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Rational design of microbial community mixtures for biogas production

Lead Research Organisation: University of York
Department Name: Biology

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Technical Summary

We have recently shown that biogas production can be enhanced through mixing multiple microbial communities together. We propose to improve this process and assess its practical application in industrial settings. We will combine high throughput laboratory experiments, genetic and metabolomic profiling and modelling to identify community combinations and invasion conditions that will enhance reactor performance. We will use this information to conduct an industrial-scale trial, the results of which will be used to assess and refine the predictive power of lab-scale measures for improving the efficiency of industrial ADs. In addition to the clear applied benefits, the results will provide fundamental and novel insights into the dynamics of microbial "community coalescence", which are likely to have relevance for the enhancement of other biotechnological, remediation and agricultural processes

Planned Impact

The project seeks to enhance the efficiency of methane production from anaerobic digestion (AD) in industrial contexts through bio-augmentation. The work will have significant direct impact for the AD industry. Impact will primarily be realised through our industrial partner, Amur, who offer services to improve the efficiency of AD throughout the UK. Amur has been closely engaged in the co-design of the proposal and exploitation of the results thereof. They will conduct a controlled, replicated trial (objective 4) and offer advice and the bio-augmentation service to their clients. To this end, we will hold regular workshops in partnership with Amur to communicate our findings to participants in the industrial trial and the wider customer base and identify IP assets and products for exploitation. Most impact will occur towards the end of the grant, when the industrial trial is complete, yet Amur, and where relevant their client base, will provide input and guidance into the earlier experimental phases of the project. There is likely to be Intellectual Property (IP) associated with the project, notably the ability to select synergistic community combinations, and identifying and protecting this will be crucial for the application of the more refined methods. We will establish IP protection (by agreement with all partners) if the lab-based results are promising. The general approach could improve a range of biotechnologies involving microbial communities (e.g. bioremediation of contaminated soils and water), hence we will communicate the results through a broader stakeholder workshop involving existing contacts (notably water industries). Finally, we will communicate the work to the general public via a range of established activities through the Universities of Exeter and York.

Publications

10 25 50
 
Description Collaboration with University of Exeter 
Organisation AB Agri Ltd
Country United Kingdom 
Sector Private 
PI Contribution MS analysis of samples plus resulting data analysis
Collaborator Contribution Collection of relevant experimental samples for analysis
Impact Collaborative research
Start Year 2020
 
Description Collaboration with University of Exeter 
Organisation University of Exeter
Country United Kingdom 
Sector Academic/University 
PI Contribution MS analysis of samples plus resulting data analysis
Collaborator Contribution Collection of relevant experimental samples for analysis
Impact Collaborative research
Start Year 2020
 
Description EBnet Collaboration 
Organisation UK Environmental Biotechnology Network
Country United Kingdom 
Sector Academic/University 
PI Contribution James Chong and Sarah Forrester are active members within the EBnet Working Group. Through their work with EBnet they are able to publicise the Cloud-SPAN project, via sharing information and delivering talks at webinars.
Collaborator Contribution EBnet support and promote the training opportunities created through the Cloud-SPAN project. The collaboration also allows members to exchange expertise in the field of HPC driven microbial genomics research, which in turn improves the quality of the Cloud-SPAN training resources.
Impact James Chong and Sarah Forrester are active members within the EBnet Working Group. Through their work with EBnet they are able to publicise the Cloud-SPAN project, via sharing information and delivering talks at webinars.
Start Year 2021
 
Description EBNet Webinar: Using Big Data Approaches to Understand Microbial Communities 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact EBNet Webinar: Using Big Data Approaches to Understand Microbial Communities
Thursday, 10th February 2022 at 13.00 - 14.15.
The SESSION RECORDING is available here https://www.youtube.com/watch?v=1QH0JK0X0Xw

EBNet are hosting a series of specialist webinars to support knowledge exchange amongst members. "Using Big Data Approaches to Understand Microbial Communities". Hear the latest developments from top speakers and participate in the online chat to engage with questions.

This fascinating session is brought to you by the Chairs: Dr Sarah Forrester, the Chong Group, Dept. of Biology, University of York & Dr Bing Guo.

