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James ODwyer (University of Illinois)12/07/2023, 09:45
In this talk we'll explore three different approaches to understanding and prediction in microbiomes. First, we'll explore commonalities between microbial community dynamics and several other complex systems, identifying where general lessons and constraints can inform our interpretation of community patterns. Second, we'll survey a range of mechanistic models, where these have given insights,...
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Giulio Biroli (ENS Paris)12/07/2023, 11:00
Using statistical physics methods we study the role of dynamical fluctuations in shaping the behavior of high-diversity and spatially extended heterogeneous ecosystems. After an introduction to the methods developed to study the dynamics of species-rich ecosystems, we shall focus on two main emerging phenomena: (i) chaotic dynamics due to endogenous fluctuations persisting for extremely long...
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Kiran Raosaheb Patil12/07/2023, 13:00
Kefir – a traditional fermented milk drink with a long history – is a fascinating example of ecological success at community-scale. The kefir microbial community stands out amongst other fermented food communities with its richness (>40 species), robustness, and spatial organisation. I will present my lab’s findings unravelling the intricate spatio-temporal interactions in the kefir...
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Ralf Steuer (Intitute for Theoretical Biology, Humboldt-University of Berlin)12/07/2023, 13:55
To understand the organization and dynamics of microbial communities is a fundamental challenge in current biology. To tackle this challenge, the construction of computational models of interacting microbes is an indispensable tool. There is, however, still a chasm between ecologically motivated descriptions of microbial growth used in typical ecosystems simulations, and the detailed metabolic...
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Jos Kramer (Department of Integrative Biology, ETH Zurich)12/07/2023, 14:45
Predation shapes biological evolution at multiple scales, from genomes and organisms to entire ecosystems. Albeit traditionally studied in larger organisms, predation also pervades the microbial world: nematodes and protists ingest prey whole via phagocytosis; many Bdellovibrio-and-like organisms (BALOs) invade their prey and reproduce in a virus-like fashion; and group-hunting myxobacteria...
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Gian Marco Palamara (University of Bern)12/07/2023, 15:15
Research on consumer-resource dynamics is vast and has been addressed in both theoretical and empirical studies. A primary goal in this research agenda is to understand how mascroscopic descriptions of trophic interactions relate to the individual processes that define the consumer-resource interaction in the first place. Despite decades of studies, there is still no clear agreement on the...
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Ana-Hermina Ghenu (Institute for Ecology and Evolution, University of Bern)12/07/2023, 17:00
Soil bacteria are critical for sustaining ecosystem functions and services. Recent studies show that soil bacterial communities are susceptible to climate change, particularly to extreme climatic events. Yet, we know little about the biotic mechanisms through which extreme climatic events, such as heat waves, restructure soil bacterial communities. Previous studies indicate that slower growing...
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Gisela Rodriguez (Microbial Population Biology Department)12/07/2023, 17:00
Glacial retreats represent a unique opportunity to study primary successional processes. The new exposed rock is a new material for the assembly of a new ecosystem. Soil formation after glacial retreat is strongly influenced by plant colonization, but this colonization depends on nutrient availability. An ongoing project in the forefront of the last Venezuelan glacier has established a...
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Alejandra Ramirez12/07/2023, 17:00
Evolutionary game dynamics is a framework used to model the evolution of strategies in a population. For finite populations, dynamics that appear to lack a pattern or principle of organisation can arise from sources like demographic noise and chaos. The former refers to the stochasticity caused by the probabilistic nature of birth and death events, while the latter is related to deterministic...
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Alyssa Henderson12/07/2023, 17:00
Microbes live in complex communities, where they continuously engage in a range of interactions with other microbes. One class of interactions is the exchange of metabolites, where one microbe synthesises a compound that is taken up by a neighboring microbe. This exchange allows some microbes to be non-producers for essential metabolites, instead relying on the biosynthetic activities of...
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Vasvi Chaudhry (University of Tübingen)12/07/2023, 17:00
Plants are associated with a diverse microbiome consisting of bacteria, fungi, and protists that play a crucial role in establishing a stable microbial community that contributes to the health of their host under atypical environmental stresses. Although these microbial communities are co-evolved with plants in either beneficial, commensal, or pathogenic lifestyles, how each member cooperates...
