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Seminars (UMC)

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Event When Speaker Title Presentation Material
UMC 21st August 2011
15:00 to 16:00
Chaos in biology: Experiments, implications and mathematical tools
UMC 12th August 2014
14:00 to 15:00
Modelling interactions between hydrodynamics and dispersal that help shape biofilm community composition across a range of scales.
(Joint with A. J. Pinto and E. Vignaga)

In any open biological community there are a few basic biological processes that shape the community composition: births, deaths, immigration and emigration. Of course there are myriad factors that influence the rate at which each of these occur in different species within a community. For bacterial biofilms, our understanding and growing ability to quantify these factors has been furnished by laboratory experimentation often at very-small scale in comparison to the system that is ultimately of interest.

Here we present circumstantial evidence that in drinking water distribution networks, where biofilm control is of paramount importance, and in river networks, where biofilms mediate biogeochemical cycling, limitations in the hydrodynamic dispersal of bacterial between locations has a strong influence on the community composition. Thus, where biofilms reside in a hydraulically connected network, immigration and emigration at the local scale can have a strong effect on the biodiversity patterns across the network. In most biofilm models, conceived on the basis of laboratory biofilms, these mechanisms assume less importance than the environmental and biological factors affecting births and deaths and are often modelled as flow-dependent biomass loss/gain terms. We present evidence and models for more complex dynamic interactions between dispersal and flow regimes. Developing a better understanding of bacterial dispersal mechanisms in networks should allow for a more robust quantification of risk in, for example, pathogen occurrence in drinking water or disturbance of river ecosystems, which should inform network management strategies.
UMC 12th August 2014
15:00 to 16:00
T Parsons A Non-exchangeable Coalescent Process Arising In Phylogenetics
(Joint with G. Achaz, A. Lambert, N. Lartillot)

A popular line of research in evolutionary biology is to use time-calibrated phylogenies in order to infer the underlying diversification process. Most models of diversification assume that species are exchangeable and lead to phylogenetic trees whose shape is the same in distribution as that of a Yule pure-birth tree. Here, we propose a non- exchangeable, individual-based, point mutation model of diversification where interspecific pairwise competition (rate d) is always weaker than intraspecific pairwise competition (rate c), and is only felt from the part of individuals belonging to younger species. The only important parameter in this model is d / c =: 1 - a, which can be seen as a selection coefficient.

We show that as the initial metapopulation size grow to infinity, the properly rescaled dynamics of species lineages converge to a `shift-down/look-up coalescent' where lineages are given levels: the species at level i is the i-th most recent extant species. At constant rate, all lineages simutaneously ``shift down'' their level by -1, while the lineage at level 1 "looks up'' to a geometrically distributed (with parameter a) level and coalesces with the lineage present there.

We propose a dimensionally-reduced version of this model allowing for fast simulation and likelihood computation of given trees. We use this algorithm and MCMC data augmentation methods to estimate a from real trees, and compare this estimate to classical measures of tree imbalance.
UMC 14th August 2014
14:00 to 15:00
Bacterial migration in porous media: new statistical physics with implications for soil bioremediation and microbial ecology
Many bacteria swim chemotactically: they are biased by chemical gradients. The importance of chemotaxis in microbial ecology is appreciated but not widely quantitated. Chemotaxis is also thought to be important in bioremediation, where it is thought to increase pollutant bioavailability. Academic chemotaxis studies focus on single bacterial species whose chemotaxis in liquid is reasonably well understood. Its study in porous media, however, has recently revealed unexpected surprises. Engineering bioremediation models describe chemotactic bacteria migrating in porous media as if they are gas particles in an external field. This description, mapping onto ordinary statistical physics (with detailed balance), fails to describe the migration of E. coli bacteria in agar (which is a porous gel). I will describe these experiments and outline the new transport theory (without detailed balance) we develope. This qualitatively accounts for observed phenomenology. I will then describe new experiments we have carried out comparing the migration of E. coli in agar with that of the soil bioremediation species Pseudomonas putida. To conclude, I will briefly connect the work to microbial ecology, and in particular algal-bacterial symbioses.
UMC 14th August 2014
15:00 to 16:00
Superbugs vs communities in environmental bioremediation
tba
UMC 19th August 2014
14:00 to 15:00
Methanogenic Communities
UMC 19th August 2014
15:00 to 16:00
C Wiuf Modelling Biochemical Pathways
UMC 21st August 2014
14:00 to 15:00
Cooperation, cheating and collapse in microbial populations
UMC 21st August 2014
15:00 to 16:00
Chaos in biology: Experiments, implications and mathematical tools
UMC 26th August 2014
14:00 to 15:00
Catalytic origami: Genetic tools and strategies for assembling 3D bacterial consortia
UMC 28th August 2014
14:00 to 15:00
Life on the edge - microbial evolution in the presence of drug gradients
UMC 2nd September 2014
14:00 to 15:00
Understanding reactions of introduced bacteria in natural and engineered environments
UMC 2nd September 2014
15:00 to 16:00
A Zelezniak Metabolic interactions in microbial communities
UMC 4th September 2014
14:00 to 15:00
Representing microbial communities in Earth system models
UMC 4th September 2014
15:00 to 16:00
Theory of adaptive evolution informed by microbial experiments
UMC 8th September 2014
16:00 to 17:00
On the (un)reasonable (in)effectiveness of mathematics in biology: Rothschild Distinguished Visiting Fellow Lecture
There is only one thing which is more unreasonable than the unreasonable effectiveness of mathematics in physics, and this is the unreasonable ineffectiveness of mathematics in biology. --Israel Gelfand
UMCW01 10th September 2014
13:30 to 14:05
Plenary Lecture 1: Contingency and convergence in microbial population dynamics
I will present some results of long-term laboratory experiments in closed microbial ecosystems. Each system is a small world in itself, with its idiosyncrasies and (hi)story to tell. Local population dynamics is monitored in dozens of replicates. Surprisingly, statistical laws governing the population fluctuations seem to be quite simple. But then, even more controlled experiments are performed...
UMCW01 10th September 2014
14:05 to 14:40
S Frank Plenary Lecture 2: Cancer-like overgrowths and genomic regulatory design in microbes
Mutant lineages may cause cancer-like overgrowths in microbial populations. Theory predicts that microbial regulatory controls may be designed to limit the origin and competitive potential of rogue lineages. The theory depends on the fundamental tradeoff between rate and yield in microbial metabolism. The rate versus yield tradeoff and the role of cancer-like overgrowths are influenced by the genetic structure of populations and by demographic processes such as how long resource patches last.
UMCW01 10th September 2014
14:40 to 15:15
T Curtis Plenary Lecture 3: Simple Theory and the Microbial World
Co-authors: Bill Sloan (Glasgow University), Dana Ofiteru (Newcastle University), Lise Ovreas (Bergen University), Joana Baptista (Newcastle University), Chris Quince (Glasgow University)

The microbial world is of astronomical dimensions and of profound practical importance. And yet, though astronomers and engineers rely heavily on quantitative theory, most microbial ecologists and associated practitioners do not. Those that do, are heavily influenced by classical ecological theory. However, most classical ecological theory is not “up to the job”. The inscrutability and practical importance of the microbial world means that prediction should be our aspiration. This imposes certain disciplines up on us. In particular, we should start as simply as possible, find and understand the parameters and what they can explain; and then move on. The simplest possible theory of community assembly in microbial communities is perhaps the work of Bill Sloan and his colleagues. The key parameters are the size of the community, the immigration rate and the size and make up of the metacommunity. The size of the community we often know. Finding the immigration par ameter yields useful insights about how communities form and change and the relative importance of immigration and evolution. The size and the nature of the metacommunity is less well understood, but its exploration hints at generic and useful rules in evolution that could be both intrinsically interesting and very important. However, we should look forward to a future in which mathematics has the stature and utility in microbial ecology, that it enjoys in physics. Then microbial ecology will done at the scale and with the rigour that the field merits.

UMCW01 10th September 2014
15:45 to 16:20
Plenary Lecture 4: Phage and Origins of the Immune System
Immune responses and mucosal surfaces of corals and humans are strikingly similar despite greater than 500 million years of divergence. Here we show that humans and phage both use bacteriophage to protect against bacteria and establish microbiomes. This Bacteriophage Adherence to Mucus (BAM) model is applicable to all metazoans. The model links hypervariable phage capsid decoration proteins with the adherence of phage to mucus and it's consequent reduced bacterial pathogenesis of underlying host epithelium. The relationships delineated make the world's most abundant biological entities central to the metazoan immune system. In so doing, they advance our understanding of immunology and the microbial ecology of a key metazoan-associated environments, and will open new directions in immunological engineering.
UMCW01 10th September 2014
16:20 to 16:55
T Rogers Plenary Lecture 5: Survival of the unfit - how demographic noise can create suboptimal species
Co-author: Alan J McKane (University of Manchester)

Competition between individuals drives the evolution of whole species. When the fittest individuals survive the longest and produce the most offspring, it is conventionally assumed that the resulting species will therefore also be optimally fit. In fact, this reasoning is not always correct. Using theoretical analysis and stochastic simulations of a simple model ecology, we demonstrate how the fitness of evolved populations depends on the detail of the competitive interaction. In particular, if competition is mediated by the consumption of a common resource then demographic noise leads to the stabilisation of species with near minimal fitness.

Related Links: •http://arxiv.org/abs/1407.3137 - Perprint describing the work in detail

UMCW01 10th September 2014
16:55 to 17:10
S Kalvala Contributed Talk 1: Computational models of spatial behaviour of microbial communities
Computational simulations are now an important component of the toolkit for studying biological systems. While it is easy to simulate well-mixed solutions in order to model intra-cellular processes, it is more difficult to capture spatial phenomena characterizing microbial communities. The problem is compounded because we need to capture not only inter-cellular communication but also changing configurations, with microbes that move, change shape, and create new communication channels.

In this talk I will review some of the methodologies that have been developed for spatially-aware computational modelling of microbial communities and the limitations of these methodologies. I will also present some of our results in capturing some of the intriguing behaviour of myxobacteria communities (namely rippling and the formation of fruiting bodies) via a spatial simulation based on the Cellular Potts Model.

UMCW01 11th September 2014
09:30 to 10:05
T Hwa Plenary Lecture 6: Mixed and Hierarchical Utilization of Carbon Substrates by Bacteria
Co-authors: Hiroyuki Okano (UC San Diego), Rutger Hermsen (Utrecht University), Conghui You (UC San Diego)

When bacteria are cultured in medium with multiple carbon substrates, some substrate combinations are consumed simultaneously while other combinations are consumed sequentially. Understanding and manipulating the order of carbon utilization is crucial in characterizing trophism in complex ecosystems such as the gut microbiota, and in optimizing synthetic biology applications such as the breakdown of cellulose for biofuel production. Building on recent advances in the understanding of metabolic coordination exhibited by Escherichia coli cells through cAMP-Crp signaling, we show that this signaling system alone gives rise to simultaneous utilization, and derive an algebraic formula describing the resulting growth rate, based only on the growth rates on individual substrates. For substrate combinations that are utilized hierarchically, we reveal a simple regulatory strategy by which the hierarchy is ordered roughly by the rate of growth on single substrates.

