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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 R Garrido Oter (Heinrich-Heine-Universität Düsseldorf)
Contributed Talk 1: Structure and functions of the bacterial root microbiota in wild and domesticated barley
The microbial communities inhabiting the interior of roots of healthy plants, as well as the rhizosphere, i.e., particles of soil firmly attached to roots, engage in symbiotic associations with their host. We employed a combination of 16S rRNA gene profiling and shotgun metagenome analysis to investigate the structural and functional diversification of the microbiota associated with wild and domesticated accessions of barley (Hordeum vulgare). Analyses of beta-diversity based on the 16S data revealed a small but significant genotype effect on the root-associated communities. In addition, functional characterization of metagenome samples allowed us to identify functional categories enriched in the rhizosphere of barley as well as protein families with evidence of being under positive selection. Our results indicate that the combined action of microbe-microbe and host-microbe interactions drives microbiota differentiation at the root-soil interface.
10:55 to 11:25 Morning Coffee
11:25 to 11:55 N Goldenfeld (University of Illinois at Urbana-Champaign)
Plenary Lecture 3: Individual-level models, demographic stochasticity and spatio-temporal variations in microbial populations
I will review recent work for modeling populations from the individual-level, using statistical mechanics to obtain a description at the population level. Topics that will be briefly covered within the time available are (1) Quasi-Turing patterns in plankton-herbivore systems and biofilms; (2) Rapid evolution and anomalous population cycles in rotifer-algae chemostats.

This work has been performed in collaboration with Tom Butler, Hong-Yan Shih and K. Michael Martini, and partially supported by the US National Science Foundation.

11:55 to 12:30 J Weitz (Georgia Institute of Technology)
Plenary Lecture 4: Modeling Ocean Viruses: From Infections to Ecosystems
Viruses are ubiquitous in the marine environment and can infect and lyse target cells. Lysis of marine host cells releases cellular debris. This debris can then be taken up by non-targeted cells, stimulating microbial production. This redirection of cellular biomass by viruses is termed the "viral shunt". Quantitative estimates of the strength of the viral shunt, first established in the late 1990s, were inferred from estimates of host and viral density, host carbon content, and viral lysis rates. Yet, these and subsequent estimates provide limited information on potential dynamic drivers and the likelihood of the viral shunt to cause other feedbacks. Here, I offer two recent perspectives on the viral shunt. First, I present an ab-initio model of the carbon and nutrient content of virus particles. In doing so, I show how the elemental stoihcoimetry of virus particles differs from that of microbial host cells. The consequences of this difference include both changes in the expected release of elements in the viral shunt as well as the potential reservoir of elements in virus particles. Second, I present a new model of a microbial community that incorporates virus-host interactions and the viral shunt. I show how virus presence in the environment may stimulate certain ecosystem-scale functions, including increased recycling of organic matter and gross primary productivity. I close with a brief discussion of ongoing challenges of translating and testing these results in the field.
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 A Haas (San Diego State University)
Contributed Talk 2: Structure, Function and Dynamics in Microbial Communities
Co-authors: Yan Wei Lim (San Diego State Universit), Craig Nelson (University of Hawai?i at Manoa), Linda W Kelly (San Diego State Universit), Jennifer Smith (Scripps Institution of Oceanography), Stuart Sandin (Scripps Institution of Oceanography), Forest Rohwer (San Diego State Universit)