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Aurore Woller12/07/2023, 17:00
Antibiotic resistance is a major threat, motivating the development of procedures to eliminate antibiotic resistant bacteria. Our collaborators (E. Slack’s lab, ETH Zürich) have shown that intestinal antibodies, raised by oral vaccines, enforce the targeted bacterial strain to undergo "enchained growth", forming large clumps, which may be flushed out of the gut faster than free bacteria. They...
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Juan Giral12/07/2023, 17:00
In recent years, great progress has been made towards understanding the properties of species-rich communities with random interactions by leveraging tools from disordered systems. In the simplest models, macroscopic simplicity comes at the expense of a lack of structure in the interaction matrix. We extend previous work to account for communities with structured weak interactions and explore...
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Amanda de Azevedo Lopes (MPI for Evolutionary Biology)12/07/2023, 17:00
Multilevel selection in host-associated microbiomes has important implications for understanding the origin and evolution of these complex associations. To date, we do not have a clear understanding of the different levels that can affect selection on microbial communities. There is evidence that the higher level of selection provided to the microbiome by the host has a significant impact on...
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Kate Williamson (MRC Toxicology Unit)12/07/2023, 17:00
The gut microbiota is now well established as a mediator of human health and disease with a central role in a myriad of host functions beyond digestion, including immune modulation, metabolic regulation and neurological signalling. Compositional changes in these bacterial communities have been causally linked to a multitude of diseases including obesity, inflammatory bowel disease, cancer,...
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medea zanoli (Mediterranean Institute for Advanced Studies (IMEDEA) , Esporles, Spain)12/07/2023, 17:00
The microbial ecosystem is full of narrow constrictions that microorganisms need to learn to navigate in order to survive. Here, we study a Nature example of a "microorganism billiard": a system composed of a population of microorganisms packed in a closed space, with only a few narrow apertures to escape from. This situation occurs when the marine parasite Parvilucifera sinerae infects and...
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Sangwon Hyun (University of California, Santa Cruz)12/07/2023, 20:00
Oceanographers can now collect flow cytometry data in real time while onboard a moving ship, which provides them with fine-scale information about the distribution of phytoplankton across thousands of kilometers. This presents an exciting opportunity to learn new insights about the microbial ecology of the ocean. We present a set of novel statistical models to estimate the time-varying...
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Ada Altieri (Université Paris Cité)13/07/2023, 09:00
In this talk, I will address some timely questions in theoretical ecology by discussing the Generalized Lotka-Volterra model in the presence of many randomly interacting species and finite demographic fluctuations. Leveraging on disordered systems’ techniques, I will unveil a rich, eventually hierarchical, organization of the equilibria and relate the slowing down of dynamical correlators to...
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Joseph Baron (LPENS)13/07/2023, 09:30
The eigenvalue spectrum of a random matrix often only depends on the first and second moments of its elements, but not on the specific distribution from which they are drawn. The validity of this universality principle is often assumed without proof in applications. In this talk, I will discuss a pertinent counterexample in the context of the generalized Lotka-Volterra equations. Using dynamic...
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Pietro Valigi (Università di Roma La Sapienza)13/07/2023, 10:00
In the very recent years, an increasing amount of interest has been devoted to the study of models of ecosystems defined on sparse random graphs.
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In this scenario both network topology and interactions nature play a relevant role in establishing the ecosystem properties.
In particular, differently from what usually happens in dense random matrices, the spectra of locally tree-like graphs... -
Daniel Amor (École Normale Supérieure)13/07/2023, 11:00
This talk aims at opening a debate on i) how to address important challenges in predicting microbial community dynamics and ii) how to leverage state-of-the-art ecology to control microbial community dynamics.
I will begin with a brief overview of the dynamics of natural communities in terms of stability in composition and functions, fluctuations, and response to perturbations. Next, I will...
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Thomas Scheuerl13/07/2023, 13:00
A major aspiration is to understand the forces that drive composition and functionality of bacterial communities. The abiotic and biotic environment, historical contingency, chance and evolutionary process are all discussed as important factors. In communities, biotic interactions may affect not only composition and functionality but also how species evolve. In the first part I will show that...
