Tag Archives: eDNA

A Celebration of World Rivers Day

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Post provided by Alfred Burian, Antonia Ford and Quentin Mauvisseau

Celebrating our river ecosystems world-wide on the 22nd of September.

Celebrating our river ecosystems world-wide on the 22nd of September. ©Bob Wick, BLM.

It’s the 22nd of September and that means it’s this year’s UN World Rivers Day! In over 60 countries around the globe events are going on today to bring attention to the many values of our waterways. And we, the Aquatic Ecology Special Interest Group of the BES, are joining in with the celebrations! We’re highlighting recent methodological advancements that will help us to manage and conserve our rivers in the future. So let’s get started…

Multiple Stressors and Molecular Tools

Today, human activities across the world are impacting rivers to varying degrees. As scientists, we frequently see the interaction of multiple different stressors such as flow regulations, pollution or climate change affecting our rivers. The combined impact of stressors like these may be worse than any of their individual impacts. To understand and manage the effect of them, we need cost-effective and reliable analytical tools that can capture site-specific and ecosystem-wide effects.

Recent methodological advances that will help us to achieve these goals often rely on the application of new or improved molecular tools. Emerging techniques include environmental DNA (eDNA) based applications to monitor endangered and invasive species as well as stable isotope ecology, which provides us with new insights into animal diets and energy flows through aquatic food webs. We’d like to take the opportunity to introduce some of the novel developments in both of these exciting fields. Continue reading →

Issue 10.9: Phenotypes, Species Interactions, Biodiversity and More

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The September issue of Methods is now online!

We’ve got another brilliant issue of Methods in Ecology and Evolution out today. In another bumper 250 page offering, you’ll find articles on identifying waterbird hotspots, identity metrics, capture-recapture methods (and the alternative close-kin mark-recpature) and way more.

Don’t have a subscription to the journal? No need to worry – this month’s issue has TEN articles that are free to access for absolutely anyone. You can find out about all 10 below.

Keep reading for a little more information on the September issue of Methods in Ecology and Evolution. Continue reading →

New eDNA Programme Makes Conservation Research Faster and More Efficient

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Below is a press release about the Methods in Ecology and Evolution article ‘Anacapa Toolkit: An environmental DNA toolkit for processing multilocus metabarcode datasets‘ taken from UCLA.

It’s estimated that a person sheds between 30,000 to 40,000 skin cells per day. These cells and their associated DNA leave genetic traces of ourselves in showers, dust — pretty much everywhere we go.

Other organisms shed cells, too, leaving traces throughout their habitats. This leftover genetic material is known as environmental DNA, or eDNA. Research using eDNA began about a decade ago, but was largely limited to a small cadre of biologists who were also experts in computers and big data. However, a new tool from UCLA could be about to make the field accessible and useful to many more scientists.

A team of UCLA researchers recently launched the Anacapa Toolkit — open-source software that makes eDNA research easier, allowing researchers to detect a broad range of species quickly and producing sortable results that are simple to understand. Continue reading →

The Self-Preserving eDNA Filter: How It Works and Why You Should Use It

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Researchers at Washington State University and Smith-Root recently invented an environmental DNA (eDNA) filter housing that automatically preserves captured eDNA by desiccation. This eliminates the need for filter handling in the field and/or liquid DNA preservatives. The new material is also biodegradable, helping to reduce long-lasting plastic waste associated with eDNA sampling.

This video explains their new innovation in the field of eDNA sampling technology:

To find out more about the self-preserving eDNA filter, read the full, Open Access Methods in Ecology and Evolution article ‘A self‐preserving, partially biodegradable eDNA filter‘
(No Subscription Required).

If you’re using interesting new field techniques like this, why not submit a Practical Tools manuscript about them? You can find out more about Practical Tools manuscripts here.

Making a Self-Preserving eDNA Filter

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Below is a press release about the Methods in Ecology and Evolution article ‘A self‐preserving, partially biodegradable eDNA filter‘ taken from the Smith-Root.

A new self-preserving filter housing automatically preserves eDNA, while reducing the risk of contamination, and creating less plastic waste.

Researcher collecting an eDNA sample using the self-preserving filter housing.

