Simone Fontana

Simone Fontana
University of Freiburg | Albert-Ludwigs-Universität Freiburg · Chair for Nature Conservation and Landscape Ecology

PhD

About

36
Publications
8,584
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552
Citations
Additional affiliations
May 2013 - November 2016
Eawag: Das Wasserforschungs-Institut des ETH-Bereichs
Position
  • PhD Student

Publications

Publications (36)
Article
Full-text available
Phenotypic variation is vital for microbial populations to survive environmental perturbations. Both genetic and non-genetic factors contribute to an organism’s phenotypic variation and therefore its fitness. To investigate the correlation between genetic diversity and phenotypic variation, we applied our recently developed mass spectrometry method...
Article
Full-text available
1.Global environmental change can influence ecosystem processes directly or through changes in the trait composition of natural communities. Traits are individual-level features of organisms, and theory predicts that diversity in traits should relate to ecosystem processes. Validated indices that account for both intra- and interspecific trait vari...
Article
Full-text available
In the context of understanding and predicting the effects of human-induced environmental change (EC) on biodiversity (BD), and the consequences of BD change for ecosystem functioning (EF), microbial ecologists face the challenge of linking individual level variability in functional traits to larger-scale ecosystem processes. Since lower level BD a...
Article
Full-text available
Ecosystem functions and underlying services are strongly influenced by multitrophic relationships, with functional traits playing a central role in structuring them. Which traits and functional metrics mediate the impact of different types of land use on ecosystem function within and across trophic levels? We studied the functional relationships be...
Article
Full-text available
Urbanization is a fundamental environmental change, today happening at accelerated speed worldwide. Despite the strong and permanent human impact, urban biodiversity has generally proved to be sur-prisingly high. Quantitative information on the effect of management actions on biodiversity is often lacking but is an indispensable basis for decisions...
Article
Ramon Margalef was a pioneering scientist who introduced an interdisciplinary approach to ecological studies. His studies were among the first to incorporate various concepts in the literature of aquatic ecology, covering topics such as organisms, ecosystem interactions and evolution. To bring Margalef’s approach into current scientific studies, in...
Article
Full-text available
Livestock grazing puts major anthropogenic pressure on biological communities worldwide. Not all species are expected to be affected in the same way, and the impacts will depend on species’ traits. Focusing on traits thus helps identify the mechanisms underlying changes in community composition under grazing pressures. We investigated how fine-scal...
Article
Full-text available
Trait‐based ecology has developed fast in the last decades, aiming to both explain mechanisms of community assembly, and predict patterns in nature, such as the effects of biodiversity shifts on key ecosystem processes. This body of work has stimulated the development of several conceptual frameworks and analytical methods, as well as the productio...
Article
Full-text available
The contrasting and idiosyncratic changes in biodiversity that have been documented across urbanization gradients call for a more mechanistic understanding of urban community assembly. The reproductive success of organisms in cities should underpin their population persistence and the maintenance of biodiversity in urban landscapes. We propose that...
Article
Full-text available
In biodiversity and ecosystem functioning research, the consideration of intraspecific trait variation and multiple trophic levels – both largely overlooked so far – has been proposed as a promising step towards a consensus about causal relationships and mechanisms. Soil invertebrates contribute crucially to leaf litter decomposition and thus to th...
Article
Full-text available
1.With urbanization identified as being one of the key drivers of change in global land use, and the rapid expansion of urban areas worldwide, it is relevant to evaluate how novel ecological conditions in cities shape species functional traits, which are essential for how species interact with their environments and with each other. 2.Despite the m...
Article
Full-text available
Individual-level variation arising from responses to environmental gradients influences population and community dynamics. How such responses empirically relate to the mechanisms that govern species coexistence is, however, poorly understood. Previous results from l ake phytoplankton communities suggested that the evenness of organismal traits in m...
Article
Drought considerably affects physiological and biochemical processes in trees and thus also reproduction. However, little is known about shifts in reproductive strategies in relation to changes in water availability. We investigated cone and seed traits as well as needle and twig growth traits in pine trees along a natural precipitation gradient (2...
Article
Full-text available
1. It has been widely recognized that species show extensive variation in form and function. Based on species' attributes, they can be positioned along major axes of variation, which are often defined by life-history traits, such as number of offspring , age at maturity or generation time. Less emphasis has been given in this respect to tolerance t...
Preprint
Full-text available
Individual-level variation arising from responses to environmental gradients influences population and community dynamics. How such responses empirically relate to the mechanisms that govern species coexistence is however not well understood. Previous results from lake phytoplankton communities suggested that the evenness of organisms in multidimen...
Article
Full-text available
Scanning flow cytometry (SFCM) is characterized by the measurement of time-resolved pulses of fluorescence and scattering, enabling the high-throughput quantification of phytoplankton morphology and pigmentation. Quantifying variation at the single cell and colony level improves our ability to understand dynamics in natural communities. Automated h...
Data
Description of CytoSense parameters. (PDF)
Data
