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Microbial ecology for engineering biology - POSTPONED

Scientific meeting

Location

Kavli Royal Society Centre, Chicheley Hall, Newport Pagnell, Buckinghamshire, MK16 9JJ

Overview

This meeting is postponed. More details to follow.

Theo Murphy international scientific meeting organised by Professor Thomas Curtis and Dr Jane Fowler.

Fluorescence in situ hybridization (FISH) of a comammox Nitrospira spp. enrichment culture from a drinking water biofilter. Image credit: Jane Fowler.

Engineered microbial systems have a crucial role to play in the development of sustainable technologies for the 21st century. The solution, ecology-based design of engineered biological systems, is urgently needed. This meeting will unite disciplines by integrating ecological theory with microbiology and engineering demands. With a focus on modelling from genome- to systems-scale, we can accelerate progress in environmental biotechnology.Speaker abstracts will be available closer to the meeting. Recorded audio of the presentations will be available on this page after the meeting has taken place. 

Attending this event

This meeting is postponed. More details to follow. 

Enquiries: contact the Scientific Programmes team

Event organisers

Select an organiser for more information

Schedule of talks

20 April

09:00-12:00

Session 1

4 talks Show detail Hide detail

Chairs

Dr Jane Fowler, Simon Fraser University, Canada

Professor Thomas Curtis, Newcastle University, UK

Dr Feng Ju, Westlake University, China

09:00-09:05 Welcome by the Royal Society

09:05-09:20 Introduction by meeting organisers

Dr Jane Fowler, Simon Fraser University, Canada
Professor Thomas Curtis, Newcastle University, UK

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09:20-10:15 When microbiology and engineering come together

Dr Beverly Stinson, AECOM Water, USA

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10:15-10:45 Coffee

10:45-12:00 From populations to ecosystems: towards a unifying ecological theory

Professor Michel Loreau, Theoretical and Experimental Ecology Station - CNRS, France

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12:00-13:00 Lunch

13:00-17:00

Session 2

6 talks Show detail Hide detail

Chairs

Dr Feng Ju, Westlake University, China

Lisa Neu, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Switzerland

13:00-14:00 Enhancing biogas production by community mixing

Professor Angus Buckling, University of Exeter, UK

Abstract

Biogas production from anaerobic digestion is likely to play an increasingly important role in future energy strategies, and hence there is a need to improve the efficiency and reliability of the process. Most refinements in biogas production have been the result of engineering solutions, with relatively little focus on direct manipulation of microbial consortia. Recent advances in ecological and evolutionary theory suggests that mixing multiple microbial communities together may provide a simple solution to enhancing biogas production. The results of experiments demonstrating the success of community mixing, its limitations and the mechanism underpinning these patterns are reported. 

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14:00-14:45 Deterministic modelling and succession of microbial communities

Professor Joana Falcão Salles,University of Groningen, The Netherlands

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14:45-15:15 Tea

15:15-15:45 Engineering the assembly of microbial communities

Professor William Sloan, University of Glasgow, UK

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15:45-16:15 Modelling of engineered biological systems

Dr Dana Ofiteru, Newcastle University, UK

Abstract

Mixed bacterial cultures are fundamental for engineered biological systems, in particular wastewater treatment. Microbes do not function in isolation but are members of communities that are complex adaptive systems. The coherent behaviour of the community arises from a variety of interactions between microbes as well as with their local environment, and some properties of the communities are not present in individual microbes. The activity at micro-scale determines the properties we measure at the macro-scale. As such, there is a wide variety of mathematical models that can be developed in order to describe and predict the microbial community behaviour. They vary from models of the mechanisms determining community assembly to the ASM/AD models used currently in plant design. Ideally, one would want to predict and understand the emergent properties using multi-scale models but it is a big challenge to model processes across different time and spatial scales. Nevertheless, bridging the gap between the macro and micro-scales would give engineers new tools that would enable them to better understand, design and optimize the novel technologies.

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16:15-16:45 Microbial community assembly processes

Professor Susann Müller, Helmholtz Centre for Environmental Research, UFZ, Germany

Abstract

Process control of bioreactors aims to create a niche defined by boundaries to strengthen and maintain an initially assembled community. Rapid detection and assessment methods are required to monitor and ultimately control assembly processes of microbial communities in such environments. Microbial flow cytometry has been used to provide high-dimensional data based on individual cells. In order to interpret the resulting time series data, inspiration was drawn from macro-ecology, which provides a multitude of concepts for describing population dynamics. In insular environments such as bioreactor systems, in contrast to natural ecosystems, microbial community structures are not affected by the immigration of new community members. When bioreactors are operated in steady-state, the impact of environmental factors on community assembly is further reduced. Under these conditions, a high degree of variability in community structures was observed over long periods of time, both between parallel reactors and within each community. It was found that both neutral and niche differentiation mechanisms are the responsible forces in community assembly processes and their respective contributions to the community assembly have been identified. The results suggest that synchronizing complex microbial communities in insular steady-state environments or keeping them in their original or desired structure can be difficult. In addition, the stability paradigm was studied in such insular environments and a fast workflow for monitoring and calculating the stability properties resistance, resilience, displacement speed, and elasticity was developed. 

