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16/05/2022, 19:45
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Paul Rainey (MPI for Evolutionary Biology)16/05/2022, 20:00
Mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long-term survival, MGEs must continuously invade new hosts by horizontal transfer. Theoretically, MGEs that persist for millions of years in single lineages, and are thus subject to vertical inheritance, should not exist....
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Seppe Kuehn (The University of Chicago)17/05/2022, 09:00
Microbial communities harbor almost unimaginable complexity at all levels of organization. Vast genomic diversity is present even within a single taxon. Diverse genomes across taxa encode complex regulatory programs that modulate physiological traits from chemotaxis to metabolic processes. From these traits emerge interactions between taxa that depend on abiotic factors. Together, these...
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Michael Manhart (ETH Zürich)17/05/2022, 09:45
Microbial growth relies on the presence of several nutrients, including elemental nutrients such as carbon and nitrogen, as well as complex nutrients like vitamins and amino acids. Evidence from biogeochemistry, especially in aquatic environments, suggests that multiple nutrients may be simultaneously rare in nature and therefore limit growth. However, we poorly understand how this...
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Alma Dal Co (University of Lausanne )17/05/2022, 10:45
Communities of interacting microbes perform fundamental processes on Earth. These processes arise from a dense network of interactions between individual cells. Most microbial communities are spatially structured systems, where cells move little, thus interactions occur mostly between cells close in space. Therefore, the spatial arrangement of different species can affect the processes that...
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Otto Cordero (MIT)17/05/2022, 11:05
Just as microbes in our guts digest the complex fibers we eat, marine bacteria break down and digest the complex forms of organic matter that phyto- and zoo-plankton produce in the surface ocean. This biological process is key for life on the planet, as it returns carbon back to the atmosphere and balances the elemental cycles that sustain life. Complex organic matter is made up of long...
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Marjon de Vos (University of Groningen - GELIFES )17/05/2022, 14:00
Bacteria derived from polymicrobial urinary tract infections (UTIs) together with commensal urinary residents can be viewed as small ecosystems. By measuring pair-wise interactions we obtained a unique insight in the ecological interactions of these microbiome members. We find that many of these bacterial interactions affect the immediate tolerance to antibiotics, as well as their ability to...
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Jeroen Meijer (Utrecht University )17/05/2022, 14:45
Jeroen Meijer, Paulien Hogeweg, Paul Rainey, Bas Dutilh.
Bacteriophages are important players in shaping microbial communities, yet their abundance and dynamics in highly diverse, natural environments remain poorly understood. In particular, many different genotypes of a single phage can be present, but their relevance for viral dynamics and ecological interactions is not currently known....
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Brandon Ogbunu (Yale University)17/05/2022, 15:05
In this talk I'll provide a survey of studies from my research program all aimed to thinking about higher-order interactions in microbial and social systems. In doing so, I propose the question of whether the science of interactions is truly headed towards being a generalizable physics, that would apply to microbial communities and other sets of actors and parcels of information.
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17/05/2022, 19:45
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Jennifer Martiny (University of California, Irvine )18/05/2022, 09:00
Microbial communities provide an excellent study system to explore the integration of ecology and evolution. At one end of the spectrum, the composition of microbial communities (assessed at broad taxonomic levels) dramatically shifts in response to environmental changes. At the other end, laboratory studies demonstrate the potential for rapid evolution in response to the similar environmental...
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Roman Zapien-Campos (MPI for Evolutionary Biology)18/05/2022, 10:00
A longstanding question in Ecology is which drivers are responsible for the difference in abundance of species within a community. While some species are relatively abundant, many others are rare. Theoretical models have been useful to investigate the drivers of community dynamics. In particular, models that consider the death, birth, and immigration of individuals have been used extensively....
