Thomas Petzoldt

Thomas Petzoldt
Technische Universität Dresden | TUD · Institut für Hydrobiologie

Dr. rer. nat.
Project KlimaKonform (https://klimakonform.uw.tu-dresden.de/) and several collaborative projects.

About

98
Publications
64,477
Reads
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4,380
Citations
Additional affiliations
January 1997 - present
Technische Universität Dresden
Position
  • Member of Academic Staff
Description
  • Ecological Modelling, Applied Statistics, Limnological Field Courses
September 1988 - December 1996
Technische Universität Dresden
Position
  • Research Assistant
Description
  • PhD, teaching
Education
September 1988 - June 1996
Technische Universität Dresden
Field of study
  • Dr. rer. nat. in Biology
September 1985 - September 1988
Technische Universität Dresden
Field of study
  • Hydrobiology
September 1983 - September 1985
University of Rostock
Field of study
  • Biology

Publications

Publications (98)
Article
Full-text available
Following the 2020 “Virtual Summit: Incorporating Data Science and Open Science in Aquatic Research” (DSOS; Meyer and Zwart 2020), a grassroots group of scientists convened the 2nd Virtual DSOS Summit on 22–23 July 2021. DSOS combined forces with the Aquatic Ecosystem MOdeling Network - Junior (AEMON-J; https://github.com/aemon-j) to host a 4-d “Ha...
Article
Full-text available
Background Climate change induced a rise in surface water temperature and a prolongation of summer stratification in drinking water reservoirs. Stratification and temperature are important factors for drinking water production because they influence bio-geo-chemical processes and thus affect water quality. Most drinking water reservoirs have outle...
Preprint
Full-text available
Strict vertical (parent-to-offspring) transmission of symbionts may be associated with benevolence and mutualism, because host reproduction and symbiont transmission are linked. Nonetheless, many such symbionts do reduce host fitness costs and the factors driving their evolution are unclear. Using microcosm populations of Caedibacter taeniospiralis...
Article
Full-text available
Increased anthropogenic nutrient input has led to eutrophication of lakes and ponds, resulting worldwide in more frequent and severe cyanobacterial blooms. In particular, enhanced availability of phosphorus (P) can promote cyanobacterial mass developments and may affect the content of secondary metabolites in cyanobacteria, such as protease inhibit...
Poster
Full-text available
Wachstums- und Verlustprozesse spielen in den ökologischen Wissenschaften eine entscheidende Rolle, nicht nur bei Symbolarten wie dem amerikanischen Bison [1], sondern auch bei Bakterien, beim Phytoplankton oder bei Fischen. Biologische Systeme besitzen eine vielfältige Dynamik und sind häufig komplex und rückgekoppelt, Simulationen und Experimente...
Article
Full-text available
The eutrophication of lakes and ponds through anthropogenic nutrient input has resulted in higher frequencies of cyanobacterial blooms worldwide. The increased availability of nitrate (NO3⁻) plays an important role for the development of such blooms and also affects the content of secondary metabolites in cyanobacteria. Cyanobacterial protease inhi...
Article
The limnology community has lost a scientist who was highly esteemed both nationally and internationally, as well as a great university lecturer. It is with deep sadness that we must report that Professor Dietrich Uhlmann, passed away in Dresden on 22 October 2018, after a short, severe illness. DietrichUhlmann was born on 4 August 1930 in Chemnitz...
Article
Feldberger Haussee (NE Germany) was polluted for almost a century. During the late 1970s, the nutrient input reached a maximum of approximately 1.9/11.5 g TP/TN m⁻² yr⁻¹. As a result, the lake became a hypertrophic ecosystem and had largely lost its recreational value. In 1980, the sewage discharge was stopped, decreasing the external loading by ap...
Article
Full-text available
Ordinary differential equations (ODE) are at the center of many environmental models. The R software is increasingly used to implement ODE-based models boosted by add-on packages providing numerical solvers. This paper introduces an R package called rodeo to facilitate the implementation of ODE-based models. It addresses a standardized model notati...
Poster
Full-text available
Overview on the R package growthrates https://CRAN.R-project.org/package=growthrates
Presentation
Full-text available
The population growth rate is a direct measure of fitness, common in many disciplines of theoretical and applied biology, e.g. physiology, ecology, eco-toxicology or pharmacology. The R package growthrates aims to streamline growth rate estimation from direct or indirect measures of population density (e.g. cell counts, optical density or fluoresce...
Article
Full-text available
Fatty acids contribute to the nutritional quality of the phytoplankton and, thus, play an important role in Daphnia nutrition. One of the polyunsaturated fatty acids (PUFAs)--eicosapentaenoic acid (EPA)--has been shown to predict carbon transfer between primary producers and consumers in lakes, suggesting that EPA limitation of Daphnia in nature is...