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16:45-17:00 Discussion

17:00-18:00

Poster session

21 April

09:00-12:00

Session 3

6 talks Show detail Hide detail

Chairs

Bastiaan Cockx, Technical University of Denmark, Denmark

Dr Leonardo Erijman, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Argentina

09:00-09:15 Introduction for day 2

Professor Thomas Curtis, Newcastle University, UK
Dr Jane Fowler, Simon Fraser University, Canada

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09:15-09:45 Individual-based modelling: what have I learnt?

Dr Jan Ulrich Kreft, University of Birmingham, UK

Abstract

For engineering systems, it is important to be able to predict the behaviour of systems before they are being engineered as prediction can avoid costly mistakes and enables optimization of systems. Mathematical models enable true predictions rather than interpolations or extrapolations from measurements of the same system, if they are mechanistic. (A similar case can be made for causal inference.) In the case of complex systems, mechanistic models have to be bottom-up models that describe the characteristics of the parts and how they interact with each other, to predict how system level behaviour emerges from these interactions. A quintessential type of bottom-up models are individual-based models, where the ‘parts’ are individual organisms, in the case of microbes often but not necessarily single cells. But how far down the scale of organization should one go when modelling individual organisms? Use Monod kinetics or incorporate gene regulatory and stoichiometric metabolic models or dynamic metabolic models? All the way to physical laws from thermodynamics and mechanics? Drawing on two case studies, the question of how to cope with the huge diversity of microbial ecotypes with their huge phenotypic flexibility, interacting with others in spatially structured and temporally fluctuating environments will be discussed with an emphasis on metabolism. The case studies are based on competing, abstract strategies rather than detailed implementations of particular manifestations of these strategies, and this choice has advantages and disadvantages. One is based on a trade-off between specific growth rate and growth yield, demonstrating the benefits of higher yields in biofilms. The second is based on a trade-off between allocating resources into repair of damaged materials or into growth and reproduction, while getting rid of damage by asymmetric damage segregation causing ageing.

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09:45-10:15 Integrating metabolic versatility into spatially-explicit models of soil bacterial life

Benedict Borer, ETH Zürich, Switzerland

Abstract

Soil is a harsh and dynamic environment for bacterial cells due to nutrient diffusion and dispersal limitations following episodic wetting events. Nevertheless, soil hosts unparalleled diversity of bacterial life where metabolic versatility is key to their success, enabling them to exploit diverse growth strategies on a wide range of resources. Soil bacterial life is governed by localized nutrient conditions at the microscale, giving rise to complex metabolic landscapes that shape bacterially-mediated processes ranging from soil nutrient cycling to greenhouse gas emissions. Interestingly, these nutrient landscapes can trigger fundamentally different growth strategies even for the same species when residing in close proximity. Most mathematical models are currently unable to capture such versatility and local adaptation, calling for a more nuanced representation of bacterial metabolism and the soil physical structure. Benedict Borer reports a mathematical framework that considers individual bacterial cell dispersal and interaction with nutrient diffusion fields in a spatial context that embrace metabolic versatility using flux balance analysis based on genome scale metabolic networks. Benedict investigates the spatial organisation of a synthetic bacterial community in artificial pore networks and reveal mechanisms promoting spatial segregation that enable coexistence. Representing the aqueous phase architecture of soil at the cell scale offers unprecedented opportunities to interrogate bacterial life in complex habitats that is typically veiled by soil opacity.

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10:15-10:45 Coffee

10:45-11:15 Upscaling and statistical emulation of individual based models

Professor Darren Wilkinson, Newcastle University, UK

Abstract

Modelling entire ecological communities of bacteria in large, complex open environments is extremely challenging. The NUFEB project involves a multi-disciplinary team of researchers developing methods and software for multiscale modelling of open engineered biological systems at scale. The group's exemplar project is focused on the modelling of wastewater treatment systems which have macro-scale characteristics arising from the micro-scale features of up to 10^18 individual interacting bacteria. They have developed an individual based model of bacterial communities in an active fluid environment, and they can use this to understand the small-scale features of the system, considering volumes containing up to a few million bacteria. At the system scale the group are developing continuum models which capture essential macro-scale properties. They propose a novel technique for coupling the two models to produce a multi-scale model by embedding fast statistical emulators of the individual based model into the macro-scale model. This talk will outline the current state of this work in progress on this ongoing project.

