Francesco Pomati

Francesco Pomati
Eawag: Das Wasserforschungs-Institut des ETH-Bereichs | Eawag · Department of Aquatic Ecology

PhD

About

188
Publications
37,674
Reads
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4,705
Citations
Additional affiliations
September 2012 - present
Eawag: Das Wasserforschungs-Institut des ETH-Bereichs
Position
  • Group Leader
July 2005 - August 2008
UNSW Sydney
Position
  • Vice Chancellor's Postdoctoral Fellow

Publications

Publications (188)
Preprint
Climate change interacts with local processes to threaten biodiversity by disrupting the complex network of ecological interactions, wherein variation in network links drastically affects ecosystems (e.g., species loss). However, how ecological networks respond to climate change is largely unknown. We herein consider 24–43 years of monthly data fro...
Preprint
Full-text available
Monitoring biodiversity is paramount to manage and protect natural resources, particularly in times of global change. Collecting images of organisms over large temporal or spatial scales is a promising practice to monitor and study biodiversity change of natural ecosystems, providing large amounts of data with minimal interference with the environm...
Article
Full-text available
Plankton are effective indicators of environmental change and ecosystem health in freshwater habitats, but collection of plankton data using manual microscopic methods is extremely labor-intensive and expensive. Automated plankton imaging offers a promising way forward to monitor plankton communities with high frequency and accuracy in real-time. Y...
Preprint
Full-text available
Plankton are effective indicators of environmental change and ecosystem health in freshwater habitats, but collection of plankton data using manual microscopic methods is extremely labor-intensive and expensive. Automated plankton imaging offers a promising way forward to monitor plankton communities with high frequency and accuracy in real-time. Y...
Article
The Dual Scripps Plankton Camera (DSPC) is a new approach for automated in-situ monitoring of phyto- and zooplankton communities based on a dual magnification dark-field imaging microscope. Here, we present the DSPC and its associated image processing while evaluating its capabilities in i) detecting and characterizing plankton species of different...
Article
Full-text available
Land use and climate change are anticipated to affect phytoplankton of lakes worldwide. The effects will depend on the magnitude of projected land use and climate changes and lake sensitivity to these factors. We used random forests (RF) fit with long‐term (1971‐2016) phytoplankton and cyanobacteria abundance time series, climate observations (1971...
Article
Full-text available
Phytoplankton blooms are complex ecological events that emerge from the dynamics of an entire ecosystem. Increasing efforts to forecast blooms are hampered by inconsistent definitions of what constitutes a bloom event, from both conceptual (mechanistic) and empirical (quantitative) perspectives. By clarifying definitions of blooms using temporal sy...
Preprint
Full-text available
We present an approach for automated in-situ monitoring of phytoplankton and zooplankton communities based on a dual magnification dark-field imaging microscope/camera. We describe the Dual Scripps Plankton Camera (DSPC) system and associated image processing, and assess its capabilities in detecting and characterizing plankton species of different...
Article
Full-text available
The study of ecosystem services requires the integration of different observational points. This is particularly true in Water, as this element continuously cycles, increasing chances of interaction among services originating in different ecosystems. However, aquatic scientists historically approached the study of inland/freshwater and open/marine...
Article
Full-text available
Key traits of unicellular species, such as cell size, often follow scale-free or self-similar distributions, hinting at the possibility of an underlying critical process. However, linking such empirical scaling laws to the critical regime of realistic individual-based model classes is difficult. Here, we reveal new empirical scaling evidence associ...
Article
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In many regions across the globe, extreme weather events such as storms have increased in frequency, intensity, and duration due to climate change. Ecological theory predicts that such extreme events should have large impacts on ecosystem structure and function. High winds and precipitation associated with storms can affect lakes via short-term run...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Drawing insights from multiple disciplines is essential for finding integrative solutions that are required to tackle complex environmental problems. Human activities are causing unprecedented influence on global ecosystems, culminating in the loss of species and fundamental changes in the selective environments of organisms across the tree of life...
Article
Full-text available
Exploiting a rich data set including both individual fishing activities and ecology, we study how eutrophication and climate warming influence plankton biodiversity in Lake Zürich and the consequent effects on fishers’ behavior and fishery yield. Our analysis indicates that changes in the fishery of Lake Zürich were driven by complex dynamic intera...
Article
Full-text available
Biomass distribution among size classes follows a power law where the Log-abundance of taxa scales to Log-size with a slope that responds to environmental abiotic and biotic conditions. The interactions between ecological mechanisms controlling the slope of locally realized size-abundance relationships (SAR) are however not well understood. Here we...
Article
Full-text available
The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear...
Article
Full-text available
Freshwaters are increasingly exposed to complex mixtures of pharmaceutical and personal care products (PPCPs) from municipal wastewater. PPCPs are known to alter freshwater communities’ structure and functioning, however, their interaction with other disturbances and whether their combined effects can impact ecological resilience (i.e. the ability...
Article
Full-text available
Disentangling the relative importance of deterministic and stochastic processes in shaping natural communities is central to ecology. studies about community assembly over broad temporal and spatial scales in aquatic microorganisms are scarce. Here, we used 16S rDNA sequence data from lake sediments to test for community assembly patterns in cyanob...
Article
Biotransformation of chemical pollutants is an ecological process requiring multifunctionality (multiple metabolic pathways) and, potentially, high biodiversity. Phytoplankton communities are highly diverse functionally and taxonomically, and co-occur with complex mixtures of organic pollutants in aquatic environments. Here, we investigated how phy...