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Rachel Szabo (Massachusetts Institute of Technology)18/05/2022, 11:00
In many natural environments, microorganisms self-assemble around heterogeneously distributed resource patches. The growth and collapse of populations on resource patches can unfold within spatial ranges of a few hundred micrometers or less, making such microscale ecosystems hotspots of biological interactions and nutrient fluxes. Despite the potential importance of patch-level dynamics for...
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Maria Rebolleda-Gomez (University of California, Irvine )18/05/2022, 11:20
Microbes affect global nutrient cycles, the development of our immune system, and resource acquisition and stress responses of multicellular organisms. In a rapidly changing world, we would like to predict the ecological and evolutionary trajectories of populations and communities. Recent efforts have shown that microbial community assembly is often fairly predictable at a functional level,...
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Reena Debray18/05/2022, 12:05
Community assembly can reach different outcomes depending on the history of species arrival, a phenomenon known as a priority effect. The study of priority effects has traditionally focused on the ecological consequences of arrival history, often assuming that evolution occurs too slowly to influence community assembly. However, recent models suggest that accounting for local adaptation would...
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Tim Barraclough (University of Oxford )18/05/2022, 13:25
Bacteria have the potential for rapid evolution thanks to short generation times, large population sizes, and mechanisms for generating genetic variation. But in the wild they live in open communities made up of hundreds of species and exposed to a constant rain of potential new colonists. This talk discusses the potential consequences of natural diversity for bacterial evolution and outlines...
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Valérie Mattelin18/05/2022, 14:10
Microbial communities in aquatic habitats, ranging from small fresh water streams to the vast oceans, are confronted with a relatively new (from an evolutionary point of view), man-made and omnipresent carbon source: plastics. Research has shown that plastic particles in marine ecosystems are rapidly colonized by microorganisms, and that microbial community in the so-called plastisphere has a...
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18/05/2022, 19:15
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Ivana Gudelj (University of Exeter )19/05/2022, 09:00
Understanding how microbial traits affect the evolution and functioning of microbial communities is fundamental for improving the management of harmful microorganisms, while promoting those that are beneficial. Decades of evolutionary ecology research has focused on examining microbial cooperation, diversity, productivity and virulence but with one crucial limitation. The traits under...
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Afra Salazar (University of Lausanne )19/05/2022, 10:00
Multispecies bacterial communities often perform functions arising from the interactions among their members. These community functions can, in principle, be improved via directed evolution. Yet, current selection methods for improved community function have shown limited success. One reason for this limited success might be that methods of community selection rely on the assumption that...
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Kristina Hillesland (School of STEM, UW Bothell, Bothell WA, USA )19/05/2022, 11:00
Mutualisms, or interactions between species where both provide a net fitness benefit to each other, are numerous and ecologically relevant. Presumably, these interactions affect the evolution of both species, possibly resulting in coevolution where evolutionary changes in one causes selection for changes in the other species. However, rigorous studies of coevolution in mutualisms have been...
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Kaitlin Schaal (ETH Zürich)19/05/2022, 11:45
Predation drives the microbial world, but trophic interactions among microbes are poorly understood. One charismatic predator, the social soil bacterium Myxococcus xanthus, is a model system for studying cooperation and aggregative multicellularity. It has been studied in bi-trophic but never tri-trophic systems, despite the proposed importance for interactions with predators in the evolution...
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Sophie de Buyl (Vrije Universiteit Brussels )19/05/2022, 12:05
We analyze properties of experimental microbial time series, from plankton and the human microbiome, and investigate whether stochastic generalized Lotka-Volterra (gLV) models could reproduce those properties. We show that this is the case when the noise term is large and a linear function of the species abundance, while the strength of the self-interactions varies over multiple orders of...
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Marta Goberna (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC) )19/05/2022, 15:30
Stressful water-limited soils are typically covered by scattered plant patches that generate a mosaic of low-productive habitats, which are almost devoid of plants and comparatively driven by abiotic filters, interspersed with high-productive habitats comparatively driven by biotic interactions. Such ecosystems provide an ideal setting to disentangle which processes dominate the community...
