Engineering Synthetic Microbial Communities for Biomethane Production

Lead Research Organisation: University of Warwick
Department Name: School of Life Sciences

Abstract

Complex microbial communities underlie natural processes such as global chemical cycles and digestion in higher animals, and are routinely exploited for industrial scale synthesis, waste treatment and fermentation. Our basic understanding of the structures, stabilities and functions of such communities is limited, leading to the declaration of their study as the next frontier in microbial ecology, microbiology, and synthetic biology. Focusing on biomethane producing microbial communities (BMCs), we will undertake a two-tiered approach of optimising natural communities and designing synthetic communities with a focus on achieving robust, high-yield biomethane production. Within this biotechnological framework, our proposal will address several fundamental scientific questions on the link between the structure and function of microbial communities.
To ensure success in this challenging project, we assembled the strongest possible interdisciplinary research team that combines significant practical and scientific expertise in microbial ecology and evolution, systems modelling, molecular microbiology, bioengineering, genomics, and synthetic biology.
We are confident that this team will deliver and that this project will result in significant impact in the scientific and industrial domains. Through our work, described in detail below, we will; significantly improve the current understanding of the structure-function relation in microbial communities, provide the scientific community with a systematic, temporal genomics and transcriptomics dataset on complex microbial communities, develop novel computational tools for microbial community (re)design, and experimentally build synthetic BMCs that will act as model ecosystems in different research fields. These scientific developments, in turn, will accumulate in the development of more sustainable bioenergy solutions for the UK economy by optimising the communities underlying biomethane production. This will help to drive the efficiency of biomethane as an alternative fuel source.

Technical Summary

We will employ both top-down (directed evolution) and bottom-up (synthetic biology) engineering of biomethane producing microbial communities (BMCs) with improved functionality. These two approaches are connected via the resulting BMCs, which will be further analysed in mid-scale reactors with the aim to impact biotechnological application of microbial communities.

Directed evolution of BMCs. We will combine our expertise in experimental evolution with applied expertise in biomethane production to use group selection on naturally derived BMCs to improve their biomethane productivity. Using the expertise and the infrastructure at TGAC, we will employ next generation sequencing to determine how communities change in response to selection, and whether significant evolutionary change has occurred in the transcriptomes of focal species. Our core experimental evolution setup will use 60 mini reactors to set up independent batch cultures, where biomethane production can be measured in real-time by automated monitoring of gas volume.

Rational engineering of synthetic BMCs. We will combine our expertise in kinetic modelling and flux balance analysis (FBA) with molecular biology to rationally design and experimentally implement synthetic BMCs. The starting point for both FBA and experimental work will be an existing co-culture that is capable of converting lactate into methane. The engineered communities and their temporal behaviour will be analysed using genomics and transcriptomics approaches.

Testing and scaling up of (re)engineered BMCs. We will test the performance and stability of evolved and synthetic BMCs under industrially realistic conditions in mid-scale reactors using our expertise and lab infrastructure in process engineering. For this task, we will use both anaerobic membrane reactors (AnMBRs), which allow for the maintenance of BMCs in the reactor without "washout" and more commonly used continuously stirred tank

Planned Impact

In line with national and international policy, this research aims to produce a step change in the efficient production of biomethane, a key renewable energy source. This, in turn, will impact on government and industrial end users, who have clearly articulated their requirements for improvements in yield and reliability of biomethane production. At the scientific level, the relations between structure, composition and function in microbial communities is at the heart of several unresolved questions in the fields of microbial ecology and evolution, microbiology and synthetic biology.

1. Academic Communities
Impact on Existing Communities. This research will benefit systems microbiologists by generating a more complete understanding of the interactions found in complex microbial communities and synthetic biologists by developing improved tools and approaches for the manipulation of microbial communities. These tools will be applicable to biomethane production but will also be of interest for the production of biofuels or bio-products by accommodating bacteria into a stable productive community. In addition, our proposed research will provide the scientific community with an unprecedented data set on the composition and structure of complex microbial communities and provide novel computational tools for their study.

Educational Impact. Today's scientific challenges require bringing together scientists from diverse fields and educating younger scientists in a genuinely cross-disciplinary fashion. Being a truly integrative project that amalgamates theory and experiment towards achieving a better understanding of complex microbial communities, the proposed research will provide an ideal setting for the development of the participating staff and PhD students, and will excite a new generation of scientists.

