Environmental DNA and environmental RNA: Current and prospective applications for biological monitoring

High Throughput Sequencing of MicroRNA in Rainbow Trout Plasma, Mucus, and Surrounding Water Following Acute Stress

(2021) Heather Ikert et al.   Frontiers in Physiology

Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects

(2020) Kingsly C. Beng et al.   BIODIVERSITY AND CONSERVATION

MicroRNA profiling identifies biomarkers in head kidneys of common carp exposed to cadmium

(2020) Qi Liu et al.   CHEMOSPHERE

DNA metabarcoding of stream invertebrates reveals spatio-temporal variation but consistent status class assessments in a natural and urban river

(2020) Vera M.A. Zizka et al.   ECOLOGICAL INDICATORS

Environmental DNA allows upscaling spatial patterns of biodiversity in freshwater ecosystems

(2020) Luca Carraro et al.   Nature Communications

Remote, autonomous real-time monitoring of environmental DNA from commercial fish

(2020) Brian K. Hansen et al.   Scientific Reports

Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment

(2020) Noriko Uchida et al.   PeerJ

Modeling the ecological status response of rivers to multiple stressors using machine learning: A comparison of environmental DNA metabarcoding and morphological data

(2020) Juntao Fan et al.   WATER RESEARCH

A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish

(2020) Shan Zhang et al.   Methods in Ecology and Evolution

Comparing fish prey diversity for a critically endangered aquatic mammal in a reserve and the wild using eDNA metabarcoding

(2020) Chanjuan Qu et al.   Scientific Reports

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

Keeping invertebrate research ethical in a landscape of shifting public opinion

(2019) Eleanor Drinkwater et al.   Methods in Ecology and Evolution

Identification and expression of microRNAs in european eels Anguilla anguilla from two natural sites with different pollution levels

(2019) Anthony Bertucci et al.   ENVIRONMENTAL POLLUTION

Developing an eDNA toolkit to quantify broadcast spawning events of the sea scallop Placopecten magellanicus: moving beyond fertilization assays

(2019) SR Bayer et al.   MARINE ECOLOGY PROGRESS SERIES

Environmental DNA provides quantitative estimates of a threatened salmon species

(2019) Andrew Olaf Shelton et al.   BIOLOGICAL CONSERVATION

Hexavalent chromium-induced toxic effects on the antioxidant levels, histopathological alterations and expression of Nrf2 and MT2 genes in the branchial tissue of Ctenopharyngodon idellus

(2019) Rajinder Jindal et al.   CHEMOSPHERE

Characterisation of the metallothionein gene in the Sydney rock oyster and its expression upon metal exposure in oysters with different prior metal exposure histories

(2019) Thanvapon Yingprasertchai et al.   MARINE ENVIRONMENTAL RESEARCH

Can Environmental RNA Revolutionize Biodiversity Science?

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

Non‐specific amplification compromises environmental DNA metabarcoding with COI

(2019) Rupert A. Collins et al.   Methods in Ecology and Evolution

Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats

(2019) Eva Egelyng Sigsgaard et al.   CONSERVATION BIOLOGY

Predicting the fate of eDNA in the environment and implications for studying biodiversity

(2019) Jori B. Harrison et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Environmental DNA size sorting and degradation experiment indicates the state of Daphnia magna mitochondrial and nuclear eDNA is subcellular

(2019) Rashnat Moushomi et al.   Scientific Reports

Monitoring spawning migrations of potamodromous fish species via eDNA

(2019) Bettina Thalinger et al.   Scientific Reports

Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis

(2018) Teresita M. Porter et al.   MOLECULAR ECOLOGY

Fluctuating interaction network and time-varying stability of a natural fish community

(2018) Masayuki Ushio et al.   NATURE

Degradation and dispersion limit environmental DNA detection of rare amphibians in wetlands: Increasing efficacy of sampling designs

(2018) Caren S. Goldberg et al.   SCIENCE OF THE TOTAL ENVIRONMENT

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

(2018) Jan Pawlowski et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Biomonitoring of intermittent rivers and ephemeral streams in Europe: Current practice and priorities to enhance ecological status assessments

(2018) Rachel Stubbington et al.   SCIENCE OF THE TOTAL ENVIRONMENT

An issue of life or death: using eDNA to detect viable individuals in wilderness restoration

(2018) Colleen Kamoroff et al.   Freshwater Science

An issue of life or death: using eDNA to detect viable individuals in wilderness restoration

(2018) Colleen Kamoroff et al.   Freshwater Science

Defence mechanisms: the role of physiology in current and future environmental protection paradigms

(2018) Chris N Glover   Conservation Physiology

Why the COI barcode should be the community DNA metabarcode for the metazoa

(2018) Carmelo Andújar et al.   MOLECULAR ECOLOGY

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

The presence of extracellular microRNAs in the media of cultured Drosophila cells

(2018) Stijn Van den Brande et al.   Scientific Reports

Identifying spawning sites and other critical habitat in lotic systems using eDNA “snapshots”: A case study using the sea lamprey Petromyzon marinus L.