Dr Sarah Forrester is a PDRA within James Chong's group within the Biology department at the University of York. She gained her PhD at the University of Liverpool in 2016 using multi 'omic approaches to analyse parasite genomic data, and has worked since then on a range of microbial systems and used a variety of bioinformatic methods. She performs HPC driven microbial genomics research and delivers bioinformatics training. As a 2022 Software Sustainability fellow and a certified Software Carpentry instructor, she is passionate about instilling good bioinformatic practises into her training. She is also involved in the preparation and delivery of the material for Cloud-SPAN: Specialised analyses for environmental 'omics with Cloud-based High Performance Computing , see https://cloud-span.york.ac.uk/.

TALK TITLE: INTRODUCTION TO THE EBNET BIOINFORMATICS WORKING GROUP
Prof James Chong is a Royal Society Industry Fellow and Professor in the Department of Biology at the University of York, where he runs a research group exploiting a range of 'omics techniques to understand microbial community dynamics, as well as leading the EBNet Working Group "Bioinformatics Training for Microbial Environmental Biotechnologies". His group is involved in generating microbial community metagenomics, meta-transcriptomics and metabolomics datasets. His group use established analytical pipelines, but also develop their own bespoke scripts for data analysis. Insight into the application of 'omics techniques, and the ways in which they can be applied to environmental biotechnology use cases to greater understand microbial community dynamics, has driven his desire to develop bioinformatic training resources. This is currently being supported by the UKRI Grant Cloud-SPAN: Specialised analyses for environmental 'omics with Cloud-based High Performance Computing, and is co-led by James, see https://cloud-span.york.ac.uk/.

Impact: enables the dissemination of the project details to a wider audience and generates registrations to current activities
Year(s) Of Engagement Activity 2022
URL https://ebnet.ac.uk/ebnet-rc22-bigdata/
 
Description EBNet Working Group Coordinator 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact James Chong is the Working Group Chair for EBnet. This WG aims to create Bioinformatics training for microbial Environmental Biotechnologies. In this role James is able to make new connections and publicise the work of Cloud-SPAN.
Year(s) Of Engagement Activity 2021
URL https://ebnet.ac.uk/about/wg-details/wg-bioinformatics/
 
Description European Biosolids and Bioresource Conference 2022. 22nd and 23rd of November in Birmingham James Chong and Sarah Forrester 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact James Chong and Sarah Forrester delivered Bioinformatics session, 40 minute Q & A on metagenomics and bioinformatics and access to training

European Biosolids and Bioresource Conference 2022. 22nd and 23rd of November in Birmingham , ~40 people attended

13:35 - 13:50 Bioinformatics-based diagnostics for monitoring AD - Professor James Chong, University of York, UK
13:50 - 14:05 Using multi-omic approaches to understand the co-digestion of wheatstraw and sewage sludge - Dr. Sarah Forrester, Senior Post Doc, University of York, UK
Year(s) Of Engagement Activity 2022
URL https://european-biosolids.com/wp-content/uploads/2022/11/European-Biosolids-Bioresources-Conference...
 
Description Metagenomics online training course April 2023 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact A training course was organised online comprising online lectures, drop in help sessions, and a slack channel for support for 30 participants.

Following completion of this course, learners will be trained to :
explain the hierarchical structure of a file system and describe the files and file structure used in the course
explain what is meant by a working directory, a path and a relative path and write down paths that they will need for the course
start a Terminal (Mac) or Git Bash Terminal (Windows)
navigate a file system using the command line
log in to and exit their AWS instance (the cloud)
use common commands such as ls, pwd and cd, on the command line
know the difference between genomics and metagenomics
describe the steps in a metagenomic workflow
perform quality control on reads and assemble them into a metagenome
perform polishing to improve an assembly
use binning to separate the metagenome into different species or MAGs (Metagenome-Assembled Genomes)
use Kraken 2 to assign taxonomy to reads and contigs and phyloseq in R to analyse taxonomic diversity
Year(s) Of Engagement Activity 2023
URL https://sites.google.com/york.ac.uk/cloud-span/train-with-us/specialised-skills#h.jqgzsdc8hbla
 
Description Participation in an activity, workshop or similar - Training Course: Genomics - 6-7 December 2022 - University of York 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Training course for 14 participants from 6 different institutions. Participants completed the interactive workshop and developed practical skills and increased their knowledge in the area of data management and analytical skills for genomic research. All participants connected to the Cloud-SPAN community via the slack channel and in person.
Year(s) Of Engagement Activity 2022
URL https://cloud-span.github.io/00genomics/