2. Industrial Communities
The innovative nature of this project and the economic and regulatory drivers related to biomethane production have already created strong interest from industry. We have engaged end users in the development of this proposal, primarily through an industrial liaison workshop held in Exeter in December 2011. Most attendees of this workshop, as well as several other industrial companies are now members of our advisory board (AB); major users of biomethane production, SME technology development companies, and a regional industry network. There is strong interest in the potential for future commercial exploitation of the proposed basic research, and we will actively seek to pursue opportunities for commercial industrial collaborations during and post-project.

3. Policy and Society
Impact on Policy. The close link between government priorities on renewable energy and greenhouse gas emission, and biomethane production through anaerobic digestion is explicitly recognised in the DECC Strategy and Action Plan, 2011. The Government has set targets to recycle 50% of household waste by 2020, reduce greenhouse gas emissions to 34% below 1990 levels by 2020 and by 80% by 2050, and achieve greater energy security. The related regulations and innovation stimulation packages developed by the Government, heavily influences the anaerobic digestion bioindustry. Recognising this link, we have already sought advice on engagement with DECC, and following this advice, we will provide them with research briefing papers as results are made available.

Social Impact. The proposed research is extremely timely and of significant social relevance since it addresses an important aspect of a "daily" challenge, namely eco-friendly and sustainable energy production. We will capitalise on this and use the project as a way to engage with the public and funding bodies and offer collaborative opportunities to think in innovative and informed ways about systems biology, synthetic biology and microbial biotechnology.

Publications


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Related Projects

Project Reference Relationship Related To Start End Award Value
BB/K003240/1 08/04/2013 24/05/2013 £3,167,919
BB/K003240/2 Transfer BB/K003240/1 01/08/2013 31/05/2018 £3,080,376
 
Title Research on synthetic microbial communities explained 
Description A 3-minute video explaining our research on microbial communities in an accesible way. 
Type Of Art Film/Video/Animation 
Year Produced 2014 
Impact The video was featured on BBSRC home page and twitter. 
URL http://osslab.lifesci.warwick.ac.uk/adLola_rsrcs.html
 
Description 1. We have shown that Anaerobic digestion (AD)-adapted communities produce more biogas compared to natural, methanogenic communities and that this is underpinned by changes in community composition following adaptation to AD conditions. We demonstrated for the first time the importance of diversity of rare species in the starting inoculum and that AD performance can be enhanced by having a mixed community inocula.

2. We have established minimal methanogenic communities at the lab scale and identified a genetic polymorphism that underpins the required syntrophy.

3. We have developed mathematical models to analyse and predict microbial community dynamics, stability and diversity by taking into account thermodynamic inhibitions.

4. We have developed a metabolic modelling platform to model ecological and evolutionary dynamics in a microbial community, allowing biologically important predictions to be made. This will help us to extend the minimal communities we are creating.

5. We have published a series of review and opinion papers, with a large number of co-authors in some cases. These have established that microbial communities, as complex dynamical systems with intertwined ecological and evolutionary processes, present themselves as the new integrated research frontier. Additional review and opinion papers highlight research priorities, such as the development of synthetic microbial fuel cells, as well as the application of synthetic biology approaches to communities, and commented on potential biotechnological routes, such as bioaugmentation, for increased biomethane generation.
Exploitation Route Our work on mixed communities (key finding 1) raises the possibility to use a large volume inoculum from a well performing AD plant to save another failing AD plant, thus reducing large costs associated with failures.

Our work on creating minimal communities (key finding 2) has provided important insights into understanding and engineering methanogenic communities.

Models developed for Key finding 3 and 4, can be extended to any microbial community to allow predictive conclusions to be drawn on their stability, dynamics and diversity, thus, facilitating the (re)engineering of microbial communities.
Sectors Agriculture, Food and Drink,Energy,Environment
URL http://osslab.lifesci.warwick.ac.uk/adLola_news.html
 
Description We have contributed to a report (prepared by the BBSRC) to the House of Lords, and relating to renewable energy We have engaged with growers and suppliers at the annual Waitrose science event, of which many use AD as part of their business. Some of our findings have been taken up by industry. In particular, results on the impact of community mixing on methane production in AD settings has been utilised by a company for the initiation of their first reactor. Further talks with this company are ongoing to explore additional applied research.
First Year Of Impact 2014
Sector Agriculture, Food and Drink,Energy,Environment,Other
Impact Types Economic
 
