One water bucket to find them all: Detecting fish, mammals, and birds from a single sample

Revolutionary environmental DNA analysis holds great potential for the future of biodiversity monitoring, concludes a new study.

Revolutionary environmental DNA analysis holds great potential for the future of biodiversity monitoring, concludes a new study

Collection of water samples for eDNA metabarcoding bioassessment.
Photo by Till-Hendrik Macher.

In times of exacerbating biodiversity loss, reliable data on species occurrence are essential, in order for prompt and adequate conservation actions to be initiated. This is especially true for freshwater ecosystems, which are particularly vulnerable and threatened by anthropogenic impacts. Their ecological status has already been highlighted as a top priority by multiple national and international directives, such as the European Water Framework Directive.

However, traditional monitoring methods, such as electrofishing, trapping methods, or observation-based assessments, which are the current status-quo in fish monitoring, are often time- and cost-consuming. As a result, over the last decade, scientists progressively agree that we need a more comprehensive and holistic method to assess freshwater biodiversity.

Meanwhile, recent studies have continuously been demonstrating that eDNA metabarcoding analyses, where DNA traces found in the water are used to identify what organisms live there, is an efficient method to capture aquatic biodiversity in a fast, reliable, non-invasive and relatively low-cost manner. In such metabarcoding studies, scientists sample, collect and sequence DNA, so that they can compare it with existing databases and identify the source organisms.

Furthermore, as eDNA metabarcoding assessments use samples from water, often streams, located at the lowest point, one such sample usually contains not only traces of specimens that come into direct contact with water, for example, by swimming or drinking, but also collects traces of terrestrial species indirectly via rainfalls, snowmelt, groundwaters etc. 

In standard fish eDNA metabarcoding assessments, these ‘bycatch data’ are typically left aside. Yet, from a viewpoint of a more holistic biodiversity monitoring, they hold immense potential to also detect the presence of terrestrial and semi-terrestrial species in the catchment.

In their new study, reported in the open-access scholarly journal Metabarcoding and MetagenomicsGerman researchers from the University of Duisburg-Essen and the German Environment Agency successfully detected an astonishing quantity of the local mammals and birds native to the Saxony-Anhalt state by collecting as much as 18 litres of water from across a two-kilometre stretch along the river Mulde.

After water filtration the eDNA filter is preserved in ethanol until further processing in the lab.
Photo by Till-Hendrik Macher.

In fact, it took only one day for the team, led by Till-Hendrik Macher, PhD student in the German Federal Environmental Agency-funded GeDNA project, to collect the samples. Using metabarcoding to analyse the DNA from the samples, the researchers identified as much as 50% of the fishes, 22% of the mammal species, and 7.4% of the breeding bird species in the region. 

However, the team also concluded that while it would normally take only 10 litres of water to assess the aquatic and semi-terrestrial fauna, terrestrial species required significantly more sampling.

Unlocking data from the increasingly available fish eDNA metabarcoding information enables synergies among terrestrial and aquatic biodiversity monitoring programs, adding further important information on species diversity in space and time. 

“We thus encourage to exploit fish eDNA metabarcoding biodiversity monitoring data to inform other conservation programs,”

says lead author Till-Hendrik Macher. 

“For that purpose, however, it is essential that eDNA data is jointly stored and accessible for different biodiversity monitoring and biodiversity assessment campaigns, either at state, federal, or international level,”

concludes Florian Leese, who coordinates the project.

Original source:

Macher T-H, Schütz R, Arle J, Beermann AJ, Koschorreck J, Leese F (2021) Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species. Metabarcoding and Metagenomics 5: e66557. https://doi.org/10.3897/mbmg.5.66557

New improvements to how impacts of non-native species are assessed recommended

A farmer sets a pheromone trap to fight tomato leaf miner. Photo by CABI.

The Centre for Agriculture and Bioscience International (CABI) has led an international team of non-native species (NNS) specialists who have compiled a list of recommendations to improve the way in which the impact of a range of invasive pests – such as the tomato leaf miner Tuta absoluta – are assessed, potentially helping towards ensuring greater global food security.

Lead authors Dr Pablo González-Moreno and Dr Marc Kenis, Senior Researchers at CABI are two of 89 NNS experts from around the world who have collaborated on the paper, published in NeoBiota, that calls for ‘more robust and user-friendly’ impact assessment protocols to predict the impacts of new or likely invaders as well as to assess the actual impact of established species.

The manuscript is the outcome of an enormous collective effort using 11 different protocols to assess the potential impact of 57 NNS to Europe yielding a total of 2614 separate assessments. This unique dataset has allowed the authors to identify which are the main factors increasing the robustness of protocols and provide recommendations on how the robustness and applicability of protocols could be enhanced for assessing NNS impacts.