UMCW01 11th September 2014
10:05 to 10:40
Plenary Lecture 7: Numerical modelling, an interdisciplinary bridge in studying microbial biofilms
Microbial biofilms inherently require multidisciplinary approaches. Numerical models can help the integration of knowledge from various disciplines into unified theories. This presentation will give examples on how mechanical models can be useful computational tools to study pattern formation due to cell motility, spreading of microbial colonies made of mixed cell morphotypes or interactions between fluid flow and biofilms, including streamer vibration effects on flow and mass transfer. Electro-active biofilms (conductive sediments, microbial fuel cells, biocorrosion) require on the other hand bridging other areas of physics and electrochemistry with biology. On the other hand, hydrology and subsurface flow models provide tools for understanding biofilm formation and their effects on multiphase flow in porous media and in biomineralization processes.
UMCW01 11th September 2014
10:40 to 10:55
Contributed Talk 2: The Initiative for the Critical Assessment of Metagenome Interpretation (CAMI)
Co-author: Alexander Sczyrba, Eddy Rubin, Nikos Kyrpides, Paul Schulze-Lefert, Julia Vorholt, Nicole Shapiro, Tanja Woyke, Hans-Peter Klenk, Stephan Majda, Johannes Droege, Ivan Gregor, Peter Hofmann, Eik Dahms, Jessika Fiedler, Ruben Garrido-Oter, Yang Bai, Girish Srinivas, Phil Blood, Mihai Pop, Aaron Darling, Matthew DeMaere, Dmitri Turaev, Chris Hill, Peter Belmann, Andreas Bremges, Thomas Rattei ()

In just over a decade, metagenomics has developed into a powerful and productive method in microbiology and microbial ecology. The ability to retrieve and organize bits and pieces of genomic DNA from any natural context has opened a window into the vast universe of uncultivated microbes. Tremendous progress has been made in computational approaches to interpret this sequence data but none can completely recover the complex information encoded in metagenomes.

A number of challenges stand in the way. Simplifying assumptions are needed and lead to strong limitations and potential inaccuracies in practice. Critically, methodological improvements are difficult to gauge due to the lack of a general standard for comparison. Developers face a substantial burden to individually evaluate existing approaches, which consumes time and computational resources, and may introduce unintended biases.

CAMI (cami-challenge.org) is a new community-led initiative designed to tackle these problems by aiming for an independent, comprehensive and bias-free evaluation of methods. We are making extensive high-quality unpublished metagenomic data sets available for developers to test their short read assembly, binning and taxonomic classification methods. The results of CAMI will provide exhaustive quantitative metrics on tool performance to serve as a guide to users under different scenarios, and to help developers identify promising directions for future work.

As a community effort, we encourage feedback by both method developers and users of metagenome analysis tools. We urge developers to already register for the competition on our website and to join our Google+ group to provide feedback on the current design phase. The competition is tentatively scheduled to open at the end of 2014. The results will be presented and discussed in a workshop after the competition. We aim for a publication of the generated insights together with all CAMI contest participants and data contributors.

UMCW01 11th September 2014
11:25 to 11:55
AG Smith Plenary Lecture 8: Algal-bacterial consortia and evolution of mutualism
Co-authors: Katherine Helliwell (University of Cambridge), Elena Kazamia (University of Cambridge), Matthew Cooper (University of Cambridge), Vaibhav Bhardwaj (University of Cambridge), Christian Ridley (University of Cambridge), Johan Kudahl (University of Cambridge)

Over half of all microalgae require an external source of vitamins, particularly vitamin B12 (cobalamin), to enable them to grow. There is no phylogenetic relationship between those that require the vitamin and those that do not. Bacteria are the only organisms that can synthesise this complex organic micronutrient, and we have shown that B12-dependent algae can grow in co-culture with bacteria that supply them the vitamin in exchange for fixed carbon. We have established a model system to study this interaction at the molecular level, and to explore reasons for why vitamin auxotrophy may have arisen so frequently across the diverse algal lineages. This may provide insights into the evolution of mutualism between algae and their bacterial partners.
UMCW01 11th September 2014
11:55 to 12:30
Plenary Lecture 9: Structure and functions of the bacterial phyllosphere microbiota
The aerial parts of the plants, which are dominated by leaves, represent one of the largest terrestrial habitats for microorganisms. This habitat, called the phyllosphere, is occupied by a diverse community of microorganisms, which is important for plant health and growth. Most of the phyllosphere inhabitants are not well investigated; however, there is a growing interest to study commensal bacteria to elucidate their interactions with the plants, among each other and to learn how they withstand the hostile conditions of their habitat. A predominance of Proteobacteria, Actinobacteria and Bacteroidetes living in the phyllosphere of numerous plants has been revealed, while metagenomics and metaproteomics approaches gave insights into the general bacterial adaptation strategies to the phyllosphere. Complementary to these cultivation-independent approaches we established a comprehensive strain collection which covers a broad diversity of strains colonizing the model plant Arabido psis thaliana. Targeted studies with model strains allowed us to identify metabolic traits important for plant colonization and to uncover a novel bacterial regulatory system essential for plant colonization which is responsible for the general stress response in Alphaproteobacteria. The establishment of a gnotobiotic system led to the identification of plant probiotic effects of commensal bacteria and candidate genes for plant protection against bacterial pathogens. Moreover, the experimental system paired with synthetic bacterial communities helped identifying plant genes involved in shaping the bacterial community structure.
UMCW01 11th September 2014
14:00 to 14:35
H Flint Plenary Lecture 10: Phylogeny and functionality in anaerobic microbial communities: making sense of metabolite outputs and population dynamics
Regions of the mammalian gut harbour dense microbial communities that derive most of their energy from the anaerobic breakdown of dietary carbohydrates that are not digested by host enzymes. Especially in herbivores, the organic acids produced by microbial fermentation in turn provide a major supply of energy for the host, while in the human colon they have an important impact on health. It is of key interest therefore to understand how the microbial communities of the rumen and human large intestine respond to dietary change and how this affects the production of alternative metabolic products. While some metabolic and degradative capabilities are widespread among the microbiota, many (eg. methanogenesis, degradation of crystalline cellulose, lactate utilization) appear to be restricted to a small number of phylogenetic groups. Information from cultured isolates, defined consortia, experimental models, metagenomics and in vivo studies is helping to define functional group s of human gut bacteria whose characteristics can be incorporated into theoretical models that explore inter-group interactions and community responses.
UMCW01 11th September 2014
14:35 to 15:10
H Kettle Plenary Lecture 11: Modelling the emergent dynamics of human colonic microbiota
Co-authors: Petra Louis (University of Aberdeen), Grietje Holtrop (Biomathematics and Statistics Scotland), Sylvia Duncan (University of Aberdeen), Harry Flint (University of Aberdeen )

We present a method for modelling the complex dynamics of the colonic microbial ecosystem that incorporates both the variation in microbial composition between people and ecosystem adaptation. The model is a Monod-equation based, ordinary differential equation model which produces computer simulations of the dynamics of the microbial population and its major metabolites. To reduce the complexity of the system we divide the bacterial community into 10 bacterial functional groups (BFGs) each distinguished by its substrate preferences, metabolic pathways, and its preferred pH range. The model simulates the growth of a large number of bacterial strains with stochastically generated traits which compete for resources. The simulation results are compared with data from four experiments in pH-controlled, anaerobic continuous flow fermentor systems that investigated the effects of pH and peptide supply. We also theoretically investigate the idea that microbial strain diversity may be promoted by a pH feedback mechanism within the colon.
UMCW01 11th September 2014
15:10 to 15:25
Contributed Talk 3: A functional population model of fiber degradation by the human intestinal microbiota
Co-authors: Marion LECLERC (MICALIS,INRA), Sebastien RAGUIDEAU (MIA-J, INRA)

The human intestinal microbiota is a complex microbial ecosystem that plays a crucial role in several aspects of human health. It is particularly involved in the metabolism of residual fibres, through anaerobic digestion, thus providing significant energy (Short Chain Fatty Acids, simple sugars) and vitamins to the host. This ecosystem remains largely unexplored as a result of its limited accessibility and its complexity. We will present the ongoing development of an in silico model of the ecosystem, in interaction with its environment and its host. Our aim is to provide a virtual platform for knowledge and data integration, and simulation. A focus will be made on the structuration of the ecosystem into functional populations. We show how Whole Genome Sequencing (WGS) data from metagenomic analyses can be used to analyse the structure of carbohydrates degradation-related functions. These data give an insight of the gene content of an entire microbial community, even if the organisms that compose it cannot be cultivated. In addition to the potential of conventional molecular inventory techniques (such as targeting ADNr16s), which allows an analysis of diversity, WGS approaches provide an access to the functions. We show how the information obtained can be integrated in the model and discuss the underlying modelling hypotheses.

UMCW01 11th September 2014
15:55 to 16:30
Plenary Lecture 12: Determining the microbial population dynamics of anaerobic digestion using metagenomics
Co-authors: Henry Nicholls (University of York), Kelly Redeker (University of York), Peter Ashton (University of York)

Anaerobic digestion (AD) is a process that uses microbial consortia to convert organic waste to methane and carbon dioxide (“biogas”) that can be burned to generate heat and electricity. This technology can be applied to both liquid and solid wastes and is in common use. While there is a broad understanding of the principles of AD, the dynamics of the microbial populations involved in AD are still poorly characterised. Recent advances in next generation DNA sequencing technologies (NGS) have made shotgun sequencing of samples a cost-effective means for determining the composition of microbial populations. We are using NGS to build a detailed catalogue of the microbes present in a bench-scale AD system and to track the dynamics of this microbial community with the goals of identifying those species that are essential for the degradation of specific molecules and how the conflicting requirements of different members of the population are met.
UMCW01 11th September 2014
16:30 to 17:05
Plenary Lecture 13 (teleconference): tba
UMCW01 11th September 2014
17:05 to 17:20
Contributed Talk 4: Metabolic Modelling in an Evolutionary Framework Predicts Phenotypic Diversification of E.coli growing on Glucose as the Single Carbon Source
Co-author: Orkun S. Soyer (University of Warwick)

Understanding microbial communities is of great importance to monitor and manipulate complex ecosystems like anaerobic digesters, wastewater removal systems or the human gut. A variety of modelling approaches have been presented to simulate microbial communities, however many imply an optimization acting at the community level, an assumption which is not well grounded in evolutionary theory. We here present an evolutionary algorithm that uses multiple instances of flux balance analysis (FBA) models and density dependant selection as the fitness function, leading to the coexistence of different phenotypes of an Escherichia coli core FBA model after 500 rounds of simulated batch-transfers in a minimal medium with Glucose as the only carbon source. The solutions are “selfish” in the way that the only optimization is to maximize individual growth rate, yet they are affected by the metabolic layout of all other members in the community through a shared culture medium. We suggest that such self-optimizing models could be used to study complex microbial communities, where competition, cross-feeding, syntrophy, symbiosis and all forms of microbial interaction arise as emergent properties of the individual optimization of the member organisms.