Description AD Network BIV
Amount £10,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 03/2017 
End 07/2017
 
Description Anaerobic Digestion Network
Amount £705,651 (GBP)
Funding ID BB/L013835/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 02/2014 
End 01/2019
 
Description Isaac Newton Institute for Mathematical Sciences research programme
Amount £200,000 (GBP)
Organisation Isaac Newton Institute for Mathematical Sciences 
Sector Academic/University
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 08/2014 
End 12/2014
 
Description SPARKS - engineering synthetic communities for algae-to-bio-methane conversion
Amount £20,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Department BBSRC Impact Award
Sector Academic/University
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start  
 
Description Technology and Resource Development Fund
Amount £151,448 (GBP)
Funding ID BB/N023285/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 07/2016 
End 09/2017
 
Description David Stahl 
Organisation University of Washington
Country United States of America 
Sector Academic/University 
PI Contribution Visited University of Washington to collaborate and discuss research findings relating to synthetic cultures.
Collaborator Contribution Hosted visit to set up collaboration and discuss research findings of overlapping interest.
Impact Submitted publication on EvoFBA
Start Year 2015
 
Description Dominique Schneider 
Organisation Joseph Fourier University
Country France, French Republic 
Sector Academic/University 
PI Contribution Hosted a visit in order to finalise joint publication on evoFBA manuscript
Collaborator Contribution Hosted a visit in order to set up collaboration on FBA technique
Impact Manuscript ready for submission
Start Year 2014
 
Description INRA-Narbonne 
Organisation French National Institute of Agricultural Research (INRA)
Country France, French Republic 
Sector Public 
PI Contribution The research team were involved in the instigation and organisation of a bilateral meeting held in Narbonne. The group travelled to Narbonne and gave a total of four presentations of their research.
Collaborator Contribution The INRA-Narbone group were involved in the organisation of the bilateral meeting. They contributed nine research presentations and a training session for PhD students.
Impact As a result of this meeting, overlaps in research interests were identified. One PDRA made an additional visit to INRA Montpellier and Narbonne to carry out specific mathematical analyses. Another PDRA hosted a follow-on meeting with scientists from INRA-Narbonne to discuss experimental results of common interest.
Start Year 2014
 
Description James Chong 
Organisation University of York
Department Department of Biology
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Visited collaborator for training and discussions
Collaborator Contribution Provided training and discussions on microbe cultivation techniques
Impact development of cultivation techniques for methanogens.
Start Year 2013
 
Description Piotr Garstecki 
Organisation Polish Academy of Sciences, Warsaw
Department Institute of Physical Chemistry
Country Poland, Republic of 
Sector Public 
PI Contribution Visited collaborator to exchange ideas on microfluidic devices for growing microbes.
Collaborator Contribution Hosted visit to exchange ideas on microfluidic devices for growing microbes.
Impact Identified common interests and potential for future experiments.
Start Year 2014
 
Description AD Science meets Industry 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact We hosted a one-day workshop to bring together anaerobic digestion (AD) practitioners and scientists. The event consisted of both science and industry focussed talks, a session from an expert on AD and an open discussion forum. We also launched a new (BBSRC) project on monitoring AD microbiomes, with 10 companies coming forward to take part. In total 68 people attended the meeting, representing 26 companies and 13 academic institutions.
Year(s) Of Engagement Activity 2016
 
Description Edinburgh Science Festival 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interest and questions from the public

Possible participation in the 2015 festival
Year(s) Of Engagement Activity 2014
URL http://www.sciencefestival.co.uk
 
Description Penny College talk 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact 40 min talk explaining biogas production and microbial ecology to grade 9 students.
Year(s) Of Engagement Activity 2015
 
Description Royal Cornwall show 2015 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact 3 h demonstration session on biomethane producing microbial communities and how it can improve a farmer's business. Approximately 60 people attended.
Year(s) Of Engagement Activity 2015
 
Description Summary for House of Lords inquiry 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? Yes
Geographic Reach National
Primary Audience Policymakers/parliamentarians
Results and Impact summary formed part of the inquiry report

None as of yet
Year(s) Of Engagement Activity 2013