(2018) Fiona S. A. Bracken et al.   Ecology and Evolution

Environmental DNA analysis as a non-invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers

(2018) Atsushi Maruyama et al.   Ecology and Evolution

Global microRNA and isomiR expression associated with liver metabolism is induced by organophosphorus flame retardant exposure in male Chinese rare minnow (Gobiocypris rarus)

(2018) Xiangsheng Hong et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Early detection monitoring for aquatic non-indigenous species: Optimizing surveillance, incorporating advanced technologies, and identifying research needs

(2017) Anett S. Trebitz et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

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

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity

(2017) Iliana Bista et al.   Nature Communications

Experimental observations on the decay of environmental DNA from bighead and silver carps

(2017) Richard Lance et al.   Management of Biological Invasions

Stability of Circulating Blood-Based MicroRNAs – Pre-Analytic Methodological Considerations

(2017) Charlotte Glinge et al.   PLoS One

The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau

(2017) Chao Tong et al.   PLoS One

A systematic approach to evaluate the influence of environmental conditions on eDNA detection success in aquatic ecosystems

(2017) Bernhard C. Stoeckle 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

Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea

(2017) Satoshi Yamamoto et al.   Scientific Reports

Hypoxia alters testicular functions of marine medaka through microRNAs regulation

(2016) Anna Chung-Kwan Tse et al.   AQUATIC TOXICOLOGY

Influence of Stream Bottom Substrate on Retention and Transport of Vertebrate Environmental DNA

(2016) Christopher L. Jerde et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Is there an ideal protocol for sampling macroinvertebrates in springs?

(2016) Melissa Rosati et al.   JOURNAL OF FRESHWATER ECOLOGY

Using environmental (e)DNA sequencing for aquatic biodiversity surveys: a beginner’s guide

(2016) Jennifer L. A. Shaw et al.   MARINE AND FRESHWATER RESEARCH

Critical considerations for the application of environmental DNA methods to detect aquatic species

(2016) Caren S. Goldberg et al.   Methods in Ecology and Evolution

The biology of environmental stress: molecular biomarkers in Sydney rock oysters (Saccostrea glomerata)

(2016) D. A. Raftos et al.   Environmental Science-Processes & Impacts

Environmental DNA detects Critically Endangered largetooth sawfish in the wild

(2016) CA Simpfendorfer et al.   Endangered Species Research

Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms

(2015) Katherine M. Strickler et al.   BIOLOGICAL CONSERVATION

Fish environmental DNA is more concentrated in aquatic sediments than surface water

(2015) Cameron R. Turner et al.   BIOLOGICAL CONSERVATION

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

(2015) Philip Francis Thomsen et al.   BIOLOGICAL CONSERVATION

Development and application of an eDNA method to detect and quantify a pathogenic parasite in aquatic ecosystems

(2015) J. R. Huver et al.   ECOLOGICAL APPLICATIONS

eDNA and specific primers for early detection of invasive species – A case study on the bivalve Rangia cuneata, currently spreading in Europe

(2015) Alba Ardura et al.   MARINE ENVIRONMENTAL RESEARCH

The Whereabouts of microRNA Actions: Cytoplasm and Beyond

(2015) Anthony K.L. Leung   TRENDS IN CELL BIOLOGY

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

Seasonal variations of gene expression biomarkers in Mytilus galloprovincialis cultured populations: Temperature, oxidative stress and reproductive cycle as major modulators

(2014) Sergio Jarque et al.   SCIENCE OF THE TOTAL ENVIRONMENT

The tiny mayfly in the room: implications of size-dependent invertebrate taxonomic identification for biomonitoring data properties

(2013) Jessica M. Orlofske et al.   AQUATIC ECOLOGY

Differential effects of metal contamination on the transcript expression of immune- and stress-response genes in the Sydney Rock oyster, Saccostrea glomerata

(2013) Daisy A. Taylor et al.   ENVIRONMENTAL POLLUTION

Effects of electric field exposure on blood pressure, cardioventilatory activity and the physiological stress response in Arctic char, Salvelinus alpinus L.

(2012) Erik Sandblom et al.   AQUACULTURE

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

Glutathione, glutathione S-transferase, and glutathione conjugates, complementary markers of oxidative stress in aquatic biota

(2012) Jocelyne Hellou et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples

(2012) Hirokazu Toju et al.   PLoS One

Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records

(2011) Arjan C. Boere et al.   ORGANIC GEOCHEMISTRY

Biological functions of microRNAs: a review

(2010) Yong Huang et al.   JOURNAL OF PHYSIOLOGY AND BIOCHEMISTRY

Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals

(2008) Andrew Grimson et al.   NATURE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Circulating microRNAs as stable blood-based markers for cancer detection

(2008) P. S. Mitchell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Vitellogenin as a biomarker of exposure to estrogenic compounds in aquatic invertebrates: A review

(2007) Valerio Matozzo et al.   ENVIRONMENT INTERNATIONAL