Technical Report
Full-text available
The growth rate of a population is a direct measure of fitness. Therefore, determination of growth rates is common in many disciplines of theoretical and applied biology, e.g. physiology, ecology, eco-toxicology or pharmacology. This package aims to streamline estimation of growth rates from direct or indirect measures of population density (e.g. c...
Technical Report
Full-text available
Stickstofflimitation in Binnengewässern - Ist Stickstoffreduktion ökologisch sinnvoll und wirtschaftlich vertretbar? Abschlussbericht NITROLIMIT Phase II
Article
Full-text available
Here, we present a community perspective on how to explore, exploit and evolve the diversity in aquatic ecosystem models. These models play an important role in understanding the functioning of aquatic ecosystems, filling in observation gaps and developing effective strategies for water quality management. In this spirit, numerous models have been...
Article
Full-text available
Water quality modelling deals with multidisciplinary questions ranging from fundamental to applied. Addressing this broad range of questions requires multiple analysis techniques and therefore multiple frameworks. Through the recently developed database approach to modelling (DATM), it has become possible to run a model in multiple software framewo...
Article
Full-text available
Simulation modelling in ecology is a field that is becoming increasingly compartmentalized. Here we propose a Database Approach To Modelling (DATM) to create unity in dynamical ecosystem modelling with differential equations. In this approach the storage of ecological knowledge is independent of the language and platform in which the model will be...
Article
Langzeitdaten von deutschen Talsperren zeigen eine Erhöhung der Temperaturen der oberen Wasserschichten vor allem im Winter, Frühling und Frühsommer. Die Trends sind regional ähnlich. Da sich geringe Temperaturerhöhungen auf die biotische und abiotische Struktur und somit auf die Wasserbeschaffenheit auswirken, ergibt sich für Trinkwassertalsperren...
Article
Full-text available
Dammed drinking water reservoirs with their catchment areas and the downstream rivers are dynamic systems that change permanently under the influence of many factors. Their multifunctional use for drinking water supply, flood control, energy production, nature conservation and recreation as well as ecological constraints for the rivers downstream r...
Article
Full-text available
To predict the coherence in local responses to large-scale climatic forcing among aquatic systems, we developed a generalized approach to compare long-term data of dimictic water bodies based on phenomenologically defined hydrographic events. These climate-sensitive phases (inverse stratification, spring overturn, early thermal stratification, summ...
Article
Full-text available
Ectothermic organisms are thought to be severely affected by global warming since their physiological performance is directly dependent on temperature. Latitudinal and temporal variations in mean temperatures force ectotherms to adapt to these complex environmental conditions. Studies investigating current patterns of thermal adaptation among popul...
Data
Parameter estimates of the Lactin-2 model. (DOC)
Data
Geographical and meteorological details for natural habitats of investigated Paramecium caudatum clones. (DOC)
Article
Full-text available
Here, we communicate a point of departure in the development of aquatic ecosystem models, namely a new community-based framework, which supports an enhanced and transparent union between the collective expertise that exists in the communities of traditional ecologists and model developers. Through a literature survey, we document the growing import...
Article
Summary1. Long‐term data on the meteorology, hydrology, physicochemistry and plankton of a reservoir and its tributaries in SE Germany run from 1976 until now. This dimictic reservoir changed from mesotrophic to eutrophic in the 1970s, remained eutrophic in the 1980s and returned to the mesotrophic state after a sharp reduction in P loading in 1990...
Article
Effects of environmental variations on microcystin (MCYST) production were tested by evaluating results obtained from batch culture experiments with Microcystis aeruginosa MASH-01A19. Time series of cell and MCYST concentrations were evaluated independently with two models, a static linear and a dynamic non-linear model. Significant influences of i...
Presentation
Full-text available
In recent years, the R software has become a well known statistics tool for many biologists, especially at the PhD and the postdoc level. R is a collection of packages and a high-level programming language that can be used for scientific computing in general. It is increasingly superseding conventional spreadsheet computing and became one of the st...
Presentation
Full-text available
The R system is not only a statistics and graphics system. It is a general-purpose high-level programming language that can be used for scientific computing in general. It is increasingly superseding conventional spreadsheet computing and became one of the standard environments for data analysis and modeling in ecology. An increasing collection of...
Article
Full-text available
1. We conducted an experimental study of predation by benthivorous fish on a natural community of stream invertebrates using a reach-scale approach. Over a 2-year period (experimental phase), the benthic invertebrate community of a stretch containing two species of benthivorous fish was compared with a fishless stretch. Thereafter, all fish were re...
