Elvira Mächler

Environmental DNA reveals that rivers are conveyer belts of biodiversity information

DNA sampled from the environment (eDNA) is a useful way to uncover biodiversity patterns. By combining a conceptual model and empirical data, we test whether eDNA transported in river networks can be used as an integrative way to assess eukaryotic biodiversity for broad spatial scales and across the land–water interface. Using an eDNA metabarcode approach, we detect 296 families of eukaryotes, spanning 19 phyla across the catchment of a river. We show for a subset of these families that eDNA samples overcome spatial autocorrelation biases associated with the classical community assessments by integrating biodiversity information over space. In addition, we demonstrate that many terrestrial species are detected; thus suggesting eDNA in river water also incorporates biodiversity information across terrestrial and aquatic biomes. Environmental DNA transported in river networks offers a novel and spatially integrated way to assess the total biodiversity for whole landscapes and will transform biodiversity data acquisition in ecology.

Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species

Abstract: Accurate knowledge of the distribution of rare, indicator, or invasive species is required for conservation and management decisions. However, species monitoring done with conventional methods may have limitations, such as being laborious in terms of cost and time, and often requires invasive sampling of specimens. Environmental DNA (eDNA) has been identified as a molecular tool that could overcome these limitations, particularly in aquatic systems. Detection of rare and invasive amphibians and fish in lake and river systems has been effective, but few studies have targeted macroinvertebrates in aquatic systems. We expanded eDNA techniques to a broad taxonomic array of macroinvertebrate species in river and lake systems. We were able to detect 5 of 6 species (Ancylus fluviatilis, Asellus aquaticus, Baetis buceratus, Crangonyx pseudogracilis, and Gammarus pulex) with an eDNA method in parallel to the conventional kicknet-sampling method commonly applied in aquatic habitats. Our eDNA method showed medium to very high consistency with the data from kicknet-sampling and was able to detect both indicator and nonnative macroinvertebrates. Furthermore, our primers detected target DNA in concentrations down to 10-5 ng/µL of total extracted tissue DNA in the absence of background eDNA in the reaction. We demonstrate that an eDNA surveillance method based on standard PCR can deliver biomonitoring data across a wide taxonomic range of macroinvertebrate species (Gastropoda, Isopoda, Ephemeroptera, and Amphipoda) in riverine habitats and may offer the possibility to deliver data on a more refined time scale than conventional methods when focusing on single or few target species. Such information based on nondestructive sampling may allow rapid management decisions and actions.

Big answers from small worlds: a user's guide for protist microcosms as a model system in ecology and evolution

Laboratory microcosm experiments using protists as model organisms have a long tradition and are widely used to investigate general concepts in population biology, community ecology and evolutionary biology. Many variables of interest are measured in order to study processes and patterns at different spatiotemporal scales and across all levels of biological organization. This includes measurements of body size, mobility or abundance, in order to understand population dynamics, dispersal behaviour and ecosystem processes. Also, a variety of manipulations are employed, such as temperature changes or varying connectivity in spatial microcosm networks. Past studies, however, have used varying methods for maintenance, measurement, and manipulation, which hinders across-study comparisons and meta-analyses, and the added value they bring. Furthermore, application of techniques such as flow cytometry, image and video analyses, and in situ environmental probes provide novel and improved opportunities to quantify variables of interest at unprecedented precision and temporal resolution. Here, we take the first step towards a standardization of well-established and novel methods and techniques within the field of protist microcosm experiments. We provide a comprehensive overview of maintenance, measurement and manipulation methods. An extensive supplement contains detailed protocols of all methods, and these protocols also exist in a community updateable online repository. We envision that such a synthesis and standardization of methods will overcome shortcomings and challenges faced by past studies and also promote activities such as meta-analyses and distributed experiments conducted simultaneously across many different laboratories at a global scale.

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

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“HTS”) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed “environmental DNA” or “eDNA”). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called “eDNA metabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.

