Engineering Synthetic Microbial Communities for Biomethane Production
Lead Research Organisation:
UNIVERSITY OF EXETER
Department Name: Engineering Computer Science and Maths
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.
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
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.
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.
Organisations
- UNIVERSITY OF EXETER (Lead Research Organisation)
- Engineering and Physical Sciences Research Council (Co-funder)
- Soehngen Institute of Anaerobic Microbiology (Collaboration)
- John Lewis Partnership (United Kingdom) (Project Partner)
- Anaerobic Digestion and Bioresources Association (Project Partner)
- iNets South West (Project Partner)
- Lawrence Berkeley National Laboratory (Project Partner)
- Centre for Process Innovation (Project Partner)
- Harvard University (Project Partner)
- Pennon Group (United Kingdom) (Project Partner)
- Veolia (United Kingdom) (Project Partner)
Publications
Du Lac M
(2017)
Predicting the Dynamics and Heterogeneity of Genomic DNA Content within Bacterial Populations across Variable Growth Regimes.
in ACS synthetic biology
Harlow CE
(2022)
Identification and single-base gene-editing functional validation of a cis-EPO variant as a genetic predictor for EPO-increasing therapies.
in American journal of human genetics
Washer SJ
(2022)
Functional characterization of the schizophrenia associated gene AS3MT identifies a role in neuronal development.
in American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics
Morley L
(2015)
Gene Loss and Lineage-Specific Restriction-Modification Systems Associated with Niche Differentiation in the Campylobacter jejuni Sequence Type 403 Clonal Complex.
in Applied and environmental microbiology
Dolfing J
(2014)
Thermodynamic constraints on syntrophic acetate oxidation.
in Applied and environmental microbiology
Buchholz HH
(2022)
A Novel and Ubiquitous Marine Methylophage Provides Insights into Viral-Host Coevolution and Possible Host-Range Expansion in Streamlined Marine Heterotrophic Bacteria.
in Applied and environmental microbiology
Dolfing J
(2013)
Syntrophic propionate oxidation via butyrate: a novel window of opportunity under methanogenic conditions.
in Applied and environmental microbiology
Shamurad B
(2020)
Stable biogas production from single-stage anaerobic digestion of food waste
in Applied Energy
La Edwards C
(2020)
Rapid Detection of Proliferative Bacteria by Electrical Stimulation.
in Bio-protocol
De Souza-Guerreiro TC
(2021)
Seeking Insights into Aging Through Yeast Mitochondrial Electrophysiology.
in Bioelectricity
Description | Please see key finding of BBSRC grant BB/K003240/2. |
Exploitation Route | Please see BBSRC grant BB/K003240/2 |
Sectors | Agriculture, Food and Drink,Energy,Environment,Other |
URL | https://warwick.ac.uk/fac/sci/lifesci/research/slola |
Description | Please see Impact Summary of BBSRC grant (BB/K003240/2) |
Sector | Agriculture, Food and Drink,Energy,Other |
Impact Types | Policy & public services |
Description | BEE BBSRC spotlight area 2022 |
Geographic Reach | National |
Policy Influence Type | Participation in a guidance/advisory committee |
URL | https://www.ukri.org/news/bbsrc-launches-new-responsive-mode-spotlight-pilot/ |
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 |
Start | 02/2014 |
End | 01/2019 |
Description | BBSRC AD Network BIV |
Amount | £10,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Department | Anaerobic Digestion Network (AD Network) |
Sector | Academic/University |
Country | United Kingdom |
Start | 03/2017 |
End | 07/2017 |
Description | BBSRC AD Network POC |
Amount | £59,970 (GBP) |
Funding ID | POC2016012 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Department | Anaerobic Digestion Network (AD Network) |
Sector | Academic/University |
Country | United Kingdom |
Start | 09/2017 |
End | 02/2018 |
Description | BBSRC Impact Acceleration Account (IAA) |
Amount | £149,790 (GBP) |
Funding ID | BB/S506783/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 06/2018 |
End | 03/2021 |
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 |
Start | 07/2016 |
End | 09/2017 |
Description | Understanding the origin and evolution of metabolic interactions using synthetic microbial communities |
Amount | £939,000 (GBP) |
Funding ID | BB/T010150/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2019 |
End | 09/2023 |
Title | Data from: Resource heterogeneity and the evolution of public-goods cooperation |
Description | Heterogeneity in resources is a ubiquitous feature of natural landscapes affecting many aspects of biology. However, the effect of environmental heterogeneity on the evolution of cooperation has been less well studied. Here, using a mixture of theory and experiments measuring siderophore production by the bacterium Pseudomonas aeruginosa as a model for public-goods based cooperation, we show that cooperation in metapopulations that were spatially heterogeneous in terms of resources can be maintained at a higher level than in homogeneous metapopulations of the same average resource value. The results can be explained by a positive covariance between fitness of cooperators, population size and resource availability, which allowed cooperators to have a disproportionate advantage within the heterogeneous metapopulations. These results suggest that natural environmental variation may help to maintain cooperation. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | http://datadryad.org/stash/dataset/doi:10.5061/dryad.rbnzs7h77 |
Title | MI-Sim |
Description | A MATLAB package for the numerical analysis of microbial ecological interactions |
Type Of Material | Computer model/algorithm |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | The publication has had over 3000 views and has been cited twice. |