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Hyejin Park (Department of Physics, Inha University; Asia Pacific Center for Theoretical Physics (APCTP))13/07/2023, 13:30
Collectives of microbes exhibit functions that individual species cannot, such as degrading waste, producing vitamins, and creating biofuels, which can benefit humans. To improve these functions, researchers suggest using artificial selection on collectives to choose the best-performing ones for the next generation. However, this method has shown that there is a limitation to improving the...
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Ruben Garrido-Oter (Max Planck Institute / Earlham Institute)13/07/2023, 14:10
Photosynthetic organisms, such as land plants and algae, release organic compounds to the surrounding environment, which create a niche for colonization by heterotrophic microbes. These microbes consume photosynthates and assemble into complex communities, often providing their host with beneficial services in exchange, such as pathogen protection, or enhanced nutrient mobilization. While...
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Divvya Ramesh (ETH Zürich and Eawag)13/07/2023, 15:30
Microbes are ubiquitous and play key roles in ecosystem functions. In nature, most microbes live in spatially structured multi-species communities. In such communities, cells live in close proximity and engage in a variety of metabolic interactions with neighbours. The overall metabolic potential of a microbial community is determined by the activities of individual cells and the interactions...
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Matti Gralka (VU Amsterdam)13/07/2023, 16:00
The enormous diversity of heterotrophic bacteria in the environment begs the question to what degree their metabolic niches can be understood in terms of a small number of simplified metabolic categories. Here, we show that, despite high variability at all levels of taxonomy, the catabolic niches of heterotrophic bacteria can be understood in terms of their preference for either glycolytic...
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Hanna Fokt14/07/2023, 09:00
The mammalian intestine is a unique ecosystem for thousands of bacterial species and strains. How naturally co-existing bacteria of the microbiota interact with each other is not yet fully understood. Here, we systematically studied over 100 interactions between bacteria of the genus Bacteroides that were isolated from the intestine of healthy mice. We find a vast diversity of interactions...
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Rachel Wheatley14/07/2023, 09:55
Antibiotic resistance poses a global health threat, but the within-host drivers of resistance remain poorly understood. Pathogen populations are often assumed to be clonal within hosts, and resistance is thought to emerge due to selection for de novo variants. Here we show that mixed strain populations are common in the opportunistic pathogen Pseudomonas aeruginosa. Crucially, resistance...
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Stephan Munch (UC Santa Cruz)14/07/2023, 11:00
There is a clear need for robust tools for prediction and inference of ecological dynamics that do not depend on precisely knowing how ecosystems work. Data-driven methods such as empirical dynamic modeling (EDM) allow us to learn dynamics with minimal assumptions. Here, I will introduce the basic ideas of EDM and then discuss two recently developed approaches to incorporating external driving...
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Jarone Pinhassi (Linnaeus University)14/07/2023, 13:00
Seasonality in the conditions for life is a ubiquitous phenomenon in the grand majority of biomes at the Earth’s surface. In aquatic environments, reasonably predictable temporal dynamics in physicochemical conditions of for example temperature and nutrients along with biotic variables set the stage for successional changes in planktonic food webs. This is frequently first noted as changes in...
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Dominic Eriksson (ETH Zürich)14/07/2023, 13:55
Marine diazotrophs convert atmospheric nitrogen gas into bioavailable nitrogen that can fuel up to 50% of the primary productivity in oligotrophic subtropical and tropical seas. Despite their importance, little is known about their global biogeography and diversity since global studies have been hampered by scarce data observations. This limitation prevents us from understanding the link...
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Alexandra Worden (Max Planck Institute for Evolutionary Biology, Plön, DE; Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, DE; Marine Biological Laboratory, Woods Hole, USA )14/07/2023, 14:45
We all know that activities and interactions of microbes in the wild underpin the biogeochemical cycles that support earth’s biomes, and the modern climate that we love so well. As in other ecosystems, in the oceans these activities can be difficult to measure particularly in connection with molecular mechanisms or in a manner that identifies the key members responsible for an activity....
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