UMCW01 11th September 2014
17:20 to 17:35
Contributed Talk 6: Metaproteomics of algal blooms
UMCW01 12th September 2014
09:30 to 10:05
K Drescher Plenary Lecture 14: Development and Evolution in Environmental Biofilms
Co-authors: Carey Nadell (Princeton University), Howard Stone (Princeton University), Ned Wingreen (Princeton University), Bonnie Bassler (Princeton University)

Biofilms are antibiotic-resistant, sessile bacterial communities that occupy most moist surfaces on Earth and cause chronic and medical device-associated infections. Despite their importance, it is largely unknown how bacteria organize their behavior inside biofilms, and how biofilms behave in natural environments. In this talk I will focus on how environmental aspects of natural habitats lead to the evolution of simple cooperative behaviors in biofilms. I will also demonstrate how biofilm development and the complex geometries of natural habitats interact to cause the sudden and rapid clogging of porous materials like soil, water filtration devices, and medical stents.
UMCW01 12th September 2014
10:05 to 10:40
Plenary Lecture 15: Geomicrobial kinetics: bridging the gap between laboratory and nature
Rates of natural microbes are a key parameter of theoretical and practical problems in environmental chemistry, microbiology, and biotechnology. Empirical models, such as the Monod equation, are standard tools for predicting microbial rates in laboratory and industrial reactors. But direct application of these models to natural environments often overestimates the significance and extent of microbial processes by orders of magnitude relative to field observations. Hence new theories and modeling approaches are required for quantifying microbial metabolism in natural environments and for simulating population dynamics of natural communities. The new theory of geomicrobial kinetics must account for dramatic differences in growth conditions between laboratory reactors and natural environments. For example, the energy available in the environment limits the metabolism of natural microbes, which can be described using the thermodynamic potential factor. According to this factor, the thermodynamic control becomes negligible where the available energy is much larger than the energy saved by microbes. But for common anaerobic respiration of natural environments, the thermodynamic control is significant because the available energy is of the same order of magnitude as the saved energy. The new theory also needs to address (1) how microbial diversity controls the rates of microbial metabolism; (2) what metabolic strategies microbes have to employ in natural environments and how these strategies impact microbial rates; and (3) how to integrate mechanisms and kinetics at different scales, from subcellular scale of enzyme kinetics and cellular scale of microbial kinetics to the field scale of watersheds and aquifers and global scale of element cycling. These questions represent current challenges of geomicrobial kinetics, and can be addressed by integrating the exciting advances in genome-scale modeling, microbial ecology, and environmental chemistry.
UMCW01 12th September 2014
10:40 to 10:55
Contributed Talk 5: Uptake levelling in chemotactic bacteria measured by the Gini index
Co-author: Raymond E. Goldstein (University of Cambridge)

Classic experiments on the accumulation of ducks around distinct food sources found consistency with the `ideal free' distribution in which the local population is proportional to the local supply rate: the animal behaviour smoothes the individual uptake over the population. Motivated by this, we examine the analogous problem in the microbial world: the distribution of chemotactic bacteria around multiple nearby food sources and their associated uptake. Through a series of simple models we illustrate how chemotaxis, nutrient consumption, and diffusion of both bacteria and nutrients conspire to produce spatial distributions with unequal resource uptake. It is suggested that the Gini index, well known in theoretical economics, provides a useful quantification of these effects.
UMCW01 12th September 2014
11:25 to 11:55
Plenary Lecture 16: Collective Functionality Through Microbial Individuality
According to the conventional view, the properties of an organism are a product of nature and nurture - of its genes and the environment it lives in. Recent experiments with unicellular organisms have challenged this view: genetically individuals living in homogeneous laboratory environments can have markedly different properties, and express different sets of genes. We are interested in the functional consequences of this variation in bacteria: is phenotypic heterogeneity sometimes beneficial, and does it provide microbes with new functionality in their natural environment? I will first present results that suggest that, for the majority of the genes in a bacterial genome, natural selection acts to reduce phenotypic variation. Then, I will present a few exception to this rule, and discuss how phenotypic variation in clonal populations of bacteria can promote interactions between individuals, lead to the division of labor, and allow clonal groups of bacteria to cope with envi ronmental uncertainty. Finally, I will present recent results that indicate that phenotypic heterogeneity in bacterial populations does not only arise through individual molecular decisions in single cells, but is also shaped by interactions between cells that impact the expression of their phenotype. The main conclusion from this work is that microbial individuality can provide groups of organisms with collective functionality.
UMCW01 12th September 2014
11:55 to 12:30
Plenary Lecture 17: Micro-scale biological interactions shape microbial community dynamics on marine particles
Particulate organic matter in aquatic environments represents a major source of nutrients for heterotrophic bacteria. To access these nutrients microbial communities need to assemble on particles and, once the ecological opportunity expires, disassemble to start migration and colonization of new nutrient sources. Because of the enormous diversity of microbes in the environment, this process is likely to involve a large number of species interacting at different points during assembly and disassembly. Using a model system based on chitin-associated communities from the coastal ocean, I will discuss ongoing work aimed at studying community assembly on particles as the behavior of a multi-species system, which we attempt to reconstruct with a combination of computational and experimental tools. Our results show that community assembly on chitin involves the fast succession of a large number of species. These complex dynamics are not driven by changes in substrates, but by local biological interactions and ecological trade-offs which structure communities at micro-meter scales. Overall, this study shows that ecological interactions impose strong selective pressures on particle-attached communities and in that micro-scale ecological processes can have a large impact on global ecosystem processes.
UMC 16th September 2014
14:00 to 15:00
Biology of Integrative and Conjugative Elements (special agents of bacterial evolution)
UMC 16th September 2014
15:00 to 16:00
Mathematical aspects of growing colonies
UMC 18th September 2014
14:00 to 14:30
A Sczyrba Metagenome, metatranscriptome and single cell genome sequencing of biogas-producing microbial communities from production-scale biogas plants
UMC 18th September 2014
14:30 to 15:00
J Droege Computational tools for the taxonomic analysis of shotgun metagenome samples
UMC 18th September 2014
15:00 to 15:30
Gaining Insights into the Uncultured Microbial World by Computational Metagenome Analysis
UMC 18th September 2014
15:30 to 16:00
Toward resolving the fine scale genetic structure of microbial populations: a metagenomic Hi-C approach
UMC 25th September 2014
14:00 to 15:00
T Parsons Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a hierarchical Dirichlet process
UMC 30th September 2014
14:00 to 15:00
Colorful niches of phototrophic microorganisms shaped by vibrations of the water molecule
UMC 2nd October 2014
14:00 to 15:00
The construction and use of bacterial bioreporters
UMC 2nd October 2014
15:00 to 16:00
Modelling electrochemically-active biofilms
UMC 7th October 2014
14:00 to 15:00
R Allen Predictability and Unpredictability in nutrient-cycling microbial ecosystems
UMC 7th October 2014
15:00 to 16:00
Impacts of rising CO2 on harmful cyanobacterial blooms
UMC 9th October 2014
09:30 to 12:30
PhreeqC tutorial session
UMC 14th October 2014
14:00 to 15:00
TBA
UMC 14th October 2014
15:00 to 16:00
Microbial communities and the structure-function twins
UMC 16th October 2014
14:00 to 15:00
Speculation about Quantum Isolation in Biology
UMC 16th October 2014
15:00 to 16:00
T Schuster Game-theoretical approaches in microbiology
UMC 20th October 2014
15:00 to 16:00
M Goddard Experimentally Quantifying Patterns in Microbial Eukaryote Populations
Due to their dissimilar life histories, it is not clear if the models developed for lager organisms apply to microbial eukaryotes. I will describe some of our attempts to elucidate patterns in microbial communities and populations, and our attempt to quantify these patterns experimentally.
UMC 20th October 2014
16:00 to 17:00
The Evolution of Multicellularity
Cooperation is central to the emergence of multicellular life, however the means by which the earliest collectives maintained integrity in the face of destructive cheating types is unclear. One idea posits cheats as a primitive germ line in a life cycle that facilitates collective reproduction. I will describe an experiment in which simple cooperating lineages of bacteria were propagated under a selective regime that rewarded collective-level persistence. Collectives reproduced via life cycles that either embraced, or purged, cheating types. When embraced, the life cycle alternated between phenotypic states. Selection fostered inception of a developmental switch that underpinned the emergence of collectives whose fitness, during the course of evolution, became decoupled from the fitness of constituent cells. Such development and decoupling did not occur when groups reproduced via a cheat-purging regime. I will discuss the findings in the context of key events in the evolution of Darwinian individuality during the transition from single cells to multicellularity.
UMC 21st October 2014
14:00 to 15:00
Outstanding Questions in the Ecology and Evolution of Coral Reef Microbes
UMC 23rd October 2014
15:00 to 16:00
TBA
UMCW02 27th October 2014
13:30 to 14:30
Plenary Lecture 1: Understanding bacterial communication and cooperation: combinatorial quorum-sensing
Quorum sensing (QS) is a cell–cell communication system that controls gene expression in many bacterial species, mediated by diffusible signal molecules. Although the intracellular regulatory mechanisms of QS are often well-understood, the functional roles of QS remain controversial. In particular, the use of multiple signals by many bacterial species poses a serious challenge to current functional theories. Here, we address this challenge by showing that bacteria can use multiple QS signals to infer both their social (density) and physical (mass-transfer) environment. Analytical and evolutionary simulation models show that the detection of, and response to, complex social/physical contrasts requires multiple signals with distinct half-lives and combinatorial (nonadditive) responses to signal concentrations. We test these predictions using the opportunistic pathogen Pseudomonas aeruginosa and demonstrate significant differences in signal decay between its two primary si gnal molecules, as well as diverse combinatorial responses to dual-signal inputs. QS is associated with the control of secreted factors, and we show that secretome genes are preferentially controlled by synergistic “AND-gate” responses to multiple signal inputs, ensuring the effective expression of secreted factors in high-density and low mass-transfer environments. Our results show that combinatorial communication is not restricted solely to primates and is computationally achievable in single-celled organisms.
UMCW02 27th October 2014
14:30 to 14:45
Contributed Talk 1: The Crabtree effect and its influences on fitness of yeast populations from natural isolates
Co-author: Thomas Pfeiffer (Massey University)

Yeasts degrade sugars in order to produce ATP. Two metabolic pathways are distinguished in ATP production: respiration and fermentation. While the respiration pathway occurs in presence of oxygen and produces up to 38 ATP to the cell, fermentation does not require oxygen but is also much less efficient (2 ATP produced by sugar converted into ethanol). Despite the low efficiency of fermentation, a certain number of yeasts species (including the brewer’s yeast Saccharomyces cerevisiae) have the ability to ferment sugar in aerobic conditions, this in addition to the respiration pathway when sugar concentration is sufficiently high. This is known as the Crabtree effect. It remains unclear why certain yeasts exhibit an aerobic alcoholic fermentation, and one explanation to this phenomenon relies on the increase in ATP production rate, which come at the cost of the production yield. This explanation is supported by the yield/rate trade-off theory. However this theory has not yet been conclusively supported by experiments. In my talk, I will introduce novel experimental approaches that might be used to investigate the yield/rate trade-off theory under the Crabtree effect in yeast from natural isolates.

UMCW02 27th October 2014
15:00 to 15:15
Contributed Talk 2: Less is more: Selective advantages can explain the loss of biosynthetic functions in bacteria
Co-authors: Silvio Waschina (Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; Research Group Theoretical Systems Biology, Friedrich Schiller University of Jena, 07743 Jena, Germany), Christoph Kaleta (Research Group Theoretical Systems Biology, Friedrich Schiller University of Jena, 07743 Jena, Germany), Christian Kost (Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany)

Bacteria that have adapted to nutrient-rich, stable environments are typically characterized by reduced genomes. The loss of biosynthetic genes frequently renders these lineages auxotroph, hinging their survival on an environmental uptake of certain metabolites. However, the factors that govern this ‘genome streamlining’ remain poorly understood. Our analysis of 1532 metabolic networks revealed that auxotrophies are likely to be highly prevalent in both symbiotic and free-living bacteria. To unravel whether selective advantages can account for the rampant loss of anabolic genes, we systematically determined the fitness consequences that result from deleting conditionally essential biosynthetic genes from the genome of Escherichia coli in the presence of the focal nutrient. Pairwise competition experiments with each of 16 mutants auxotrophic for different amino acids, vitamins, and nucleobases against the prototrophic wild type unveiled a pronounced, concentration-dependent growth advantage of around 13% for virtually all mutants tested. Our in silico analysis also suggests that bacteria are frequently auxotrophic for multiple metabolites. Also bacteria are frequently subjected to changes in resource environments. Hence we also determined the effect of different carbon environments and epistasis on the fitness of Escherichia coli genotypes from whose genome one, two, or three different amino acid biosynthesis genes have been deleted. Competition experiments between auxotrophic mutants and prototrophic wild type cells in one of two carbon environments revealed that plasticity and epistasis strongly affected the mutants’ fitness individually and interactively. Taken together, our findings suggest adaptive benefits could drive the loss of conditionally essential biosynthetic genes and that both the genetic background and environmental conditions determine the adaptive value of the loss of these biosynthetic functions.