URL | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0173249#ack |
Title | MetQy |
Description | MetQy is a R package to ease interfacing with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to query metabolic functions of genes and genomes |
Type Of Material | Computer model/algorithm |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | None to report |
URL | https://academic.oup.com/bioinformatics/article/34/23/4134/5033387 |
Title | Micodymora |
Description | Micodymora is a python package allowing to simulate Ordinary Differential Equations (ODE) models of microbial population dynamics, while providing gas/liquid transfer and acide/base equilibria as additional features |
Type Of Material | Computer model/algorithm |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | None as yet |
URL | https://github.com/OSS-Lab/micodymora |
Title | On the genetic architecture of rapidly adapting and convergent life history traits in guppies |
Description | The genetic basis of traits shapes and constrains how adaptation proceeds in nature; rapid adaptation can be facilitated by polygenic traits, which subsequently provide multiple, redundant, genetic routes to adaptive phenotypes, reducing re-use of the same genes (genetic convergence). Guppy life history traits evolve rapidly and convergently among natural high- (HP) and low-predation (LP) environments in northern Trinidad. This system has been studied extensively at the phenotypic level, but little is known about the underlying genetic architecture. Here, we use an F2 QTL design to examine the genetic basis of seven (five female, two male) guppy life history phenotypes to assess whether the genetic architecture of these traits reflects theoretical predictions. We use RAD-sequencing data (16,539 SNPs) from 370 male and 267 female F2 individuals. We perform linkage mapping, estimates of genome-wide and per-chromosome heritability (multi-locus associations), and QTL ma pping (single-locus associations). Our results are consistent with architectures of many-loci of small effect for male age and size at maturity and female interbrood period. Male trait associations are clustered on specific chromosomes, but female interbrood period exhibits a weak genome-wide signal suggesting a potentially highly polygenic component. Offspring weight and female size at maturity are also associated with a single significant QTL each. These results suggest rapid phenotypic evolution of guppies may be facilitated by polygenic trait architectures, but these could fuel redundancy and limit gene re-use across populations, in agreement with an absence of strong signatures of genetic convergence from recent population genomic analyses of wild HP-LP guppies. |
Type Of Material | Database/Collection of data |
Year Produced | 2022 |
Provided To Others? | Yes |
URL | http://datadryad.org/stash/dataset/doi:10.5061/dryad.w3r2280sk |
Description | SIAM |
Organisation | Soehngen Institute of Anaerobic Microbiology |
Country | Netherlands |
Sector | Private |
PI Contribution | The sLola research team plus other PDRAs from the Soyer group visited the Netherlands for a research exchange workshop with researchers from the SIAM research program. Research talks and poster presentations were given at the workshop as well as participation in round table discussions on Anaerobic digestion microbiology topics and potentials for future collaboration. |
Collaborator Contribution | The SIAM group hosted the workshop and also gave research talks and poster presentations and participated in round table discussions on Anaerobic digestion microbiology topics and potentials for future collaboration. |
Impact | None to report yet. |
Start Year | 2017 |
Title | MicrobeMeter |
Description | MicrobeMeter is a high-resolution photometer with continuous measurement and wireless capabilities. It allows measuring of microbial growth dynamics, as used in many disciplines of life sciences, such as molecular biology, systems biology and synthetic biology. |
IP Reference | |
Protection | Copyrighted (e.g. software) |
Year Protection Granted | 2018 |
Licensed | No |
Impact | more than 50 units sold. Manuscript describing the blueprint of the MicrobeMeter on bioRxix has been downloaded 2373 (https://www.biorxiv.org/content/10.1101/407742v1.article-metrics). |
Description | AAAS annual meeting - invited talk |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I was invited speaker at the annual meeting of the American Association of the Advancement of Science (AAAS). |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.aaas.org/events/2020-aaas-annual-meeting |
Description | AD Monitoring Project Stakeholder Meeting |
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 | An online meeting was held with key industrial participants of this project. Results of the project were clearly presented together with plans to publish the data. Also discussed were options for applying for future funding with industrial support. |
Year(s) Of Engagement Activity | 2021 |
Description | Isaac Newton Institute Workshop on Microbial communities: current approaches and open challenges |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | This is a 4-month residential workshop we have organised at the Isaac Newton Institute. It aimed to assess the state of the microbial communities research field and resulted in significant impact on the development of the field. The 2022 follow on workshop took place over four days and included 20 invited and 25 contributed talks that covered broad and recent topics in microbial community research. |
Year(s) Of Engagement Activity | 2014,2015,2022 |
URL | https://www.newton.ac.uk/event/umc/ |