Florian Altermatt

Last Name

Altermatt

First Name

Florian

ORCID

0000-0002-4831-6958

Organisational unit

01709 - Lehre Umweltsystemwissenschaften

Show all metadata

Search Results

Publications 1 - 10 of 38

Fewer non-native insects in freshwater than in terrestrial habitats across continents
Sendek, Agnieszka; Baity-Jesi, Marco; Altermatt, Florian; et al. (2022)
Diversity and Distributions
Aim Biological invasions are a major threat to biodiversity in aquatic and terrestrial habitats. Insects represent an important group of species in freshwater and terrestrial habitats, and they constitute a large proportion of non-native species. However, while many non-native insects are known from terrestrial ecosystems, they appear to be less represented in freshwater habitats. Comparisons between freshwater and terrestrial habitats of invader richness relative to native species richness are scarce, which hinders syntheses of invasion processes. Here, we used data from three regions on different continents to determine whether non-native insects are indeed under-represented in freshwater compared with terrestrial assemblages. Location Europe, North America, New Zealand. Methods We compiled a comprehensive inventory of native and non-native insect species established in freshwater and terrestrial habitats of the three study regions. We then contrasted the richness of non-native and native species among freshwater and terrestrial insects for all insect orders in each region. Using binomial regression, we analysed the proportions of non-native species in freshwater and terrestrial habitats. Marine insect species were excluded from our analysis, and insects in low-salinity brackish water were considered as freshwater insects. Results In most insect orders living in freshwater, non-native species were under-represented, while they were over-represented in a number of terrestrial orders. This pattern occurred in purely aquatic orders and in orders with both freshwater and terrestrial species. Overall, the proportion of non-native species was significantly lower in freshwater than in terrestrial species. Main conclusions Despite the numerical and ecological importance of insects among all non-native species, non-native insect species are surprisingly rare in freshwater habitats. This is consistent across the three investigated regions. We review hypotheses concerning species traits and invasion pathways that are most likely to explain these patterns. Our findings contribute to a growing appreciation of drivers and impacts of biological invasions.
Food for people and planet
Niggli, Urs; Altermatt, Florian; Finger, Robert; et al. (2020)
Swiss Academies Reports ~ Priority Themes for Swiss Sustainability Research
Current high-input and high-output food systems have many negative consequences for producers, consumers, and natural environments worldwide. Projections based on the increasing wealth of low- and middle-income countries suggest that meat consumption will continue to grow, which will only increase pressure on the environment. It remains unclear how to develop a sustainable food system that is beneficial to all actors and contributes to a global system capable of feeding 9–10 billion people by 2050.
Integrating Environmental DNA Metabarcoding and Remote Sensing Reveals Known and Novel Fish Diversity Hotspots in a World Heritage Area
Bizzozzero, Manuela R.; Marfurt, Svenja M.; Altermatt, Florian; et al. (2025)
Diversity and Distributions
Aim: Shark Bay, a UNESCO World Heritage site in Western Australia, is highly vulnerable to climate change, yet its fish biodiversity remains poorly understood at fine spatial scales. We integrated environmental DNA (eDNA) metabarcoding with high-resolution remote sensing to assess and extrapolate fish diversity patterns, providing a scalable framework for biodiversity monitoring in dynamic coastal ecosystems. Location: Shark Bay, Western Australia. Methods: We analysed 270 water samples across 560 km² using fish-specific 16S and 12S rRNA metabarcoding, comparing our results to earlier studies using conventional methods including seining, trawling, fisheries reports, and fish traps. We linked biodiversity patterns to key environmental variables, including depth, salinity, sea surface temperature, and habitat characteristics derived from high-resolution satellite imagery. To predict fish biodiversity across unsampled areas, we employed machine-learning models, enabling spatial extrapolation of eDNA data across the seascape. Results: eDNA metabarcoding identified 106 fish species across 132 genera and 71 families, with substantial overlap with conventional monitoring but broader coverage at higher taxonomic levels. Fish richness increased with decreasing salinity, high channel habitat coverage, and moderate depths with high seagrass coverage. We delineated five distinct fish communities (A–E): two shallow seagrass communities—one in sparse seagrass (A) and another in dense seagrass (B), one in channel habitats (C) with the greatest fish diversity; one in deep sandy waters (D) and one in medium-depth, seagrass-free areas (E). Additionally, we detected several tropical species, suggesting poleward shifts due to rising water temperatures. Main Conclusions: This study highlights the utility of combining marine eDNA metabarcoding with remote sensing to detect fine-scale biodiversity. The integration of machine learning enables spatial upscaling and timely responses to habitat changes, enhancing marine conservation and management. By identifying key environmental drivers of fish diversity, this approach supports proactive conservation strategies, providing a scalable model for biodiversity monitoring under climate change.
