Biology subjects

Carraro, L.

Publications and source records attributed to Carraro, L..

8 recordsLinked to original sources

bioRxiv2025

Tracking the phenology of riverine insect communities using environmental DNA

Aquatic insects are iconic and ecologically highly relevant inhabitants of riverine ecosystems. They are also often the target of monitoring programs to assess the ecological status of these lotic habitats. Environmental DNA (eDNA) techniques have been widely and successfully implemented to investigate freshwater insects and other macroinvertebrates. Commonly, such monitoring is conducted at one or two timepoints per year, despite the known strong seasonality and phenology of aquatic insects. Here, we assessed if and how eDNA can capture the temporal changes of the orders Ephemeroptera (mayflies), Plecoptera (stoneflies), Trichoptera (caddisflies) and Diptera (true flies). We carried out eDNA sampling at roughly monthly intervals from April to October at 25 sites across a whole river catchment in the northeastern part of Switzerland. We found pronounced, cyclic phenological trends in all orders but Trichoptera: the communities diverged from spring to summer and then in fall gradually returned closer to the spring state. The four orders exhibited different predominance in gains or losses of species detection throughout this time interval. Lastly, we found that field replicates, despite showing a relatively high local stochasticity, were able to provide a more complete assessment of aquatic communities and could thus be used as a proxy for the frequency of observation of a species through the seasons. In fact, this approach yielded comparable temporal patterns to the ones extracted from the Global Biodiversity Information Facility (GBIF). Overall, our findings demonstrate that eDNA techniques can be used to reveal intra-annual dynamics of aquatic insects. Given the current necessity to assess and monitor the biodiversity status of ecosystems, we therefore show that eDNA methods are a viable option to obtain a deeper understanding of the structuring of freshwater communities over time.

ecology↗

bioRxiv2024

eDITH: an R-package to spatially project eDNA-based biodiversity across river networks with minimal prior information

O_LIEcological and ecosystem monitoring is rapidly shifting towards using environmental DNA (eDNA) data, particularly in aquatic systems. This approach enables a combined coverage of biodiversity across all major organismal groups and the assessment of ecological indices. Yet, most current approaches are not exploiting the full potential of eDNA data, largely interpreting results in a localized perspective. In riverine networks, by explicitly modelling hydrological transport and associated DNA decay, hydrology-based models enable upscaling eDNA-based diversity information, providing spatially integrated inference. To capitalize from these unprecedented biodiversity data and translate into space-filling biodiversity projections, a streamlined implementation is needed. C_LIO_LIHere, we introduce the eDITH R-package, implementing the eDITH model to project biodiversity across riverine networks with minimal prior information. eDITH couples a species distribution model relating a local taxons eDNA shedding rate in streamwater to environmental covariates, a mass balance expressing the eDNA concentration at a rivers cross-section as a weighted sum of upstream contributions, and an observational model accounting for uncertainties in eDNA measurements. By leveraging on spatially replicated eDNA measurements and minimal hydromorphological data, eDITH enables disentangling the various upstream eDNA sources, and produces space-filling maps of a taxons spatial distribution at any chosen resolution. eDITH is applicable to both eDNA concentration and metabarcoding data, and to any taxon whose DNA can be retrieved in streamwater. C_LIO_LIThe eDITH package provides user-friendly functions for single-run execution and fitting of eDITH to eDNA data with both Bayesian methods (via the BayesianTools package) and non-linear optimization. An interface to the DHARMa package allows model validation via posterior predictive checks. Necessary preliminary steps such as watershed delineation and hydrological characterization are implemented via the rivnet package. We illustrate eDITHs workflow and functionalities with two case studies from published fish eDNA data. C_LIO_LIThe eDITH package provides a user-friendly implementation of eDITH, specifically intended for ecologists and conservation biologists. It can be used without previous modelling knowledge but also allows customization for experienced users. Ultimately, eDITH allows upscaling eDNA biodiversity data for any river globally, transforming how state and change of biodiversity in riverine systems can be tracked at high resolution in a highly versatile manner. C_LI

ecology↗

bioRxiv2022

Modelling eDNA transport in river networks reveals highly resolved spatio-temporal patterns of freshwater biodiversity