UMCW02 27th October 2014
15:30 to 16:30
J Weitz Plenary Lecture 2: Theoretical principles of virus-host population dynamics
In this talk I will introduce theoretical principles underlying the study of virus-host interactions from an ecological perspective. In doing so, I will show how viruses can affect population dynamics, evolutionary dynamics and ecosystem functioning.

Related Links

•http://ecotheory.biology.gatech.edu

UMCW02 27th October 2014
16:30 to 17:30
Plenary Lecture 3: Are simple models more general?
Co-author: Robert J Clegg (University of Birmingham)

Using some examples I will show that simpler models can be less general and that complex models can be less realistic. It is therefore important to vary the complexity of a model to test the structural robustness of models, not just checking off the parameter sensitivity box. For example, one ought to test which processes (e.g. growth, diffusion, migration, predation, …) need to be included in a model, but having to spend a lot of time implementing further processes that may turn out not to matter means that this is often not done, especially towards the end of a project. Open-source, individual-based modelling platforms can help here if many groups contribute by implementing further processes enabling the user to quickly try out a bunch of processes. In the end, models are more useful if they are less wrong.
UMCW02 28th October 2014
09:30 to 10:30
Plenary Lecture 4: Biofilms, particularly Biofilm Models
UMCW02 28th October 2014
11:00 to 12:00
Plenary Lecture 5: Biogeochemical Reaction Modeling: Theory and Application
Biogeochemical reaction modeling (BGRM) is a computational framework that couples the simulation of microbial metabolism with the simulation of chemical reactions. BGRM simulates chemical reactions using the classical approaches of geochemical reaction modeling. Specifically, it builds on the equilibrium simulation of chemical speciation, and applies kinetic or equilibrium modeling approach to redox reaction, mineral precipitation and dissolution, and other chemical reactions. BGRM simulates the metabolism of microbial groups in terms of the rates of microbial respiration/fermentation, growth, and maintenance. It describes microbial rates using rate laws that consider the availability of electron donors, acceptors, and growth nutrients, the thermodynamics of the environment, and the energetics of microbial metabolism. By capturing the thermodynamics and kinetics of chemical and microbial reactions, BGRM can be applied to assess the habitability and potential metabolic activit ies of natural environments, and to predict the dynamics of microbial populations and environmental chemistry. By simulating simultaneously chemical and microbial reactions, BGRM can also be applied to investigate the interactions among different microbial groups, and between microbes and their environment.
UMCW02 28th October 2014
12:00 to 12:15
ER Watkins Contributed Talk 3: The role of metabolic and immunological competition in structuring pneumococcal populations and the effects of vaccination
Streptococcus pneumoniae (the pneumococcus) is a major cause of bacterial pneumonia, septicemia and meningitis worldwide. Traditional serotyping methods have demonstrated that pneumococcal populations are highly diverse, with over 90 capsular serotypes. More recently, whole genome sequencing has revealed extensive diversity among the metabolic genes, and that metabolic alleles tend to segregate in non-overlapping associations with the antigenic serotype. Here, we use a multilocus model in which strains are composed of metabolic, antigenic and virulence components to explain these patterns of structuring through ecological and immunological competition in the host.

Currently, pneumococcal protein conjugate vaccines target only a small subset of its >90 known capsular serotypes. We use our model to show that a strain-targeted vaccination strategy could alter the genomic profile of non-vaccine strains, potentially leading to an increase in their transmissibility and virulence. The results are consistent with data on the changes in the population structure of the pneumococcus following vaccination, including support at the whole genome level in a collection of 600 pneumococcal genomes.

Similar non-overlapping associations among metabolic and antigenic alleles have been observed in a number of other bacterial pathogens, suggesting that metabolic and immunological competition may play important roles in the maintenance of pathogen population structure more generally. Our vaccination findings also have implications for strain-targeted vaccination in a range of bacterial and viral systems.

UMCW02 28th October 2014
12:15 to 12:30
Contributed Talk 4: How the coexistence of specialist and generalist species is influenced by the size of environmental graining
Co-authors: Rosalind Allen (University of Edinburgh), Richard Blythe (University of Edinburgh)

Consider an ecosystem with limited space. For a specialist species to survive, there must be enough of its favoured habitat to support itself. If there is a lot of a particular habitat, then necessarily there must be less of another type of habitat.

A central question in ecology is why so many types of species can coexist in the same place. A popular explanation is niche partitioning, in which different species adopt different strategies and thus avoid competition. A possible difference in strategies is to either become a specialist, which uses one resource very well but cannot use anything else, or a generalist, which can use many resources, but less well. Specialist and generalist species coexist in many environments on earth, but why?

One possible factor is the size of similar patches that occur in the environment, which can also be thought of as the coarseness of environmental grain. Using an agent-based model, I investigate the effects of grain size on the coexistence of specialists and generalists and show why intermediately sized graining encourages coexistence and a higher overall species diversity.

UMCW02 28th October 2014
14:00 to 15:00
Plenary Lecture 6: Resolving microbial community structure and function using next generation sequencing
Co-authors: Dr Konstantinos Gerasimidis (University of Glasgow), Dr Nick Loman (University of Birmingham)

I will give an overview of bioinformatics for analysing microbial communities using next generation sequence data. Determination of community structure from 16S rRNA gene sequencing and potential function from shotgun metagenomics data will be covered. There will be an emphasis on the relative merits of different techniques and analysis strategies. To illustrate these methods an example analysis from a longitudinal study of changes in the gut microbiome of children with Crohn's disease undergoing treatment with a therapeutic diet (exclusive enteral nutrition) will be presented.

UMCW02 28th October 2014
15:00 to 15:15
F Goldschmidt Contributed Talk 5: Successive range expansions of interacting microbial populations promote spatial diversity
Succession of species is a process that is widespread in nature. Succession occurs when a pioneering species that expands into new territory is followed by a secondary species that depends on the change in the formerly pristine environment caused by the primary species. It is known that when species expand their territory, genetic drift leads to a reduction of diversity in this species. On the other hand was recently shown that interactions between species, like mutualistic dependencies, can oppose genetic drift during simultaneous expansion. However, it remains unclear how genetic drift affects diversity during successive expansions of interacting species. Our main questions are two-fold; first, can a temporally segregated interaction can oppose genetic drift during the succession and if this affects mainly the secondary or also the primary pioneer?

To address our questions, we constructed a system of two syntrophic bacteria that undergo successive range expansions. The producing strain degrades a parent substrate into an intermediate, which is then excreted. The consuming strain then consumes the secreted intermediate. We manipulate the interaction between the two strains from commensal to a non-obligate mutualism by changing the reactivity of the intermediate using the pH (i.e., the toxicity of the intermediate increases as the pH decreases).

We found that the producing strain forms a regular wave front, while the consuming strain, which has to penetrate the biofilm of the producing strain, forms dendritic structures with fractal properties. There are two processes that oppose the diversity reducing effect of genetic drift during the successive expansion. First the number of expanding dendrites is higher at non-obligate mutualistic conditions. This process maintains the initial diversity. Second the degree of dendritic branching is higher at commensal conditions. Branching generates new spatial diversity by splitting up the populations into small sub-populations. In short we find that successive expansion promotes diversity by maintenance of pre-existing diversity and generation of new diversity during the expansion.

UMCW02 28th October 2014
15:15 to 15:30
Contributed Talk 6: Carbon source-dependent metabolic costs of amino acid biosynthesis in Escherichia coli
Co-authors: Glen D'Souza (Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology), Christian Kost (Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology), Christoph Kaleta (Theoretical Systems Biology Research Group, FSU Jena)

Bacteria invest a significant proportion of their available energy and resources into the biosynthesis of amino acids, which are required for cell growth and maintenance. As a consequence, the costs of amino acid biosynthesis profoundly limit the growth rate and, hence, the fitness of a bacterial species. Despite the substantial role for the metabolic economics of a cell, little is known about how these costs may shape the dynamics of cooperative cross-feeding interactions in bacterial communities. Here we show that the growth rates of Escherichia coli amino acid auxotrophic strains relative to the growth rate of the E. coli wild type are strongly carbon source-dependent, when amino acid availability is limiting. To understand these differences we developed a computational framework to quantitatively estimate biosynthetic costs of amino acid anabolism. This approach is based on a genome-scale metabolic network of E. coli and essentially estimates the amount of a given carbon source which is needed to synthesize a specific amino acid. The observed carbon source-dependent increase of the auxotroph's maximum growth rate µmax with increasing amino acid concentration correlated positively with the predicted biosynthetic costs. We conclude that the differences in the increase of µmax are due to the metabolic costs, which the auxotrophs save by taking up the focal amino acid from the environment. These findings imply that there is a high potential for mutualistic amino acid cross-feeding interactions to evolve among sympatric populations of the same bacterial species that specialize in the utilization of different substrates when multiple carbon sources are available in the environment.

UMCW02 28th October 2014
16:00 to 17:00
Discussion Session: Different approaches to the modelling of microbial communities
UMCW02 29th October 2014
09:30 to 10:30
C Tarnita Plenary Lecture 7: Mathematics of social behavior
I will begin with a discussion and mathematical description of the two different types of social construction: `staying together' and `coming together' (or aggregation). Staying together means that individuals form larger units (complexes, groups) by not separating after reproduction (eg. ant colonies, most multicellular organisms), while coming together means that independent individuals form aggregates (eg. most animal groups, including humans). For each of these operations I will discuss its strengths and vulnerabilities in promoting social behavior, which will lead naturally into a discussion of the various mechanisms (and the relationships between them) that have been proposed to explain the evolution and maintenance of social behavior and cooperation: direct and indirect reciprocity, kin selection, group/multilevel selection, spatial structure, punishment/ostracism, rewards. I will discuss the theoretical frameworks in which these mechanisms are generally studied and for each mechanism I will present a simple model that captures the essence of how it can be described mathematically. Examples will be given from multicellularity, eusociality, bacterial biofilms, animal and human behavior.
UMCW02 29th October 2014
10:30 to 10:45
Contributed Talk 7: Social evolution of toxic metal bioremediation in P.aeruginosa
Bacteria are often iron-limited, hence produce extracellular iron-scavenging siderophores. A crucial feature of siderophore production is that it can be an altruistic behaviour (individually costly but benefitting neighbouring cells), thus siderophore producers can be invaded by non-producing social “cheats”. Recent studies have shown that siderophores can also bind other heavy metals (such as Cu and Zn), but in this case siderophore chelation actually reduces metal uptake by bacteria. These complexes reduce heavy metal toxicity, hence siderophore production may contribute to toxic metal bioremediation. Here, we show that siderophore production in the context of bioremediation is also an altruistic trait and can be exploited by cheating phenotypes in the opportunistic pathogen Pseudomonas aeruginosa. Specifically, we show that in toxic copper concentrations: 1) siderophore non-producers evolve de novo and reach high frequencies; and 2) that producing stra in s are fitter than isogenic non-producing strains in monoculture, and vice versa in co-culture. Moreover, we show that the evolutionary effect copper has on reducing siderophore production is greater than the reduction observed under iron-limited conditions. We discuss the relevance of these results to the evolution of siderophore production in natural communities and heavy metal bioremediation.
UMCW02 29th October 2014
11:30 to 12:30
Plenary Lecture 8: Game theory for modelling microbial communities
UMC 29th October 2014
14:00 to 15:00
UMC Discussion Session
UMCW03 30th October 2014
09:30 to 10:05
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.
UMCW03 30th October 2014
10:05 to 10:40
Plenary Lecture 2: tba
UMCW03 30th October 2014
10:40 to 10:55
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.
UMCW03 30th October 2014
11:25 to 11:55
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.

