Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Freshwater Microbial Ecology

Freshwater Microbial Ecology

Freshwater systems such as streams, rivers, and lakes exhibit distinct physical and biological characteristics that influence their microbial communities. These environments are broadly categorized into lotic systems—those with flowing waters like streams and most rivers—and lentic systems, which include still or slow-moving waters such as lakes, ponds, and marshes.In lentic systems, phytoplankton drive primary production, generating autochthonous organic carbon. In contrast, lotic systems...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Testing the waters: A comparison of DNA extraction methods for the metabarcoding of microbial communities.

Marine environmental research·2026

Same author

Asymmetrical hybridization and environmental factors influence the spatial genetic structure of a killifish hybrid zone.

Evolution; international journal of organic evolution·2024

Same author

Geographic genetic variation in the Coral Hawkfish, <i>Cirrhitichthys oxycephalus</i> (Cirrhitidae), in relation to biogeographic barriers across the Tropical Indo-Pacific.

PeerJ·2024

Same author

Isolation, whole-genome sequencing, and annotation of two antibiotic-producing and antibiotic-resistant bacteria, Pantoea rodasii RIT 836 and Pseudomonas endophytica RIT 838, collected from the environment.

PloS one·2024

Same author

Perceptions of Palliative and End-Of-Life Care Capacity Among Frontline Staff and Administrators in Long-Term Care Homes During the COVID-19 Pandemic in Ontario, Canada: A Mixed-Methods Evaluation.

Journal of the American Medical Directors Association·2023

Same author

Importance of timely metadata curation to the global surveillance of genetic diversity.

Conservation biology : the journal of the Society for Conservation Biology·2023

Search research articles

Related Experiment Video

Updated: Jun 27, 2026

Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA

Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA

Published on: November 25, 2016

Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary.

Girish Kumar¹, Ashley M Reaume¹, Emily Farrell¹

¹Department of Biology, University of Central Florida, Genomics and Bioinformatics Cluster, Orlando, FL, United States of America.

|June 17, 2022

Summary

Comparing environmental DNA (eDNA) metabarcoding primers for fish surveys revealed the Riaz_12S primer set as most effective. This study highlights the importance of selecting appropriate primers for accurate aquatic biodiversity assessments.

More Related Videos

Laboratory Protocol for Genetic Gut Content Analyses of Aquatic Macroinvertebrates Using Group-specific rDNA Primers

Laboratory Protocol for Genetic Gut Content Analyses of Aquatic Macroinvertebrates Using Group-specific rDNA Primers

Published on: October 5, 2017

The Floating Lab: Standard Operational Procedure for Collecting and Filtering Seawater Samples from Operating Ferries for Environmental DNA Analysis

The Floating Lab: Standard Operational Procedure for Collecting and Filtering Seawater Samples from Operating Ferries for Environmental DNA Analysis

Published on: August 1, 2025

Related Experiment Videos

Last Updated: Jun 27, 2026

Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA

Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA

Published on: November 25, 2016

Laboratory Protocol for Genetic Gut Content Analyses of Aquatic Macroinvertebrates Using Group-specific rDNA Primers

Laboratory Protocol for Genetic Gut Content Analyses of Aquatic Macroinvertebrates Using Group-specific rDNA Primers

Published on: October 5, 2017

The Floating Lab: Standard Operational Procedure for Collecting and Filtering Seawater Samples from Operating Ferries for Environmental DNA Analysis

The Floating Lab: Standard Operational Procedure for Collecting and Filtering Seawater Samples from Operating Ferries for Environmental DNA Analysis

Published on: August 1, 2025

Area of Science:

Environmental DNA (eDNA) metabarcoding
Aquatic biodiversity assessment
Molecular ecology

Background:

Metabarcoding of environmental DNA is a powerful tool for assessing aquatic biodiversity.
Primer selection significantly impacts the efficiency and outcomes of eDNA metabarcoding studies.
Limited comparative studies exist for marine and estuarine fish metabarcoding primers.

Purpose of the Study:

To evaluate and compare the performance of five commonly used fish metabarcoding primer sets.
To identify the most effective primer set for eDNA-based fish surveys in estuarine systems.

Main Methods:

Collected water samples from estuarine sites in the Indian River Lagoon, Florida.
Amplified target genes (12S, 16S, 18S rRNA) using five different primer sets.
Analyzed metabarcoding reads to identify fish species and compare primer set efficacy.

Main Results:

The Riaz_12S and Berry_16S primer sets detected a comparable and higher number of fish species (55 and 49) than MiFish_12S and Valentini_12S (34 and 32).
The 18S primer set showed poor specificity, with most reads assigned to non-fish taxa.
The Riaz_12S primer set detected the most elasmobranch species (six) and was identified as the most effective overall for fish surveys.

Conclusions:

Primer choice critically influences the results of eDNA metabarcoding for fish biodiversity assessments.
The Riaz_12S primer set demonstrated superior performance for detecting fish diversity in this estuarine system.
Employing multiple primer sets targeting different genomic regions can enhance comprehensive biodiversity detection.