Characteristics of major functional groups based on lab training data. (PDF)
Data
Animated 3D plots showing identified clusters in cleaned data, shown on Red1.Red2.ratio, FL.Orange.Range & FWS.Length axes. (MP4)
Data
Cluster characteristics of cleaned data and the designated identities for the most abundant clusters. Trait values indicate the value at the centre of the clusters. (PDF)
Data
Animated 3D plots showing identified clusters in raw data, shown on FWS.Range, X2.FL.Red.Range & FL.Red.Range axes. All clusters except #1 (black) were manually designated as belonging to phytoplankton cells. Clusters 2–8 were subsequently re-clustered (Fig 1, S4 Fig) for phytoplankton group identification based primarily on their high fluorescence...
Data
Animated 3D plots showing identified clusters in cleaned data, shown on FL.Red.First, X2.FL.Red.Gradient & FL.Orange.Range axes. (MP4)
Data
Example 3D plots showing identified clusters in raw data. All clusters except #1 (black) were manually designated as belonging to phytoplankton cells based primarily on their high fluorescence signals. Clusters 2–8 were subsequently re-clustered (Fig 1, S4 Fig) for phytoplankton group identification, because the large proportion in cluster #1 rende...
Data
Cluster characteristics of raw data and designated identities of the clusters based on visual inspection. Trait values indicate the value at the centre of the clusters (PDF)
Data
Dynamics of cell density (per mL) of individual phytoplankton species within the lake, identified and quantified by microscopy. (CSV)
Data
Mean biovolumes (μm3) of phytoplankton species within the lake, identified and quantified by microscopy in previous years (Buergi unpublished). Column ‘name_size_corrected’ contains the corrected taxon names that may be used for matching with other databases, with rare exceptions for taxa that could not be identified to a species level (e.g. 2018Di...
Data
Scanning flow cytometry pulse measurement, by the CytoSense. The instrument measures 6 independent pulses: Forward Scatter (FWS), Sideward Scatter (SWS), Red Fluorescence 1 (FL.Red), Red Fluorescence 2 (X2.FL.Red), Orange Fluorescence (FL.Orange) and Yellow Fluorescence (FL.Yellow). Details of the specific wavelengths of these pulses may be found i...
Data
Using lab cultures to identify the variables that most strongly distinguish between live cells and other signals. Based on prior knowledge, we manually identified the live cells and other signals in lab cultures of phytoplankton. Here we show two examples (a) Chlorella sp. and (b) Microcystis aeruginosa that illustrate this separation, using Maximu...
Data
Example 3D plots showing identified clusters in cleaned data. Axes for the plots are (a) Red1.Red2.ratio, FL.Orange.Range & FWS.Length, and (b) FL.Red.First, X2.FL.Red.Gradient & FL.Orange.Range. Animated versions of these plots can be found in S3 and S4 Videos. (PDF)
Data
Random forest variable importance for estimation of cell biovolumes, determined using laboratory culture measurements. Importance is estimated using % change in mean squared error between trees that include individual variables and those that have those variables omitted. The 30 most important variables are shown here, but all variables were used i...
Data
Animated 3D plots showing identified clusters in raw data, shown on FL.Red.Fill.factor, FL.Yellow.Range & X2.FL.Red.Last axes. All clusters except #1 (black) were manually designated as belonging to phytoplankton cells based primarily on their high fluorescence signals. Clusters 2–8 were subsequently re-clustered (Fig 1, S4 Fig) for phytoplankton g...
Article
Full-text available
Forecasting changes to ecological communities is one of the central challenges in ecology. However, nonlinear dependencies, biotic interactions and data limitations have limited our ability to assess how predictable communities are. Here, we used a machine learning approach and environmental monitoring data (biological, physical and chemical) to as...
Preprint
Full-text available
Scanning flow cytometry (SFCM) is characterized by the measurement of time-resolved pulses of fluorescence and scattering, enabling the high-throughput quantification of phytoplankton morphology and pigmentation. Quantifying variation at the single cell and colony level improves our ability to understand dynamics in natural communities. Automated h...
Preprint
Full-text available
Forecasting anthropogenic changes to ecological communities is one of the central challenges in ecology. However, nonlinear dependencies, biotic interactions and data limitations have limited our ability to assess how predictable communities are. Here we used a machine learning approach and environmental monitoring data (biological, physical and ch...
Article
Full-text available
Understanding how microbial diversity influences ecosystem properties is of paramount importance. Cellular traits—which determine responses to the abiotic and biotic environment—may help us rigorously link them. However, our capacity to measure traits in natural communities has thus far been limited. Here we compared the predictive power of trait r...

Projects

Projects (5)
Project
Urban beekeeping is increasing fast in many European cities, including Swiss cities. The main goal of this project is to improve the understanding on: - Urban beekeeping trends in Switzerland -Motivations and driving forces of urban beekeeping - Effects of beekeeping intensity and resource availability in urban wild bee communities
Project
At the beginning of this century, numerous pines in the Rhone Valley, one of the driest inner alpine valleys of the European Alps, situated between Brig and Sion (Canton Valais), started showing symptoms of drought; several older trees having already died. With a view to uncovering the causes of these pines dying, the Swiss Federal Institute for Forest, Snow and Landscape Research (WSL) launched a long-term irrigation experiment in summer 2003 in the Nature Park of Pfyn-Finges. Since then, the WSL has been comparing the growth of several hundred pines in irrigated forest plots with trees that only receive the natural amount of precipitation. More infos can be found at https://www.wsl.ch/en/about-wsl/instrumented-field-sites-and-laboratories/experimental-sites-in-forests/pfynwald.html
Project
To explore how needle and twig nutrients content and stoichiometry change respond to contrasting water availability. Which factor (climatic and/or edaphic) affect Scots pine needle and twig nutrient content and stoichiometry diversity