Diversity and Distribution of Freshwater Amphipod Species in Switzerland (Crustacea: Amphipoda)

Amphipods are key organisms in many freshwater systems and contribute substantially to the diversity and functioning of macroinvertebrate communities. Furthermore, they are commonly used as bioindicators and for ecotoxicological tests. For many areas, however, diversity and distribution of amphipods is inadequately known, which limits their use in ecological and ecotoxicological studies and handicaps conservation initiatives. We studied the diversity and distribution of amphipods in Switzerland (Central Europe), covering four major drainage basins, an altitudinal gradient of>2,500 m, and various habitats (rivers, streams, lakes and groundwater). We provide the first provisional checklist and detailed information on the distribution and diversity of all amphipod species from Switzerland. In total, we found 29 amphipod species. This includes 16 native and 13 non-native species, one of the latter (Orchestia cavimana) reported here for the first time for Switzerland. The diversity is compared to neighboring countries. We specifically discuss species of the genus Niphargus, which are often receiving less attention. We also found evidence of an even higher level of hidden diversity, and the potential occurrence of further cryptic species. This diversity reflects the biogeographic past of Switzerland, and suggests that amphipods are ideally suited to address questions on endemism and adaptive radiations, post-glaciation re-colonization and invasion dynamics as well as biodiversity-ecosystem functioning relationships in aquatic systems.

Fishing in the Water: Effect of Sampled Water Volume on Environmental DNA-Based Detection of Macroinvertebrates

Accurate detection of organisms is crucial for the effective management of threatened and invasive species because false detections directly affect the implementation of management actions. The use of environmental DNA (eDNA) as a species detection tool is in a rapid development stage; however, concerns about accurate detections using eDNA have been raised. We evaluated the effect of sampled water volume (0.25 to 2 L) on the detection rate for three macroinvertebrate species. Additionally, we tested (depending on the sampled water volume) what amount of total extracted DNA should be screened to reduce uncertainty in detections. We found that all three species were detected in all volumes of water. Surprisingly, however, only one species had a positive relationship between an increased sample volume and an increase in the detection rate. We conclude that the optimal sample volume might depend on the species-habitat combination and should be tested for the system where management actions are warranted. Nevertheless, we minimally recommend sampling water volumes of 1 L and screening at least 14 μL of extracted eDNA for each sample to reduce uncertainty in detections when studying macroinvertebrates in rivers and using our molecular workflow.

Spatial patterns of genetic diversity, community composition and occurrence of native and non-native amphipods in naturally replicated tributary streams

BackgroundWorldwide, natural communities are invaded by non-native species, with potentially devastating effects on the native communities. A large part of past research aimed at finding traits and characteristics of the invading species or the invaded community explaining observed invasions. Only recently, the focus shifted on the spatial patterns during invasions per se. Empirical data, however, are limited, as invasions are often unique incidences of a complex spatio-temporal process. In order to identify generalities of invasion patterns, we studied 13 naturally replicated tributary streams draining into Lake Constance, and studied the occurrence of native and non-native amphipods along linear transects from the stream outlets to the upstream headwater reaches.ResultsWe found repeated spatial patterns of community composition and the occurrence of native and non-native amphipod species across two different years. Specifically, occurrence as well as abundance of two non-native amphipod species decreased from the stream outlets at the lake site towards upstream headwater reaches. Populations of the most common native amphipod species were largest at the uppermost headwater reaches. All populations of this native species, however, showed significant signals of recent genetic bottlenecks, irrespective of the stream position and occurrence of non-native species. Contrary to our expectations, this native species also showed no longitudinal genetic differentiation within individual tributaries as postulated for headwater versus outlet populations.ConclusionsOur results indicate that invasions of river-systems may overall follow predictable patterns on the level of spatial distributions and community composition. However, effects of invading organisms on the genetic diversity and genetic structure of native populations observed at larger scales may not necessarily be directly reflected at the scale of smaller tributaries.