Urbanisation Drives the Decoupling, Simplification, and Homogenization of Aquatic and Terrestrial Food Webs
Perrelet , Kilian; Cook , Lauren M.; Reji Chacko , Merin; et al. (2025)
Ecology Letters
Aquatic and terrestrial communities often co-occur at close distances, enabling biotic interactions across ecosystem boundaries. While such interactions in natural habitats contribute to complex, coupled food webs, their dynamics in engineered and fragmented urban habitats are hardly known. Using environmental DNA metabarcoding and a metaweb approach, we examined food web structure at 54 paired aquatic-terrestrial sites along an urbanisation gradient in Zurich, Switzerland. We found that urbanisation led to simpler, less connected, and more homogeneous food webs by replacing high-trophic-level predators with low-trophic-level basal consumers. This shift towards basal consumers, dependent on distinct aquatic or terrestrial basal resources, subsequently weakened the links between aquatic and terrestrial food webs. Conversely, enhancing habitat quantity and landscape connectivity bolstered predator diversity, promoting vertically diverse, connected, complex, and stable food webs. Our findings reveal that while urbanisation can disrupt aquatic-terrestrial food webs, careful urban habitat planning can enhance biodiversity and food web stability.
An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding
Perry, William Bernard; Seymour, Mathew; Orsini, Luisa; et al. (2024)
Nature Communications
Anthropogenically forced changes in global freshwater biodiversity demand more efficient monitoring approaches. Consequently, environmental DNA (eDNA) analysis is enabling ecosystem-scale biodiversity assessment, yet the appropriate spatio-temporal resolution of robust biodiversity assessment remains ambiguous. Here, using intensive, spatio-temporal eDNA sampling across space (five rivers in Europe and North America, with an upper range of 20-35 km between samples), time (19 timepoints between 2017 and 2018) and environmental conditions (river flow, pH, conductivity, temperature and rainfall), we characterise the resolution at which information on diversity across the animal kingdom can be gathered from rivers using eDNA. In space, beta diversity was mainly dictated by turnover, on a scale of tens of kilometres, highlighting that diversity measures are not confounded by eDNA from upstream. Fish communities showed nested assemblages along some rivers, coinciding with habitat use. Across time, seasonal life history events, including salmon and eel migration, were detected. Finally, effects of environmental conditions were taxon-specific, reflecting habitat filtering of communities rather than effects on DNA molecules. We conclude that riverine eDNA metabarcoding can measure biodiversity at spatio-temporal scales relevant to species and community ecology, demonstrating its utility in delivering insights into river community ecology during a time of environmental change.
A triad of kicknet sampling, eDNA metabarcoding, and predictive modeling to assess richness of mayflies, stoneflies and caddisflies in rivers
Keck, François; Hürlemann, Samuel; Locher, Nadine; et al. (2022)
Metabarcoding and Metagenomics
Monitoring biodiversity is essential to understand the impacts of human activities and for effective management of ecosystems. Thereby, biodiversity can be assessed through direct collection of targeted organisms, through indirect evidence of their presence (e.g. signs, environmental DNA, camera trap, etc.), or through extrapolations from species distribution and species richness models. Differences in approaches used in biodiversity assessment, however, may come with individual challenges and hinder cross-study comparability. In the context of rapidly developing techniques, we compared three different approaches in order to better understand assessments of aquatic macroinvertebrate diversity. Specifically, we compared the community composition and species richness of three orders of aquatic macroinvertebrates (mayflies, stoneflies, and caddisflies, hereafter EPT) obtained via eDNA metabarcoding and via traditional in situ kicknet sampling to catchment-level based predictions of a species richness model. We used kicknet data from 24 sites in Switzerland and compared taxonomic lists to those obtained using eDNA amplified with two different primer sets. Richness detected by these methods was compared to the independent predictions made by a statistical species richness model, that is, a generalized linear model using landscape-level features to estimate EPT diversity. Despite the ability of eDNA to consistently detect some EPT species found by traditional sampling, we found important discrepancies in community composition between the kicknet and eDNA approaches, particularly at a local scale. We found the EPT-specific primer set fwhF2/EPTDr2n, detected a greater number of targeted EPT species compared to the more general primer set mlCOIintF/HCO2198. Moreover, we found that the species richness measured by eDNA from either primer set was poorly correlated to the richness measured by kicknet sampling (Pearson correlation = 0.27) and that the richness estimated by eDNA and kicknet were poorly correlated with the prediction of the species richness model (Pearson correlation = 0.30 and 0.44, respectively). The weak relationships between the traditional kicknet sampling and eDNA with this model indicates inherent limitations in upscaling species richness estimates, and possibly a limited ability of the model to meet real world expectations. It is also possible that the number of replicates was not sufficient to detect ambiguous correlations. Future challenges include improving the accuracy and sensitivity of each approach individually, yet also acknowledging their respective limitations, in order to best meet stakeholder demands and address the biodiversity crisis we are facing.