In 2015 the inventor of the Keurig disposable coffee cartridge (K-Cups) told reporters that sometimes he regrets ever inventing the technology. The single-use design simply produces too much non-recyclable trash. Well, that very same problem is what ultimately led to the creation of a self-preserving filter for environmental DNA (eDNA); a recently reported Practical Tool in Methods in Ecology and Evolution.

eDNA scientists rely on single-use sampling equipment because eDNA surveys are highly sensitive to potential contamination. “We started out simply looking for biodegradable plastics that could be molded into a filter housing, with the objective of reducing plastic waste.” says Dr. Austen Thomas who led the team of researchers and engineers who invented the Smith-Root eDNA Sampler. “That’s when we realized that some of the biodegradable compounds function by being highly hydrophilic.” Continue reading →

Using the Smith-Root ANDe System for Wildlife Conservation

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POST PROVIDED BY TRACIE SEIMON, PHD

The ANDe system can help researchers tell whether endangered species are present.

The ANDe system can help researchers tell whether endangered species are present.

In recent years, there have been a lot of studies on the use of environmental DNA (eDNA) for species detection and monitoring. This method takes advantage of the fact that organisms shed DNA into the environment in the form of urine, feces, or cells from tissue such as skin. As this DNA stays in the environment, we can use molecular techniques to search for traces of it. By doing this, we can determine if a species lives in a particular place.

At the Wildlife Conservation Society (WCS), we’re integrating and using the ANDe system in combination with ultra-portable qPCR (quantitative polymerase chain reaction) and DNA extraction technologies developed by Biomeme Inc. for eDNA capture and species detection of endangered turtles, and other aquatic organisms. This helps us to better monitor species within our global conservation programs. Continue reading →

Editor Recommendation: Assessing Strengths and Weaknesses of DNA Metabarcoding-Based Macroinvertebrate Identification for Routine Stream Monitoring

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Post provided by Andrew R. Mahon

The use of molecular methods for monitoring and surveillance of organisms in aquatic and marine systems has become more and more common. We’ve since expanded this technology this through using both captured whole organisms and collecting/filtering environmental DNA (eDNA).  These methods naturally migrated from single species, active surveillance methods towards using high throughput sequencing as a method of passive surveillance via metabarcoding.

In this virtual issue, the article “Assessing strengths and weaknesses of DNA metabarcoding-based macroinvertebrate identification for routine stream monitoring” by Vasco Elbrecht et al. provides an excellent overview to the field. It also helps to clarify the work being done to provide interested groups, including management agencies, with the best practices for utilising these new methods for monitoring and surveillance.  This work will help the field, particularly for those searching for rare species of organisms in aquatic systems.

I’d recommend this paper to all researchers and management groups interested in applying metabarcoding techniques to answer both experimental and applied questions. The design of this article will provide both experienced researchers and those new to the field with important information to further this rapidly expanding field.

To find out more about, read the full Methods in Ecology and Evolution article ‘Assessing strengths and weaknesses of DNA metabarcoding-based macroinvertebrate identification for routine stream monitoring’

 This article is part of ‘Practical Tools: A Field Methods Virtual Issue’. All articles in this Virtual Issue will be available for a limited time.

ANDe™: High‐Throughput eDNA Sampling in a Fully Integrated System

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Current eDNA sampling technologies consist mainly of do‐it‐yourself solutions. The lack of purpose‐built sampling equipment is limiting the efficiency and standardization of eDNA studies. So, Thomas et al. (a team of molecular ecologists and engineers) designed ANDe™.

In this video, the authors highlight the key features and benefits of ANDe™. This integrated system includes a backpack-portable pump that integrates sensor feedback, a pole extension with remote pump controller, custom‐made filter housings in single‐use packets for each sampling site and on-board sample storage. 

This video is based on the article ‘ANDe™: A fully integrated environmental DNA sampling system‘ by Thomas et al.

Uncertainties in Species Occurrence Data: How to deal with False Positives and False Negatives

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Post provided by Gurutzeta Guillera-Arroita

Species Surveys: New Opportunities and Ongoing Data Challenges

Technologies, such as drones, open new opportunities for wildlife monitoring ©J. Lahoz-Monfort, UMelb.

Technologies, such as drones, open new opportunities for wildlife monitoring ©J. Lahoz-Monfort, UMelb.

Monitoring is a fundamental step in the management of any species. The collection and careful analysis of species data allows us to make informed decisions about management priorities and to critically evaluate our actions. There are many aspects of a natural system that we can measure and, when it comes to monitoring the status of species, occurrence is a commonly used metric.

Ecologists have a long history of collecting species occurrence data from systematic surveys and our ability to gather species data is only going to grow! This is partly enabled by the fact that citizen science programs are starting to gain a prominent role in wildlife monitoring. There’s a growing recognition that well-managed citizen science surveys can produce useful data, while scaling up monitoring effort thanks to the increased human-power from large numbers of committed volunteers. Continue reading →