Conference Paper
Full-text available
Over the past decade, there has been a drastic increase in the amount of data collected for environmental monitoring in both engineered and natural systems. In order to manage this vast quantity of data, dedicated tools are required; this includes implementing standard procedures for sensor validation, data importation and storage, as well as data...
Article
Full-text available
The phylum Cyanobacteria comprises a non-photosynthetic lineage. The diversity and distribution of non-photosynthetic cyanobacteria (NCY) across aquatic environments are currently unknown, including their ecology. Here, we report about composition and phylogenetic diversity of two clades of NCY in ten lakes of the European peri-Alpine region, over...
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...
Preprint
Full-text available
Disentangling the relative importance of deterministic and stochastic processes in shaping natural communities is central to ecology. Studies on community assembly over broad temporal and spatial scales in aquatic microorganisms are scarce. Here, we used 16S rDNA sequence data from lake sediments to test for deterministic and stochastic assembly pa...
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
Motivation: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community led open-source database of biodiversity time se...
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...
Article
Occurrence and fate of glyphosate, a widely used herbicide, and its main metabolite AMPA was investigated in Lake Greifensee, Switzerland. Monthly vertical concentration profiles in the lake showed an increase of glyphosate concentrations in the epilimnion from 15 ng/L in March to 145 ng/L in July, followed by a sharp decline to <5 ng/L in August....
Article
Full-text available
Human impacts on biodiversity are well recognized, but uncertainties remain regarding patterns of diversity change at different spatial and temporal scales. Changes in microbial assemblages are, in particular, not well understood, partly due to the lack of community composition data over relevant scales of space and time. Here, we investigate biodi...
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...
Article
Full-text available
Eutrophication generally favours the growth of cyanobacteria over eukaryotic green algae in freshwater lakes. Cyanobacteria constitute a poor food source for the waterflea Daphnia, an important primary consumer of phytoplankton in lakes. While it is known that some Daphnia species are adapted to eutrophic conditions and can cope with cyanobacteria...
Article
Full-text available
There has been considerable focus on the impacts of environmental change on ecosystem function arising from changes in species richness. However, environmental change may affect ecosystem function without affecting richness, most notably by affecting population densities and community composition. Using a theoretical model, we find that, despite in...
Article
Phytoplankton constitute an important component of surface water ecosystems; however little is known about their contribution to biotransformation of organic micropollutants. To elucidate biotransformation processes, batch experiments with two cyanobacterial species (Microcystis aeruginosa, Synechococcus sp.) and one green algal species (Chlamydomo...
Article
Full-text available
Chemical micropollutants occur worldwide in the environment at low concentrations and in complex mixtures, and how they affect the ecology of natural systems is still uncertain. Dynamics of natural communities are driven by the interaction between individual organisms and their growth environment, which is mediated by the organisms' expressed pheno...
Data
This file contains SI methods, results, discussion and references. Specific results include Tables A-H and Figures A-H. (DOCX)
Article
Full-text available
The composition and dynamics of plankton communities are critically affected by human-induced environmental changes. We analysed 33 years of phytoplankton monthly data collected in Lake Zurich (Switzerland), assigning organisms (genus level) to taxonomic groups (class, family), Reynolds associations and size categories. The aim was to understand ho...
Preprint
Full-text available
Perfluorinated compounds have raised concern due to their potential association with detrimental postnatal outcomes in animals and humans. We tested the effects of perfluorooctane sulfonate (PFOS) on a human pluripotent teratocarcinoma (known as NCCIT) cells as an in vitro prototype for developmental toxicity in mammals. NCCIT contains stem-cells a...
Article
The seasonal dominance of cyanobacteria in the phytoplankton community of lake ecosystems can have severe implications for higher trophic levels. For herbivorous zooplankton such as Daphnia, cyanobacteria have poor nutritional value and some species can produce toxins affecting zooplankton survival and reproduction. Here, we present another, hither...
Article
Full-text available
The use of high-frequency sensors on pro ling buoys to investigate physical, chemical, and biological processes in lakes is increasing rapidly. Profiling buoys with automated winches and sensors that collect high-frequency chlorophyll uorescence (ChlF) profiles in 11 lakes in the Global Lake Ecological Observatory Network (GLEON) allowed the study...
Article
Full-text available
For the past 20 years, research on biodiversity and ecosystem functioning (B-EF) has only implicitly considered the underlying role of environmental change. We illustrate that explicitly reintroducing environmental change drivers in B-EF research is needed to predict the functioning of ecosystems facing changes in biodiversity. Next we show how thi...
Article
Importance: Cyanobacterial blooms can produce toxins that affect water quality, especially under eutrophic conditions, which are a consequence of human-induced climate warming and increased nutrient availability. Lakes worldwide have suffered from regular cyanobacterial blooms over the last century. The lack of long-term data limits our understand...
Article
Full-text available
Zooplankton communities can be strongly affected by cyanobacterial blooms, especially species of genus Daphnia, which are key-species in lake ecosystems. Here, we explored the effect of microcystin/non-microcystin (MC/non-MC) producing cyanobacteria in the diet of experimental Daphnia galeata populations composed of eight genotypes. We used D. gale...
Article
Full-text available
The ecosystem services (EcoS) concept is being used increasingly to attach values to natural systems and the multiple benefits they provide to human societies. Ecosystem processes or functions only become EcoS if they are shown to have social and/or economic value. This should assure an explicit connection between the natural and social sciences, b...