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11:15-11:30 Discussion

11:30-12:00 Computational modelling of microbial communities

Professor Ines Thiele, National University of Ireland, Ireland

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12:00-13:00 Lunch

13:00-17:00

Session 4

5 talks Show detail Hide detail

Chairs

Dr Leonardo Erijman, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Argentina

Dr Sukhwan Yoon, Korea Advanced Institute of Science and Technology, South Korea

Dr Jane Fowler, Simon Fraser University, Canada

13:00-13:30 Unravelling and rewiring anaerobic microbiome metabolism with microbial systems ecology

Dr Christopher Lawson, Joint BioEnergy Institute, Lawrence Berkeley National Lab, USA

Abstract

Microbial communities ('microbiomes') have been employed to benefit society for thousands of years. However, the vast majority of the microbial world’s transformative capabilities have yet to be unlocked and harnessed for engineering applications. A key reason for this is the lack of tools available to quantitatively probe and experimentally discover the structure and in situ activity (ie fluxes) of biochemical networks operating in poorly characterized and uncultivated microorganisms. While understanding and control of microbiome metabolic flux is the ultimate goal, we have started with unravelling metabolism and fluxes in microbial communities of anaerobic ammonium oxidizing (anammox) bacteria and other nitrogen-cycling organisms. Together, these microbes are responsible for controlling nitrogen flux to the atmosphere on a global-scale and for performing sustainable nitrogen removal from wastewater through complex metabolic network interactions. Dr Lawson will show how isotopic tracers combined with quantitative metabolomic analysis were used to probe and illuminate the biochemical pathways operating in anammox bacteria. He will also discuss how the integration of metagenomics, 13C-metaproteomics, and metabolic modelling were used to determine metabolic interactions between anammox, nitrifying, and denitrifying bacteria in complex microbiomes. These analyses have resulted in several key discoveries on the enigmatic metabolism of anammox bacteria and their metabolic interactions with other poorly characterized nitrogen cycle bacteria. He will conclude with discussion on preliminary efforts to assemble and engineer synthetic consortia of anaerobic fungi and bacteria to recover valuable products from renewable biomass sources, while unmasking basic principles for microbiome engineering.

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13:30-13:45 Discussion

13:45-14:45 The role of the pulmonary microbial community in cystic fibrosis lung disease

Dr Stefanie Widder, Medical University of Vienna, Austria

Abstract

People with cystic fibrosis (CF) suffer from persistent, poly-microbial infections in the lung. This lung microbiome is a dynamical, evolving ecosystem that displays classic features of a complex system. It shows temporal changes in composition, is spatially stratified in the alveolar microenvironment and microbial interactions generate an ecological dependency structure in the community. The emergent disease dynamics are characterized by abrupt inflammatory aggravation (pulmonary exacerbations) that cause irreversible lung damage and drive patient mortality. Dr Widder and others hypothesize that the ecological state of the lung microbiome, in particular dysbiosis and the loss of interactions is directly related to resulting disease dynamics. They use 16S and metagenomic sequencing data derived from large sputum collections and apply complex systems theory, network science and modelling techniques to dig deep into the community structure of the airway microbiome. Comparing the airway microbiome during clinical baseline symptoms or acute exacerbation, reveals rearrangements in taxa dominance, interactions and metabolic activity of the community. Moreover, also the analysis of microbiome time series suggests that in exacerbation the microbiome shifts from self-organization to neutral and competitive dynamics driving dysbiosis. In summary, these results indicate that microbial community properties and their dynamics, rather than individual pathogens strongly contribute to CF lung disease dynamics. The vision is to build new treatment strategies building on the underlying ecological dependencies in the CF lung microbiome with the goal to avoid exacerbation and prolong patient’s lives. 

 

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14:45-15:15 Tea

15:15-15:45 Integrating ecological theory and data

Dr Timothée Poisot, Université de Montréal, Canada

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15:45-17:00 Final discussion and summary

Microbial ecology for engineering biology - POSTPONED

Theo Murphy international scientific meeting organised by Professor Thomas Curtis and Dr Jane Fowler.

Kavli Royal Society Centre, Chicheley Hall Newport Pagnell Buckinghamshire MK16 9JJ
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