UMCW03 30th October 2014
11:55 to 12:30
J Weitz 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.
UMCW03 30th October 2014
14:00 to 14:35
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.
UMCW03 30th October 2014
14:35 to 15:10
C Tarnita 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.
UMCW03 30th October 2014
15:10 to 15:25
A Haas 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.

UMCW03 30th October 2014
15:55 to 16:30
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.
UMCW03 30th October 2014
16:30 to 17:05
J Tasoff 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.
UMCW03 30th October 2014
17:05 to 17:20
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.

UMCW03 31st October 2014
09:30 to 10:05
B Teusink Plenary Lecture 9: tba
UMCW03 31st October 2014
10:05 to 10:40
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.
UMCW03 31st October 2014
10:40 to 10:55
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.

UMCW03 31st October 2014
11:25 to 11:55
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.
UMCW03 31st October 2014
11:55 to 12:30
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.
UMC 3rd November 2014
09:00 to 17:00
COMSOL tutorial
UMCW05 4th November 2014
10:05 to 10:20
Taking a bottom-up approach: using metabolic models to study how interactions shape natural-occurring microbial communities
Co-authors: Rafi Zareki (Tel Aviv University), Omer Eilam (Tel Aviv University), Eytan Ruppin (Tel Aviv University)

Revealing the ecological principles that shape communities is a major challenge of the post-genomic era. To date, a systematic approach for describing inter-species interactions has been lacking. Using CBM, we independently predict the competitive and cooperative potential between 6,903 bacterial pairs derived from a collection of 118 species ’ metabolic models and chart an intricate association between competition and cooperation. Utilizing ecological data from 2,801 samples, we explore the associations between bacterial interactions and coexistence patterns. The high level of competition observed between species with mutual-exclusive distribution patterns supports the role of competition in community assembly. Cooperative interactions are typically unidirectional with no obvious benefit to the giver. However, within their natural communities, bacteria typically form close cooperative loops resulting in indirect benefit to all species involved.

UMCW05 4th November 2014
10:20 to 10:35
tba
UMCW05 4th November 2014
10:35 to 10:50
D Fell Issues in Flux Balance Analysis
Co-authors: Mark Poolman (Oxford Brookes University), Hassan Hartman (Oxford Brookes University)

As the practice of genome scale metabolic modelling by FBA has become more widespread, certain procedures and assumptions have been automatically adopted, almost as a standard, whereas their utility and applicability should be assessed for each specific model and investigation. In addition, there are some recurrent biochemical errors that are not always being filtered out.

Amongst the procedures not being given sufficient thought are: 1. Optimisation by maximisation or minimisation? Maximisation is generally adopted even though the way that the linear programming algorithm operates results in artefacts in the solutions that are not present on minimisation and that require post-processing to remove. 2. Expressing the biomass formation as a pseudo-reaction with non-integer stoichiometry or as part of the constraints in the analysis. Again the former is more general even though it is almost impossible to ensure it is correctly stoichiometrically balanced and feasible. 3. Substrate consumption for non-growth associated cell maintenance is for ATP generation. We have shown that part of this extra substrate consumption in Arabidopsis cells is for NADPH, presumably to combat oxidative damage, and this has consequences for the predicted fluxes in central carbon metabolism.

Recurrent errors include: 1. Writing enzyme prosthetic groups as substrates and products of enzyme reactions. FAD and FADH are the most frequent culprits. This creates pool metabolites that could generate spurious redox interactions across the network that will not exist because these groups are contained and recycled entirely within the enzyme reaction. 2. ATP from nothing. There are published models that can generate the ATP to satisfy maintenance requirements without any flows into the metabolic network from external material. Needless to say, all subsequent analysis of such a model is valueless. Preventing this is an elementary reality check during model construction.

UMCW05 4th November 2014
11:15 to 11:30
Importance of Standardising Genome-Scale Stoichiometric Models
Co-author: Orkun Soyer (University of Warwick)

Genome-scale stoichiometric model based approaches are increasingly being used for studying cellular metabolism, which has resulted in the development of stoichiometric models for a verity of organisms and cell types. However, many of these models vary significantly in terms of their syntax, chemical/reaction naming conventions, data structures, etc., mostly due to the use of different tools/methods for developing them. These variations often make the models incompatible; therefore, comparison/integration of multiple models become very difficult. In this talk I discuss about certain issues related to the lack of a common standard and emphasis the importance of standardising stoichiometric models.

UMCW05 4th November 2014
11:30 to 11:45
Standardisation of stoichiometric models: how and why
Interest in constraint-based modelling of metabolism using stoichiometric models has grown significantly over the last 10-15 years. Hundreds of curated models [1], and thousands of automatically generated models [2] are now publicly available, covering organisms in all three domains.

Despite attempts of standardising their representation, using community-developed formats such as the Systems Biology Markup Language, SBML [3], many tasks surrounding model building and analysis are hampered by a lack of interoperability between models.

Based on the speaker's experience in co-leading two large international community efforts in the development of consensus models for yeast [4] and human [5], approaches to model standardisation will be discussed. Moreover, the benefits of adopting a disciplined approach to model standardisation - automated model building, model checking, and 'omics data integration - will be demonstrated.

Such reliance on automated techniques will be of particular relevance to stoichiometric modelling of microbial communities, where the complexity of such models is likely to far exceed that of even the largest existing models of mammalian metabolism.

[1] Optimizing genome-scale network reconstructions. Monk J, et al. Nat Biotechnol. 2014, 32(5):447-52. [2] Path2Models: large-scale generation of computational models from biochemical pathway maps. Büchel F, et al. BMC Syst Biol. 7:116. [3] The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Hucka M, et al. Bioinformatics. 2003, 19(4):524-31. [4] A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Herrgård MJ, et al. Nat Biotechnol. 2008, 26(10):1155-60. [5] A community-driven global reconstruction of human metabolism. Thiele I, et al. Nat Biotechnol. 2013, 31(5):419-25.

UMCW05 4th November 2014
11:45 to 12:00
A Heinken Constraint-based modeling of microbial communities and their interaction with the host
Co-author: Ines Thiele (Luxembourg Centre for Systems Biomedicine)

The gut microbiota performs a central role in human well-being and disease, yet few constraint-based efforts have investigated the metabolic interaction between the host and this important ecosystem. In a first effort, we constructed an in silico model of a gnotobiotic mouse colonized with a single microbial species by joining a genome-scale, manually curated and validated reconstruction of the prominent human and mouse gut symbiont Bacteroides thetaiotaomicron and a previously published mouse reconstruction, iMM1415. We depicted the trade-off between host and microbe biomass and predicted that the microbe rescued lethal host phenotypes (1). Subsequently, we developed a framework of alternating in silico and in vitro steps to elucidate the metabolic potential of a poorly studied gut microbe relevant for human health, Faecalibacterium prausnitzii. The combination of metabolic modeling and in vitro culture revealed novel carbon sources and secretion products and allowed the definition of a chemically defined growth medium for the microbe (2). We then constructed an in silico gut microbial community model consisting of 11 microbes spanning three phyla. The community model was joined with the global human reconstruction Recon2 and the effects of the microbes on human metabolic phenotypes were systematically predicted. The microbes had a global effect on the predicted host body fluid metabolome that was significantly more pronounced for commensal than for pathogenic microbes. Finally, we discuss challenges that need to be considered when constructing a well-curated, representative gut microbial community model. We demonstrate that constraint-based multi-species modeling can accurately capture the interaction between the gut microbiota and the human host and should prove useful for modeling the influence of the microbiota in human health and disease.

1. A. Heinken et al., Gut Microbes 4, 28-40 (2013). 2. A. Heinken et al., J Bacteriol, (2014).

UMCW05 4th November 2014
13:00 to 13:15
B Olivier Exchanging stoichiometric models: interoperability at genome scale
Advances in the methods used to construct genome scale constraint based models and the wider adoption of constraint based modeling in biotechnological and medical applications have led to a rapid increase in both the number of models being constructed and the tools used to analyze them.

Faced with such growth, both in number and diversity, the need for a standardized data format for the definition, exchange and annotation of constraint based models has become critical. As the core model components (e.g. species, reactions, stoichiometry) can already be efficiently described in the Systems Biology Markup Language (SBML) the Flux Balance Constraints (FBC) package aims to extend SBML Level 3 core by adding the elements necessary to encode current and future constraint based model.

In this presentation, focusing on how they might be utilized in modelling microbial ecosystems, I will introduce the SBML Level 3 FBC package and two related standards, SED-ML and the COMBINE archive.

I will also explain the need for the consistent use of reaction/species identifiers and a tool that is being developed to address this issue.

UMCW05 4th November 2014
13:15 to 13:30
tba
UMCW05 4th November 2014
13:30 to 13:45
Optimal metabolic dynamics resolved by cyclic FBA
Co-authors: Willi Gottstein (Humboldt University Berlin, Institute of Theoretical Biology, Germany), Rainer Machne (Charité Universitätsmedizin Berlin, Institute of Theoretical Biology, Berlin, Germany), Ralf Steuer (Humboldt University Berlin, Institute of Theoretical Biology, Germany), Douglas Murray (Keio University, Institute for Advanced Biosciences, Japan)

We present a new variant of Flux Balance Analysis (FBA) that allows for dynamic modelling of metabolic cycles. In contrast to traditional dynamic FBA, which performs a series of simulations, discrete time frames are optimized simultaneously. The network is expanded to represent all species in every time frame and time transition fluxes are added to allow an exchange of metabolites between adjacent time frames. The steady state condition only holds true for the total process, and storage or depletion of metabolites throughout the cycle can be predicted. We apply this method to respiration cycles of continous yeast cultures to evaluate preferences of metabolic syntheses towards different energetic cellular states.

UMCW05 4th November 2014
13:45 to 14:00
Implementing Trade-offs in FBA
Co-author: Orkun Soyer (University of Warwick)

The implementation of higher level constraints in flux balance analysis, that impose global limits on flux rates, could considerably limit the amount of apriori kinetic information that needs to go into an FBA model. Two promising approaches in this direction are the notion of "molecular crowding", that sets a limit on the total allowable flux within a model and the membrane-space limitation approach, that limits total uptake flux. We use membrane-space limitation in an evolutionary scenario to find uptake fluxes on FBA models that lead to higher growth rates given a certain medium. Depending on the complexity of the medium, the trade offs forbid a unique solution and hence we see the emergence of multiple co-existing model "species" sharing a given medium.