O_LIThe ever-increasing threats to riverine biodiversity call for the development of novel approaches for a complete assessment of biodiversity across highly resolved spatial, temporal and taxonomic scales. Past studies on riverine biodiversity patterns were often restricted to spatially scattered data, focused on specific taxonomic groups, and disregarded the temporal dimension, preventing a universal understanding of relationships between biodiversity and stream size across spatial, temporal and taxonomic scales. Recent advances in the joint use of environmental DNA (eDNA) data and novel mechanistic models for eDNA transport in river networks have the potential to uncover the full structure of riverine biodiversity at an unprecedented spatial resolution, hence providing fundamental insights into ecosystem processes and offering a basis for targeted conservation measures. C_LIO_LIHere, we applied a mechanistic model (i.e., the eDITH model) to a metabarcoding dataset covering three taxonomic groups (fish, invertebrates and bacteria) and three seasons (spring, summer and autumn) for a 740-km2 Swiss catchment, sampled for eDNA at 73 sites. C_LIO_LIUsing the mechanistic model, we upscaled eDNA-based biodiversity predictions to more than 1900 individual reaches, allowing an assessment of patterns of - and {beta}-diversity across seasons and taxonomic groups at a space-filling, fine scale over the whole network. C_LIO_LIWe found that both predicted - and {beta}-diversity varied considerably depending on both season and taxonomic group. Predicted fish -diversity increased in the downstream direction at all seasons, while invertebrate and bacteria -diversity either decreased downstream or was not significantly related to position within network, depending on the season. Spatial {beta}-diversity was mostly found to be decreasing in the downstream direction, and this was the case for all seasons for bacteria. Temporal {beta}-diversity was mostly found to be increasing downstream. In general, genus richness values predicted by the model were found to be higher than those obtained by directly analyzing the eDNA data. Overall, stream size (subsumed by drainage area) was generally a poor predictor of patterns of predicted - and {beta}-diversities. Conversely, riverine biodiversity is shaped by a complex interplay of environmental variables, abiotic and biotic factors, which need be taken into account for a correct assessment of its structure. C_LI

ecology↗

bioRxiv2021

Meta-ecosystem dynamics drive the spatial distribution of functional groups in river networks

The meta-ecosystem concept provides a theoretical framework to study the effect of local and regional flows of resources on ecosystem dynamics. Meta-ecosystem theory has hitherto been applied to highly abstract landscapes, and meta-ecosystem dynamics in real-world landscapes remain largely unexplored. River networks constitute a prime example of meta-ecosystems, being characterized by directional resource flows from upstream to downstream communities and from the terrestrial to the aquatic realm. These flows have been thoroughly described by the River Continuum Concept (RCC), a seminal concept in freshwater ecology, stating that observed spatial variations in the relative abundances of invertebrate functional groups reflect systematic shifts in types and locations of food resources, which are in turn determined by the physical attributes of river reaches. Hence, the RCC represents a solid conceptual basis for determining how changes in landscape structure and resource flows will translate into local and regional changes in community composition. Here, we develop and analyse a riverine meta-ecosystem model inspired by the RCC, which builds upon a physically-based landscape model of dendritic river networks. We show that the spatial distributions and regional biomass of invertebrate functional groups observed in stream communities are determined by the spatial structure and scaling attributes of dendritic river networks, as well as by specific rates of resource flows. Neglecting any of these aspects in modelling river meta-ecosystems would result in unrealistic community patterns. Moreover, we observed that high rates of resource flow, for example due to river anthropization, have a negative effect on the regional biomass of all functional groups studied, and can lead to cascading extinctions at the meta-ecosystem scale. Our work paves the way for the development of physically-based meta-ecosystem models to understand the structure and functioning of real-world ecosystems.

ecology↗

bioRxiv2021

South American freshwater fish diversity shaped by Andean uplift since the Late Cretaceous

South America is home to the highest freshwater fish biodiversity on Earth1,2. The hotspot of species richness is located in the western Amazon Basin, and richness decreases downstream along the Amazon River towards the mouth at the Atlantic coast (Fig. 1b, c)3,4, which contradicts the positive relationship between stream size and biodiversity that is commonly observed in river systems across the world5,6. We investigate the role of river rerouting events caused by Andean mountain building and repeated episodes of flooding in western Amazonia in shaping the modern-day richness pattern of freshwater fishes in South America. To this end, we combine a reconstruction of river networks following Andean surface uplift since 80 million years ago with a mechanistic biological model simulating dispersal, allopatric speciation and extinction over the dynamic landscape of rivers and lakes. We show that the numerous small river rerouting events in western Amazonia resulting from mountain building produced highly dynamic riverine habitats that caused high diversification rates, shaping the exceptional present-day richness of this region. The history of marine incursions and lakes, including the Miocene Pebas megawetland system in western Amazonia, played a secondary role. This study is a major step towards the understanding of the processes involved in the interactions between the solid Earth, landscapes, and life of extraordinary biodiverse South America. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/444133v1_fig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@c4643forg.highwire.dtl.DTLVardef@1916aa5org.highwire.dtl.DTLVardef@1f0900forg.highwire.dtl.DTLVardef@81ea9b_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1.C_FLOATNO a, Major rivers and drainage basins of South America. HydroRIVERS data from the HydroSHEDS database17; rivers shown that drain a surface area of >4000 km2. b, Freshwater fish species richness per sub-basin (level 5 HydroBASINS17), reproduced from data from Cassemiro, et al. 4. c and d, Richness versus distance to outlet per sub-basins (as shown in panel b), illustrating the positive relationship (richness decreases towards the mouth of the river) for the Amazon (c), and, for comparison, a negative relationship for the Parana-Paraguay river basin (d). C_FIG

evolutionary biology↗

bioRxiv2020

How to design optimal eDNA sampling strategies for biomonitoring in river networks