Shedding light on eDNA: neither natural levels of UV radiation nor the presence of a filter feeder affect eDNA-based detection of aquatic organisms

Abstract The use of environmental DNA (eDNA) as a species detection tool is attracting attention from both scientific and applied fields, especially for detecting invasive or rare species. In order to use eDNA as an efficient and reliable tool, however, we need to understand its origin and state as well as factors affecting its degradation. Various biotic and abiotic environmental factors have been proposed to affect degradation of eDNA in aquatic environments and thus to influence detection rates of species. Here, we were interested in two of them, namely UV light, which can break down DNA, and the presence of filter feeders, which can remove DNA and DNA-bound particles. A few, mostly laboratory-based studies have found minor effects of UVB on the degradation of eDNA. Ultraviolet A radiation (UVA), however, has been neglected although it also causes DNA lesions and is 10- to 100-fold more prevalent than UVB when reaching the earth’s surface. Filter feeders are common in aquatic ecosystem, but their effects on eDNA has hitherto been ignored. We conducted a full-factorial aquatic mesocosm experiment under near-natural outdoor conditions manipulating UV radiation as well as the presence of Dreissena polymorpha, a strong filter feeder capable of filtering cells or organelles containing DNA. Surprisingly, we found that neither UV radiation nor the presence of the filter feeder affected eDNA-based detection rates of macroinvertebrates, even though the experiment took place in summer when UV radiation intensity and filtration activity is high for the chosen experimental site and conditions. These results, in combination with studies from marine or laboratory settings finding no effect of sunlight and its UV components on the detectability of eDNA, suggest that eDNA based species assessments could be relatively robust with respect to our two factors studied.

Biodiversity increases and decreases ecosystem stability

Losses and gains in species diversity affect ecological stability1–7 and the sustainability of ecosystem functions and services8–13. Experiments and models have revealed positive, negative and no effects of diversity on individual components of stability, such as temporal variability, resistance and resilience2,3,6,11,12,14. How these stability components covary remains poorly understood15. Similarly, the effects of diversity on overall ecosystem stability16, which is conceptually akin to ecosystem multifunctionality17,18, remain unknown. Here we studied communities of aquatic ciliates to understand how temporal variability, resistance and overall ecosystem stability responded to diversity (that is, species richness) in a large experiment involving 690 micro-ecosystems sampled 19 times over 40 days, resulting in 12,939 samplings. Species richness increased temporal stability but decreased resistance to warming. Thus, two stability components covaried negatively along the diversity gradient. Previous biodiversity manipulation studies rarely reported such negative covariation despite general predictions of the negative effects of diversity on individual stability components3. Integrating our findings with the ecosystem multifunctionality concept revealed hump- and U-shaped effects of diversity on overall ecosystem stability. That is, biodiversity can increase overall ecosystem stability when biodiversity is low, and decrease it when biodiversity is high, or the opposite with a U-shaped relationship. The effects of diversity on ecosystem multifunctionality would also be hump- or U-shaped if diversity had positive effects on some functions and negative effects on others. Linking the ecosystem multifunctionality concept and ecosystem stability can transform the perceived effects of diversity on ecological stability and may help to translate this science into policy-relevant information.Species richness was found to increase temporal stability but decrease resistance to warming in an experiment involving 690 micro-ecosystems consisting of 1 to 6 species of bacterivorous ciliates that were sampled over 40 days.

Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds

Environmental DNA (eDNA) analysis is a rapid, non-invasive, cost-efficient biodiversity monitoring tool with enormous potential to inform aquatic conservation and management. Development is ongoing, with strong commercial interest, and new uses are continually being discovered. General applications of eDNA and guidelines for best practice in freshwater systems have been established, but habitat-specific assessments are lacking. Ponds are highly diverse, yet understudied systems that could benefit from eDNA monitoring. However, eDNA applications in ponds and methodological constraints specific to these environments remain unaddressed. Following a stakeholder workshop in 2017, researchers combined knowledge and expertise to review these applications and challenges that must be addressed for the future and consistency of eDNA monitoring in ponds. The greatest challenges for pond eDNA surveys are representative sampling, eDNA capture, and potential PCR inhibition. We provide recommendations for sampling, eDNA capture, inhibition testing, and laboratory practice, which should aid new and ongoing eDNA projects in ponds. If implemented, these recommendations will contribute towards an eventual broad standardisation of eDNA research and practice, with room to tailor workflows for optimal analysis and different applications. Such standardisation will provide more robust, comparable, and ecologically meaningful data to enable effective conservation and management of pond biodiversity.