The shift in benthic reef communities from coral to algae dominated systems as a result of anthropogenic influences is widely documented. Recent research has focused on the biogeochemical impacts of these shifts and on the resulting reciprocal influences between macro- and microbial communities. Although non calcifying algae release significantly higher amounts of dissolved organic carbon (DOC) than calcifying organisms, declines in the DOC standing stock with increasing algal cover have been described in multiple locations. This discrepancy of “more DOC gives less DOC” may be explained by an algal exudate fueled, enhanced microbial community metabolism. Our recent studies support this theory and provide potential mechanisms on how this “super-heterotrophic” community may facilitate long-term depletion of ambient DOC stocks. Data from 60 sampling sites across 3 different ocean systems link increased algal cover to low DOC concentrations and elevated mi crobial abundance. Comparison of microbial metagenomes across a gradient of benthic cover shows higher relative abundance of genes encoding for the citric acid cycle and changes in the preference of glycolytic pathways from the EMP to the ED and PP pathways with increasing algal abundance. Although the EMP pathway is, based on stoichiometry of reactants and products, the most effective pathway, it requires up to 3.5 times higher enzyme levels to counterbalance its low thermodynamic driving force to support the same metabolic rate than the EMP pathway. This becomes increasingly important for microbial growth on more oxidized carbon sources. A shift towards the PP pathway may open up additional carbon resources especially in pentose rich systems. In concert these findings indicate that an increase in the overall heterotrophic metabolism and a change in pathways of carbohydrate breakdown to pyruvate enables algal fostered microbial communities to tap deeper, but more inefficiently into the refractory carbon pool.

15:25 to 15:55 Afternoon Tea
15:55 to 16:30 D Segre (Boston University)
Plenary Lecture 7: Spatio-temporal dynamics of microbial ecosystem metabolism
Metabolism, in addition to being the “engine” of every living cell, plays a major role in the cell-cell and cell-environment relations that shape the dynamics and evolution of microbial communities, e.g. by mediating competition and cross-feeding interactions between different species. Despite the increasing availability of metagenomic sequencing data for numerous microbial ecosystems, fundamental aspects of these communities, such as the unculturability of most isolates, and the conditions necessary for taxonomic or functional stability, are still poorly understood. In the past few years we have been developing new computational methods for studying these ecosystems based on genome scale stoichiometric models of metabolism (such as flux balance analysis), showing for example how one can computationally identify minimal growth media that could induce metabolic cross-feeding between two microbial species – an approach that has applications in the nascent fiel d of synthetic ecology. A more comprehensive understanding of the role of metabolic networks in the dynamics of microbial communities will require a broader theoretical framework capable of dealing with the multi-scale spatio-temporal complexity of these ecosystems. Our new, experimentally validated, open source platform for the Computation of Microbial Ecosystems in Time and Space (COMETS), addresses this challenge by combining flux balance analysis with diffusion equations to simulate the 3D spatio-temporal dynamics of metabolism in microbial communities. While some COMETS predictions are non-intuitive and surprisingly accurate, abundant work is still needed in order to bridge the gap between the dynamics of small engineered communities, and the huge diversity and complexity of natural ecosystems.
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 S Freilich (Agricultural Research Organization)
Contributed Talk 3: Metabolic Network Approaches for delineating functional division within Bacterial Communities
Co-authors: Shani Ofaim (ARO), Tamar Lahav (ARO)

Rapid advances in metagenomics and genome sequencing have led to the accumulation of vast amounts of empirical ecological data. With the increase in ecological data production, the need for robust automated functional community analysis approaches rises. The genomic-based construction of a communal metabolic network allows the investigation of the functional division between its participants, showing the metabolic hierarchy in the sampled environment. More specifically, such hierarchy allows the identification of key reaction allowing the environment-specific metagenome to make use of the available resources allowing, for example N- and S assembly as well as the utilization of complex carbohydrates. Taxonomic classification of such reactions further allows delineating the corresponding functional significance of species-groups and their specific contribution to the meta-level metabolism. Here, I will discuss the use of such metabolic network approaches for carrying a functio nal division analysis of communities in the rhizosphere and bulk soil environments based on RNA Seq data.

17:20 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 G Nicol (University of Aberdeen)
Contributed Talk 4: Understanding microbial networks driving nitrogen cycling in soil
Co-author: James I. Prosser (University of Aberdeen)

Since their discovery a decade ago, the activities of ammonia oxidising archaea (AOA) in soil (and other environments) are now recognised as a central component to the cycling of reactive nitrogen. However, despite being considered functionally analogous to their bacterial counterparts (AOB), current work indicates that archaeal-specific adaptations may separate the ecological niches of AOA and AOB to such an extent that any interactions may not actually be competitive, and hint at a more complex microbial network of interactions cycling nitrogen in soil.

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