The current biodiversity crisis calls for appropriate and timely methods to assess state and change of bio-diversity. In this respect, environmental DNA (eDNA) is a highly promising tool, especially for aquatic ecosystems. While initial eDNA studies assessed biodiversity at a few sites, technology now allows analyses of samples from many points at a time. However, the selection of these sites has been mostly motivated on an ad-hoc basis, and it is unclear where to position sampling sites in a river network to most effectively sample biodiversity. To this end, hydrology-based models might offer a unique guidance on where to sample eDNA to reconstruct the spatial patterns of taxon density based on eDNA data collected across a watershed. Here, we performed computer simulations to identify best-practice criteria for the choice of positioning of eDNA sampling sites in river networks. To do so, we combined a hydrology-based eDNA transport model with a virtual river network reproducing the scaling features of real rivers. In particular, we conducted simulations investigating scenarios of different number and location of eDNA sampling sites in a riverine network, different spatial taxon distributions, and different eDNA measurement errors. We identified best practices for sampling site selection for taxa that have a scattered versus an even distribution across the network. We observed that, due to hydrological controls, non-uniform patterns of eDNA concentration arise even if the taxon distribution is uniform and decay is neglected. We also found that uncertainties in eDNA concentration estimates do not necessarily hamper model predictions. Knowledge of eDNA decay rates improves model predictions, highlighting the need for empirical estimates of these rates under relevant environmental conditions. Our simulations help define strategies for the design of eDNA sampling campaigns in river networks, and can guide the sampling effort of field ecologists and environmental authorities.

ecology↗

bioRxiv2020

Generation and application of river network analogues for use in ecology and evolution

O_LISeveral key processes in freshwater ecology and evolution are governed by the connectivity inherent to dendritic river networks. These networks have extensively been analyzed from a geomorphological and hydrological viewpoint, yet network structures classically used in modelling have only been partially representative of the structure of real river basins, and have often failed to capture well known scaling features of real river networks. Pioneering work has identified optimal channel networks (OCNs) as spanning trees that reproduce all scaling features characteristic of real, natural stream networks worldwide. While these networks have been used to generate landscapes for studies on metapopulations, biodiversity and epidemiology, their generation has not been generally accessible. C_LIO_LIGiven the increasing interest in dendritic riverine networks by ecologists and evolutionary biologists, we here present a method to generate OCNs and, to facilitate its application, we also provide the R-package OCNet. Owing to the random search process that generates OCNs, multiple network replicas spanning the same surface can be built, allowing one to perform computational experiments whose results do not depend on the particular shape of a single river network. The OCN construct also enables the generation of elevational gradients derived from the optimal network configuration, which can constitute three-dimensional landscapes for spatial studies in both terrestrial and freshwater realms. Moreover, the OCNet package provides functions that aggregate the OCN into an arbitrary number of nodes, calculate several metrics and descriptors of river networks, and draw relevant features of the network. C_LIO_LIWe describe the main functionalities of the package and present how it can be integrated into other R-packages commonly used in spatial ecology. Moreover, we exemplify the generation of OCNs and discuss an application to a metapopulation model for an invasive riverine species. C_LIO_LIIn conclusion, OCNet provides a powerful tool to generate and use realistic river network analogues for various applications. It thereby allows the design of spatially realistic studies in increasingly impacted ecosystems, and enhances our knowledge on spatial processes in freshwater ecology in general. C_LI

ecology↗

bioRxiv2019

Diauxie and co-utilization are not exclusive during growth in nutritionally complex environments

The classic view of microbial growth strategy when multiple carbon sources are available states that they either metabolize them sequentially (diauxic growth) or simultaneously (co-utilization). This perspective is biased by the fact that this process has been mainly analysed in over-simplified laboratory settings, i.e. using a few model microorganisms and growth media containing only two alternative compounds. Models concerning the mechanisms and the dynamics regulating nutrients assimilation strategies in conditions that are closer to the ones found in natural settings (i.e. with many alternative carbon/energy sources) are missing. Here, we show that bacterial co-utilization and sequential uptake of multiple substrates can coexist when multiple possible nutrients are provided in the same growth experiment, leading to an efficient exploitation of nutritionally complex settings. The order of nutrient uptake is determined by the actual biomass yield (and growth rate) that can be achieved when the same compounds are provided as single carbon sources. Finally, using two alternative theoretical models we show that this complex metabolic phenotype can be explained by a tight regulation process that allows microbes to actively modulate the different assimilatory pathways involved.

systems biology↗