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A. Delphine Tripp19/05/2022, 16:15
Poor predictability of stable microbial colonization undermines our ability to harness probiotics and phage therapy in human health applications. Person-specific diversity contributes to this unpredictability; it is unclear how microbes colonize and evolve on individuals to create microbiomes with unique compositions, in which most genetic variation occurs within species boundaries....
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19/05/2022, 19:00
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Alejandra Rodriguez Verdugo (University of California Irvine )20/05/2022, 09:00
Microbial communities are incredibly diverse. Molecular techniques such as ‘omics’ have uncovered a vast number of microbial ‘species’ in communities from natural environments. Yet, the ecological and evolutionary processes originating this diversity remain understudied. This study investigated the ecological and evolutionary forces by which new bacterial ‘species’ emerge and coexist in...
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Duhita Sant (Monash University)20/05/2022, 09:45
Duhita G. Sant 1, Aysha L. Sezmis 1, Laura C. Woods 1 and Mike J. McDonald1* 1 School of Biological Sciences, Monash University, Monash, Australia * Correspondence should be addressed to: mike.mcdonald@monash.edu
Microbial communities comprised of many interacting species sustain all ecosystems and are essential for life. A major goal is to be able to intervene when microbiomes become...
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Sara Mitri (University of Lausanne )20/05/2022, 10:45
Microbial communities in soil or the mammalian gut are constantly changing, as they first assemble and as species adapt to each other and to their environment. Being able to predict how these dynamics play out is crucial, as these communities greatly affect us and our environment. But since studying co-evolutionary dynamics in natural systems is extremely challenging, in my lab we study small...
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Elze Hesse (University of Exeter, Penryn Campus)20/05/2022, 11:30
Evolutionary dynamics can occur over similar time scales as ecological selection, meaning that there can be feedback between ecology and evolution. However, evidence of concordant eco-evolutionary selection often comes from in vitro studies, where there necessarily will be strong selection. Moreover, these studies have typically focussed on different focal traits meaning ecological and...
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Saheli Saha (Indian Institute of Science, Bangalore, India)20/05/2022, 11:50
Reciprocal interactions such as cooperation, parasitism, altruism, etc are strongly affected by population mixing and modes of transmission. However, the effect of population mixing on the evolutionary dynamics of prey-predator interactions remains largely unexplored. Hence, in a laboratory evolution experiment, we propagated bacterial predator-prey communities in two distinct transfer...
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Ayari Fuentes Hernandez (Center for Genomic Sciences, UNAM )20/05/2022, 13:15
Microbial ecosystems are composed of multiple species in constant metabolic exchange. A pervasive interaction in microbial communities is metabolic cross-feeding. The metabolic burden of producing costly metabolites is distributed between community members, in some cases for the benefit of all interacting partners. In particular, amino acid auxotrophies generate obligate metabolic...
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Josie Elliott (University of Bath )20/05/2022, 14:00
Authors: Josie Elliott, Bridget Watson, Edze Westra, Tiffany Taylor
CRISPR-Cas is an adaptive bacterial defence system that offers protection against foreign DNA, including phages. This antiviral system allows bacteria to acquire resistance to new infections, providing a powerful weapon in the evolutionary arms races that exist between bacteria and their phage. Despite these systems being...
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20/05/2022, 17:00
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Luis Valentin (University of California Berkeley)
Discharging deeply-sourced groundwater can contain reduced inorganic sulfur compounds that sustain chemoautotrophic ecosystems, yet questions remain regarding the role of CPR bacteria within these complex subsurface communities. Here, we studied two sites where microbial biofilms grow in cold, sulfide-rich groundwater derived from deep crustal and meteoric sources. Profiling of biofilms and...
