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Timetable (UMCW03)

Structure, Function and Dynamics in Microbial Communities

Thursday 30th October 2014 to Friday 31st October 2014

Wednesday 29th October 2014
19:30 to 22:00 Conference Dinner at Emmanuel College
Thursday 30th October 2014
09:00 to 09:20 Registration
09:20 to 09:30 Welcome from Christie Marr (INI Deputy Director)
09:30 to 10:05 J Huisman (Universiteit van Amsterdam)
Plenary Lecture 1: Non-Equilibrium Dynamics in Ecological Communities
Co-authors: Elisa Beninca (University of Amsterdam), Stephen Ellner (Cornell University)

Many ecological studies have focused on equilibrium dynamics. Examples in microbial ecology are provided by chemostat studies in which species interactions are investigated until steady state is reached. In this presentation, I will take a different perspective by highlighting non-equilibrium dynamics in ecological communities.

First, I will show that interaction networks consisting of multiple species can produce permanent changes in community structure, with chaotic ups and downs in species abundances such that the species composition never reaches an equilibrium state. This is illustrated by several controlled laboratory experiments with microbial food webs.

Next, I will discuss possible underlying mechanisms that may generate such complex dynamics. For instance, predator and prey species can display classical predator-prey oscillations. Analysis of experimental data shows that the coupling of several predator-prey systems can cause intriguing species fluctuations, in which the community shifts back and forth between different predator-prey cycles in a chaotic fashion.

Finally, I present field data of a cyclic succession sustained by rock-paper-scissors dynamics over many years. Analysis of the population dynamics reveals that the cyclic species replacement moves back and forth between stabilizing and chaotic dynamics. The results are supported by a simple community model, which shows that seasonal variation is likely the environmental driver that pushes this cyclic succession to the edge of chaos.

Microbial communities typically consist of numerous species, involved in a multitude of species interactions. Hence, this non-equilibrium perspective may find application in a wide range of different fields. Examples include studies of natural communities in terrestrial, freshwater and marine ecosystems, but also the microbial gut flora, microbial disease dynamics, or the use of microbial communities in wastewater treatment and other biotechnological applications.
10:05 to 10:40 P Rainey (Massey University)
Plenary Lecture 2: tba
10:40 to 10:55 Contributed Talk 1: tba INI 1
10:55 to 11:25 Morning Coffee
11:25 to 11:55 N Goldenfeld (University of Illinois at Urbana-Champaign)
Plenary Lecture 3: tba
11:55 to 12:30 J Weitz (Georgia Institute of Technology)
Plenary Lecture 4: tba
12:30 to 13:30 Lunch at Wolfson Court
14:00 to 14:35 P Warren (Unilever R&D)
Plenary Lecture 5: Neutral models on island chains: biodiversity measures, and the 'everything is everywhere' problem.
Personal care products such as deodorants, anti-dandruff treatments, and toothpastes, impact directly on human-associated microbial communities. Recent progress in next generation sequencing, and large scale microbiomics projects, have revealed the startling diversity of these communities: sequence deep enough and (almost) everything is everywhere. Conversely, it appears that everyone carries around their own personal microflora. This begs the question: how do human-associated microbial communities get to be the way they are? How much is due to chance? In this talk, simulations of neutral community assembly models on island chains indicate how measurements of inter-individual and intra-individual beta-diversity may give insights into assembly mechanisms. Additionally, the analysis suggests biodiversity measures which remain well defined in the 'microbial limit' of an infinite population, escaping the 'everything is everywhere' problem.
14:35 to 15:10 C Tarnita (Princeton University)
Plenary Lecture 6: Ecology and the evolution of multicellularity
Co-authors: Alex Washburne (Princeton University), Simon Levin (Princeton University), Allyson Sgro (Princeton University), Martin Nowak (Harvard University), Cliff Taubes (Harvard University)

