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.

An Isotopic Tune

A couple of years ago, Brian Fry, one of the founders of stable isotope ecology, was – in his own words – “touring through Europe” (yes, there are some similarities between good scientists and rock stars). During the insightful talk he gave at Stockholm University, he compared the periodic table and the 25 elements essential to life to a keyboard ready to be played by isotope ecologists. But to his concern, all that we are doing is constantly hitting two keys – carbon and nitrogen – over and over again.

Cave Angel Fish in Mae Hongson, Thailand. ©Chulabush Khatancharoen

In this regard, Dr Jia Liew and colleagues started to make some music in their recent paper ‘Quantifying terrestrial carbon in freshwater food webs using amino acid isotope analysis’. They use improved isotope-based methods to quantify terrestrial carbon inputs into aquatic food webs. Instead of applying a bulk isotope approaches, Liew et al. rely on analyses of isotopic ratios in individual amino acids. This substantially extends the number of available tracers, boosting the power of their analysis. By combining literature data with their own measurements, they show that essential amino acids have consistent differences in isotopic values between autochthonous (aquatic) and allochthonous (terrestrial) carbon sources.

A remarkable finding was that these differences in the isotopic fingerprints of terrestrial plants and aquatic derived biomass were consistent and largely independent from sampling location. These universal differences might help us to trace carbon pathways across ecosystem boundaries and represent an exciting opportunity for future research and method development.

There are still a number of hurdles to overcome for broad-scale application of this method. Sample sizes are small and the assumption that isotope values of essential amino acid do not change with trophic transfer still requires thorough testing. But the first sounds of this isotopic tune are very promising. They might well be picked up by a marching band soon.

Mapping Habitat Use Across River Basins

A second exciting application of stable isotopes is the study of changes in dietary habits across space and time. Migratory patterns of fish can be hard to study. They truly embrace complexity and often switch habitats throughout their life cycle. Stable isotopes have been widely used across ecological studies to study resource use and food webs. Increasingly, they’re being used to study animal migration too. The term ‘isoscapes’ was coined by West et al. to describe the use of isotope patterns across landscapes to study such movement.

A large male Chinook salmon that returned from the ocean. ©California Sea Grant

A recent study made use of stable isotopes from continuously growing tissues to create something like a dietary time series for individuals. Tissues like hair, otoliths, and teeth grow continuously and their chemical composition varies depending on what resources the animal was feeding on during their production. That means they contain a collection of isotopic traces from an animal’s dietary past.

Brennan et al. used this principle to develop a novel model investigating habitat use of migratory fish over time: the space‐time isotope model of provenance (STIMP). STIMP integrates data on stable isotopes, habitat, and fish movement patterns, and the authors demonstrate its applicability with Chinook salmon in Alaska, USA. They show that individuals use many different habitat types during juvenile life stage and that habitat may vary spatially across river basins.

Being able to identify habitat use at different stages of a species’ life and across their spatial distribution is important for species management and conservation. Advances in integrating diverse information sources as done by Brennan et al. hold great potential for understanding migratory species behaviour and changing use of resources. It highlights the importance of detailed data collection for the study and conservation of riverine systems.

Improving the Detection of Closely Related Species Based on Environmental DNA

Detection of DNA traces left by organisms in aquatic environments is now routinely used for rare species monitoring and early detection of invasive species. But, DNA sequences from co-occurring or closely related species can be difficult to distinguish, even when using species-specific detection methods.

Fish – a diverse resource in rivers targeted in studies on Chinook salmon, Lake whitefish and cave fish. ©Marco Verch

Since the publication of ‘Species detection using environmental DNA from water samples’ by Ficetola et al., a number of studies have reported difficulties targeting specific species. This is usually due to the lack of sequence polymorphism with congeneric species. In ‘Use of RNase H‐dependent PCR for discrimination and detection of closely related species from environmental DNA’ Rodgers et al.  provide a potential solution to this problem.

The use of a novel primer technology allows them to detect and discriminate between closely related species using eDNA samples. Specifically, they rely on a RNase H-dependant PCR (rhPCR). This method uses cleavable primers in combination with the enzyme RNase H2 to increase the specificity of PCR/qPCR reaction. The authors design two assays using rhPCR for detecting two closely related Coregonus species: C. sardinella (least cisco) and C. nasus (broad whitefish). After proper validation of their methods, they managed to monitor both species using eDNA detection from locations previously sampled with conventional methods.

The application of rhPCR represents an advance in eDNA research, but the authors highlighted the rhPCR was highly sensitive to inhibition. In this study, the use of an inhibition removal kit reduced those effects. But the usage such kits comes at the cost of removing also target eDNA and so it lowers the sensitivity of eDNA detection. It’s intriguing to think about future combinations of rhPCR and ddPCR, which is much less sensitive to inhibition. Using them together could give both high specificity and sensitivity of eDNA-based measurements.

Salmon spawning grounds in Alaska.

The environmental threats to our river systems are numerous. But so are the methodological advancements which can be used for river management and conservation. Stable isotopes and eDNA techniques are only some of the tools that can reveal complex ecological dynamics. And they can be used to demonstrate a wide public audience who care about our waterways and how to protect and restore them.

Isn’t that a good reason to celebrate? A happy World Rivers Day to everyone!