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Gisela Tatianna Rodriguez Sanchez
Gisela T. Rodriguez1,4, Barbara Huber1,3, 4, Alejandra Melfo2, Luis D. Llambi3 and Kristin Saltonstall4 1Laboratorio de Microbiología Molecular y Biotecnología, Universidad de los Andes, Mérida, Venezuela. 2Centro de Física Fundamental, Universidad de Los Andes, Mérida, Venezuela. 3Instituto de Ciencias Ambientales y Ecológicas, Universidad de Los Andes, Mérida, Venezuela. 4Smithsonian...
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Nittay Meroz (The Hebrew University of Jerusalem)
Managing and engineering microbial communities relies on the ability to predict their composition. While progress has been made on predicting compositions on short, ecological timescales, there is still little work aimed at predicting compositions on evolutionary timescales. Therefore, it is still unknown for how long communities typically remain stable after reaching ecological equilibrium,...
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Marie Rescan (Catalan Institute for Water Research )
City sewers shelter rich and diverse bacterial communities that are continuously exposed to antibiotic residues from human excreta, thus becoming a reservoir of resistance. Predicting the risk of antibiotic resistance evolution in city sewers thus requires a comprehensive understanding of the dynamics and evolution of wastewater bacterial communities. However, interactions between species...
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Michael Raatz (MPI for Evolutionary Biology)
Microbial communities comprise an astonishing diversity. Decomposing these often complex communities into small community modules holds the promise to elucidate the mechanisms behind the assembly and maintenance of this diversity. Among these, the apparent competition module, where two prey types compete and are preyed on by a shared predator, has received particular attention, often with a...
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Miguel Díez Fernández de Bobadilla (IRYCIS (Ramón y Cajal Institute for Health Research) )
Hospital-built environments, and especially Intensive Care Units (ICUs), are hotspots for the emergence, transmission, and evolution of antimicrobial resistance (AMR). Most bacterial species able to acquire genes encoding resistance to antibiotics (ARGs), heavy metals (MRGs) or biocides (BcRGs) are colonizing opportunistic pathogens able to survive in abiotic systems (surfaces, medical...
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Luis Zaman (University of Michigan )
Most of Earth's diversity has been produced in rounds of adaptive radiation, but the ecological drivers of diversification, such as abiotic complexity (i.e., ecological opportunity) or predation and parasitism (i.e., ecological necessity), are hard to disentangle. However, most of these radiations occurred hundreds of thousands if not millions of years ago, and the mechanisms promoting...
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José Carlos Ramón Hernández Beltrán (Max-Planck Institute for Evolutionary Biology )
The study of evolution has traditionally focused on the effects of selection on individuals. In recent years, attention has turned to the possibility of selection on communities. Yet much remains to be understood about the conditions necessary for selection to work on collectives. Previous theoretical works have shown that communities can evolve as units of selection provided that the...
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52. Experimental (co)evolution in a multi‐species microbial community results in local maladaptationMeaghan Castledine (University of Exeter )
Interspecific coevolutionary interactions can result in rapid biotic adaptation, but most studies have focused only on species pairs. Here, we (co)evolved five microbial species in replicate polycultures and monocultures for 10 weeks (~100 generations) and quantified local adaptation. Specifically, growth rate assays were used to determine adaptations of each species’ populations to (1) the...
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Maxime Ardre (ESPCI )
Colonization of a pristine environment by bacterial communities is a crucial step for the co-evolutionnary dynamics followed by bacteria, in the wild as well as in laboratories. A key phase for the fixation of a strain in a new environment is the primary phase of growth: the lag phase- where cells adapt to their new conditions. For a population composed of several settlers, an essential...
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Ben Kerr
The passage of genes from parents to offspring is a fundamental rule of heredity. However, bacteria violate this rule of strict vertical inheritance by shuttling DNA between cells through horizontal gene transfer (HGT). Common vehicles for HGT are conjugative plasmids, extrachromosomal pieces of DNA encoding the machinery for their own transfer. In addition to standard vertical transmission,...