The evolutionary trajectory of life on earth is one of increasing size and complexity. Yet the standard equations of evolutionary dynamics describe mutation and selection among similar organisms that compete on the same level of organization. I will try to outline a mathematical theory that might help to explore how evolution can be constructive. I will distinguish and compare two fundamental operations -- ‘staying together’ (individuals form larger units by not separating after reproduction) and ‘coming together’ (individuals form aggregates). Both operations have been identified in the context of multicellularity, but they can be found at every level of biological construction. Although staying together is considered to be the primary mechanism for the evolution of complex multicellularity, I will argue that it is the comparison between coming together and staying together in the right ecological contexts that sheds most light on the evolution of mul ticellularity.
15:10 to 15:25 Contributed Talk 2: tba INI 1
15:25 to 15:55 Afternoon Tea
15:55 to 16:30 D Segre (Boston University)
Plenary Lecture 7: tba
16:30 to 17:05 J Tasoff (Claremont Graduate University)
Plenary Lecture 8: An Economic Framework of Microbial Trade
A large fraction of microbial life on earth exists in complex communities where metabolic exchange is vital. Microbes trade essential resources to promote their own growth in an analogous way to countries that exchange goods in modern economic markets. Inspired by these similarities, we developed a framework based on general equilibrium theory (GET) from economics to predict the population dynamics of trading microbial communities. Our biotic GET (BGET) model provides an a priori theory of the growth benefits of microbial trade, yielding several novel insights relevant to understanding microbial ecology and engineering synthetic communities. We find that the economic concept of comparative advantage is a crucial condition for mutualistic trade. Our model suggests that microbial communities can grow faster when species are unable to produce essential resources that are obtained through trade, thereby promoting metabolic specialization and increased intercellular interactions. Furthermore, we find that species engaged in trade exhibit a fundamental tradeoff between growth rate and relative population abundance, and that different environments may promote varying strategies along this growth-abundance spectrum. We experimentally tested this tradeoff using a synthetic consortium of Escherichia coli cells and found the results to match the predictions of the model. This quantitative framework provides a foundation to study natural and engineered microbial communities through a new lens based on economic theories developed over the past century.
17:05 to 17:20 G Nicol (University of Aberdeen)
Contributed Talk 3: tba
17:20 to 17:35 S Freilich ([Newe-Ya'ar Research Center])
Contributed Talk 4: tba
17:35 to 18:30 Wine Reception and Poster Session
Friday 31st October 2014
09:30 to 10:05 B Teusink (Vrije Universiteit Amsterdam)
Plenary Lecture 9: tba
10:05 to 10:40 A Buckling (University of Exeter)
Plenary Lecture 10: Feedback between microevolution and community structure
Community context drives microevolution, and in turn microevolution can drive community structure. Here, we report the real-time feedback between microevolution of an ecologically important and well-studied soil bacterium (Pseudomonas fluorescens SBW25) and the structure and function of the rest of the microbial community in soil.
10:40 to 10:55 Contributed Talk 5: tba INI 1
10:55 to 11:25 Morning Coffee
11:25 to 11:55 S de Monte (École Normale Supérieure)
Plenary Lecture 11: The evolution of groups and microbial collectives
Co-authors: Thomas Garcia (IBENS, Paris), Paul Rainey (NZIAS, Auckland/MPI, Ploen)

Microbial populations display a number of collective forms of organization, some of which have been integrated into complex life cycles. For instance, clusters or flakes of cells confer protection against stress to yeast and bacteria, swarming powers collective foraging in Myxobacteria, and recurrent aggregation of sparse cells allows the development of fruiting bodies in Myxobacteria and social amoebas. In this talk, I will present different ways natural selection can drive the evolution of groups composed of replicating particles. In particular, I will focus on settings when collectives are composed of particles of two types, which provide different contributions to collective functionality. A classical conundrum associated with such systems is that functional collectives exist, in spite of the disruptive effects of free-riding on groups composed of cooperative particles. I will use mathematical models that take explicitly into account the process of group formation to show that the evolution of functional collectives can stem from simple features of the composing particles, such as differential stickiness. However, something more is required if selection is to shift to the collective level. In concluding, I will discuss the value of a mechanistic perspective on the evolutionary emergence of multicellular life forms.
11:55 to 12:30 D Johnson (ETH Zürich)
Plenary Lecture 12: The causes and consequences of metabolic specialization
Co-authors: Elin E Lilja (ETH Zürich and Eawag), Felix Goldschmidt (ETH Zürich and Eawag), Martin Ackermann (ETH Zürich and Eawag)

Consider a microbial cell residing within a lake, soil, or the human gut. This cell encounters a myriad of different substrates that could theoretically satisfy its growth requirements. Yet, even if this cell were near starvation, it would only consume a subset of the available substrates. Why is this? What is the advantage of consuming only a subset of the available substrates rather than all of them? We hypothesize that particular metabolic processes are in biochemical conflict with each other, thus causing those processes to be more effectively performed by different strains than by the same strain. A biochemical conflict could occur, for example, if different metabolic processes compete for the same pool of limiting intracellular resources or if different metabolic processes produce products that inhibit other metabolic processes. In this talk, I first present a general theoretical model that uses information about biochemical conflicts to predict whether any two metaboli c processes will be retained by a single metabolic generalist strain or will segregate into different metabolic specialist strains over evolutionary time. I next present empirical evidence of specific environmental conditions when consortia of metabolically specialized strains consume substrates more rapidly than a single metabolic generalist strain. Our findings are potentially relevant for any pair of metabolic processes and could therefore be useful for predicting how best to distribute different metabolic processes among different cells in order to maximize the conversion of a substrate into a desired product.
12:30 to 13:30 Lunch at Wolfson Court
University of Cambridge Research Councils UK
    Clay Mathematics Institute The Leverhulme Trust London Mathematical Society Microsoft Research NM Rothschild and Sons