Unearthing the Potential of Soil eDNA Metabarcoding—Towards Best Practice Advice for Invertebrate Biodiversity Assessment

Comparing diversity levels in environmental samples: DNA sequence capture and metabarcoding approaches using 18S and COI genes

(2020) H Giebner et al.   Molecular Ecology Resources

Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches

(2019) Daniel Marquina et al.   Molecular Ecology Resources

COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems

(2019) Mehrdad Hajibabaei et al.   PLoS One

Validation of COI metabarcoding primers for terrestrial arthropods

(2019) Vasco Elbrecht et al.   PeerJ

Variations in terrestrial arthropod DNA metabarcoding methods recovers robust beta diversity but variable richness and site indicators

(2019) Teresita M. Porter et al.   Scientific Reports

A DNA metabarcoding approach to characterize soil arthropod communities

(2018) Angela M. Oliverio et al.   SOIL BIOLOGY & BIOCHEMISTRY

Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities

(2018) Guang K. Zhang et al.   Evolutionary Applications

New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods

(2018) Daniel Marquina et al.   Molecular Ecology Resources

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

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

PER-SIMPER-A new tool for inferring community assembly processes from taxon occurrences

(2018) Corentin Gibert et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Body size determines soil community assembly in a tropical forest

(2018) Lucie Zinger et al.   MOLECULAR ECOLOGY

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

Circular linkages between soil biodiversity, fertility and plant productivity are limited to topsoil at the continental scale

(2017) Manuel Delgado-Baquerizo et al.   NEW PHYTOLOGIST

Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

(2017) Tobias Guldberg Frøslev et al.   Nature Communications

Sorting things out: Assessing effects of unequal specimen biomass on DNA metabarcoding

(2017) Vasco Elbrecht et al.   Ecology and Evolution

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

(2017) Laurence J. Clarke et al.   Ecology and Evolution

Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA

(2016) Lucie Zinger et al.   SOIL BIOLOGY & BIOCHEMISTRY

iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

(2016) T. C. Hsieh et al.   Methods in Ecology and Evolution

The ecologist's field guide to sequence-based identification of biodiversity

(2016) Simon Creer et al.   Methods in Ecology and Evolution

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

DNA metabarcoding of insects and allies: an evaluation of primers and pipelines

(2015) G.-J. Brandon-Mong et al.   BULLETIN OF ENTOMOLOGICAL RESEARCH

Evaluating a multigene environmental DNA approach for biodiversity assessment

(2015) Alexei J. Drummond et al.   GigaScience

DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match

(2014) B. E. Deagle et al.   Biology Letters

Using metabarcoding to ask if easily collected soil and leaf-litter samples can be used as a general biodiversity indicator

(2014) Chenxue Yang et al.   ECOLOGICAL INDICATORS

A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

(2013) Matthieu Leray et al.   Frontiers in Zoology

Linking invertebrate communities to decomposition rate and nitrogen availability in pine forest soils

(2012) D.A. Neher et al.   APPLIED SOIL ECOLOGY

Tracking earthworm communities from soil DNA

(2012) FRIEDERIKE BIENERT et al.   MOLECULAR ECOLOGY

New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

(2012) LAURA S. EPP et al.   MOLECULAR ECOLOGY

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

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

(2012) C. Q. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity

(2012) ChenXue Yang et al.   Science China-Life Sciences

Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

(2012) Douglas W. Yu et al.   Methods in Ecology and Evolution

betapart: an R package for the study of beta diversity

(2012) Andrés Baselga et al.   Methods in Ecology and Evolution

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos

(2011) Mehrdad Hajibabaei et al.   PLoS One

Accessing the Soil Metagenome for Studies of Microbial Diversity

(2010) Tom O. Delmont et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The Enigma of Soil Animal Species Diversity Revisited: The Role of Small-Scale Heterogeneity

(2010) Uffe N. Nielsen et al.   PLoS One

Extracellular DNA in soil and sediment: fate and ecological relevance

(2008) G. Pietramellara et al.   BIOLOGY AND FERTILITY OF SOILS