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Pauline Buffard (MPI for Evolutionary Biology)
Recent work from our lab showed that it is possible to use selfish genetic elements (SGEs) to link genes to community function. My project uses this same experimental approach and applies it to understand how horizontal gene transfer (HGT) might affect the establishment of the microbiome of the well-studied nematode Caenorhabditis elegans. To achieve this, I am experimentally evolving C....
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Nanami Kubota (University of Pittsburgh )
Bacteriophage integrated in bacterial chromosomes (prophages) can act as mobile genetic elements, making them important drivers of rapid bacterial evolution. The Pf phages are filamentous Inoviruses that are integrated in most Pseudomonas aeruginosa genomes and they are unusual because they can reproduce without lysing their host. Pf prophage particles have been shown to contribute to P....
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Akos Kovacs (Technical University of Denmark )
Synthetic communities provide a proxy to reveal the ecological interaction between microbes, including metabolic cross feeding and inter-species signals that influence growth and differentiation. Among these laboratory communities, biofilm retains a spatially organized niche. We have recently demonstrated how metabolic interaction between Bacilli and Pseudomonads in biofilms is translated to...
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Sijmen Schoustra (Wageningen University)
Microbial ecosystems generally consist of communities with a complex composition. Prolonged propagation in a new environment may impose various selective pressures that can change species composition. Over the short term, ecological processes such as species sorting may be most prominent. Over the longer term, novel mutations in specific players of the community may add to the shaping of...
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Peter Deines (CAU Kiel, GEOMAR)
Organisms and their resident microbial communities form a complex and mostly stable ecosystem. Of particular relevance are the factors that shape the stability and resilience of such communities, despite different fitness trajectories of the microbiome members. Our work addresses microbial interactions within the microbiome of the simple metaorganism, Hydra. Firstly, we ask whether the...
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Brendan Bohannan (University of Oregon/CAU-Kiel )
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Sebastien Wielgoss (ETH Zurich)
Among group-forming microbes, the predatory myxobacteria represent important model organisms in developmental biology and social evolution. Many important aspects of their multicellular life cycles have been studied in great molecular detail. We recently showed that individuals of the myxobacterium Myxococcus xanthus stay together as kin groups over extended periods of time in soil, thereby...
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Sebastian Gude (Technical University of Denmark (DTU) )
Bacteria require a diverse set of metabolites to proliferate. While some bacteria fulfil their metabolic needs through de novo biosynthesis, others rely on uptake. Mechanisms enabling stable metabolite provisioning among free-living bacteria, i.e., in the absence of means for positive assortment, remain largely unclear. Particularly, since the production of ‘public goods’ bares the inherent...
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Chih-Fu Yeh (Stanford University )
Ecological theory suggests spatial synchrony in population fluctuation can be generated via three mechanisms: (1) dispersal between populations; (2) environmental forcing, known as the Moran effect; and (3) biotic interactions with synchronized or mobile species. Although both experimental and theoretical works have been conducted to examine the relative importance of these mechanisms,...
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Siobhan O'Brien (Trinity College Dublin )
Slowing the spread of antimicrobial resistance is urgent if we are to continue treating infectious diseases successfully. There is increasing evidence microbial interactions between and within species are significant drivers of resistance. On one hand, cross-protection by resistant genotypes can shelter susceptible microbes from the adverse effects of antibiotics, reducing the advantage of...
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James Hall (Department of Evolution, Ecology and Behaviour, University of Liverpool )
Mobile genetic elements (MGEs) are integral members of microbial communities, interacting with cellular microbes as well as other mobile genetic elements (MGEs), and affecting the dynamics and evolution of cells, populations, and microbiomes. Conjugative plasmids are MGEs that can transfer themselves between bacteria, forming a major route for the transmission of diverse adaptive traits in...
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Yansong Zhao
Yansong Zhao1, Andrew D. Farr1 & Paul B. Rainey1,2 1 Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany. 2 Laboratory of Biophysics and Evolution, ESPCI, Paris, France.
Microbial communities have intrinsic complexity in their composition, totality of interaction and function, which has been an inspiration for scientific curiosity and, at...
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