Article
The ongoing climate change has motivated numerous studies investigating the temperature response of various organisms, especially that of ectotherms. To correctly describe the thermal performance of these organisms, functions are needed which sufficiently fit to the complete optimum curve. Surprisingly, model-comparisons for the temperature-depende...
Article
A pronounced pollution of surface water bodies in the Western Bug River Basin, Ukraine, has been caused by outdated or overloaded wastewater treatment plants, agriculture, industry and coal mining. These pressures have led to a generally poor state of both chemical and microbiological variables creating health risks of various kinds. The state of s...
Article
The open-source problem solving software R [1] has become one of the most widely used systems for statistical data analysis. As it is a powerful interpreted language, it is also very well suited for other disciplines in scientific computing. One of the fields where considerable progress has been made is the solution of differential equations. In th...
Article
The open-source software R has become one of the most widely used systems for statistical data analysis and for making graphs, but it is also well suited for other disciplines in scientific computing. One of the fields where considerable progress has been made is the solution of differential equations. Here we first give an overview of the types of...
Article
Full-text available
A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others (‘reinventing the wheel’). The other challenge is to avoid focusi...
Chapter
Seen und Talsperren sind dynamische Systeme, die gleichermaßen durch externe wie interne Prozesse gesteuert werden. Das Verständnis dieser Dynamik ist ein zentrales Anliegen der Limnologie und Grundvoraussetzung für zielführendes und kreatives Management. In diesem Zusammenhang sind komplexe dynamische Seenmodelle (KDS) ein unentbehrliches Hilfsmit...
Technical Report
Full-text available
This document describes how to use the deSolve package (Soetaert, Petzoldt, and Setzer 2010a) to solve models that are written in FORTRAN or C.
Article
Full-text available
Mathematical simulation models are commonly applied to analyze experimental or environmental data and eventually to acquire predictive capabilities. Typically these models depend on poorly defined, unmeasurable parameters that need to be given a value. Fitting a model to data, so-called inverse modelling, is often the sole way of finding reasonable...
Article
Full-text available
In this paper we present the R package deSolve to solve initial value problems (IVP) written as ordinary differential equations (ODE), differential algebraic equations (DAE) of index 0 or 1 and partial differential equations (PDE), the latter solved using the method of lines approach. The differential equations can be represented in R code or as co...
Article
Full-text available
R package deSolve (Soetaert, Petzoldt, and Setzer 2010a,b) the successor of R package odesolve is a package to solve initial value problems (IVP) of: ordinary differential equations (ODE), differential algebraic equations (DAE) and partial differential equations (PDE). delay differential equations (DeDE). The implementation includes stiff integrati...
Article
Full-text available
Although R is still predominantly applied for statistical analysis and graphical representation, it is rapidly becoming more suitable for mathematical computing. One of the fields where considerable progress has been made recently is the solution of differential equations. Here we give a brief overview of differential equations that can now be solv...
Article
Full-text available
In temperate regions, the warming trends of the last decades have been observed primarily in winter and early spring. Accordingly, changes in the phenology of individual species, e.g. sprouting in plants or spawning of fish, occurred mainly in spring. Although the general pattern is earlier and faster development in response to warming, differences...
Presentation
Full-text available
The talk will focus on practical experience with implementing and using dynamic models in R as seen from a biological scientist’s perspective. A series of concrete case studies was performed analysing particular aspects of ecological interactions. These are presented together with the applied modelling techniques, e.g. sensitivity analysis, paramet...
Article
A mechanistic model was applied to study the influence of diurnal vertical migration (DVM) of planktonic crustaceans on the succession and composition of the phytoplankton community. While zooplankton was restricted to only one functional group, the phytoplankton community was divided into two functional groups which are distinguished by their maxi...
Article
In temperate regions, the warming trends of the last decades have been observed primarily in winter and early spring. Accordingly, changes in the phenology of individual species, e.g. sprouting in plants or spawning of fish, occurred mainly in spring. Although the general pattern is earlier and faster development in response to warming, differences...
Article
Full-text available
Hypothesis: Divergence in thermal preference, in combination with temperature-related metabolic adaptations, promotes ecological specialization and co-existence of a sympatric species pair of coregonid fish. Background: The coregonids show substantially lower divergence in diet composition than other sympatric fish pairs in temperate freshwater lak...
Article
Diel vertical migration (DVM) of Daphnia is a well-studied inducible defence mechanism against predation by fish. Our study is anchored in constructing an individual-based model of DVM in order to bring established knowledge about essential key processes into a synthesis. For that purpose, we combined information about both proximate and ultimate f...
Article
The quantitative description of phytoplankton growth, dynamic photoacclimation and photosynthesis in dependence on temperature, irradiance, trace element and nutrient availability is still a matter of debate and competing ideas in the literature, mainly due to a lack of new critical experiments and to non-unique mathematical descriptions. This pape...
