro et al.   Science Advances

Next-Generation Environmental Diversity Surveys of Foraminifera: Preparing the Future

(2016) J. Pawlowski et al.   BIOLOGICAL BULLETIN

High-Throughput Sequencing Characterizes Intertidal Meiofaunal Communities in Northern Gulf of Mexico (Dauphin Island and Mobile Bay, Alabama)

(2016) Pamela M. Brannock et al.   BIOLOGICAL BULLETIN

Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria

(2016) Christina Bienhold et al.   PLoS One

A comparison of DNA extraction methods for biodiversity studies of eukaryotes in marine sediments

(2015) K Lekang et al.   AQUATIC MICROBIAL ECOLOGY

Towards a better quantitative assessment of the relevance of deep-sea viruses, Bacteria and Archaea in the functioning of the ocean seafloor

(2015) R Danovaro et al.   AQUATIC MICROBIAL ECOLOGY

Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity

(2015) Philip Francis Thomsen et al.   BIOLOGICAL CONSERVATION

Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries

(2015) Anthony A. Chariton et al.   ENVIRONMENTAL POLLUTION

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

(2015) Joana Amorim Visco et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Use of continuous, real-time observations and model simulations to achieve autonomous, adaptive sampling of microbial processes with a robotic sampler

(2015) Lydie Herfort et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Meiofaunal community analysis by high-throughput sequencing: Comparison of extraction, quality filtering, and clustering methods

(2015) Pamela M. Brannock et al.   Marine Genomics

Metagenetic tools for the census of marine meiofaunal biodiversity: An overview

(2015) Laura Carugati et al.   Marine Genomics

Is there a possibility of ranking benthic quality assessment indices to select the most responsive to different human pressures?

(2015) Ángel Borja et al.   MARINE POLLUTION BULLETIN

Microbial Surface Colonization and Biofilm Development in Marine Environments

(2015) Hongyue Dang et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Complex archaea that bridge the gap between prokaryotes and eukaryotes

(2015) Anja Spang et al.   NATURE

Virus decomposition provides an important contribution to benthic deep-sea ecosystem functioning

(2015) Antonio Dell’Anno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Agricultural insecticides threaten surface waters at the global scale

(2015) Sebastian Stehle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats

(2015) Jizhong Zhou et al.   mBio

Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors

(2015) Mark B. Smith et al.   mBio

A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types

(2015) Mark A. Lever et al.   Frontiers in Microbiology

Patterns of benthic bacterial diversity in coastal areas contaminated by heavy metals, polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs)

(2015) Grazia Marina Quero et al.   Frontiers in Microbiology

Is the meiofauna a good indicator for climate change and anthropogenic impacts?

(2015) Daniela Zeppilli et al.   Marine Biodiversity

Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data

(2015) Katrin Panzer et al.   PLoS One

Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons

(2015) Magdalena Guardiola et al.   PLoS One

Machine Learning methods for Quantitative Radiomic Biomarkers

(2015) Chintan Parmar et al.   Scientific Reports

High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems

(2015) Franck Lejzerowicz et al.   Scientific Reports

Patchiness of deep-sea benthic Foraminifera across the Southern Ocean: Insights from high-throughput DNA sequencing

(2014) Franck Lejzerowicz et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

A molecular-based approach for examining responses of eukaryotes in microcosms to contaminant-spiked estuarine sediments

(2014) Anthony A. Chariton et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes

(2014) Vera G. Fonseca et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems

(2014) Delphine Lallias et al.   ISME Journal

A procedure for separate recovery of extra- and intracellular DNA from a single marine sediment sample

(2014) Mashal Alawi et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data

(2014) Gentile F. Ficetola et al.   Molecular Ecology Resources

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

(2014) Jonas Zimmermann et al.   Molecular Ecology Resources

Fungal diversity from various marine habitats deduced through culture-independent studies

(2013) Cathrine Sumathi Manohar et al.   FEMS MICROBIOLOGY LETTERS

Dispersal and gene flow in free-living marine nematodes

(2013) Sofie Derycke et al.   Frontiers in Zoology

Analysis of the bacterial community in the two typical intertidal sediments of Bohai Bay, China by pyrosequencing

(2013) Liping Wang et al.   MARINE POLLUTION BULLETIN

From research to operational biomonitoring of freshwaters: a suggested conceptual framework and practical solutions

(2013) Michel Lafont et al.   ECOHYDROLOGY & HYDROBIOLOGY

PCR inhibitors - occurrence, properties and removal

(2012) C. Schrader et al.   JOURNAL OF APPLIED MICROBIOLOGY

The use of benthic macroinvertebrates to establish a benchmark for evaluating the environmental quality of microtidal, temperate southern hemisphere estuaries

(2012) J.R. Tweedley et al.   MARINE POLLUTION BULLETIN

Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil Spill

(2012) Holly M. Bik et al.   PLoS One

Do nematode and macrofauna assemblages provide similar ecological assessment information?

(2011) Joana Patrício et al.   ECOLOGICAL INDICATORS

Three hundred ways to assess Europe's surface waters: An almost complete overview of biological methods to implement the Water Framework Directive

(2011) Sebastian Birk et al.   ECOLOGICAL INDICATORS

Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton

(2011) Elizabeth A Ottesen et al.   ISME Journal

Response of single benthic metrics and multi-metric methods to anthropogenic pressure gradients, in five distinct European coastal and transitional ecosystems

(2011) Angel Borja et al.   MARINE POLLUTION BULLETIN

Two decades of describing the unseen majority of aquatic microbial diversity

(2011) LUCIE ZINGER et al.   MOLECULAR ECOLOGY

The use of nematodes in assessing ecological quality status in the Mediterranean coastal ecosystems

(2010) Mariapaola Moreno et al.   ECOLOGICAL INDICATORS

Life history allometries and production of small fauna

(2010) Julia Reiss et al.   ECOLOGY

On the quantitative distribution and community structure of the meio and macrofaunal communities in the coastal area of the Central Adriatic Sea (Italy)

(2010) Fabrizio Frontalini et al.   ENVIRONMENTAL MONITORING AND ASSESSMENT

Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

(2010) Anthony A Chariton et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

First audit of macroinvertebrate samples from an EU Water Framework Directive monitoring program: human error greatly lowers precision of assessment results

(2010) Peter Haase et al.   JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

(2010) S. CREER et al.   MOLECULAR ECOLOGY

Second-generation environmental sequencing unmasks marine metazoan biodiversity

(2010) Vera G. Fonseca et al.   Nature Communications

Assessment of Bias Associated with Incomplete Extraction of Microbial DNA from Soil

(2009) L. M. Feinstein et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantitative PCR methods for RNA and DNA in marine sediments: maximizing yield while overcoming inhibition

(2009) Karen G. Lloyd et al.   FEMS MICROBIOLOGY ECOLOGY

Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands

(2009) Simone I Böer et al.   ISME Journal

Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor

(2009) F. Scheckenbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Refinement of biomonitoring of urban water courses by combining descriptive and ecohydrological approaches

(2009) Michel Lafont et al.   ECOHYDROLOGY & HYDROBIOLOGY

Overview of integrative tools and methods in assessing ecological integrity in estuarine and coastal systems worldwide

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