UMC 5th November 2014
14:00 to 15:00
Energetic feedback on chromatin state defines a system-wide reset point
UMC 5th November 2014
15:00 to 16:00
W Shou Interaction driven spatial patterning in microbial communities
UMC 6th November 2014
14:00 to 15:00
D Franco Controlling chaos in population models
UMC 6th November 2014
15:00 to 16:00
How microbial communities drove the evolution of the genetic code more than 3.8 billion years ago
Relics of early life, preceding even the last universal common ancestor of all life on Earth, are present in the structure of the modern day canonical genetic code --- the map between DNA sequence and amino acids that form proteins. The code is not random, as often assumed, but instead is now known to have certain error minimisation properties. How could such a code evolve, when it would seem that mutations to the code itself would cause the wrong proteins to be translated, thus killing the organism? Using digital life simulations, I show how a unique and optimal genetic code can emerge over evolutionary time, but only if horizontal gene transfer within early microbial communities --- a network effect --- was a much stronger characteristic of early life than it is now. These results suggest a natural scenario in which evolution exhibits three distinct dynamical regimes, differentiated respectively by the way in which information flow, genetic novelty and complexity emerge.
UMC 10th November 2014
14:00 to 15:00
Understanding the structure and function of microbes involved in cycling of trace gases in the environment
My research over the last 30 years has centred around the physiology, biochemistry, molecular biology, genetics and ecology of bacteria that grow on one carbon compounds such as methane, methanol, methylated amines and dimethyl sulphide (methylotrophs). A particular focus has been on the physiology, biochemistry and molecular biology of methane oxidising bacteria (methanotrophs) and their role in carbon cycling in the environment. One of the major challenges in microbial ecology is to define "who does what" in the environment; ie which groups of microbes are carrying out specific processes in the environment. We developed the technique of DNA Stable Isotope Probing (SIP) to define the structure and function of microbes in studies on the methane cycle. SIP allows the capture of specific information from key groups of microbes in the environment that are carrying out a specific process. $^1$$^3$C- labelled substrate is incorporated into cell material of the active microbial community involved in a specific process in environmental samples, eg methane oxidation. This $^1$$^3$C-labelled material can be separated from non-labelled ($^1$$^2$C) cell components from all other non- utilizers or "dormant" methane oxidizers. $^1$$^3$C-labelled RNA provides phylogenetic information on active cells and $^1$$^3$C-labelled DNA yields information on key functional genes encoding key steps in biogeochemical processes eg methane monooxygenase. These techniques help us to define the function of microbes involved in key biogeochemical cycles. DNA-SIP can be used in gene mining studies and has the additional advantage of allowing access to the genomes of whole communities of microbes carrying out a specific process in the environment. Targeted metagenomics, focusing down on key processes in the environment, will provide substantial information on major physiological groups of organisms involved in cycling of trace gases such as methane, dimethylsulfide and isoprene and volatile organic compounds such as methanol in the marine and terrestrial environment.

Lab: www.jcmurrell.co.uk The Earth & Life Systems Alliance:www.elsa.co.uk
UMC 13th November 2014
14:00 to 15:00
Why are there so few microbial species?
UMC 13th November 2014
15:00 to 16:00
R Quinn Omics approaches reveal how chemistry governs the biology of cystic fibrosis lung infections
UMC 14th November 2014
11:00 to 12:00
Modelling Macro Ecological Patterns: Neutral Theory and Beyond
Classical ecological theory suggests that two species can only coexist if they use resources differently. By contrast, "Neutral" theory proposes that ecological drift allows species to coexist even if they are ecologically equivalent. Neutral models give a surprisingly good description of several well-known macroecological patterns, but require numerous biologically unpalatable assumptions. I shall discuss how these assumptions can be relaxed to produce more realistic, yet still mathematically tractable ecological theories. I will begin my talk with a short introduction to a variety of modelling frameworks used to describe ecological patterns of abundance.

Video for an earlier version of this talk is available.

UMC 18th November 2014
14:00 to 15:00
Sexual signals between yeast cells
UMC 21st November 2014
14:00 to 15:00
Life at High Reynolds Number
Microorganisms living in the ocean can be subject to strong turbulence, with cell division times in the middle of a cascade of eddy turnover times. We explore the dynamics of a Fisher equation describing cell proliferation in one and two dimensions, with cellular diffusion as well as a coupling to turbulent advection. Due to inertial effects and cell buoyancy, we argue that the effective advecting velocity field is compressible. For strong enough compressible turbulence, microorganisms such as bacteria and phytoplankton track, in a quasilocalized fashion, sinks in the turbulent velocity field, with important consequences for the carrying capacity and for fixation times when two genetically different species compete
UMC 25th November 2014
14:00 to 15:00
S Guptal The role of immune selection on the population structure of metabolic genes in pathogenic bacteria
We have developed multilocus models for pathogen evolution (1) that resolve the paradox that many pathogen populations exist, either stably or unstably, as discrete antigenic types, which may then circulate as independently transmitted strains with their own particular virulence characteristics. This hypothesis was originally formulated in the context of Plasmodium falciparum malaria but its principal conclusions have received strongest support so far from studies of bacterial pathogens such as Neisseria meningitis and Streptoccocus pneumonaie. We have also used this general framework to address the long-standing conundrum of why bacterial lineages (as defined by combinations of housekeeping genes) persist over long time periods despite frequent genetic exchange. Our analyses reveal that these genes can exhibit long-term linkage disequilibrium as a consequence of immune-mediated competition, even though they are not themselves under immune selection (2). I will attempt to discuss the implications of these results for microbial communities in general.

1. Gupta S, Ferguson NM & Anderson RM (1998) Chaos, persistence and the evolution of strain structure in populations of antigenically variable infectious agents. Science 240:912 915.

2. Buckee CO, Jolley KA, Recker M, Penman B, Kriz P, Gupta S & Maiden M. (2008) Role of selection in the emergence of lineages and the evolution of virulence in Neisseria meningitidis. Proc Natl Acad Sci U S A :15082-7.
UMC 25th November 2014
15:00 to 16:00
M Mobilia Spiralling patterns in models inspired by bacterial games with cyclic competition
Evolutionary game theory, where the success of one species depends on what the others are doing, provides a promising framework to investigate the mechanisms allowing the maintenance of biodiversity. Experiments on microbial populations have shown that cyclic local interactions promote species coexistence. In this context, rock-paper-scissors games are used to model populations in cyclic competition.

After the survey of some inspiring experiments, I will discuss the subtle interplay between the individuals' mobility and local interactions in two-dimensional rock-paper-scissors systems. This leads to the loss of biodiversity above a certain mobility threshold, and to the formation of spiralling patterns below that threshold. I will then discuss a generic rock-paper-scissors metapopulation model formulated on a two-dimensional grid of patches. When these have a large carrying capacity, the model's dynamics is faithfully described in terms of the system's complex Ginzburg-Landau equation suitably derived from a multiscale expansion. The properties of the ensuing complex Ginzburg-Landau equation are exploited to derive the system's phase diagram and to characterize the spatio-temporal properties of the spiralling patterns in each phase. This enables us to analyse the spiral waves stability, the influence of linear and nonlinear diffusion, and the far-field breakup of the spiralling pattern.
UMCW04 26th November 2014
13:30 to 14:05
Plenary Lecture 1: Engineering syntrophic exchange in synthetic microbial communities
Co-authors: Michael T. Mee (Boston University), James J. Collins (Boston University), George M. Church (Harvard Medical School)

Metabolic crossfeeding is an important process that can broadly shape microbial communities. However, little is known about specific crossfeeding principles that drive the formation and maintenance of individuals within a mixed population. Here, we describe the construction of a series of synthetic syntrophic communities to probe the complex interactions underlying metabolic exchange of amino acids. We experimentally analyzed multimember, multidimensional communities of Escherichia coli of increasing sophistication to assess the outcomes of synergistic crossfeeding. We find that biosynthetically costly amino acids including methionine, lysine, isoleucine, arginine, and aromatics, tend to promote stronger cooperative interactions than amino acids that are cheaper to produce. Furthermore, cells that share common intermediates along branching pathways yielded more synergistic growth, but exhibited many instances of both positive and negative epistasis when these interactions sca led to higher dimensions. In more complex communities, we find certain members exhibiting keystone species-like behavior that drastically impact the community dynamics. Based on comparative genomic analysis of >6,000 sequenced bacteria from diverse environments, we present evidence suggesting that amino acid biosynthesis has been broadly optimized to reduce individual metabolic burden in favor of enhanced crossfeeding to support synergistic growth across the biosphere. These results improve our basic understanding of microbial syntrophy while also highlighting the utility and limitations of current modeling approaches to describe the dynamic complexities underlying microbial ecosystems. This work sets the foundation for future endeavors to resolve key questions in microbial ecology and evolution, and presents a platform to develop better and more robust engineered synthetic communities for industrial biotechnology.

Related links: http://wanglab.c2b2.columbia.edu/ - Wang Lab at Columbia University
UMCW04 26th November 2014
14:05 to 14:40
K Foster Plenary Lecture 2: Cooperation and competition in microbial communities
Since Darwin, evolutionary biologists have been fascinated by cooperative behavior. Honeybee workers labor their whole life without reproducing, birds make alarm calls, and humans often help one another. One major group that remains relatively unexplored, however, is the microbes whose full spectrum of sociality only recently came to light. Microbes often live in large dense groups where one cell can strongly affect the survival and reproduction of others. But do microbes typically help or harm those around them? We study this question using a diversity of systems, including computer simulations, pseudomonad bacteria and budding yeast. We find that single-genotype patches naturally emerge in microbial groups, which creates favorable conditions for cooperation within a particular genotype. Moreover, some microbes actively adjust both genotypic assortment and investment into social traits in a way that promotes cooperation within a genotype. However, our work on interactions be tween different microbial genotypes suggests that, here, the evolution of competitive phenotypes is more likely than cooperation. This leads us to a simple model – the genotypic view – that predicts microbes will evolve to help their own genotype but harm most other strains and species that they meet. We are now moving to understand how our understanding of cooperation and competition in microbial communities can contribute to design principles associated with synthetic and natural systems.
UMCW04 26th November 2014
14:40 to 15:15
Plenary Lecture 3: Bacterial interactions in synthetic communities and in the wild
Predicting how bacterial community structure impacts ecosystem functioning requires quantifying how bacteria interact in natural environments. Our past research has used synthetic communities to characterise the ecology and evolution of bacterial interactions. Results indicate that: (i) interactions tend to be antagonistic, (ii) community complexity mollifies antagonisms and favours positive interactions, (iii) interactions evolve rapidly with repercussions for ecosystem functioning, and (iv) higher-order interactions are relatively unimportant. However, extrapolating these results to natural environments is challenging because of the complexity these communities. I will discuss one potential solution, which uses common garden experiments to quantify interactions in complex communities collected from nature.
UMCW04 26th November 2014
15:45 to 16:20
Plenary Lecture 4: Eco-engineering of fermentative microbial communities: the role of keystone species

Microbial mixed cultures present a broad metabolic flexibility and allow considering complex organic biomass as potential resources for biomolecules and hydrogen production in dark fermentation processes. A wide number of microbial species are able to ferment carbohydrates, but a high microbial diversity is often detrimental to bioprocess operation since it leads to process instability. To date, only few controllers, essentially physicochemical, are available to control finely the multiplicity of bacterial metabolisms in mixed cultures. And no strong or very specific selection pressure could be applied to enrich in efficient and robust microbial communities. One possibility would be to engineer ecologically these communities to better control the metabolic networking. For that, we investigated the use of keystone species as biotic triggers of the fermentative metabolism in mixed cultures. First some keystone species, often low in abundance but having a major role on metabolic networks, were identified from several natural ecosystems. Different strategies of biotic control of the fermentative microbial communities were then investigated, confirming the important role of these species and the possibility of using them as biotic controllers of the overall community. Artificial co-cultures were also carried out, and a specific type of interaction was characterized. Beyond this study, it is expected that these findings lead to new biotechnological or environmental applications through the use of biotic control of microbial metabolisms.