Unravelling large-scale patterns and drivers of biodiversity in dry rivers
Foulquier, Arnaud; Datry, Thibault; Corti, Roland; et al. (2024)
Nature Communications
More than half of the world’s rivers dry up periodically, but our understanding of the biological communities in dry riverbeds remains limited. Specifically, the roles of dispersal, environmental filtering and biotic interactions in driving biodiversity in dry rivers are poorly understood. Here, we conduct a large-scale coordinated survey of patterns and drivers of biodiversity in dry riverbeds. We focus on eight major taxa, including microorganisms, invertebrates and plants: Algae, Archaea, Bacteria, Fungi, Protozoa, Arthropods, Nematodes and Streptophyta. We use environmental DNA metabarcoding to assess biodiversity in dry sediments collected over a 1-year period from 84 non-perennial rivers across 19 countries on four continents. Both direct factors, such as nutrient and carbon availability, and indirect factors such as climate influence the local biodiversity of most taxa. Limited resource availability and prolonged dry phases favor oligotrophic microbial taxa. Co-variation among taxa, particularly Bacteria, Fungi, Algae and Protozoa, explain more spatial variation in community composition than dispersal or environmental gradients. This finding suggests that biotic interactions or unmeasured ecological and evolutionary factors may strongly influence communities during dry phases, altering biodiversity responses to global changes.
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities
Deiner, Kristy; Bik, Holly M.; Mächler, Elvira; et al. (2017)
Molecular Ecology
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.
Linking human impacts to community processes in terrestrial and freshwater ecosystems
McFadden, Ian R.; Sendek, Agnieszka; Brosse, Morgane; et al. (2023)
Ecology Letters
Human impacts such as habitat loss, climate change and biological invasions are radically altering biodiversity, with greater effects projected into the future. Evidence suggests human impacts may differ substantially between terrestrial and freshwater ecosystems, but the reasons for these differences are poorly understood. We propose an integrative approach to explain these differences by linking impacts to four fundamental processes that structure communities: dispersal, speciation, species-level selection and ecological drift. Our goal is to provide process-based insights into why human impacts, and responses to impacts, may differ across ecosystem types using a mechanistic, eco-evolutionary comparative framework. To enable these insights, we review and synthesise (i) how the four processes influence diversity and dynamics in terrestrial versus freshwater communities, specifically whether the relative importance of each process differs among ecosystems, and (ii) the pathways by which human impacts can produce divergent responses across ecosystems, due to differences in the strength of processes among ecosystems we identify. Finally, we highlight research gaps and next steps, and discuss how this approach can provide new insights for conservation. By focusing on the processes that shape diversity in communities, we aim to mechanistically link human impacts to ongoing and future changes in ecosystems.
SWECO25: a cross-thematic raster database for ecological research in Switzerland
Külling, Nathan; Adde, Antoine; Fopp, Fabian; et al. (2024)
Scientific Data
Standard and easily accessible cross-thematic spatial databases are key resources in ecological research. In Switzerland, as in many other countries, available data are scattered across computer servers of research institutions and are rarely provided in standard formats (e.g., different extents or projections systems, inconsistent naming conventions). Consequently, their joint use can require heavy data management and geomatic operations. Here, we introduce SWECO25, a Swiss-wide raster database at 25-meter resolution gathering 5,265 layers. The 10 environmental categories included in SWECO25 are: geologic, topographic, bioclimatic, hydrologic, edaphic, land use and cover, population, transportation, vegetation, and remote sensing. SWECO25 layers were standardized to a common grid sharing the same resolution, extent, and geographic coordinate system. SWECO25 includes the standardized source data and newly calculated layers, such as those obtained by computing focal or distance statistics. SWECO25 layers were validated by a data integrity check, and we verified that the standardization procedure had a negligible effect on the output values. SWECO25 is available on Zenodo and is intended to be updated and extended regularly.

Publications 1 - 10 of 38

Florian Altermatt

Last Name

First Name

ORCID

Organisational unit

Filters

Search Results