As reported in the study, entitled ‘Consistency of impact assessment protocols for Non-Native Species’, Dr González-Moreno and fellow scientists – from 80 institutions including the UK-based Centre for Ecology & Hydrology (CEH), University of Milan, University of Bern and Queens University Belfast – argue that ‘assessment of the realised or potential impacts of NNS is particularly important for the prioritization of management actions.’

Millions of the world’s most vulnerable people face problems with invasive weeds, insects and plant diseases, which are out of control and have a major impact on global prosperity, communities and the environment. Developing countries are disproportionately affected.

The global cost of the world’s 1.2 million invasive species is estimated at $1.4 trillion per year – close to 5 percent of global gross domestic product. In East Africa, five major invasive species alone cause $1 billion in economic losses to smallholder farmers each year.

The scientists believe that, currently, the large variety of metrics adopted to measure the impacts of invasive species undermines direct comparison of impacts across species, groups of taxa, localities or regions. They go on to argue that in general we have ‘little understanding of the patterns in consistency of impact scores across assessors and protocols, and more importantly, which factors contribute to high levels of consistency.’

Dr González-Moreno said,

“There is an increasing demand for robust and user-friendly impact assessment protocols to be used by professionals with different levels of expertise and knowledge.
Robust NNS impact protocols should ideally result in accurate and consistent impact scores for a species even if applied by different assessors, as long as they have the adequate expertise in the assessed species and context.
Several key factors should be taken into account when selecting or designing an NNS risk assessment protocol, such as the aim, the scope, the consistency and the accuracy of the outcomes, and the resources available to perform the assessment – for example time or information available.”

In compiling a list of recommendations for improved NNS impact protocols, Dr González-Moreno and the team of researchers used 11 different protocols to assess the potential impact of 57 species not native to Europe and belonging to a very large array of taxonomic groups (plants, animals, pathogens) from terrestrial to freshwater and marine environments.

They agree that using a ‘5-level scoring, maximum aggregation method and the moderation of expertise requirements’ offers a good compromise to reducing inconsistencies in research findings without losing discriminatory power or usability.

Dr González-Moreno added, “In general, we also advise protocol developers to perform sensibility tests of consistency before final release or adoption. This is crucial as if a protocol yields inconsistent outcomes when used by different assessors, then it is likely that decisions taken based on the results could be variable and disproportionate to the actual impacts.”

Original source:

González-Moreno P, Lazzaro L, Vilà M, Preda C, Adriaens T, Bacher S, Brundu G, Copp GH, Essl F, García-Berthou E, Katsanevakis S, Moen TL, Lucy FE, Nentwig W, Roy HE, Srėbalienė G, Talgø V, Vanderhoeven S, Andjelković A, Arbačiauskas K, Auger-Rozenberg M-A, Bae M-J, Bariche M, Boets P, Boieiro M, Borges PA, Canning-Clode J, Cardigos F, Chartosia N, Cottier-Cook EJ, Crocetta F, D’hondt B, Foggi B, Follak S, Gallardo B, Gammelmo Ø, Giakoumi S, Giuliani C, Guillaume F, Jelaska LS, Jeschke JM, Jover M, Juárez-Escario A, Kalogirou S, Kočić A, Kytinou E, Laverty C, Lozano V, Maceda-Veiga A, Marchante E, Marchante H, Martinou AF, Meyer S, Michin D, Montero-Castaño A, Morais MC, Morales-Rodriguez C, Muhthassim N, Nagy ZA, Ogris N, Onen H, Pergl J, Puntila R, Rabitsch W, Ramburn TT, Rego C, Reichenbach F, Romeralo C, Saul W-C, Schrader G, Sheehan R, Simonović P, Skolka M, Soares AO, Sundheim L, Tarkan AS, Tomov R, Tricarico E, Tsiamis K, Uludağ A, van Valkenburg J, Verreycken H, Vettraino AM, Vilar L, Wiig Ø, Witzell J, Zanetta A, Kenis M (2019) Consistency of impact assessment protocols for non-native species. NeoBiota 44: 1-25. https://doi.org/10.3897/neobiota.44.31650

Additional information:

The paper is based upon work from the COST Action TD1209: ALIEN Challenge. COST (European Cooperation in Science and Technology) is a pan-European intergovernmental framework. The mission of COST is to enable scientific and technological developments leading to new concepts and products and thereby contribute to strengthening Europe’s research and innovation capacities.

Dr Pablo González-Moreno was supported by the CABI Development Fund (with contributions from ACIAR (Australia) and DFID (UK) and by Darwin plus, DPLUS074 ‘Improving biosecurity in the SAUKOTs through Pest Risk Assessments’.

 

Text originally published by CABI.