UMCW04 26th November 2014
16:20 to 16:55
Plenary Lecture 5: Engineering microbial community architecture to set community metabolism
The composition of a microbial community is a major indicator of a community’s metabolic potential. However, the spatial structure of that community, imposed or inherently present, can dictate its extant activity. We are keen to explore how we can steer the spatial structure of open and synthetic microbial communities to select or stabilize a target community metabolism from its constituent members. I will provide experimental and computational insights in our efforts to engineer spatially structured communities to generate redox-stratified biofilms for autotrophic nitrogen removal. These communities can provide test grounds for ecological enquiries and building blocks for technological applications.
UMCW04 26th November 2014
16:55 to 17:10
JF Poyatos Contributed Talk 1: Synthetic microbial systems as ecosystems simulators
Co-authors: Clara Moreno (CNB-CSIC), Matteo Cavaliere (CNB-CSIC), Esteban Martinez-Garcia (CNB-CSIC)

An ideal ecosystem “simulator” would permit the study of ecological questions that are difficult to analyze in the field, and whose details are sometimes not easy to incorporate by means of ab initio computer models. Here, I propose the use of synthetic bacterial systems as such “simulators” by discussing one case study. This is focused on the issue of how certain stressors impact ecosystems that rest on public resources, a fundamental question for risk assessment. We will thus engineer a community that relies on public goods to manage stress. With this “simulator”, I will try to show how the availability of essential resources, and the presence of habitat heterogeneities eventually influence the effect of the stressor. Some surprises are guaranteed.

UMCW04 27th November 2014
09:30 to 10:05
Plenary Lecture 6: Metabolic conflicts drive multi-scale organization of microbial activities
Biological bottlenecks for microbial biodegradation of recalcitrant compounds in the environment include [i] unfavourable thermodynamics of (bio)chemical reactions at stake, [ii] lack of specificity of existing pathways and enzymes for novel substrates, and [iii] physicochemical stress encountered in polluted sites. Besides these limitations, bacterial cells also experience increased endogenous oxidative stress during metabolism of aromatic compounds, which is exacerbated when enzymes meet suboptimal substrates. Evolving bacterial metabolism is thus shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks -and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. These features suggest that the physical structure of existing biosystems, from operon assemblies to multi-cellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. We have examined oxidative stress brought about by the still-evolving 2,4-dinitrotoluene biodegradative pathway in Burkholderia sp. DNT. The dnt pathway of this bacterium apparently evolved from a precursor naphthalene degradation route and the first enzyme (2,4-dinitrotoluene dioxygenase) maintains some activity towards its earlier substrate. Examination of both in vivo reactions and the associated regulatory system suggests that ROS production is the first bottleneck that evolving pathways have to overcome for dealing with novel compounds. Evolutionary consequences -and some hints and genetic tools for engineering multi-strain biocatalysts- will be discussed.
UMCW04 27th November 2014
10:05 to 10:40
Plenary Lecture 7: Lignocellulose degradation by enriched microbial consortia from cow rumen and termite gut
Co-authors: Lucas Auer (idem), Adèle Lazuca (idem), Maider Abadie (idem), Gunnar Oelker (idem)

Bioconversion of lignocellulosic biomass into energy and synthons of industrial interest is of current concern to reduce the fossil energy dependence. Lignocellulose can be converted into carboxylates which can be used to produce added-value products (e.g biofuels or bioplastics). Such transformation can be realized by microbial consortia issued from the digestive tract ruminants and phytophage insects. Our aim was to produce microbial consortia displaying stable microbial diversity, high lignocellulolytic potential and high capacity to produce carboxylates using termite gut and cow rumen microbiomes. We also wanted to correlate the functional diversity of these consortia with their enzymatic activity and lignocellulose degradation profiles. To this aim, we studied the lignocellulolytic capacities of cow rumen and gut microbiomes of four species of tropical termites (Termes hospes, Microcerotermes parvus, Nasutitermes lujae and N. ephratae). Lignocellulose transformation was tested in anaerobic reactors (35°C) using wheat straw as sole carbon source. Carboxylate production and residual lignocellulosic substrate were regularly monitored during the incubation period (15 d). Our data showed that gut microbiomes from N. ephratae displayed high capacities to degrade lignocellulose. N. ephratae cow rumen microbiomes were selected to enrich the most active lignocellulolytic spe cies by sequencing batch reactor process. After 10-12 cycles, stable consortia were obtained. Sequencing of 16S rRNA gene showed important differences in the functional species present in these ecosystems compared to the initial communities. The enzymatic activities (endoglucanase, ß-glucosidase, xylanase, ß-xylosidase), mainly associated to the cell biomass, suggested the production of cellulosome-like systems. In this presentation, insights in enzymes activities and diversity will be discussed, providing better understanding of lignocellulose deconstruction by microbial consortia.

UMCW04 27th November 2014
10:40 to 10:55
Contributed Talk 2: Long distance relationships between algae and bacteria
Co-authors: F. Peaudecerf (Department of Applied Mathematics and Theoretical Physics (DAMTP), University of Cambridge), M. A. Bees (Department of Mathematics, University of York), R. E. Goldstein (Department of Applied Mathematics and Theoretical Physics (DAMTP), University of Cambridge), A. G. Smith (Department of Plant Sciences, University of Cambridge)

Microbial interactions are often predicated on metabolism: e.g. auxotrophs depend on nutrients made by other microbes. Many algae are vitamin auxotrophs, with several known species requiring exogenous vitamin B12 [1]. This vitamin must be obtained from bacteria, as only they can synthesise it. Laboratory experiments have demonstrated mutualistic interactions between bacteria and B12-dependent algae. Populations of the bacterium Mesorhizobium loti (B12 producer, carbon requirer) and the green alga Lobomonas rostrata (B12 requirer, carbon producer) in co-culture stabilise to an algae/bacteria ratio of 1/30, independent of initial inoculum ratio [2]. system [3].

Here we consider the interactions between microbial populations separated in space. Experiments on hard agarose indicate that mutualistic interactions exist at a distance. We present a mathematical model capturing the essence of these experiments: growing populations of algae and bacteria coupled by a diffusive channel. Solutions to the model reveal rich dynamics. We will discuss these and speculate on the ecological significance of our findings for understanding environmental biofilms and microbial mats.

[1] Croft, M. T. et al. Nature 483:90–93 (2005) [2] Kazamia, E. et al. Environ. Microbiol. 14, 1466 (2012)

UMCW04 27th November 2014
11:25 to 11:55
Plenary Lecture 8: Towards a predictive framework for microbial community dynamics in drinking water systems
The abundant and diverse drinking water microbiome migrates daily from the drinking water treatment plant through the distribution systems into our homes, offices, schools, etc. Every litre of water emerging from our taps has tens of millions of microbes – bacteria, archaea, eukaryotes, and viruses – all of which constitute a complex microbial community. Effectively managing this diverse microbial community is not only critical from a public health perspective, but also has implications for our water infrastructure (e.g. microbially mediated corrosion). Efforts to manage the drinking water microbiome would be well served by a framework that can predict its dynamics as a function of process operations, environmental conditions, and water supply infrastructure over relevant spatial and temporal scales. A predictive framework would pave the way for a nuanced control of the drinking water microbiome, which will save labour, energy and may also ultimately promote heal th. This presentation will outline efforts to develop a such predictive framework for water systems in the US and Europe.
UMCW04 27th November 2014
11:55 to 12:30
N Krasnogor Plenary Lecture 9: Computation and Polymer Synthesis for Designer Quorum Sensing Behaviour
Bacteria deploy a range of chemistries to regulate their behaviour and respond to their environment. Quorum sensing is one method by which bacteria use chemical reactions to modulate pre-infection behaviour such as surface attachment. A combination of polymer and analytical chemistry, biological assays and computational modelling has been used to characterize the feedback between bacteria clustering and quorum sensing signalling. We have also derived design principles and chemical strategies for controlling bacterial behaviour at the population level. In this talk I will summarise our work on the utilisation of computational modelling for the design of synthetic polymers affecting QS phenotypes and, , time permitting, the combinatorial DNA library design tool (DNALD).
UMCW04 27th November 2014
14:00 to 14:35
Plenary Lecture 10: tba
UMCW04 27th November 2014
14:35 to 15:10
M Barer Plenary Lecture 11: The good the bad and the irrelevant. Sequential analyses of the sputum microbiome in patients with Chronic Obstructive Pulmonary Disease
Co-authors: Koirobi Haldar (University of Leiceister), Mona Bafadhel (University of Oxford), Chris Brightling (University of Leiceister)

COPD is a chronic respiratory disease associated with progressive deterioration of lung function and eventually death from respiratory failure; chronic exposure to smoke is the major aetiological risk factor and the disease is a major WHO priority. COPD patients have excess production of mucus in their lower airways and this is coughed up as sputum which supports an abundant and diverse microbiome. The course of the disease is characterised by exacerbations in which cough and sputum production increase and lung function worsens. The causes of COPD exacerbations are hotly debated and are likely to be multiple. The view that infections, attributable to one or more microbial pathogen, are the primary cause of exacerbations is widely accepted by physicians and sanctioned by the almost universal use of antibiotics. However, rigorous evidence in support of this view is lacking. We have conducted the first sequential study of the sputum microbiome in COPD patients with samples taken when stable, at the time of exacerbation (prior to antibiotics) then 2 and six weeks later, when all had recovered from the episode. Microbiome profiling was based on Roche 454 sequencing of 16S-rDNA amplicons. With the exception of a small group of virus positive exacerbations the events could not be explained by the arrival or increased abundance of recognised pathogens. Microbiome analyses revealed a high frequency of 20 different phyla in most samples but consistent dominance of Proteobacteria and Firmicutes. No clear pattern with respect to composition or diversity of the microbiome was associated with exacerbations. However, cluster analysis revealed a subgroup of exacerbations in which disturbance of the ratio between Proteobacteria and Firmicutes occurred and subsequently returned to the stable value following therapy. We propose that this subgroup may be patients who need antibiotics while they are unnecessary or even harmful for patients whose microbiomes did not show this pattern.

UMCW04 27th November 2014
15:10 to 15:25
Contributed Talk 3: Flux analysis in microbial ecosystems
Environmental bioprocess modeling has proven as a very useful tool for analysis of natural and man-made ecosystems. Attributing specific redox reactions to specific microbial groups allows for investigating a complex microbial community as the sum of the different reactions in the system. Inclusion of the microbial redox reactions in bioreactor systems and by including thermodynamic equilibria, phase transfer reactions, and spatial distribution of reactions allows for establishment of an overall system description. This kind of models have been used for analysis of numerous wastewater treatment related processes like the activated sludge process, anaerobic digestion, and biofilm processes. In recent years metaproteogenomic methods have become available to investigate microbial ecosystems. To which extent these methods and the corresponding modeling tools are of interest for research in the field of applied environmental microbiology will be the topic of this presentation. First I will present an overview of recent modeling efforts in our research group, and based on that experience I will discuss the potential role of metaproteogenomic tools in the field of environmental microbiology.
UMCW04 27th November 2014
15:55 to 16:30
J Prosser Plenary Lecture 12: The paradox of nitrification in acid soils and lessons for microbial community ecology
Co-author: Cecile Gubry-Rangin (University of Aberdeen)

A major, long-standing question in nitrifier ecology has been the paradox of nitrification in acid soils: cultivated ammonia oxidisers cannot growth in liquid batch culture below pH 7 but gross nitrification rate in soil is unaffected by pH and some of the highest rates are seen in soils of pH 4 – 5. This question is of both scientific interest and significant global economic importance, as approximately 30% of the world’s soils are acidic, including 50% of arable soils, and up to 70% of ammonia-based nitrogen fertiliser is lost through nitrification and leaching or denitrification of nitrate. Although several mechanisms were proposed for growth of bacterial ammonia oxidisers in acid soils, a major breakthrough was evidence that the ratio of archaeal:bacterial amoA genes and gene transcripts increase as pH decreases, suggesting that acidophilic archaeal ammonia oxidisers may exist. Further evidence for this hypothesis was a global study of the distribution of archaeal amoA genes, which indicated that pH was a major factor determining archaeal ammonia oxidiser distribution in soil and identifying clusters associated with soils of different pH. The pH preference for these clusters was confirmed by predictions of their distribution in a large number of UK soil covering a range of pH values. The second line of evidence was the isolation of an acidophilic archaeal ammonia oxidisers, Nitrosotalea devanaterra, which belongs to one of the acidophilic clusters characterised in the global study, and demonstration of its growth in acid soil. While discussing this specific question in ammonia oxidiser community ecology, the different approaches used will be discussed and compared and will be used to exemplify the current state of microbial community ecology and ways in which new technologies may help and hinder future studies.