Article
Laboratory experiments revealed a relationship between microcystin (MCYST) production and cell division. In order to evaluate this relationship, a model with two differential equations describing population growth and MCYST production was applied. It is demonstrated that MCYST production and expected maximum values of MCYST cell quota are generally...
Article
Drift as a low-energy cost means of migration may enable stream invertebrates to leave risky habitats or to escape after encountering a predator. While the control of the diurnal patterns of invertebrate drift activity by fish predators has received considerable interest, it remains unclear whether benthivorous fish reduce or increase drift activit...
Presentation
Full-text available
Conference slides about obect-oriented implementation of ecological models with R package simecol. Abstract: https://www.r-project.org/conferences/useR-2008/abstracts/Petzoldt.pdf Slides: https://www.r-project.org/conferences/useR-2008/slides/Petzoldt.pdf
Technical Report
Full-text available
This document is a loose collection of chapters that describe dierent aspects of modelling and model implementation in R with the simecol package. It supplements the original publication of Petzoldt and Rinke (2007) from which an updated version, simecol-introduction, is also part of this package. Please refer to the JSS publication when citing thi...
Technical Report
Full-text available
The cardidates package provides methods for fitting four resp. six parametric Weibull functions to environmental data. Heuristics are applied for finding initial parameters in the six parametric case. As a second step, the fitted functions can be used to identify maximum, beginning and end of peaks by using a quantile-like approach.
Conference Paper
So far, seasonal management strategies for water withdrawal from drinking water reservoirs in Germany are based on the hydrological regime and use Monte-Carlo-simulations in order to provide recommendations with certain probability thresholds. Long-term experience on the annual development and composition of phytoplankton is used for ad-hoc adjustm...
Article
Full-text available
Batch culture experiments with the cyanobacterium Microcystis aeruginosa PCC 7806 were performed in order to test the hypothesis that microcystins (MCYSTs) are produced in response to a relative deficiency of intracellular inorganic carbon (Ci,i). In the first experiment, MCYST production was studied under increased Ci,i deficiency conditions, achi...
Article
Phenology and seasonal succession in aquatic ecosystems are strongly dependent on physical factors. In order to promote investigations into this coupling, methods of characterising annual time series of phytoplankton were derived and applied to a 31-year data set from Saidenbach Reservoir (Saxony, Germany). Field data are often scarce and irregular...
Article
Full-text available
The third special volume in the "Foometrics in R" series of the Journal of Statistical Software collects a number of contributions describing statistical methodology and corresponding implementations related to ecology and ecological modelling. The scope of the papers ranges from theoretical ecology and ecological modelling to statistical methodolo...
Article
Full-text available
Results of ecological models differ, to some extent, more from measured data than from empirical knowledge. Existing techniques for validation based on quantitative assessments sometimes cause an underestimation of the performance of models due to time shifts, accelerations and delays or systematic differences between measurement and simulation. Ho...
Article
Full-text available
The simecol package provides an open structure to implement, simulate and share ecological models. A generalized object-oriented architecture improves readability and potential code re-use of models and makes simecol-models freely extendable and simple to use. The simecol package was implemented in the S4 class system of the programming language R....
Article
The influence of Daphnia galeata×hyalina grazing and of infochemicals released by the daphnids on the colony size and growth rate of the colonial gelatinous green alga Sphaerocystis schroeteri (Chlorococcales) was investigated in laboratory batch experiments run for 96 h. High zooplankton grazing pressure was exerted by a final concentration of 100...
Article
1. We present data with a high spatio-temporal resolution from a 72-h field survey in Bautzen Reservoir (Saxony, Germany). The aims of this survey were to observe hydrophysical processes during a period of unstable stratification in spring and investigate the effect of wind-induced internal waves on the vertical distribution of zooplankton. 2. Win...
Article
Full-text available
The third special volume in the "Foometrics in R" series of the Journal of Statistical Software collects a number of contributions describing statistical methodology and corresponding implementations related to ecology and ecological modelling. The scope of the papers ranges from theoretical ecology and ecological modelling to statistical methodolo...
Poster
Full-text available
Simulations of reservoir ecosystems were carried out by means of the coupled hydrodynamical ecological model SALMO which is vertically resolved. It comprises modules for (i) turbulent diffusion, seiches and the hydrological balance, (ii) advection and sedimentation and (iii) the internal biological/chemical reactions (photosynthesis, grazing, nutri...
Article
Excessive inputs of phosphorus and nitrogen are the main reasons of eutrophication of inland waters and coastal areas. Large efforts have been made to control phosphorus, but the measures to reduce nitrogen emissions failed at least partly. While it was possible to reduce nitrogen emissions from industry and municipal wastewater treatment plants, d...