UMCW04 27th November 2014
16:30 to 17:05
Plenary Lecture 13: Variability and Alternative Community States in Microbial Communities
Co-authors: Eulyn Pagaling1,2*, Katsiaryna Usachova1,3, Liudmila Usachova4, Fiona Strathdee1, Kristin Vassileva1, Rocky Kindt1, Rosalind J. Allen2

The ability to control and engineer complex microbial communities for particular purposes or functions depends on the reproducibility and stability of community structure and function under controlled conditions. Natural microbial communities contain many low-abundance species, comprising the so-called "rare biosphere", which may be selected when the environmental parameters governing the system are altered. Current data suggest that the stochastic selection of rare species, together with the complex, non-linear dynamics of these communities, can lead to unpredictability of community structure and function following environmental selection. This can also result in alternative stable states of the system which may be difficult to interconvert.

We give an example of a wastewater treatment plant processing urban waste streams, describing the operational problems caused by the emergence of stable undesirable community states and challenges in recovering the diversity, structure and function. We then investigate the phenomena of alternative states and unpredictability using a simple, replicable laboratory model system (microcosm) containing diverse microbial ecotypes which cycle nutrients such as carbon and sulphur compounds and generate community function in the form of a redox potential gradient. Variability in the microbial community composition of this model system is observed following a selective bottleneck in the system caused by anaerobiosis. Concomitant variation in the development of the redox gradient is also seen. However, stable final microcosm communities re-inoculated into the same environment exhibit much less variability than the original communities and a final organisational state which is closely related to their initial state at inoculation. These results suggest that selection under novel environmental conditions can cause unpredictability in microbial community structure and function, but that repeated selection can be a means to ensure predictability. We discuss these phenomena with reference to microbial photobioreactor systems containing low microbial diversity which are amenable to engineering by "synthetic ecology".

UMCW04 27th November 2014
17:05 to 17:20
M Ortiz Contributed Talk 4: Optimization-based tools for bacterial ecology design
Bacteriophage-based cell-cell communication allows users to create genetically dynamic bacterial ecologies by transmitting DNA molecules between E. coli cells. In previous work, I demonstrated how such a system could be used to transmit DNA messages having different functionalities to develop ecologies over hours-long time courses in liquid or over solid media. If well-designed, such ecologies have the ability to compute, amplify, or report state as a population.

One immediate problem encountered in designing stable bacterial ecologies is that relatively small differences in individual growth rates can impact the resulting population mix in little time. As such, we have focused on developing optimization-based tools for relating the initial and final states of heterogeneous baterial ecologies. We have created a scalable model of the phage-based communication platform to aid development of more complex engineered bacterial ecologies. By inputting few experimental parameters as well as an arbitrary desired output behavior, users can easily obtain the necessary inputs to their engineered system. As phage-based communication via DNA transmission inherently creates genetically distinct species as phage infection proceeds, this tool also enables the user to design and optimize for time-varying behaviors. Overall, it is hoped that such tools will enable greater complexity of heterogeneous bacterial mixtures, help us better understand ec ologies, and allow us to narrow the gap between natural and synthetic systems.

UMCW04 27th November 2014
17:20 to 17:35
Contributed Talk 5: Numerical Continuation of Equilibria of Cell Population Models with Internal Cell Cycle
I will discuss the behavior of a model describing unicellular organisms living in a continuous culture. We do this mainly numerically, with the help of an extended version of bifurcation analysis adapted to this type of quite complex (structured) population dynamics. The complexity is induced by attaching a whole physiological structure to each of these cells, which in the present case describes the states of their internal cell cycle. Other pathways based on biochemistry would entirely fit into the modeling framework as well. In our example the cycling speed through the cell cycle will depend on the environment, which in a bioreactor environment is just the concentration of some limiting nutrient in the main tank where microbial growth takes place. The model serves well as a basis of multi-scale mathematical modeling of microbial activity, from internal cell biochemistry up to the population level, like distributions of microbial biomasses in the environment. Howev er, medical applications can be covered as well.
UMCW04 28th November 2014
09:30 to 10:05
Plenary Lecture 14: Ecosystems Biology: from data to control of microbial communities
Co-authors: Emilie Muller (University of Luxembourg), Anna Heintz-Buschart (University of Luxembourg), Shaman Narayanasamy (University of Luxembourg), Cédric Laczny (University of Luxembourg)

Mixed microbial communities are complex and dynamic systems. Integrated omics (combined metagenomics, metatranscriptomics, metaproteomics and metabolomics) are currently gaining momentum for detailed descriptions of community structure, function and dynamics in situ as well as offering the potential to discover novel functionalities within the framework of Eco-Systems Biology. We have developed an integrative workflow comprising wet- and dry-lab methodologies to enable systematic measurements of microbial communities over space and time, and the integration and analysis of the resulting “multi-meta-omic” data. Two distinct approaches have been developed allowing the deconvolution of integrated omic data either at the population- or community-level. By resolving multi-omic data at the population-level, we have uncovered patterns which suggest that in our model microbial community (lipid accumulating microbial consortia from a biological wastewater treatment tank) t he dominance of a microbial generalist is linked to finely tuned resource usage. Analysis of reconstructed metabolic networks has resulted in the identification of possible “keystone genes”, analogous to keystone species in species interaction networks. Integrated omics will likely become the future standard for the large-scale characterization of microbial consortia within an Eco-Systems Biology framework. In particular, by integrating information from genome to metabolome, integrated omics allows deconvoluton of structure-function relationships by identifying key members and functionalities. For example, identified keystone species and/or genes likely represent driver nodes which may be exploited in view of future control strategies. However, to test emerging hypotheses and formulate predictive models, which support such endeavours, an iterative discovery-driven planning approach is required. This should ultimately allow the manipulation of microbial communities and steer them towards desired outcomes.

UMCW04 28th November 2014
10:05 to 10:40
Plenary Lecture 15: Can bioenergetics tell us more about microbial ecosystems activity than community identity?
Co-authors: Rebeca González-Cabaleiro (University of Santiago de Compostela (ES)), Robbert Kleerebezem (Delft University of Technology (NL)), Juan M. Lema (University of Santiago de Compostela (ES))

Bioenergetic considerations appear to play a central role in defining microbial ecosystems activity irrespective of the microbial community identity. Our modelling results suggest that mainly bioenergetics can define the activity of microbial ecosystems at three different levels: (1) When a generalized bioenergy-based model is used to describe the competition between a number of existing and postulated microbial metabolisms, the prevailing successful ones, the reasons behind their success and some syntrophisms are correctly predicted. This has been applied to glucose fermentation and to nitrogen oxidation and reduction ecosystems. Metabolic activities appear to be selected by maximum energy harvest rate. Based on this we postulate that it is primarily energetics who defined the today existing microbial metabolisms, pathway lengths and synergisms among them. (2) When specific anaerobic fermentative reactions of interest are studied under a thermodynamic perspective, conclusions can be drawn out about their potential reversibility. Quasi equilibrium calculations can be used to estimate concentration limits for the feasibility of pathway steps and compares with physiological and kinetic limits. Based on this we postulate that in energy limited microbial ecosystems, thermodynamic limitations can impose unfeasible intermediate metabolite concentrations rendering a metabolic pathway impossible or reversing it. (3) When anaerobic fermentation microbial ecosystems are described as one mass and electron balanced metabolic network, an optimisation of the network for maximum energy yield can provide an accurate prediction of the product formation. This has been successfully applied to the prediction of products and their shifts as a function of the environmental pH. Based on this we postulate that in energy limited microbial ecosystems such as fermentations, a bioenergetic maximum energy harvest rate criteria defines the product spectrum irrespective of the microbial community.

UMCW04 28th November 2014
11:25 to 11:55
L Raskin Plenary Lecture 16: Managing microbial communities in anaerobic membrane bioreactors
Anaerobic membrane bioreactor (AnMBR) systems have recently come to the forefront as promising options for mainstream anaerobic treatment of domestic wastewater. Our research has demonstrated with a bench-scale AnMBR that this technology can produce effluent quality comparable to activated sludge treatment at temperatures as low as 6°C. However, we have also demonstrated that this technology can only become competitive as an alternative domestic wastewater treatment option after addressing its high global warming potential due to the presence of dissolved methane in the permeate and the high energy demand for fouling control. While these appear to be typical process engineering problems, we contend that management of the complex anaerobic microbial communities in AnMBR is an essential component of solving these challenges and will show experimental data in support of this statement.
UMCW04 28th November 2014
11:55 to 12:30
Plenary Lecture 17: Modeling biofilm formation in porous media and fouling in membrane processes
Biofilm formation in porous media is determined by a multitude of processes not only different in nature, but also in spatial and temporal scales, making in general the whole system challenging to study. This presentation will introduce concepts and approaches to biofilm modeling at pore scale. We couple two- or three-dimensional fluid dynamics models with solute transport supplying nutrients for biofilm development in complex geometry media. The biofilm formation can be described by particle-based models, with growth dependent of nutrient concentrations and detachment as a function of shear stress induced by flow. Mineral precipitation can also be introduced in the particle-based framework. A first application evaluates the impact of biofilms on proppant packed fractures in shale gas reservoirs. Simulations of two-phase flow indicated that although hydrophobic proppant grains provide better dewatering than hydrophilic surfaces, biofilms can worsen the dewatering. Model extensions show how biofilm lysis can create flow paths continuously changing position even after the medium permeability reached steady state. The second series of examples describes the effect of biofilm growth in spacer-filled channels of reverse osmosis membrane devices for water desalination. The 3-d numerical simulations show how biofilm accumulation strongly affects the feed channel pressure drop and liquid channeling. Furthermore, accumulation of salts near the membrane and mineral precipitation is stimulated by the biofilm. The micro-scale models can explain experimental observations on particle deposition patterns, biofilm and crystal formation.
UMC 4th December 2014
13:30 to 13:45
Welcome & Introduction
UMC 4th December 2014
13:45 to 14:10
T Curtis Mathematical Computational Approaches to Understanding Microbial Communities
UMC 4th December 2014
14:10 to 14:40
Innovation and Technology Transfer in Anaerobic Digestion
UMC 4th December 2014
14:40 to 15:10
Industrialisation of a Biotech Process - a Multidisciplinary Approach
UMC 4th December 2014
15:30 to 16:00
Microbial Dysbiosis - A Personal Care Perspective
UMC 4th December 2014
16:00 to 16:30
Harnessing the Wonders of the Microbial World to Solve Environmental Problems
UMC 4th December 2014
16:30 to 17:00
Questions & Open Discussion
University of Cambridge Research Councils UK
    Clay Mathematics Institute London Mathematical Society NM Rothschild and Sons